search

pombase / fypo

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

closes #4386 #4387

Closed manulera closed 1 year ago

github-actions[bot] commented 1 year ago

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

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 ### abnormal distribution of interpolar microtubule rescue during anaphase B `http://purl.obolibrary.org/obo/FYPO_0007975` #### Removed - [abnormal distribution of interpolar microtubule rescue during anaphase B](http://purl.obolibrary.org/obo/FYPO_0007975) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed during anaphase B in which the distribution of the positions of interpolar microtubule rescues is abnormal. The positions of interpolar microtubule rescues are where the transitions from shrinkage to growth occur." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [abnormal distribution of interpolar microtubule rescue during anaphase B](http://purl.obolibrary.org/obo/FYPO_0007975) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed during anaphase B in which the distribution of the positions of interpolar microtubule rescues is abnormal. The positions of interpolar microtubule rescues are where the transitions from shrinkage to growth occur." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### abnormal duration of microtubule growth event `http://purl.obolibrary.org/obo/FYPO_0007956` #### Removed - [abnormal duration of microtubule growth event](http://purl.obolibrary.org/obo/FYPO_0007956) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which the duration of microtubule growth events is abnormal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [abnormal duration of microtubule growth event](http://purl.obolibrary.org/obo/FYPO_0007956) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which the duration of microtubule growth events is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### abnormal rate of microtubule depolymerization during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0007954` #### Removed - [abnormal rate of microtubule depolymerization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0007954) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which the rate or speed of microtubule depolymerization, i.e. the removal of tubulin dimers from a microtubule, is abnormal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:val" #### Added - [abnormal rate of microtubule depolymerization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0007954) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which the rate or speed of microtubule depolymerization, i.e. the removal of tubulin dimers from a microtubule, is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:val" ### cut with mitotic spindle microtubules protruding beyond spindle pole body `http://purl.obolibrary.org/obo/FYPO_0007968` #### Removed - [cut with mitotic spindle microtubules protruding beyond spindle pole body](http://purl.obolibrary.org/obo/FYPO_0007968) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An inviable phenotype observed in the vegetative growth phase of the life cycle after normal chromosome separation in which pushing forces exerted by microtubules protruding from the spindle pole bodies displace one of the daughter nuclei to the site of cytokinesis. The septum then physically divides that nucleus into two parts, giving rise to inviable daughter cell." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:26031557" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [cut with mitotic spindle microtubules protruding beyond spindle pole body](http://purl.obolibrary.org/obo/FYPO_0007968) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An inviable phenotype observed in the vegetative growth phase of the life cycle after normal chromosome separation in which pushing forces exerted by microtubules protruding from the spindle pole bodies displace one of the daughter nuclei to the site of cytokinesis. The septum then physically divides that nucleus into two parts, giving rise to inviable daughter cell." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26031557" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### decreased mating efficiency during phosphate starvation `http://purl.obolibrary.org/obo/FYPO_0008064` #### Removed - [decreased mating efficiency during phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A biological process phenotype in which the observed mating efficiency, as determined by counting zygotes, asci, and sometimes spores, is lower than normal after phosphate removal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:36779416" #### Added - [decreased mating efficiency during phosphate starvation](http://purl.obolibrary.org/obo/FYPO_0008064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A biological process phenotype in which the observed mating efficiency, as determined by counting zygotes, asci, and sometimes spores, is lower than normal after phosphate removal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36779416" ### decreased rate of interpolar microtubule polymerization during mitotic anaphase B `http://purl.obolibrary.org/obo/FYPO_0007972` #### Removed - [decreased rate of interpolar microtubule polymerization during mitotic anaphase B](http://purl.obolibrary.org/obo/FYPO_0007972) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a lower rate, or speed, than normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [decreased rate of interpolar microtubule polymerization during mitotic anaphase B](http://purl.obolibrary.org/obo/FYPO_0007972) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a lower rate, or speed, than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### decreased rate of microtubule catastrophe involved in meitotic centromere clustering during meiotic prophase I `http://purl.obolibrary.org/obo/FYPO_0009057` #### Removed - [decreased rate of microtubule catastrophe involved in meitotic centromere clustering during meiotic prophase I](http://purl.obolibrary.org/obo/FYPO_0009057) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process in which catastrophe rate (i.e. the frequency of transition from pause or growth to shrinkage) of microtubules is lower than normal as part of centromere clustering during meiotic prophase I." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:36435910" #### Added - [decreased rate of microtubule catastrophe involved in meitotic centromere clustering during meiotic prophase I](http://purl.obolibrary.org/obo/FYPO_0009057) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process in which catastrophe rate (i.e. the frequency of transition from pause or growth to shrinkage) of microtubules is lower than normal as part of centromere clustering during meiotic prophase I." