closes #4574

[ValWood]

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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 protein localization to chromatin at MCB promoters http://purl.obolibrary.org/obo/FYPO_0005460

Added

• abolished protein localization to chromatin at MCB promoters SubClassOf decreased protein localization to chromatin at protein coding gene

decreased LTR-derived RNA level http://purl.obolibrary.org/obo/FYPO_0008248

Added

• decreased LTR-derived RNA level label "decreased LTR-derived RNA level"@en

• decreased LTR-derived RNA level creation_date "2024-07-04T10:31:20Z"^^dateTime

• decreased LTR-derived RNA level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is lower than normal."

  • comment "PMID:25356590"

  • database_cross_reference "PomBase:pc"

• decreased LTR-derived RNA level created_by "vw"

• decreased LTR-derived RNA level has_obo_namespace "fission_yeast_phenotype"

• Class: decreased LTR-derived RNA level

• decreased LTR-derived RNA level SubClassOf decreased RNA level during vegetative growth

decreased cenH-derived RNA level http://purl.obolibrary.org/obo/FYPO_0008251

Added

• decreased cenH-derived RNA level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is lower than normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:25356590"

• decreased cenH-derived RNA level has_obo_namespace "fission_yeast_phenotype"

• decreased cenH-derived RNA level created_by "vw"

• decreased cenH-derived RNA level creation_date "2024-07-04T11:13:18Z"^^dateTime

• decreased cenH-derived RNA level label "decreased cenH-derived RNA level"@en

• Class: decreased cenH-derived RNA level

• decreased cenH-derived RNA level SubClassOf decreased RNA level during vegetative growth

decreased histone H2B localization to chromatin at protein coding gene http://purl.obolibrary.org/obo/FYPO_0005223

Removed

• decreased histone H2B localization to chromatin at protein coding gene SubClassOf abnormal protein localization to chromatin during vegetative growth

Added

• decreased histone H2B localization to chromatin at protein coding gene SubClassOf decreased protein localization to chromatin at protein coding gene

decreased histone H3-K4 acetylation at LTR during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008256

Added

• decreased histone H3-K4 acetylation at LTR during vegetative growth label "decreased histone H3-K4 acetylation at LTR during vegetative growth"@en

• decreased histone H3-K4 acetylation at LTR during vegetative growth created_by "vw"

• decreased histone H3-K4 acetylation at LTR during vegetative growth creation_date "2024-07-04T12:13:44Z"^^dateTime

• decreased histone H3-K4 acetylation at LTR during vegetative growth has_obo_namespace "fission_yeast_phenotype"

• decreased histone H3-K4 acetylation at LTR 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 4 of histone H3 occurs to a lower extent than normal at long terminal repeat (LTR) regions."

  • database_cross_reference "PMID:25356590"

• Class: decreased histone H3-K4 acetylation at LTR during vegetative growth

• decreased histone H3-K4 acetylation at LTR during vegetative growth SubClassOf decreased histone H3-K4 acetylation during vegetative growth

decreased histone H3-K4 acetylation at protein coding gene during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008255

Added

• decreased histone H3-K4 acetylation at protein coding gene 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 4 of histone H3 occurs to a lower extent than normal in regions containing protein-coding genes."

  • database_cross_reference "PMID:25356590"

• decreased histone H3-K4 acetylation at protein coding gene during vegetative growth created_by "vw"

• decreased histone H3-K4 acetylation at protein coding gene during vegetative growth has_obo_namespace "fission_yeast_phenotype"

• decreased histone H3-K4 acetylation at protein coding gene during vegetative growth creation_date "2024-07-04T12:08:52Z"^^dateTime

• decreased histone H3-K4 acetylation at protein coding gene during vegetative growth label "decreased histone H3-K4 acetylation at protein coding gene during vegetative growth"@en

• Class: decreased histone H3-K4 acetylation at protein coding gene during vegetative growth

• decreased histone H3-K4 acetylation at protein coding gene during vegetative growth SubClassOf decreased histone H3-K4 acetylation during vegetative growth

decreased protein localization to chromatin at protein coding gene http://purl.obolibrary.org/obo/FYPO_0008249

Added

• decreased protein localization to chromatin at protein coding gene created_by "vw"

• decreased protein localization to chromatin at protein coding gene label "decreased protein localization to chromatin at protein coding gene"@en

• decreased protein localization to chromatin at protein coding gene creation_date "2024-07-04T10:46:57Z"^^dateTime

• decreased protein localization to chromatin at protein coding gene has_obo_namespace "fission_yeast_phenotype"

