closes #4563; closes #4560; closes #4559; closes #4558; closes #4557;…

[ValWood]

… closes #4549;

[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

abolished MBF complex assembly during mitotic G1 phase http://purl.obolibrary.org/obo/FYPO_0006563

Removed

• abolished MBF complex assembly during mitotic G1 phase EquivalentTo has_part some
  (lacking processual parts and (inheres_in some MBF transcription complex assembly) and (qualifier some abnormal))

abolished nuclear RNA-directed RNA polymerase complex assembly http://purl.obolibrary.org/obo/FYPO_0008235

Added

• abolished nuclear RNA-directed RNA polymerase complex assembly creation_date "2024-06-17T11:49:20Z"^^dateTime

• abolished nuclear RNA-directed RNA polymerase complex assembly label "abolished nuclear RNA-directed RNA polymerase complex assembly"@en

• abolished nuclear RNA-directed RNA polymerase complex assembly definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which the assembly of the nuclear RNA-directed RNA polymerase complex is abolished."

  • comment "PomBase:vw"

• abolished nuclear RNA-directed RNA polymerase complex assembly created_by "vw"

• abolished nuclear RNA-directed RNA polymerase complex assembly has_obo_namespace "fission_yeast_phenotype"

• Class: abolished nuclear RNA-directed RNA polymerase complex assembly

• abolished nuclear RNA-directed RNA polymerase complex assembly SubClassOf abnormal protein complex assembly

abolished siRNA loading onto RITS complex http://purl.obolibrary.org/obo/FYPO_0008011

Added

• abolished siRNA loading onto RITS complex has_exact_synonym "decreased siRNA localization to RITS complex"

decreased cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0008024

Removed

• decreased cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of polyphosphate measured in a cell is lower than normal."
  • database_cross_reference "PMID:35012333"

Added

• decreased cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of polyphosphate measured in a cell (total or free) is lower than normal."
  • database_cross_reference "PMID:35012333"

decreased free cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0008241

Added

• decreased free cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of free polyphosphate measured in a cell is lower than normal."

  • database_cross_reference "PomBase:vw"

• decreased free cellular polyphosphate level creation_date "2024-06-17T12:22:45Z"^^dateTime

• decreased free cellular polyphosphate level label "decreased free cellular polyphosphate level"@en

• decreased free cellular polyphosphate level created_by "vw"

• decreased free cellular polyphosphate level has_obo_namespace "fission_yeast_phenotype"

• Class: decreased free cellular polyphosphate level

• decreased free cellular polyphosphate level SubClassOf decreased cellular polyphosphate level

decreased total cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0008240

Added

• decreased total cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the total amount of polyphosphate measured in a cell is lower than normal."

  • database_cross_reference "PomBase:vw"

• decreased total cellular polyphosphate level has_obo_namespace "fission_yeast_phenotype"

• decreased total cellular polyphosphate level creation_date "2024-06-17T12:19:59Z"^^dateTime

• decreased total cellular polyphosphate level label "decreased total cellular polyphosphate level"@en

• decreased total cellular polyphosphate level created_by "vw"

• Class: decreased total cellular polyphosphate level

• decreased total cellular polyphosphate level SubClassOf decreased cellular polyphosphate level

increased cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0007816

Removed

• increased cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of polyphosphate measured in a cell is higher than normal."

  • database_cross_reference "PMID:34147496"

  • database_cross_reference "PomBase:mah"

Added

• increased cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of polyphosphate measured in a cell (total or free) is higher than normal."

  • database_cross_reference "PMID:34147496"

  • database_cross_reference "PomBase:mah"

increased free cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0008239

Added

• increased free cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of free polyphosphate measured in a cell is higher than normal."

  • database_cross_reference "PomBase:vw"

• increased free cellular polyphosphate level creation_date "2024-06-17T12:17:20Z"^^dateTime

• increased free cellular polyphosphate level has_obo_namespace "fission_yeast_phenotype"

• increased free cellular polyphosphate level created_by "vw"

• increased free cellular polyphosphate level label "increased free cellular polyphosphate level"@en

• Class: increased free cellular polyphosphate level

• increased free cellular polyphosphate level SubClassOf increased cellular polyphosphate level

increased total cellular polyphosphate level http://purl.obolibrary.org/obo/FYPO_0008238

Added

• increased total cellular polyphosphate level creation_date "2024-06-17T12:16:18Z"^^dateTime

• increased total cellular polyphosphate level has_obo_namespace "fission_yeast_phenotype"

• increased total cellular polyphosphate level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the total amount of polyphosphate measured in a cell is higher than normal."

  • database_cross_reference "PomBase:vw"

• increased total cellular polyphosphate level created_by "vw"

• increased total cellular polyphosphate level label "increased total cellular polyphosphate level"@en

• Class: increased total cellular polyphosphate level

• increased total cellular polyphosphate level SubClassOf increased cellular polyphosphate level

microtubule bundles present in increased numbers during mitotic M phase http://purl.obolibrary.org/obo/FYPO_0008232

Added

• microtubule bundles present in increased numbers during mitotic M phase created_by "vw"

• microtubule bundles present in increased numbers during mitotic M phase label "microtubule bundles present in increased numbers during mitotic M phase"@en

• microtubule bundles present in increased numbers during mitotic M phase definition "A physical cellular phenotype in which cells contain more microtubule bundles than normal during mitotic M-phase."