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36435910" ### decreased vegetative cell population growth after short incubation in hydroxyurea `http://purl.obolibrary.org/obo/FYPO_0009109` #### Added - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased vegetative cell population growth after short incubation in hydroxyurea" - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell growth phenotype in which cell population growth is decreased relative to normal after short incubation in hydroxyurea." - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [date](http://purl.org/dc/elements/1.1/date) "2023-07-10T09:12:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [creator](http://purl.org/dc/elements/1.1/creator) "PomBase:mlr" - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37200372" - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "decreased vegetative cell population growth after acute hydroxyurea treatment"@en - Class: [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) SubClassOf [increased sensitivity to chemical](http://purl.obolibrary.org/obo/FYPO_0002683) - [decreased vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009109) SubClassOf [decreased vegetative cell population growth](http://purl.obolibrary.org/obo/FYPO_0001355) ### dihydrouridine absent from cell `http://purl.obolibrary.org/obo/FYPO_0007934` #### Removed - [dihydrouridine absent from cell](http://purl.obolibrary.org/obo/FYPO_0007934) [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 dihydrouridine measured in a cell is too low to detect." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" #### Added - [dihydrouridine absent from cell](http://purl.obolibrary.org/obo/FYPO_0007934) [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 dihydrouridine measured in a cell is too low to detect." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" ### increased duration of interpolar microtubule growth events during anaphase B `http://purl.obolibrary.org/obo/FYPO_0007976` #### Removed - [increased duration of interpolar microtubule growth events during anaphase B](http://purl.obolibrary.org/obo/FYPO_0007976) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during anaphase B in which the duration of interpolar microtubule growth events is longer." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [increased duration of interpolar microtubule growth events during anaphase B](http://purl.obolibrary.org/obo/FYPO_0007976) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during anaphase B in which the duration of interpolar microtubule growth events is longer." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### increased length of chromatin loops during meiotic prophase I `http://purl.obolibrary.org/obo/FYPO_0007942` #### Removed - [increased length of chromatin loops during meiotic prophase I](http://purl.obolibrary.org/obo/FYPO_0007942) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which chromatin loop formation during meiotic prophase I results in chromatin loops of increased length." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:val" #### Added - [increased length of chromatin loops during meiotic prophase I](http://purl.obolibrary.org/obo/FYPO_0007942) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which chromatin loop formation during meiotic prophase I results in chromatin loops of increased length." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:val" ### increased mating efficency during nitrogen stress `http://purl.obolibrary.org/obo/FYPO_0007950` #### Removed - [increased mating efficency during nitrogen stress](http://purl.obolibrary.org/obo/FYPO_0007950) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A biological process phenotype in which the observed mating efficiency, as determined by counting zygotes, asci, and sometimes spores, is higher than normal when a cell is subject to nitrogen stress." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:val" #### Added - [increased mating efficency during nitrogen stress](http://purl.obolibrary.org/obo/FYPO_0007950) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A biological process phenotype in which the observed mating efficiency, as determined by counting zygotes, asci, and sometimes spores, is higher than normal when a cell is subject to nitrogen stress." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:val" ### increased rate of interpolar microtubule polymerization during mitotic anaphase B `http://purl.obolibrary.org/obo/FYPO_0007971` #### Removed - [increased rate of interpolar microtubule polymerization during mitotic anaphase B](http://purl.obolibrary.org/obo/FYPO_0007971) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a higher rate, or speed, than normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [increased rate of interpolar microtubule polymerization during mitotic anaphase B](http://purl.obolibrary.org/obo/FYPO_0007971) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a higher rate, or speed, than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### increased rate of interpolar microtubule polymerization inside the mitotic nuclear membrane bridge `http://purl.obolibrary.org/obo/FYPO_0007974` #### Removed - [increased rate of interpolar microtubule polymerization inside the mitotic nuclear membrane bridge](http://purl.obolibrary.org/obo/FYPO_0007974) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization occurs at a higher rate, or speed, than normal for microtubules with their plus ends inside the nuclear membrane bridge formed during mitotic anaphase B." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [increased rate of interpolar microtubule polymerization inside the mitotic nuclear membrane bridge](http://purl.obolibrary.org/obo/FYPO_0007974) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed during mitotic anaphase B in which interpolar microtubule polymerization occurs at a higher rate, or speed, than normal for microtubules with their plus ends inside the nuclear membrane bridge formed during mitotic anaphase B." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### increased rate of microtuble polymerization during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0007970` #### Removed - [increased rate of microtuble polymerization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0007970) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a higher rate, or speed, than normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35293864" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [increased rate of microtuble polymerization during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0007970) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A microtubule cytoskeleton organization phenotype observed in the vegetative growth phase of the life cycle in which microtubule polymerization, i.e. the addition of tubulin dimers to the plus end of a microtubule occurs at a higher rate, or speed, than normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35293864" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### increased sensitivity to chemical in stationary phase `http://purl.obolibrary.org/obo/FYPO_0008000` #### Removed - [increased sensitivity to chemical in stationary phase](http://purl.obolibrary.org/obo/FYPO_0008000) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype in which cells show increased sensitivity to a chemical when the cell population is in stationary phase. Cells stop growing (and may die) at a concentration of that chemical that allows wild type cells to grow." