closes #4770,#4783,#4785,#4787,#4788,#4789,#4790,#4791

[PCarme]

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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 histone H3-K9 dimethylation at rDNA during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010028

Added

• abolished histone H3-K9 dimethylation at rDNA during vegetative growth created_by "PomBase:pc"

• abolished histone H3-K9 dimethylation at rDNA during vegetative growth creation_date "2026-02-25T11:00:38Z"^^dateTime

• abolished histone H3-K9 dimethylation at rDNA during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the dimethylation of lysine at position 9 of histone H3 at ribosomal DNA does not occur."

  • database_cross_reference "PomBase:pc"

• abolished histone H3-K9 dimethylation at rDNA during vegetative growth label "abolished histone H3-K9 dimethylation at rDNA during vegetative growth"@en

• Class: abolished histone H3-K9 dimethylation at rDNA during vegetative growth

• abolished histone H3-K9 dimethylation at rDNA during vegetative growth SubClassOf abolished histone H3-K9 methylation during vegetative growth

abolished histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth http://purl.obolibrary.org/obo/FYPO_0006111

Removed

• abolished histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth SubClassOf abnormal histone H3-K9 methylation during vegetative growth

Added

• abolished histone H3-K9 dimethylation at subtelomeric heterochromatin during vegetative growth SubClassOf abnormal histone H3-K9 dimethylation during vegetative growth

abolished histone H3-K9 dimethylation during vegetative growth http://purl.obolibrary.org/obo/FYPO_0007886

Removed

• abolished histone H3-K9 dimethylation during vegetative growth SubClassOf abolished histone H3-K9 methylation during vegetative growth

Added

• abolished histone H3-K9 dimethylation during vegetative growth SubClassOf abnormal histone H3-K9 dimethylation during vegetative growth

abolished mitotic recombination at centromere http://purl.obolibrary.org/obo/FYPO_0010026

Added

• abolished mitotic recombination at centromere label "abolished mitotic recombination at centromere"@en

• abolished mitotic recombination at centromere created_by "PomBase:pc"

• abolished mitotic recombination at centromere definition "A cellular process phenotype in which mitotic recombination does not occur in centromeric regions."

  • database_cross_reference "PomBase:pc"

• abolished mitotic recombination at centromere creation_date "2026-02-25T10:48:31Z"^^dateTime

• Class: abolished mitotic recombination at centromere

• abolished mitotic recombination at centromere EquivalentTo has_part some
  (PATO_0001558 and (happens_during some GO_0072690) and (occurs_at some SO_0000577) and (inheres_in some GO_0006312))

• abolished mitotic recombination at centromere SubClassOf abnormal mitotic recombination

abolished nuclear pore clustering during cellular response to hydroxyurea http://purl.obolibrary.org/obo/FYPO_0010034

Added

• abolished nuclear pore clustering during cellular response to hydroxyurea creation_date "2026-02-25T11:52:12Z"^^dateTime

• abolished nuclear pore clustering during cellular response to hydroxyurea definition "A localization phenotype observed in the vegetative growth phase of the life cycle in which nuclear pore clustering during cellular response to hydroxyurea does not occur."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:41259369"

• abolished nuclear pore clustering during cellular response to hydroxyurea label "abolished nuclear pore clustering during cellular response to hydroxyurea"@en

• abolished nuclear pore clustering during cellular response to hydroxyurea created_by "PomBase:pc"

• Class: abolished nuclear pore clustering during cellular response to hydroxyurea

• abolished nuclear pore clustering during cellular response to hydroxyurea SubClassOf abnormal nuclear pore localization

abolished protein localization to P-bodies during mating http://purl.obolibrary.org/obo/FYPO_0010020

Added

• abolished protein localization to P-bodies during mating created_by "PomBase:pc"

• abolished protein localization to P-bodies during mating creation_date "2026-02-25T10:01:59Z"^^dateTime

• abolished protein localization to P-bodies during mating definition "A cell phenotype in which the localization of a protein to P-bodies during conjugation is abolished."

  • database_cross_reference "PomBase:pc"

• abolished protein localization to P-bodies during mating label "abolished protein localization to P-bodies during mating"@en

• Class: abolished protein localization to P-bodies during mating

• abolished protein localization to P-bodies during mating EquivalentTo has_part some
  (PATO_0001558 and (happens_during some GO_0000747) and (inheres_in some GO_0110012))

• abolished protein localization to P-bodies during mating SubClassOf abnormal protein localization to P-bodies during mating

circularized chromosome during mitotic G1 phase http://purl.obolibrary.org/obo/FYPO_0002907

Added

• circularized chromosome during mitotic G1 phase has_related_synonym "chromosome ends fusion during mitotic G1 phase"
  • database_cross_reference "PomBase:vw"

circularized chromosome during mitotic G2 phase http://purl.obolibrary.org/obo/FYPO_0004789

