#4422, #4421, #4422 ,#4415, #4414

[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

abnormal de novo SAGA complex assembly http://purl.obolibrary.org/obo/FYPO_0008117

Added

• abnormal de novo SAGA complex assembly created_by "vw"

• abnormal de novo SAGA complex assembly creation_dat "2023-09-05T16:22:58Z"^^dateTime

• abnormal de novo SAGA complex assembly comment "Note that this term refers to the abnormal biogenesis of the complex, i.e. the process of building the complex from individual subunits. For assays identifyion alterations in complex subunit composition use 'abnormal protein complex composition FYPO:0005003' or 'abnormal protein-protein interaction" (FYPO:0000704) or their descendants."

• abnormal de novo SAGA complex assembly definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which de novo assembly of the SAGA complex is abnormal."

  • database_cross_reference "PMID:31748520"

• abnormal de novo SAGA complex assembly label "abnormal de novo SAGA complex assembly"@en

• Class: abnormal de novo SAGA complex assembly

• abnormal de novo SAGA complex assembly SubClassOf abnormal protein complex assembly

decreased protein level in NuA4 complex http://purl.obolibrary.org/obo/FYPO_0008121

Added

• decreased protein level in NuA4 complex created_by "vw"

• decreased protein level in NuA4 complex definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of a protein measured in the NuA4 complex is lower than normal."

  • database_cross_reference "PMID:31748520"

• decreased protein level in NuA4 complex label "decreased protein level in NuA4 complex"@en

• decreased protein level in NuA4 complex creation_dat "2023-09-05T16:40:45Z"^^dateTime

• Class: decreased protein level in NuA4 complex

• decreased protein level in NuA4 complex SubClassOf abnormal protein complex composition

decreased protein level in SAGA complex http://purl.obolibrary.org/obo/FYPO_0008120

Added

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

  • database_cross_reference "PMID:31748520"

• decreased protein level in SAGA complex created_by "vw"

• decreased protein level in SAGA complex label "decreased protein level in SAGA complex"@en

• decreased protein level in SAGA complex creation_dat "2023-09-05T16:37:08Z"^^dateTime

• Class: decreased protein level in SAGA complex

• decreased protein level in SAGA complex SubClassOf abnormal protein complex composition

increased mitochondrial fusion http://purl.obolibrary.org/obo/FYPO_0008122

Added

• increased mitochondrial fusion created_by "vw"

• increased mitochondrial fusion label "increased mitochondrial fusion"@en

• increased mitochondrial fusion creation_dat "2023-09-05T16:53:41Z"^^dateTime

• increased mitochondrial fusion definition "A cellular process phenotype in which mitochondrion fusion is increased."

  • definition "PMID:37590302"

• Class: increased mitochondrial fusion

• increased mitochondrial fusion SubClassOf abnormal mitochondrial fusion

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

Added

• loss of viability in stationary phase upon phopshate starvation definition "A cell population phenotype in which a smaller than normal proportion of cells in the population remains viable after entering stationary phase, when cells the population are subject to phosphate starvation."

  • database_cross_reference "PMID:36794724"

• loss of viability in stationary phase upon phopshate starvation has_exact_synonym "decreased chronological lifespan of phosphate-starved cells"

• loss of viability in stationary phase upon phopshate starvation creation_dat "2023-09-05T16:57:32Z"^^dateTime

• loss of viability in stationary phase upon phopshate starvation created_by "vw"

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

• Class: loss of viability in stationary phase upon phopshate starvation

• loss of viability in stationary phase upon phopshate starvation SubClassOf loss of viability in stationary phase

small mitochondria http://purl.obolibrary.org/obo/FYPO_0007193

Added

• small mitochondria SubClassOf abnormal mitochondrial morphology

small mitochondria present in increased numbers, with normal total mitochondrial volume http://purl.obolibrary.org/obo/FYPO_0003810

Removed

• small mitochondria present in increased numbers, with normal total mitochondrial volume label "small mitochondria present in increased numbers, with normal total mitochondrial volume"

• small mitochondria present in increased numbers, with normal total mitochondrial volume definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which total mitochondrial volume is normal, but mitochondria are smaller and more numerous than normal."

  • database_cross_reference "PomBase:mah"

Added

• small mitochondria present in increased numbers, with normal total mitochondrial volume label "small fragmented mitochondria present in increased numbers"

• small mitochondria present in increased numbers, with normal total mitochondrial volume definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which mitochondria are smaller and more numerous than normal. Total mitochondrial volume is usually similar to normal."

  • database_cross_reference "PomBase:mah"

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