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:35618649" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" #### Added - [increased sensitivity to chemical in stationary phase](http://purl.obolibrary.org/obo/FYPO_0008000) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype in which cells show increased sensitivity to a chemical when the cell population is in stationary phase. Cells stop growing (and may die) at a concentration of that chemical that allows wild type cells to grow." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35618649" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### meiotic cell cycle entry in haploid cell `http://purl.obolibrary.org/obo/FYPO_0006670` #### Removed - [meiotic cell cycle entry in haploid cell](http://purl.obolibrary.org/obo/FYPO_0006670) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which a haploid cell undergoes meiotic cell cycle." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9755190" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:mlr" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31278118" #### Added - [meiotic cell cycle entry in haploid cell](http://purl.obolibrary.org/obo/FYPO_0006670) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype in which a haploid cell undergoes meiotic cell cycle." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9755190" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mah" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31278118" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:mlr" ### normal mitochondrial distribution `http://purl.obolibrary.org/obo/FYPO_0007912` #### Removed - [normal mitochondrial distribution](http://purl.obolibrary.org/obo/FYPO_0007912) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which mitochondrial localization is normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:10641037" - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" #### Added - [normal mitochondrial distribution](http://purl.obolibrary.org/obo/FYPO_0007912) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which mitochondrial localization is normal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10641037" ### normal mono ubiquitin binding `http://purl.obolibrary.org/obo/FYPO_0008060` #### Removed - [normal mono ubiquitin binding](http://purl.obolibrary.org/obo/FYPO_0008060) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the binding of one protein to a ubiquitin monomer is normal (i.e. indistinguishable from wild type)." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PMID:16138082" #### Added - [normal mono ubiquitin binding](http://purl.obolibrary.org/obo/FYPO_0008060) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the binding of one protein to a ubiquitin monomer is normal (i.e. indistinguishable from wild type)." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16138082" ### normal vegetative cell population growth after short incubation in hydroxyurea `http://purl.obolibrary.org/obo/FYPO_0009110` #### Added - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [creator](http://purl.org/dc/elements/1.1/creator) "PomBase:mlr" - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell growth phenotype in which cell population growth is normal after short incubation in hydroxyurea." - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [date](http://purl.org/dc/elements/1.1/date) "2023-07-10T09:26:07Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37200372" - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "normal vegetative cell population growth after acute hydroxyurea treatment" - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) [label](http://www.w3.org/2000/01/rdf-schema#label) "normal vegetative cell population growth after short incubation in hydroxyurea"@en - Class: [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) - [normal vegetative cell population growth after short incubation in hydroxyurea](http://purl.obolibrary.org/obo/FYPO_0009110) SubClassOf [normal vegetative cell population growth](http://purl.obolibrary.org/obo/FYPO_0001357) ### sensitive to calcofluor and potassium chloride `http://purl.obolibrary.org/obo/FYPO_0007926` #### Removed - [sensitive to calcofluor and potassium chloride](http://purl.obolibrary.org/obo/FYPO_0007926) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to a combination of calcofluor and potassium chloride. Cells stop growing (and may die) at concentrations of calcofluor and potassium chloride that allow wild type cells to grow." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" #### Added - [sensitive to calcofluor and potassium chloride](http://purl.obolibrary.org/obo/FYPO_0007926) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to a combination of calcofluor and potassium chloride. Cells stop growing (and may die) at concentrations of calcofluor and potassium chloride that allow wild type cells to grow." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" ### sensitive to egtazic acid `http://purl.obolibrary.org/obo/FYPO_0007931` #### Removed - [sensitive to egtazic acid](http://purl.obolibrary.org/obo/FYPO_0007931) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to egtazic acid. Cells stop growing (and may die) at a concentration of egtazic acid that allows wild type cells to grow." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" #### Added - [sensitive to egtazic acid](http://purl.obolibrary.org/obo/FYPO_0007931) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to egtazic acid. Cells stop growing (and may die) at a concentration of egtazic acid that allows wild type cells to grow." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" ### sensitive to ethylenediaminetetraacetic acid `http://purl.obolibrary.org/obo/FYPO_0007928` #### Removed - [sensitive to ethylenediaminetetraacetic acid](http://purl.obolibrary.org/obo/FYPO_0007928) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to ethylenediaminetetraacetic acid (EDTA). Cells stop growing (and may die) at a concentration of ethylenediaminetetraacetic acid (EDTA) that allows wild type cells to grow." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" #### Added - [sensitive to ethylenediaminetetraacetic acid](http://purl.obolibrary.org/obo/FYPO_0007928) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phenotype observed in the vegetative growth phase of the life cycle in which cells show increased sensitivity to ethylenediaminetetraacetic acid (EDTA). Cells stop growing (and may die) at a concentration of ethylenediaminetetraacetic acid (EDTA) that allows wild type cells to grow." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw"
# 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 ```
manulera commented 1 year ago