Added

• circularized chromosome during mitotic G2 phase has_related_synonym "chromosome ends fusion during mitotic G2 phase"
  • database_cross_reference "PomBase:vw"

decreased CCR4-NOT complex binding http://purl.obolibrary.org/obo/FYPO_0010031

Added

• decreased CCR4-NOT complex binding creation_date "2026-02-25T11:33:56Z"^^dateTime

• decreased CCR4-NOT complex binding definition "A molecular function phenotype in which occurrence of CCR4-NOT complex binding by a gene product (usually a protein) in a mutant is decreased. The affected gene product may be encoded by the mutated gene, or by a different gene."

  • database_cross_reference "PMID:41184513"

  • database_cross_reference "PomBase:vw"

• decreased CCR4-NOT complex binding label "decreased CCR4-NOT complex binding"@en

• decreased CCR4-NOT complex binding created_by "PomBase:pc"

• Class: decreased CCR4-NOT complex binding

• decreased CCR4-NOT complex binding EquivalentTo has_part some
  (PATO_0002052 and (inheres_in some GO_0044877) and (towards some GO_0030014) and (qualifier some PATO_0000460))

• decreased CCR4-NOT complex binding SubClassOf abnormal protein complex binding

• decreased CCR4-NOT complex binding SubClassOf decreased protein-protein interaction

decreased mitotic recombination at centromere http://purl.obolibrary.org/obo/FYPO_0006281

Added

• decreased mitotic recombination at centromere EquivalentTo has_part some
  (PATO_0002052 and (happens_during some GO_0072690) and (occurs_at some SO_0000577) and (inheres_in some GO_0006312))

decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010037

Added

• decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth label "decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth"@en

• decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth created_by "PomBase:pc"

• decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to the medial cortex of a cell is decreased, and the protein is present in the cytoplasm instead. There may be little or no protein detected at the medial cortex."

  • database_cross_reference "PomBase:pc"

• decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth creation_date "2026-02-25T13:22:21Z"^^dateTime

• Class: decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth

• decreased protein localization to medial cortex with protein mislocalized to cell tip during vegetative growth SubClassOf decreased protein localization to medial cortex during vegetative growth

decreased sumoylated protein-protein interaction http://purl.obolibrary.org/obo/FYPO_0010025

Added

• decreased sumoylated protein-protein interaction definition "A molecular function phenotype in which the binding of a sumoylated protein to another protein occurs to a lower extent than normal. The relevant proteins may include the one encoded by the mutated gene, or may both be encoded by different genes."

  • database_cross_reference "PomBase:pc"

• decreased sumoylated protein-protein interaction label "decreased sumoylated protein-protein interaction"@en

• decreased sumoylated protein-protein interaction created_by "PomBase:pc"

• decreased sumoylated protein-protein interaction creation_date "2026-02-25T10:36:44Z"^^dateTime

• Class: decreased sumoylated protein-protein interaction

• decreased sumoylated protein-protein interaction SubClassOf decreased protein-protein interaction

increased duration of double-strand break repair via homologous recombination http://purl.obolibrary.org/obo/FYPO_0010021

Added

• increased duration of double-strand break repair via homologous recombination definition "A cellular process phenotype in which the duration of repair of double-strand breaks via homologous recombination is longer than normal."

  • database_cross_reference "PomBase:pc"

• increased duration of double-strand break repair via homologous recombination label "increased duration of double-strand break repair via homologous recombination"@en

• increased duration of double-strand break repair via homologous recombination created_by "PomBase:pc"

• increased duration of double-strand break repair via homologous recombination creation_date "2026-02-25T10:11:26Z"^^dateTime

• Class: increased duration of double-strand break repair via homologous recombination

• increased duration of double-strand break repair via homologous recombination EquivalentTo has_part some
  (PATO_0000498 and (inheres_in some GO_0000724))

• increased duration of double-strand break repair via homologous recombination SubClassOf abnormal double-strand break repair during vegetative growth

increased mitotic recombination at centromere http://purl.obolibrary.org/obo/FYPO_0010024

Added

• increased mitotic recombination at centromere creation_date "2026-02-25T10:31:26Z"^^dateTime

• increased mitotic recombination at centromere label "increased mitotic recombination at centromere"@en

• increased mitotic recombination at centromere created_by "PomBase:pc"

• increased mitotic recombination at centromere definition "A cellular process phenotype in which the occurrence of mitotic recombination is increased in centromeric regions."

