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pombase / fypo

Fission Yeast Phenotype Ontology
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‘closes #4550

Closed ValWood closed 1 month ago

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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 DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0008216` #### Added - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of DNA N-glycosylase activity is abnormal." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) [label](http://www.w3.org/2000/01/rdf-schema#label) "abnormal DNA N-glycosylase activity"@en - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T14:25:17Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([quality](http://purl.obolibrary.org/obo/PATO_0000001) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [DNA N-glycosylase activity](http://purl.obolibrary.org/obo/GO_0019104)) and ([qualifier](http://purl.obolibrary.org/obo/RO_0002573) some [abnormal](http://purl.obolibrary.org/obo/PATO_0000460))) - [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) ### abnormal DNA-1,N6-ethenoadenine N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0000692` #### Removed - [abnormal DNA-1,N6-ethenoadenine N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0000692) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal DNA-1,N6-ethenoadenine N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0000692) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abnormal hypoxanthine DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0004279` #### Removed - [abnormal hypoxanthine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004279) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal hypoxanthine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004279) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abnormal oxanine DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0004283` #### Removed - [abnormal oxanine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004283) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal oxanine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004283) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abnormal purine-specific mismatch base pair DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0004676` #### Removed - [abnormal purine-specific mismatch base pair DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004676) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal purine-specific mismatch base pair DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004676) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abnormal uracil DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0004277` #### Removed - [abnormal uracil DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004277) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal uracil DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004277) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abnormal xanthine DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0004281` #### Removed - [abnormal xanthine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004281) SubClassOf [abnormal catalytic activity](http://purl.obolibrary.org/obo/FYPO_0000661) #### Added - [abnormal xanthine DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0004281) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### abolished chromatin binding at promoter region `http://purl.obolibrary.org/obo/FYPO_0008210` #### Added - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which occurrence of chromatin binding by a gene product (usually a protein) at one or more promoter regions does not occur." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished chromatin binding at promoter region"@en - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T13:40:02Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) - [abolished chromatin binding at promoter region](http://purl.obolibrary.org/obo/FYPO_0008210) SubClassOf [abolished chromatin binding](http://purl.obolibrary.org/obo/FYPO_0001093) ### abolished histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0006112` #### Removed - [abolished histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0006112) SubClassOf [abolished histone methylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002565) #### Added - [abolished histone H3-K9 dimethylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0006112) SubClassOf [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) ### abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008212` #### Added - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) [label](http://www.w3.org/2000/01/rdf-schema#label) "abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth"@en - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which methylation of lysine at position 9 of histone H3 in silent mating-type cassettes does not occur." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T13:50:33Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - Class: [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) - [abolished histone H3-K9 methylation at silent mating-type cassette during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008212) SubClassOf [abolished histone H3-K9 methylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0002566) ### abolished protein neddylation during vegetative growth `http://purl.obolibrary.org/obo/FYPO_0008208` #### Added - [abolished protein neddylation during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0008208) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" ### decreased antisense RNA level during heat stress `http://purl.obolibrary.org/obo/FYPO_0008211` #### Added - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T13:47:34Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) [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 antisense RNA measured in a cell is lower than normal duing heat stress. Antisense RNA is transcribed from the coding, rather than the template, strand of DNA." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased antisense RNA level during heat stress"@en - Class: [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) - [decreased antisense RNA level during heat stress](http://purl.obolibrary.org/obo/FYPO_0008211) SubClassOf [decreased antisense RNA level](http://purl.obolibrary.org/obo/FYPO_0004816) ### decreased pre-mRNA level during cellular response to heat `http://purl.obolibrary.org/obo/FYPO_0008214` #### Added - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) [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 pre-mRNA measured in a cell during a cellular response to heat is lower than normal. Total pre-mRNA or a specific pre-mRNA may be affected." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T14:12:11Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) [label](http://www.w3.org/2000/01/rdf-schema#label) "decreased pre-mRNA level during cellular response to heat"@en - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - Class: [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) SubClassOf [decreased RNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0002287) - [decreased pre-mRNA level during cellular response to heat](http://purl.obolibrary.org/obo/FYPO_0008214) SubClassOf [decreased pre-mRNA level](http://purl.obolibrary.org/obo/FYPO_0002937) ### increased DNA N-glycosylase activity `http://purl.obolibrary.org/obo/FYPO_0008217` #### Added - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T14:33:49Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased DNA N-glycosylase activity"@en - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A molecular function phenotype in which the observed rate of DNA N-glycosylase activity is increased." - Class: [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) EquivalentTo [has_part](http://purl.obolibrary.org/obo/BFO_0000051) some ([increased rate](http://purl.obolibrary.org/obo/PATO_0000912) and ([inheres_in](http://purl.obolibrary.org/obo/RO_0000052) some [DNA N-glycosylase activity](http://purl.obolibrary.org/obo/GO_0019104))) - [increased DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008217) SubClassOf [abnormal DNA N-glycosylase activity](http://purl.obolibrary.org/obo/FYPO_0008216) ### increased vegetative cell population growth on lactate carbon source `http://purl.obolibrary.org/obo/FYPO_0008213` #### Added - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T14:06:36Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vegetative cell population phenotype in which cell growth is increased relative to normal in a medium containing lactate as the carbon source." - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PomBase:vw" - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased vegetative cell population growth on lactate carbon source"@en - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - Class: [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) - [increased vegetative cell population growth on lactate carbon source](http://purl.obolibrary.org/obo/FYPO_0008213) SubClassOf [increased vegetative cell population growth](http://purl.obolibrary.org/obo/FYPO_0004557) ### resistance to Rho GTPase inhibitor O1 `http://purl.obolibrary.org/obo/FYPO_0008215` #### Added - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) [creation_date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2024-05-08T14:17:51Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "fission_yeast_phenotype" - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) [created_by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) [label](http://www.w3.org/2000/01/rdf-schema#label) "resistance to Rho GTPase inhibitor O1"@en - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An increased chemical resistance phenotype observed in the vegetative growth phase of the life cycle in which cells grow in the presence of a higher concentration of GTPase inhibitor O1 than normal." - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "PomBase:vw" - Class: [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) - [resistance to Rho GTPase inhibitor O1](http://purl.obolibrary.org/obo/FYPO_0008215) SubClassOf [increased resistance to chemical during vegetative growth](http://purl.obolibrary.org/obo/FYPO_0000126)
# 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 ```