closes #4454; closes #4449; part of others

[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 nuclear envelope morphology during mitosis http://purl.obolibrary.org/obo/FYPO_0003779

Removed

• abnormal nuclear envelope morphology during mitosis has_exact_synonym "abnormal nuclear envelope morphology during mitosis during vegetative growth"

  • database_cross_reference "PomBase:mah"

• abnormal nuclear envelope morphology during mitosis SubClassOf abnormal nuclear morphology during vegetative growth

• abnormal nuclear envelope morphology during mitosis SubClassOf abnormal endomembrane system morphology

Added

• abnormal nuclear envelope morphology during mitosis SubClassOf abnormal nuclear envelope morphology during vegetative growth

decreased RNA level during meiosis II http://purl.obolibrary.org/obo/FYPO_0008141

Added

• decreased RNA level during meiosis II has_exact_synonym "decreased RNA level during second meiotic nuclear division"

• decreased RNA level during meiosis II has_exact_synonym "reduced RNA level during meiosis II"

• decreased RNA level during meiosis II comment "Consider annotating to a term describing abnormal transcription or abnormal regulation of transcription, but note that changes in RNA levels may result from changes in RNA stability as well as changes in transcription. We recommend noting which RNA(s) were used in the assay when annotating to this term."

• decreased RNA level during meiosis II has_obo_namespace "fission_yeast_phenotype"

• decreased RNA level during meiosis II creation_date "2023-12-29T19:18:34Z"^^dateTime

• decreased RNA level during meiosis II created_by "vw"

• decreased RNA level during meiosis II label "decreased RNA level during meiosis II"@en

• decreased RNA level during meiosis II has_exact_synonym "decreased transcript level during meiosis II"

  • database_cross_reference "PomBase:vw"

• decreased RNA level during meiosis II definition "A cell phenotype in which the amount of RNA measured in a cell is lower than normal during the second meiotic nuclear division. Total RNA or a specific RNA may be affected."

  • database_cross_reference "PMID:16272747"

• decreased RNA level during meiosis II has_related_synonym "decreased RNA accumulation during meiosis II"

• decreased RNA level during meiosis II id "FYPO:0004937"

• Class: decreased RNA level during meiosis II

• decreased RNA level during meiosis II EquivalentTo has_part some
  (decreased concentration and (exists_during some meiosis II) and (inheres_in some fungal cell) and (towards some ribonucleic acid))

• decreased RNA level during meiosis II SubClassOf decreased RNA level during meiosis

decreased level of heme O in cell http://purl.obolibrary.org/obo/FYPO_0008145

Added

• decreased level of heme O in cell definition "A cell phenotype in which the amount of heme O measured in a cell is lower than normal."

  • database_cross_reference "PMID:11248251"

• decreased level of heme O in cell has_exact_synonym "decreased heme O level"

• decreased level of heme O in cell created_by "vw"

• decreased level of heme O in cell label "decreased level of heme O in cell"@en

• decreased level of heme O in cell creation_date "2023-12-29T19:32:33Z"^^dateTime

• decreased level of heme O in cell has_obo_namespace "fission_yeast_phenotype"

• Class: decreased level of heme O in cell

• decreased level of heme O in cell SubClassOf decreased level of substance in cell

decreased size and number of lipid droplets http://purl.obolibrary.org/obo/FYPO_0008137

Added

• decreased size and number of lipid droplets definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which lipid droplets are smaller and more numerous than normal."

  • database_cross_reference "PMID:35658118"

• decreased size and number of lipid droplets creation_date "2023-12-29T18:29:47Z"^^dateTime

• decreased size and number of lipid droplets created_by "vw"

• decreased size and number of lipid droplets label "decreased size and number of lipid droplets"@en

• Class: decreased size and number of lipid droplets

• decreased size and number of lipid droplets SubClassOf abnormal lipid droplet organization

dilated endoplasmic reticulum lumen http://purl.obolibrary.org/obo/FYPO_0008139

Added

• dilated endoplasmic reticulum lumen creation_date "2023-12-29T18:58:59Z"^^dateTime

• dilated endoplasmic reticulum lumen label "dilated endoplasmic reticulum lumen"@en

• dilated endoplasmic reticulum lumen has_exact_synonym "dialted ER lumen"

• dilated endoplasmic reticulum lumen definition "A physical cellular phenotype observed in the vegetative growth phase of the life cycle in which the endoplasmic reticulum lumen is larger than normal."

  • database_cross_reference "PMID:11839792"

• dilated endoplasmic reticulum lumen created_by "vw"

• Class: dilated endoplasmic reticulum lumen

• dilated endoplasmic reticulum lumen SubClassOf abnormal endoplasmic reticulum morphology

dilated nuclear envelope lumen http://purl.obolibrary.org/obo/FYPO_0008140

Added

• dilated nuclear envelope lumen creation_date "2023-12-29T19:09:04Z"^^dateTime

• dilated nuclear envelope lumen definition "An abnormal nuclear envelope morpbology in the vegetative growth phase of the life cycle in which the nuclear envelope lumen is larger than normal."