  • database_cross_reference "PomBase:pc"

• Class: increased mitotic recombination at centromere

• increased mitotic recombination at centromere EquivalentTo has_part some
  (PATO_0002051 and (happens_during some GO_0072690) and (occurs_at some SO_0000577) and (inheres_in some GO_0006312))

• increased mitotic recombination at centromere SubClassOf increased mitotic recombination

increased protein localization to centromeric chromatin during mitotic G1 phase http://purl.obolibrary.org/obo/FYPO_0005898

Removed

• increased protein localization to centromeric chromatin during mitotic G1 phase SubClassOf abnormal protein localization to centromeric chromatin during vegetative growth

Added

• increased protein localization to centromeric chromatin during mitotic G1 phase SubClassOf increased protein localization to centromeric chromatin during vegetative growth

increased protein localization to centromeric chromatin during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010023

Added

• increased protein localization to centromeric chromatin during vegetative growth definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to centromeric chromatin is higher than normal."

  • database_cross_reference "PomBase:pc"

• increased protein localization to centromeric chromatin during vegetative growth created_by "PomBase:pc"

• increased protein localization to centromeric chromatin during vegetative growth label "increased protein localization to centromeric chromatin during vegetative growth"@en

• increased protein localization to centromeric chromatin during vegetative growth creation_date "2026-02-25T10:26:26Z"^^dateTime

• Class: increased protein localization to centromeric chromatin during vegetative growth

• increased protein localization to centromeric chromatin during vegetative growth EquivalentTo has_part some
  (PATO_0002051 and (happens_during some GO_0072690) and (occurs_at some SO_0001795) and (inheres_in some GO_0071168))

• increased protein localization to centromeric chromatin during vegetative growth SubClassOf abnormal protein localization to centromeric chromatin during vegetative growth

medial cortical nodes present in decreased number http://purl.obolibrary.org/obo/FYPO_0010030

Added

• medial cortical nodes present in decreased number creation_date "2026-02-25T11:21:52Z"^^dateTime

• medial cortical nodes present in decreased number definition "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which cells contain fewer medial cortical nodes than normal."

  • database_cross_reference "PomBase:vw"

• medial cortical nodes present in decreased number label "medial cortical nodes present in decreased number"@en

• medial cortical nodes present in decreased number created_by "PomBase:pc"

• Class: medial cortical nodes present in decreased number

• medial cortical nodes present in decreased number SubClassOf abnormal subcellular component during vegetative growth

normal chromosome end protection http://purl.obolibrary.org/obo/FYPO_0010036

Added

• normal chromosome end protection created_by "PomBase:pc"

• normal chromosome end protection creation_date "2026-02-25T13:09:05Z"^^dateTime

• normal chromosome end protection definition "A cellular process phenotype in which any chromosome end protection is normal (i.e. indistinguishable from wild type). Chromosome end protection protects chromosome ends from potentially harmful DNA repair pathways, such as non homologous end joining."

  • database_cross_reference "PMID:41201383"

  • database_cross_reference "PomBase:vw"

• normal chromosome end protection label "normal chromosome end protection"@en

• Class: normal chromosome end protection

• normal chromosome end protection SubClassOf normal cellular process during vegetative growth

normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010032

Added

• normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth creation_date "2026-02-25T11:39:23Z"^^dateTime

• normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth label "normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth"@en

• normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth created_by "PomBase:pc"

• normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the trimethylation of lysine at position 36 of histone H3 at the centromere outer repeat is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:pc"

• Class: normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth

• normal histone H3-K36 trimethylation at centromere outer repeat during vegetative growth SubClassOf normal histone H3-K36 trimethylation during vegetative growth

normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010033

Added

• normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth label "normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth"@en

• normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth created_by "PomBase:pc"

• normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the dimethylation of lysine at position 9 of histone H3 in one or more heterochromatin domains is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:pc"

• normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth creation_date "2026-02-25T11:43:05Z"^^dateTime

• Class: normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth

• normal histone H3-K9 dimethylation at heterochromatin domain during vegetative growth SubClassOf normal histone H3-K9 methylation at heterochromatin domain during vegetative growth

normal histone H3-K9 dimethylation at rDNA during vegetative growth http://purl.obolibrary.org/obo/FYPO_0010029

Added

• normal histone H3-K9 dimethylation at rDNA during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the dimethylation of lysine at position 9 of histone H3 at ribosomal DNA is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:pc"

• normal histone H3-K9 dimethylation at rDNA during vegetative growth created_by "PomBase:pc"

• normal histone H3-K9 dimethylation at rDNA during vegetative growth creation_date "2026-02-25T11:05:52Z"^^dateTime

• normal histone H3-K9 dimethylation at rDNA during vegetative growth label "normal histone H3-K9 dimethylation at rDNA during vegetative growth"@en

• Class: normal histone H3-K9 dimethylation at rDNA during vegetative growth

• normal histone H3-K9 dimethylation at rDNA during vegetative growth SubClassOf normal histone H3-K9 methylation at rDNA during vegetative growth

normal mitotic recombination frequency at centromere http://purl.obolibrary.org/obo/FYPO_0010027

Added

• normal mitotic recombination frequency at centromere creation_date "2026-02-25T10:52:21Z"^^dateTime

• normal mitotic recombination frequency at centromere definition "A cellular process phenotype in which the frequency of occurrence of mitotic recombination is normal (i.e. indistinguishable from wild type) at centromeric regions."

