closes #4618; closes #4617; closes #4616; closes #4615; closes #4614;…

[ValWood]

… closes #4607

[github-actions]

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

abnormal DNA repair during vegetative growth http://purl.obolibrary.org/obo/FYPO_0000188

Removed

• abnormal DNA repair during vegetative growth has_related_synonym "abnormal DNA repair during mitotic cell cycle"
  • database_cross_reference "PomBase:mah"

Added

• abnormal DNA repair during vegetative growth has_related_synonym "abnormal DNA repair during mitotic cell cycle"

abnormal punctate nuclear protein localization during meiotic prophase I http://purl.obolibrary.org/obo/FYPO_0008300

Added

• abnormal punctate nuclear protein localization during meiotic prophase I created_by "vw"

• abnormal punctate nuclear protein localization during meiotic prophase I label "abnormal punctate nuclear protein localization during meiotic prophase I"@en

• abnormal punctate nuclear protein localization during meiotic prophase I definition "A cell phenotype observed during prophase of the first division of the meiotic cell cycle in which a protein that is normally localized to discrete regions in the nucleus, visible as foci or dots by microscopy, is abnormally localized."

  • database_cross_reference "PomBase:pc"

• abnormal punctate nuclear protein localization during meiotic prophase I creation_date "2024-10-07T10:00:27Z"^^dateTime

• abnormal punctate nuclear protein localization during meiotic prophase I has_obo_namespace "fission_yeast_phenotype"

• Class: abnormal punctate nuclear protein localization during meiotic prophase I

• abnormal punctate nuclear protein localization during meiotic prophase I SubClassOf abnormal protein localization during meiosis

abolished protein localization to nucleus during meiosis http://purl.obolibrary.org/obo/FYPO_0008304

Added

• abolished protein localization to nucleus during meiosis created_by "vw"

• abolished protein localization to nucleus during meiosis has_obo_namespace "fission_yeast_phenotype"

• abolished protein localization to nucleus during meiosis label "abolished protein localization to nucleus during meiosis"@en

• abolished protein localization to nucleus during meiosis creation_date "2024-10-07T10:12:16Z"^^dateTime

• abolished protein localization to nucleus during meiosis definition "A cell phenotype in which the localization of a protein to the nucleus during one or both meiotic nuclear divisions is abolished."

  • database_cross_reference "PomBase:pc"

• Class: abolished protein localization to nucleus during meiosis

• abolished protein localization to nucleus during meiosis SubClassOf abnormal protein localization to nucleus during meiosis

abolished punctate nuclear protein localization during meiotic prophase I http://purl.obolibrary.org/obo/FYPO_0008302

Added

• abolished punctate nuclear protein localization during meiotic prophase I created_by "vw"

• abolished punctate nuclear protein localization during meiotic prophase I definition "A cell phenotype observed during prophase of the first division of the meiotic cell cycle in which the localization of a protein to discrete regions in the nucleus, visible as foci or dots by microscopy, is abolished."

  • database_cross_reference "PomBase:pc"

• abolished punctate nuclear protein localization during meiotic prophase I has_obo_namespace "fission_yeast_phenotype"

• abolished punctate nuclear protein localization during meiotic prophase I label "abolished punctate nuclear protein localization during meiotic prophase I"@en

• abolished punctate nuclear protein localization during meiotic prophase I creation_date "2024-10-07T10:03:21Z"^^dateTime

• Class: abolished punctate nuclear protein localization during meiotic prophase I

• abolished punctate nuclear protein localization during meiotic prophase I SubClassOf abnormal punctate nuclear protein localization during meiotic prophase I

decreased cell diameter at division http://purl.obolibrary.org/obo/FYPO_0008307

Added

• decreased cell diameter at division creation_date "2024-10-07T10:31:53Z"^^dateTime

• decreased cell diameter at division has_obo_namespace "A cell phenotype in which a cell divides with a smaller diameter than normal (i.e. compared to wild-type cells under the same conditions)."