Hi @matentzn. I recently did the upgrade to Protege 5.6 for this repository following your instructions in #4366. I saved the file with Protege and that made a lot of changes in the formatting in https://github.com/pombase/fypo/pull/4385, as expected.

However, now I have edited the ontology in the same computer, without other changes going in, and there is a few changes in the diff that simply switch the positions of annotations of a term without making a real change, see this PR's diff. Will this stop in the future after all inconsistencies are picked up, or is this something like the xsd_string that will happen every time we save the ontology in Protege?

cc: @ValWood

matentzn commented 1 year ago

I cant tell you that unfortunately @manulera - some things look odd, like you are using a wrong annotation property for your pmids in some cases (rdfs:comment instead of hasDbXref));

This kind of serialisation fluctuation should not generally happen! cc @anitacaron if she has an idea

anitacaron commented 1 year ago

I have seen this happens in other ontologies too. Somehow, Protégé doesn't apply all changes for the new serialization in the whole file. Checking the diffs, these are expected and will stop in the future.

github-actions[bot] commented 1 year ago

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

manulera commented 1 year ago

Thanks both@anitacaron and @matentz for the very fast response, as usual! And thanks nico for catching that those were errors (some of my first fypo edits). I have fixed them and will do the release after the merge. Thanks!

github-actions[bot] commented 1 year ago

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

ValWood commented 1 year ago

And thanks nico for catching that those were errors (some of my first fypo edits).

Is it possible to get error messages if we use the wrong properties. We get those with the GO pull requests is there something we need to do to make that happen?

matentzn commented 12 months ago

In mondo we have a strict system:

Test for permitted properties: https://github.com/monarch-initiative/mondo/blob/master/src/sparql/qc/general/qc-permitted-properties.sparql

Test for illegal axiom annotations: https://github.com/monarch-initiative/mondo/blob/master/src/sparql/qc/general/qc-illegal-axiom-annotation.sparql

You could adapt them to FYPO and integrate in QC!