• decreased protein localization to chromatin at protein coding gene definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is decreased."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:25356590"

• Class: decreased protein localization to chromatin at protein coding gene

• decreased protein localization to chromatin at protein coding gene SubClassOf decreased protein localization to chromatin during vegetative growth

decreased subtelomeric heterochromatin RNA level http://purl.obolibrary.org/obo/FYPO_0008247

Added

• decreased subtelomeric heterochromatin RNA level has_obo_namespace "fission_yeast_phenotype"

• decreased subtelomeric heterochromatin RNA level created_by "vw"

• decreased subtelomeric heterochromatin RNA level definition "A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin regions is lower than normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:25356590"

• decreased subtelomeric heterochromatin RNA level label "decreased subtelomeric heterochromatin RNA level"@en

• decreased subtelomeric heterochromatin RNA level creation_date "2024-07-04T10:28:51Z"^^dateTime

• Class: decreased subtelomeric heterochromatin RNA level

• decreased subtelomeric heterochromatin RNA level SubClassOf decreased RNA level during vegetative growth

increased histone H3-K4 acetylation at LTR during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008257

Added

• increased histone H3-K4 acetylation at LTR during vegetative growth label "increased histone H3-K4 acetylation at LTR during vegetative growth"@en

• increased histone H3-K4 acetylation at LTR 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 4 of histone H3 occurs to a greater extent than normal at long terminal repeat (LTR) regions."

  • database_cross_reference "PMID:25356590"

• increased histone H3-K4 acetylation at LTR during vegetative growth creation_date "2024-07-04T12:30:40Z"^^dateTime

• increased histone H3-K4 acetylation at LTR during vegetative growth created_by "vw"

• increased histone H3-K4 acetylation at LTR during vegetative growth has_obo_namespace "fission_yeast_phenotype"

• Class: increased histone H3-K4 acetylation at LTR during vegetative growth

• increased histone H3-K4 acetylation at LTR during vegetative growth SubClassOf increased histone H3-K4 acetylation during vegetative growth

increased histone H3-K4 acetylation at protein coding gene during vegetative growth http://purl.obolibrary.org/obo/FYPO_0008254

Added

• increased histone H3-K4 acetylation at protein coding gene during vegetative growth has_obo_namespace "fission_yeast_phenotype"

• increased histone H3-K4 acetylation at protein coding gene during vegetative growth creation_date "2024-07-04T12:06:21Z"^^dateTime

• increased histone H3-K4 acetylation at protein coding gene 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 4 of histone H3 occurs to a greater extent than normal in regions containing protein-coding genes."

  • database_cross_reference "PMID:25356590"

• increased histone H3-K4 acetylation at protein coding gene during vegetative growth created_by "vw"

• increased histone H3-K4 acetylation at protein coding gene during vegetative growth label "increased histone H3-K4 acetylation at protein coding gene during vegetative growth"@en

• Class: increased histone H3-K4 acetylation at protein coding gene during vegetative growth

• increased histone H3-K4 acetylation at protein coding gene during vegetative growth SubClassOf increased histone H3-K4 acetylation during vegetative growth

normal LTR-derived RNA level http://purl.obolibrary.org/obo/FYPO_0008252

Added

• normal LTR-derived RNA level has_obo_namespace "fission_yeast_phenotype"

• normal LTR-derived RNA level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PMID:25356590"

• normal LTR-derived RNA level label "normal LTR-derived RNA level"@en

• normal LTR-derived RNA level created_by "vw"

• normal LTR-derived RNA level creation_date "2024-07-04T11:16:06Z"^^dateTime

• Class: normal LTR-derived RNA level

• normal LTR-derived RNA level SubClassOf normal RNA level during vegetative growth

normal cenH-derived RNA level http://purl.obolibrary.org/obo/FYPO_0008246

Added

• normal cenH-derived RNA level creation_date "2024-07-04T10:22:47Z"^^dateTime

• normal cenH-derived RNA level created_by "vw"

• normal cenH-derived RNA level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs."