  • database_cross_reference "PomBase:pc"

• decreased cell diameter at division has_obo_namespace "fission_yeast_phenotype"

• decreased cell diameter at division label "decreased cell diameter at division"@en

• decreased cell diameter at division created_by "vw"

• Class: decreased cell diameter at division

• decreased cell diameter at division SubClassOf viable thin vegetative cell

decreased protein kinase activity during cellular response to osmotic stress http://purl.obolibrary.org/obo/FYPO_0005270

Removed

• decreased protein kinase activity during cellular response to osmotic stress has_exact_synonym "reduced protein kinase activity during cellular response to salt stress"

  • database_cross_reference "PomBase:mah"

• decreased protein kinase activity during cellular response to osmotic stress definition "A molecular function phenotype in which the observed rate of a protein kinase activity is decreased during a cellular response to salt stress."

  • database_cross_reference "PomBase:mah"

• decreased protein kinase activity during cellular response to osmotic stress label "decreased protein kinase activity during cellular response to salt stress"

Added

• decreased protein kinase activity during cellular response to osmotic stress definition "A molecular function phenotype in which the observed rate of a protein kinase activity is decreased during a cellular response to osmotic stress."

  • database_cross_reference "PomBase:mah"

• decreased protein kinase activity during cellular response to osmotic stress label "decreased protein kinase activity during cellular response to osmotic stress"

decreased punctate nuclear protein localization during meiotic prophase I http://purl.obolibrary.org/obo/FYPO_0008301

Added

• decreased punctate nuclear protein localization during meiotic prophase I creation_date "2024-10-07T10:02:04Z"^^dateTime

• decreased punctate nuclear protein localization during meiotic prophase I has_obo_namespace "fission_yeast_phenotype"

• decreased punctate nuclear protein localization during meiotic prophase I definition "A cell phenotype observed during prophase of the first division of the meiotic cell cycle in which a protein that is normally localized to discrete regions in the nucleus, visible as foci or dots by microscopy, is abnormally localized such that fewer dots are observed than in normal (wild type) cells."

  • database_cross_reference "PomBase:pc"

• decreased punctate nuclear protein localization during meiotic prophase I created_by "vw"

• decreased punctate nuclear protein localization during meiotic prophase I label "decreased punctate nuclear protein localization during meiotic prophase I"@en

• Class: decreased punctate nuclear protein localization during meiotic prophase I

• decreased punctate nuclear protein localization during meiotic prophase I SubClassOf abnormal punctate nuclear protein localization during meiotic prophase I

decreased rate of protein exchange at plasma membrane http://purl.obolibrary.org/obo/FYPO_0008299

Added

• decreased rate of protein exchange at plasma membrane label "decreased rate of protein exchange at plasma membrane"@en

• decreased rate of protein exchange at plasma membrane creation_date "2024-10-07T09:51:54Z"^^dateTime

• decreased rate of protein exchange at plasma membrane created_by "vw"

• decreased rate of protein exchange at plasma membrane definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the rate, or speed, of protein exchange between the plasma membrane and the cytosol is decreased."

  • database_cross_reference "PomBase:pc"

• decreased rate of protein exchange at plasma membrane has_obo_namespace "fission_yeast_phenotype"

• Class: decreased rate of protein exchange at plasma membrane

• decreased rate of protein exchange at plasma membrane SubClassOf abnormal protein localization to plasma membrane at cell division site during vegetative growth

increased cell surface area at division http://purl.obolibrary.org/obo/FYPO_0008309

Added

• increased cell surface area at division definition "A cell phenotype in which a cell divides with a greater surface area than normal (i.e. compared to wild-type cells under the same conditions)."

