closes #4485; closes #4483; closes #4482; closes #4476

[ValWood]

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Changes added to the edit file this PR

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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

RNA absent from cell during cellular response to glucose starvation http://purl.obolibrary.org/obo/FYPO_0008156

Added

• RNA absent from cell during cellular response to glucose starvation definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA measured in a cell is too low to detect during a cellular response to glucose starvation. Total RNA or a specific RNA may be affected."

  • database_cross_reference "PMID:18820678"

• RNA absent from cell during cellular response to glucose starvation label "RNA absent from cell during cellular response to glucose starvation"@en

• RNA absent from cell during cellular response to glucose starvation created_by "vw"

• RNA absent from cell during cellular response to glucose starvation creation_date "2024-01-30T16:15:37Z"^^dateTime

• Class: RNA absent from cell during cellular response to glucose starvation

• RNA absent from cell during cellular response to glucose starvation SubClassOf RNA absent from cell during vegetative growth

abnormal histone deacetylation at the silent mating-type locus during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008157

Added

• abnormal histone deacetylation at the silent mating-type locus during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which histone deacetylation is abnormal at the silent-mating type locus."

• abnormal histone deacetylation at the silent mating-type locus during vegetative growth created_by "vw"

• abnormal histone deacetylation at the silent mating-type locus during vegetative growth creation_date "2024-01-30T16:18:53Z"^^dateTime

• abnormal histone deacetylation at the silent mating-type locus during vegetative growth label "abnormal histone deacetylation at the silent mating-type locus during vegetative growth"@en

• Class: abnormal histone deacetylation at the silent mating-type locus during vegetative growth

• abnormal histone deacetylation at the silent mating-type locus during vegetative growth SubClassOf abnormal histone deacetylation during vegetative growth

abnormal regulatory lncRNA 3'-end processing http://purl.obolibrary.org/obo/FYPO_0008155

Added

• abnormal regulatory lncRNA 3'-end processing created_by "vw"

• abnormal regulatory lncRNA 3'-end processing definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which regulatory lncRNA 3' end processing is abnormal."

  • database_cross_reference "PMID:32415063"

• abnormal regulatory lncRNA 3'-end processing creation_date "2024-01-30T16:09:16Z"^^dateTime

• abnormal regulatory lncRNA 3'-end processing label "abnormal regulatory lncRNA 3'-end processing"@en

• Class: abnormal regulatory lncRNA 3'-end processing

• abnormal regulatory lncRNA 3'-end processing SubClassOf abnormal RNA 3'-end processing

abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008159

Added

• abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth created_by "vw"

• abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth creation_date "2024-01-30T16:23:13Z"^^dateTime

• abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth label "abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth"@en

• abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which histone phosphorylation at the silent mating-type locus does not occur. All histone phosphorylation may be affected, or phosphorylation of specific sites on specific histones may be abolished."

  • database_cross_reference "PMID:16246721"

• Class: abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth

• abolished histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth SubClassOf abolished histone phosphorylation during vegetative growth

increased activation of S-phase DNA damage checkpoint http://purl.obolibrary.org/obo/FYPO_0008162

Added

• increased activation of S-phase DNA damage checkpoint creation_date "2024-01-30T16:40:47Z"^^dateTime

• increased activation of S-phase DNA damage checkpoint definition "A cell cycle checkpoint phenotype in which the incidence of mitotic cell cycle arrest or delay due to regulation by the mitotic S-phase DNA damage checkpoint is greater than in wild type under any specified set of conditions."

  • database_cross_reference "PMID:18344406"

• increased activation of S-phase DNA damage checkpoint label "increased activation of S-phase DNA damage checkpoint"@en

• increased activation of S-phase DNA damage checkpoint created_by "vw"

• Class: increased activation of S-phase DNA damage checkpoint

• increased activation of S-phase DNA damage checkpoint SubClassOf increased mitotic DNA damage checkpoint activation

• increased activation of S-phase DNA damage checkpoint SubClassOf abnormal S-phase DNA damage checkpoint

increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008158

Added

• increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth creation_date "2024-01-30T16:21:20Z"^^dateTime

• increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth created_by "vw"

• increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which phosphorylation of serine at position 10 of histone H3 is increased at the silent mating-type locus."

  • comment "PMID:16246721"

• increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth label "increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth"@en

• Class: increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth

• increased histone H3-S10 phosphorylation at the silent mating-type locus during vegetative growth SubClassOf increased histone H3-S10 phosphorylation during vegetative growth

normal histone H3-K56 acetylation during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008160

Added

• normal histone H3-K56 acetylation during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 56 of histone H3 is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PMID:18344406"

• normal histone H3-K56 acetylation during vegetative growth creation_date "2024-01-30T16:33:35Z"^^dateTime

• normal histone H3-K56 acetylation during vegetative growth created_by "vw"

• normal histone H3-K56 acetylation during vegetative growth label "normal histone H3-K56 acetylation during vegetative growth"@en

• Class: normal histone H3-K56 acetylation during vegetative growth

• normal histone H3-K56 acetylation during vegetative growth SubClassOf normal histone acetylation during vegetative growth

normal histone H4-K16 acetylation during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008161

Added

• normal histone H4-K16 acetylation during vegetative growth label "normal histone H4-K16 acetylation during vegetative growth"@en

• normal histone H4-K16 acetylation during vegetative growth definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 16 of histone H4 is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PMID:18344406"

• normal histone H4-K16 acetylation during vegetative growth created_by "vw"

• normal histone H4-K16 acetylation during vegetative growth creation_date "2024-01-30T16:36:56Z"^^dateTime

• Class: normal histone H4-K16 acetylation during vegetative growth

• normal histone H4-K16 acetylation during vegetative growth SubClassOf normal histone acetylation during vegetative growth

Changes to ontology after reasoner runs

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Coming soon

Errors reported

Level	Rule Name	Subject	Property	Value
WARN	missing_definition	abolished protein localization to heterochromatin at silent mating-type cassette during vegetative growth	definition	
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