  • database_cross_reference "PomBase:vw"

• microtubule bundles present in increased numbers during mitotic M phase creation_date "2024-06-17T11:30:48Z"^^dateTime

• Class: microtubule bundles present in increased numbers during mitotic M phase

• microtubule bundles present in increased numbers during mitotic M phase EquivalentTo has_part some
  (has extra parts of type and (exists_during some mitotic interphase) and (towards some microtubule bundle))

• microtubule bundles present in increased numbers during mitotic M phase SubClassOf microtubule bundles present in increased numbers

microtubule bundles present in normal numbers http://purl.obolibrary.org/obo/FYPO_0008233

Added

• microtubule bundles present in normal numbers created_by "vw"

• microtubule bundles present in normal numbers definition "A physical cellular phenotype in which cells contain a normal number of microtubule bundles."

  • database_cross_reference ""

  • comment "PomBase:vw"

• microtubule bundles present in normal numbers label "microtubule bundles present in normal numbers"@en

• microtubule bundles present in normal numbers has_obo_namespace "fission_yeast_phenotype"

• microtubule bundles present in normal numbers creation_date "2024-06-17T11:41:37Z"^^dateTime

• Class: microtubule bundles present in normal numbers

• microtubule bundles present in normal numbers SubClassOf normal microtubule cytoskeleton organization during vegetative growth

normal glycerophospholipid level during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008237

Added

• normal glycerophospholipid level during vegetative growth definition "A cell phenotype in which the amount of glycerophospholipid measured in a cell is normal (i.e. indistinguishable from wild type) when the cell is in the vegetative growth phase of the life cycle."

  • comment "PomBase:vw"

• normal glycerophospholipid level during vegetative growth creation_date "2024-06-17T12:03:23Z"^^dateTime

• normal glycerophospholipid level during vegetative growth has_obo_namespace "fission_yeast_phenotype"

• normal glycerophospholipid level during vegetative growth created_by "vw"

• normal glycerophospholipid level during vegetative growth label "normal glycerophospholipid level during vegetative growth"@en

• Class: normal glycerophospholipid level during vegetative growth

• normal glycerophospholipid level during vegetative growth SubClassOf normal level of substance in cell

normal protein localization to cytoplasmic puncta http://purl.obolibrary.org/obo/FYPO_0008234

Added

• normal protein localization to cytoplasmic puncta definition "A cell phenotype in which a protein is localized to discrete regions in the cytoplasm, visible as foci or dots by microscopy, to the same extent as observed in normal (wild type) cells."

  • database_cross_reference "PomBase:vw"

• normal protein localization to cytoplasmic puncta has_obo_namespace "fission_yeast_phenotype"

• normal protein localization to cytoplasmic puncta creation_date "2024-06-17T11:44:21Z"^^dateTime

• normal protein localization to cytoplasmic puncta label "normal protein localization to cytoplasmic puncta"@en

• normal protein localization to cytoplasmic puncta created_by "vw"

• Class: normal protein localization to cytoplasmic puncta

• normal protein localization to cytoplasmic puncta SubClassOf normal protein localization to cytoplasm

normal protein localization to cytoplasmic stress granule http://purl.obolibrary.org/obo/FYPO_0004024

Removed

• normal protein localization to cytoplasmic stress granule SubClassOf normal protein localization during vegetative growth

Added

• normal protein localization to cytoplasmic stress granule SubClassOf normal protein localization to cytoplasm

normal replication fork arrest at MPS1 barrier http://purl.obolibrary.org/obo/FYPO_0008230

Added

• normal replication fork arrest at MPS1 barrier definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which replication fork arrest at the MPS1 barrier located in the mating-type region is normal (i.e. indistinguishable from wild-type)."

  • database_cross_reference ""

  • comment "PomBase:vw"

• normal replication fork arrest at MPS1 barrier created_by "vw"

• normal replication fork arrest at MPS1 barrier label "normal replication fork arrest at MPS1 barrier"@en

• normal replication fork arrest at MPS1 barrier creation_date "2024-06-17T11:26:44Z"^^dateTime

• normal replication fork arrest at MPS1 barrier has_obo_namespace "fission_yeast_phenotype"

• Class: normal replication fork arrest at MPS1 barrier

• normal replication fork arrest at MPS1 barrier SubClassOf normal replication fork arrest

normal siRNA loading onto RITS complex http://purl.obolibrary.org/obo/FYPO_0008236

Added

• normal siRNA loading onto RITS complex creation_date "2024-06-17T11:59:07Z"^^dateTime

• normal siRNA loading onto RITS complex definition "An RNA localization phenotype where the loading of siRNAs onto the RITs complex is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:vw"

• normal siRNA loading onto RITS complex label "normal siRNA loading onto RITS complex"@en

• normal siRNA loading onto RITS complex has_obo_namespace "fission_yeast_phenotype"

• normal siRNA loading onto RITS complex created_by "vw"

• Class: normal siRNA loading onto RITS complex

• normal siRNA loading onto RITS complex SubClassOf normal RNA localization to chromatin

Changes to ontology after reasoner runs

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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