  • database_cross_reference "PMID:11839792"

• dilated nuclear envelope lumen created_by "vw"

• dilated nuclear envelope lumen label "dilated nuclear envelope lumen"@en

• Class: dilated nuclear envelope lumen

• dilated nuclear envelope lumen SubClassOf abnormal nuclear envelope morphology during vegetative growth

excess endoplasmic reticulum membrane present http://purl.obolibrary.org/obo/FYPO_0001784

Added

• excess endoplasmic reticulum membrane present has_exact_synonym "accumulated ER membrane"

• excess endoplasmic reticulum membrane present has_exact_synonym "accumulated endoplasmic reticulum membrane"

heme A absent from cell http://purl.obolibrary.org/obo/FYPO_0008143

Added

• heme A absent from cell label "heme A absent from cell"@en

• heme A absent from cell created_by "vw"

• heme A absent from cell creation_date "2023-12-29T19:25:56Z"^^dateTime

• heme A absent from cell definition "A cell phenotype in which the amount heme A measured in a cell is too low to detect."

  • database_cross_reference "PMID:11248251"

• Class: heme A absent from cell

• heme A absent from cell SubClassOf heme absent from cell

heme O absent from cell http://purl.obolibrary.org/obo/FYPO_0008144

Added

• heme O absent from cell definition "A cell phenotype in which the amount heme O measured in a cell is too low to detect."

  • database_cross_reference "PMID:11248251"

• heme O absent from cell creation_date "2023-12-29T19:29:25Z"^^dateTime

• heme O absent from cell label "heme O absent from cell"@en

• heme O absent from cell created_by "vw"

• Class: heme O absent from cell

• heme O absent from cell SubClassOf heme absent from cell

heme absent from cell http://purl.obolibrary.org/obo/FYPO_0008142

Added

• heme absent from cell created_by "vw"

• heme absent from cell creation_date "2023-12-29T19:25:56Z"^^dateTime

• heme absent from cell definition "A cell phenotype in which the amount heme measured in a cell is too low to detect."

  • database_cross_reference "PMID:11248251"

• heme absent from cell label "heme absent from cell"@en

• Class: heme absent from cell

• heme absent from cell EquivalentTo has_part some
  (lacks all parts of type and (inheres_in some fungal cell) and (towards some heme))

• heme absent from cell SubClassOf substance absent from cell

increased antisense RNA level http://purl.obolibrary.org/obo/FYPO_0003557

Removed

• increased antisense RNA level SubClassOf increased RNA level during vegetative growth

Added

• increased antisense RNA level SubClassOf increased ncRNA level during vegetative growth

increased centromeric transcript level http://purl.obolibrary.org/obo/FYPO_0004982

Removed

• increased centromeric transcript level SubClassOf increased RNA level during vegetative growth

Added

• increased centromeric transcript level SubClassOf increased ncRNA level during vegetative growth

increased level of mitochondrial tRNA processing intermediates with 3' extensions http://purl.obolibrary.org/obo/FYPO_0002590

Removed

• increased level of mitochondrial tRNA processing intermediates with 3' extensions SubClassOf increased RNA level during vegetative growth

Added

• increased level of mitochondrial tRNA processing intermediates with 3' extensions SubClassOf increased ncRNA level during vegetative growth

increased level of nuclear tRNA processing intermediates with 3' extensions http://purl.obolibrary.org/obo/FYPO_0002581

Removed

• increased level of nuclear tRNA processing intermediates with 3' extensions SubClassOf increased RNA level during vegetative growth

Added

• increased level of nuclear tRNA processing intermediates with 3' extensions SubClassOf increased ncRNA level during vegetative growth

increased lncRNA level http://purl.obolibrary.org/obo/FYPO_0005995

Removed

• increased lncRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased lncRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature 25S rRNA level http://purl.obolibrary.org/obo/FYPO_0006075

Removed

• increased mature 25S rRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased mature 25S rRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature 5.8SL rRNA level http://purl.obolibrary.org/obo/FYPO_0003675

Removed

• increased mature 5.8SL rRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased mature 5.8SL rRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature ncRNA level http://purl.obolibrary.org/obo/FYPO_0006467

Removed

• increased mature ncRNA level EquivalentTo has_part some
  (increased concentration and (exists_during some single-celled organism vegetative growth phase) and (inheres_in some vegetative cell (sensu Fungi)) and (towards some ncRNA))

• increased mature ncRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased mature ncRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature rRNA level http://purl.obolibrary.org/obo/FYPO_0005507

Removed

• increased mature rRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased mature rRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature snRNA level http://purl.obolibrary.org/obo/FYPO_0004206

Removed

• increased mature snRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased mature snRNA level SubClassOf increased ncRNA level during vegetative growth

increased mature tRNA level during vegetative growth http://purl.obolibrary.org/obo/FYPO_0002564

Removed

• increased mature tRNA level during vegetative growth SubClassOf increased RNA level during vegetative growth

Added

• increased mature tRNA level during vegetative growth SubClassOf increased ncRNA level during vegetative growth

increased ncRNA level during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008146

Added

• increased ncRNA level during vegetative growth definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of non-coding RNA transcribed measured in a cell is higher than normal."