  • database_cross_reference "PomBase:pc"

• normal mitotic recombination frequency at centromere label "normal mitotic recombination frequency at centromere"@en

• normal mitotic recombination frequency at centromere created_by "PomBase:pc"

• Class: normal mitotic recombination frequency at centromere

• normal mitotic recombination frequency at centromere EquivalentTo has_part some
  (PATO_0000057 and (happens_during some GO_0072690) and (occurs_at some SO_0000577) and (inheres_in some GO_0006312) and (qualifier some PATO_0000461))

• normal mitotic recombination frequency at centromere SubClassOf normal mitotic recombination frequency

normal nuclear pore clustering during cellular response to hydroxyurea http://purl.obolibrary.org/obo/FYPO_0010035

Added

• normal nuclear pore clustering during cellular response to hydroxyurea creation_date "2026-02-25T11:54:39Z"^^dateTime

• normal nuclear pore clustering during cellular response to hydroxyurea created_by "PomBase:pc"

• normal nuclear pore clustering during cellular response to hydroxyurea label "normal nuclear pore clustering during cellular response to hydroxyurea"@en

• normal nuclear pore clustering during cellular response to hydroxyurea definition "A localization phenotype observed in the vegetative growth phase of the life cycle in which nuclear pore clustering during cellular response to hydroxyurea is normal (i.e. indistinguishable from wild type). Nuclear pore complexes aggregate into discrete clusters in presence of hydroxyurea."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:41259369"

• Class: normal nuclear pore clustering during cellular response to hydroxyurea

• normal nuclear pore clustering during cellular response to hydroxyurea SubClassOf normal nuclear pore localization

normal number of Rad52 foci during cellular response to bleomycin http://purl.obolibrary.org/obo/FYPO_0005437

Removed

• normal number of Rad52 foci during cellular response to bleomycin SubClassOf cellular physical quality phenotype during vegetative growth

normal number of Rad52 foci during cellular response to methyl methanesulfonate http://purl.obolibrary.org/obo/FYPO_0010022

Added

• normal number of Rad52 foci during cellular response to methyl methanesulfonate creation_date "2026-02-25T10:20:41Z"^^dateTime

• normal number of Rad52 foci during cellular response to methyl methanesulfonate has_related_synonym "normal number of Rad52 foci during cellular response to MMS"

  • database_cross_reference "PomBase:pc"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the number of sites at which the protein Rad52 (also called Rad22) accumulates is normal (i.e. indistinguishable from wild type) during a cellular response to methyl methanesulfonate."

  • database_cross_reference "PomBase:pc"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate has_related_synonym "normal number of Rad52 foci during cellular response to DNA damage"

  • database_cross_reference "PomBase:pc"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate label "normal number of Rad52 foci during cellular response to methyl methanesulfonate"@en

• normal number of Rad52 foci during cellular response to methyl methanesulfonate has_exact_synonym "normal number of Rad22 foci during cellular response to methyl methanesulfonate"

  • database_cross_reference "PomBase:pc"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate created_by "PomBase:pc"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate has_obo_namespace "fission_yeast_phenotype"

• normal number of Rad52 foci during cellular response to methyl methanesulfonate has_exact_synonym "normal number of Rad52 foci during cellular response to methyl methanesulfonate during vegetative growth"

  • database_cross_reference "PomBase:pc"

• Class: normal number of Rad52 foci during cellular response to methyl methanesulfonate

• normal number of Rad52 foci during cellular response to methyl methanesulfonate SubClassOf normal number of Rad52 foci during vegetative growth

normal protein localization to medial cortex during vegetative growth http://purl.obolibrary.org/obo/FYPO_0002558

Added

• normal protein localization to medial cortex during vegetative growth SubClassOf normal protein localization to lateral cell cortex during vegetative growth

Changes to ontology after reasoner runs

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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	
WARN	missing_obsolete_label	DEPRECATED increased subtelomere-derived RNA level	rdfs:label	DEPRECATED increased subtelomere-derived RNA level
WARN	missing_obsolete_label	DEPRECATED increased protein localization to chromatin at centromere outer repeat	rdfs:label	DEPRECATED increased protein localization to chromatin at centromere outer repeat
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