  • database_cross_reference "PomBase:pc"

• increased cell surface area at division creation_date "2024-10-07T10:42:26Z"^^dateTime

• increased cell surface area at division label "increased cell surface area at division"@en

• increased cell surface area at division has_obo_namespace "fission_yeast_phenotype"

• increased cell surface area at division created_by "vw"

• Class: increased cell surface area at division

• increased cell surface area at division SubClassOf viable swollen vegetative cell

increased cell volume at division http://purl.obolibrary.org/obo/FYPO_0008308

Added

• increased cell volume at division creation_date "2024-10-07T10:39:11Z"^^dateTime

• increased cell volume at division created_by "vw"

• increased cell volume at division definition "A cell phenotype in which a cell divides with a greater volume than normal (i.e. compared to wild-type cells under the same conditions)."

  • database_cross_reference "PomBase:pc"

• increased cell volume at division has_obo_namespace "fission_yeast_phenotype"

• increased cell volume at division label "increased cell volume at division"@en

• Class: increased cell volume at division

• increased cell volume at division SubClassOf viable swollen vegetative cell

increased inter-sister chromatid meiotic recombination http://purl.obolibrary.org/obo/FYPO_0008305

Added

• increased inter-sister chromatid meiotic recombination definition "A cellular process phenotype in which the occurrence of meiotic recombination between alleles on different sister chromatids (inter-sister recombination) is increased."

  • database_cross_reference "PomBase:pc"

• increased inter-sister chromatid meiotic recombination created_by "vw"

• increased inter-sister chromatid meiotic recombination has_obo_namespace "fission_yeast_phenotype"

• increased inter-sister chromatid meiotic recombination creation_date "2024-10-07T10:17:50Z"^^dateTime

• increased inter-sister chromatid meiotic recombination label "increased inter-sister chromatid meiotic recombination"@en

• Class: increased inter-sister chromatid meiotic recombination

• increased inter-sister chromatid meiotic recombination SubClassOf increased meiotic recombination

increased mitotic DNA replication initiation from late origin http://purl.obolibrary.org/obo/FYPO_0008306

Added

• increased mitotic DNA replication initiation from late origin has_obo_namespace "fission_yeast_phenotype"

• increased mitotic DNA replication initiation from late origin creation_date "2024-10-07T10:25:43Z"^^dateTime

• increased mitotic DNA replication initiation from late origin created_by "vw"

• increased mitotic DNA replication initiation from late origin definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the frequency of DNA replication initiation is higher than normal at layte origins."

• increased mitotic DNA replication initiation from late origin label "increased mitotic DNA replication initiation from late origin"@en

• Class: increased mitotic DNA replication initiation from late origin

• increased mitotic DNA replication initiation from late origin SubClassOf abnormal mitotic DNA replication initiation

loss of viability in stationary phase upon phosphate starvation http://purl.obolibrary.org/obo/FYPO_0008123

Removed

• loss of viability in stationary phase upon phosphate starvation label "loss of viability in stationary phase upon phopshate starvation"@en

Added

• loss of viability in stationary phase upon phosphate starvation label "loss of viability in stationary phase upon phosphate starvation"

normal number of Rad51 foci during meiotic prophase I http://purl.obolibrary.org/obo/FYPO_0008303

Added

• normal number of Rad51 foci during meiotic prophase I label "normal number of Rad51 foci during meiotic prophase I"@en

• normal number of Rad51 foci during meiotic prophase I created_by "vw"

• normal number of Rad51 foci during meiotic prophase I has_obo_namespace "fission_yeast_phenotype"

• normal number of Rad51 foci during meiotic prophase I creation_date "2024-10-07T10:06:50Z"^^dateTime

• normal number of Rad51 foci during meiotic prophase I definition "A cell phenotype observed during prophase of the first division of the meiotic cell cycle in which the number of sites at which the protein Rad51 accumulates is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:pc"

• Class: normal number of Rad51 foci during meiotic prophase I

• normal number of Rad51 foci during meiotic prophase I SubClassOf normal protein localization during meiosis

Changes to ontology after reasoner runs

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Coming soon

Errors reported

Level	Rule Name	Subject	Property	Value
WARN	missing_definition	decreased cell diameter at division	definition	
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
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