  • database_cross_reference "PMID:25989903"

• increased ncRNA level during vegetative growth creation_date "2023-12-29T19:42:09Z"^^dateTime

• increased ncRNA level during vegetative growth label "increased ncRNA level during vegetative growth"@en

• increased ncRNA level during vegetative growth created_by "vw"

• Class: increased ncRNA level during vegetative growth

• increased ncRNA level during vegetative growth EquivalentTo has_part some
  (increased concentration and (exists_during some single-celled organism vegetative growth phase) and (inheres_in some vegetative cell (sensu Fungi)) and (towards some ncRNA))

• increased ncRNA level during vegetative growth SubClassOf increased RNA level during vegetative growth

increased polyadenylated rRNA level http://purl.obolibrary.org/obo/FYPO_0008091

Removed

• increased polyadenylated rRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased polyadenylated rRNA level SubClassOf increased ncRNA level during vegetative growth

increased pre-tRNA level during vegetative growth http://purl.obolibrary.org/obo/FYPO_0006749

Removed

• increased pre-tRNA level during vegetative growth SubClassOf increased RNA level during vegetative growth

Added

• increased pre-tRNA level during vegetative growth SubClassOf increased ncRNA level during vegetative growth

increased rRNA precursor level http://purl.obolibrary.org/obo/FYPO_0003600

Removed

• increased rRNA precursor level SubClassOf increased RNA level during vegetative growth

Added

• increased rRNA precursor level SubClassOf increased ncRNA level during vegetative growth

increased siRNA level http://purl.obolibrary.org/obo/FYPO_0004207

Removed

• increased siRNA level SubClassOf increased RNA level during vegetative growth

Added

• increased siRNA level SubClassOf increased ncRNA level during vegetative growth

increased telomeric transcript level http://purl.obolibrary.org/obo/FYPO_0004573

Removed

• increased telomeric transcript level SubClassOf increased RNA level during vegetative growth

Added

• increased telomeric transcript level SubClassOf increased ncRNA level during vegetative growth

normal nuclear export http://purl.obolibrary.org/obo/FYPO_0000509

Removed

• normal nuclear export SubClassOf normal cellular process during vegetative growth

Added

• normal nuclear export SubClassOf normal nucleocytoplasmic transport

normal nuclear import http://purl.obolibrary.org/obo/FYPO_0000516

Removed

• normal nuclear import SubClassOf normal cellular process during vegetative growth

Added

• normal nuclear import SubClassOf normal nucleocytoplasmic transport

normal nucleocytoplasmic transport http://purl.obolibrary.org/obo/FYPO_0008138

Added

• normal nucleocytoplasmic transport created_by "vw"

• normal nucleocytoplasmic transport definition "A cellular process phenotype observed in the vegetative growth phase of the life cycle in which nucleocytoplasmic tranport is normal (i.e. indistinguishable from wild type). Nucleocytoplasmic transportport is the directed movement of any substance into or out of the nucleus; import or export of all substances or a specific substance may be affected."

  • database_cross_reference "PMID:11839792"

• normal nucleocytoplasmic transport label "normal nucleocytoplasmic transport"@en

• normal nucleocytoplasmic transport creation_date "2023-12-29T18:52:02Z"^^dateTime

• Class: normal nucleocytoplasmic transport

• normal nucleocytoplasmic transport EquivalentTo has_part some
  (quality and (happens_during some single-celled organism vegetative growth phase) and (inheres_in some nucleocytoplasmic transport) and (qualifier some normal))

• normal nucleocytoplasmic transport SubClassOf normal cellular process during vegetative growth

nuclear envelope protrusion present during mitosis http://purl.obolibrary.org/obo/FYPO_0003788

Removed

• nuclear envelope protrusion present during mitosis SubClassOf abnormal nuclear envelope morphology during vegetative growth

Added

• nuclear envelope protrusion present during mitosis SubClassOf abnormal nuclear envelope morphology during mitosis

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

Removed

• small mitochondria label "small mitochondria"

Added

• small mitochondria label "small fragmented mitochondria"

small mitochondria with decreased mitochondrial volume http://purl.obolibrary.org/obo/FYPO_0007611

Removed

• small mitochondria with decreased mitochondrial volume definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which mitochondria are smaller, and the total volume of all mitochondria in the cell is lower, than normal."

  • database_cross_reference "PMID:31562247"

  • database_cross_reference "PomBase:mah"

• small mitochondria with decreased mitochondrial volume label "small mitochondria with decreased mitochondrial volume"

Added

• small mitochondria with decreased mitochondrial volume definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which mitochondria are smaller, and the total number of mitochondria in the cell is lower, than normal. Total mitochondrial volume is therefore lower than normal normal."

  • database_cross_reference "PMID:31562247"

  • database_cross_reference "PomBase:mah"

• small mitochondria with decreased mitochondrial volume label "small fragmented mitochondria present in decreased numbers"

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