  • database_cross_reference "PomBase:pc"

• normal cenH-derived RNA level label "normal cenH-derived RNA level"@en

• normal cenH-derived RNA level has_obo_namespace "fission_yeast_phenotype"

• Class: normal cenH-derived RNA level

• normal cenH-derived RNA level SubClassOf normal RNA level during vegetative growth

normal protein localization during vegetative growth http://purl.obolibrary.org/obo/FYPO_0000644

Removed

• normal protein localization during vegetative growth EquivalentTo has part some
  (quality and (happens_during some single-celled organism vegetative growth phase) and (characteristic of some GO_0034613) and (has modifier some normal))

Added

• normal protein localization during vegetative growth EquivalentTo has part some
  (quality and (happens_during some single-celled organism vegetative growth phase) and (characteristic of some protein localization) and (has modifier some normal))

normal protein localization to chromatin at gene promoter region http://purl.obolibrary.org/obo/FYPO_0008245

Added

• normal protein localization to chromatin at gene promoter region label "normal protein localization to chromatin at gene promoter region"@en

• normal protein localization to chromatin at gene promoter region creation_date "2024-07-04T09:30:07Z"^^dateTime

• normal protein localization to chromatin at gene promoter region definition "A cell phenotype in which the localization of a protein to chromatin at one or more specific promoter elements is normal (i.e. indistinguishable from wild type) during vegetative growth."

  • database_cross_reference "PMID:27538348"

• normal protein localization to chromatin at gene promoter region has_obo_namespace "fission_yeast_phenotype"

• normal protein localization to chromatin at gene promoter region created_by "vw"

• Class: normal protein localization to chromatin at gene promoter region

• normal protein localization to chromatin at gene promoter region EquivalentTo has part some
  (quality and (happens_during some single-celled organism vegetative growth phase) and (occurs_at some promoter_element) and (characteristic of some protein localization to chromatin) and (has modifier some normal))

• normal protein localization to chromatin at gene promoter region SubClassOf normal protein localization to chromatin during vegetative growth

normal protein localization to chromatin at protein coding gene http://purl.obolibrary.org/obo/FYPO_0008250

Added

• normal protein localization to chromatin at protein coding gene has_obo_namespace "fission_yeast_phenotype"

• normal protein localization to chromatin at protein coding gene label "normal protein localization to chromatin at protein coding gene"@en

• normal protein localization to chromatin at protein coding gene created_by "vw"

• normal protein localization to chromatin at protein coding gene definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PomBase:pc"

  • database_cross_reference "PMID:25356590"

• normal protein localization to chromatin at protein coding gene creation_date "2024-07-04T10:57:44Z"^^dateTime

• Class: normal protein localization to chromatin at protein coding gene

• normal protein localization to chromatin at protein coding gene EquivalentTo has part some
  (quality and (happens_during some single-celled organism vegetative growth phase) and (occurs_at some protein_coding_gene) and (characteristic of some protein localization to chromatin) and (has modifier some normal))

• normal protein localization to chromatin at protein coding gene SubClassOf normal protein localization to chromatin during vegetative growth

normal subtelomeric heterochromatin RNA level http://purl.obolibrary.org/obo/FYPO_0005602

Removed

• normal subtelomeric heterochromatin RNA level has_related_synonym "normal subtelomere-derived RNA level during mitotic cell cycle"

  • database_cross_reference "PomBase:mah"

• normal subtelomeric heterochromatin RNA level definition "A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from sub-telomeric regions measured in a cell is normal (i.e. indistinguishable from wild type)."

  • database_cross_reference "PMID:27183912"

  • database_cross_reference "PomBase:mah"

• normal subtelomeric heterochromatin RNA level label "normal subtelomere-derived RNA level"

• normal subtelomeric heterochromatin RNA level has_related_synonym "normal subtelomere-derived RNA accumulation"

  • database_cross_reference "PomBase:mah"

Added

• normal subtelomeric heterochromatin RNA level label "normal subtelomeric heterochromatin RNA level"

• normal subtelomeric heterochromatin RNA level has_exact_synonym "normal subtelomere-derived RNA level"

• normal subtelomeric heterochromatin RNA level definition "A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin forming regions is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected."

  • database_cross_reference "PMID:27183912"

  • database_cross_reference "PMID:25356590"

normal telomere repeat region derived RNA level http://purl.obolibrary.org/obo/FYPO_0008253

Added

• normal telomere repeat region derived RNA level has_obo_namespace "fission_yeast_phenotype"

• normal telomere repeat region derived RNA level created_by "vw"

• normal telomere repeat region derived RNA level label "normal telomere repeat region derived RNA level"@en

• normal telomere repeat region derived RNA level definition "A cell phenotype in which the amount of telomere repeat derived RNA 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."

  • database_cross_reference "PMID:27183912"

• normal telomere repeat region derived RNA level creation_date "2024-07-04T11:56:39Z"^^dateTime

• Class: normal telomere repeat region derived RNA level

• normal telomere repeat region derived RNA level SubClassOf normal RNA level during vegetative growth

Changes to ontology after reasoner runs

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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