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Obsoleted 15 terms; fixes #29219 #29377

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merged 2 commits into from
Dec 4, 2024
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Obsoleted 15 terms; fixes #29219 #29377

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1d4c942
Obsoleted 15 terms; fixes #29219
raymond91105 Dec 4, 2024
53cc920
Merge branch 'master' into issue-29219
raymond91125 Dec 4, 2024
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139 changes: 75 additions & 64 deletions src/ontology/go-edit.obo
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Expand Up @@ -60431,11 +60431,12 @@ is_a: GO:0071103 ! DNA conformation change

[Term]
id: GO:0006266
name: DNA ligation
name: obsolete DNA ligation
namespace: biological_process
def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [ISBN:0815316194]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process
def: "OBSOLETE. The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [ISBN:0815316194]
comment: The reason for obsoletion is that the term represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0006267
Expand Down Expand Up @@ -60664,11 +60665,12 @@ relationship: part_of GO:0006284 ! base-excision repair

[Term]
id: GO:0006288
name: base-excision repair, DNA ligation
name: obsolete base-excision repair, DNA ligation
namespace: biological_process
def: "The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair." [ISBN:1550091131]
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0006284 ! base-excision repair
def: "OBSOLETE. The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair." [ISBN:1550091131]
comment: The reason for obsoletion is that the term represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0006289
Expand Down Expand Up @@ -320984,64 +320986,70 @@ intersection_of: regulates GO:0003677 ! DNA binding

[Term]
id: GO:0051102
name: DNA ligation involved in DNA recombination
name: obsolete DNA ligation involved in DNA recombination
namespace: biological_process
def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA recombination." [GOC:ai]
def: "OBSOLETE. The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA recombination." [GOC:ai]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation during DNA recombination" RELATED [GOC:dph, GOC:tb]
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0006310 ! DNA recombination
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051103
name: DNA ligation involved in DNA repair
name: obsolete DNA ligation involved in DNA repair
namespace: biological_process
def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair." [GOC:ai]
def: "OBSOLETE. The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA repair." [GOC:ai]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation during DNA repair" RELATED [GOC:dph, GOC:tb]
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0006281 ! DNA repair
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051104
name: DNA-dependent DNA replication DNA ligation
name: obsolete DNA-dependent DNA replication DNA ligation
namespace: biological_process
def: "The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA-dependent DNA replication." [GOC:ai, GOC:dph, GOC:tb]
def: "OBSOLETE. The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA-dependent DNA replication." [GOC:ai, GOC:dph, GOC:tb]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation during DNA-dependent DNA replication" RELATED [GOC:dph, GOC:tb]
synonym: "DNA ligation involved in DNA-dependent DNA replication" EXACT []
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0006261 ! DNA-templated DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051105
name: regulation of DNA ligation
name: obsolete regulation of DNA ligation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006266 ! DNA ligation
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
comment: The reason for obsoletion is that the term represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051106
name: positive regulation of DNA ligation
name: obsolete positive regulation of DNA ligation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "activation of DNA ligation" NARROW []
synonym: "stimulation of DNA ligation" NARROW []
synonym: "up regulation of DNA ligation" EXACT []
synonym: "up-regulation of DNA ligation" EXACT []
synonym: "upregulation of DNA ligation" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0006266 ! DNA ligation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051107
name: negative regulation of DNA ligation
name: obsolete negative regulation of DNA ligation
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of DNA ligation, the re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase." [GOC:ai]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "down regulation of DNA ligation" EXACT []
synonym: "down-regulation of DNA ligation" EXACT []
synonym: "downregulation of DNA ligation" EXACT []
synonym: "inhibition of DNA ligation" NARROW []
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006266 ! DNA ligation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0051108
Expand Down Expand Up @@ -507948,12 +507956,13 @@ creation_date: 2013-07-09T13:45:43Z

[Term]
id: GO:1902291
name: cell cycle DNA replication DNA ligation
name: obsolete cell cycle DNA replication DNA ligation
namespace: biological_process
def: "Any DNA ligation that is involved in cell cycle DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
def: "OBSOLETE. Any DNA ligation that is involved in cell cycle DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation involved in cell cycle DNA replication" EXACT []
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0044786 ! cell cycle DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2013-07-09T16:05:45Z

Expand Down Expand Up @@ -508482,12 +508491,13 @@ creation_date: 2013-07-24T22:47:37Z

[Term]
id: GO:1902327
name: bacterial-type DNA replication DNA ligation
name: obsolete bacterial-type DNA replication DNA ligation
namespace: biological_process
def: "Any DNA ligation that is involved in bacterial-type DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
def: "OBSOLETE. Any DNA ligation that is involved in bacterial-type DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation involved in bacterial-type DNA replication" EXACT []
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0044787 ! bacterial-type DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2013-07-25T10:47:46Z

Expand Down Expand Up @@ -508555,15 +508565,16 @@ creation_date: 2013-07-25T10:48:34Z

[Term]
id: GO:1902333
name: nuclear DNA replication DNA ligation
name: obsolete nuclear DNA replication DNA ligation
namespace: biological_process
def: "Any DNA ligation that is involved in nuclear cell cycle DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
def: "OBSOLETE. Any DNA ligation that is involved in nuclear cell cycle DNA replication." [GOC:mtg_cell_cycle, GOC:TermGenie]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation involved in DNA replication during S phase" RELATED [GOC:TermGenie]
synonym: "DNA ligation involved in DNA replication involved in S phase" EXACT [GOC:TermGenie]
synonym: "DNA ligation involved in DNA replication involved in S-phase" EXACT [GOC:TermGenie]
synonym: "DNA ligation involved in nuclear cell cycle DNA replication" EXACT []
intersection_of: GO:0006266 ! DNA ligation
intersection_of: part_of GO:0033260 ! nuclear DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2013-07-25T10:55:56Z

Expand Down Expand Up @@ -519252,25 +519263,27 @@ creation_date: 2014-05-06T15:20:47Z

[Term]
id: GO:1902972
name: premeiotic DNA replication DNA ligation
name: obsolete premeiotic DNA replication DNA ligation
namespace: biological_process
def: "Any DNA ligation involved in meiotic cell cycle DNA replication." [GO_REF:0000060, GOC:TermGenie]
def: "OBSOLETE. Any DNA ligation involved in meiotic cell cycle DNA replication." [GO_REF:0000060, GOC:TermGenie]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation involved in meiotic cell cycle DNA replication" RELATED []
synonym: "DNA ligation involved in meiotic DNA replication" EXACT []
intersection_of: GO:1902333 ! nuclear DNA replication DNA ligation
intersection_of: part_of GO:0006279 ! premeiotic DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2014-05-06T15:20:53Z

[Term]
id: GO:1902973
name: mitotic DNA replication DNA ligation
name: obsolete mitotic DNA replication DNA ligation
namespace: biological_process
def: "Any DNA ligation involved in mitotic cell cycle DNA replication." [GO_REF:0000060, GOC:TermGenie]
def: "OBSOLETE. Any DNA ligation involved in mitotic cell cycle DNA replication." [GO_REF:0000060, GOC:TermGenie]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "DNA ligation involved in mitotic cell cycle DNA replication" EXACT []
synonym: "DNA ligation involved in mitotic DNA replication" EXACT []
intersection_of: GO:1902333 ! nuclear DNA replication DNA ligation
intersection_of: part_of GO:1902969 ! mitotic DNA replication
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2014-05-06T15:20:59Z

Expand Down Expand Up @@ -554208,13 +554221,12 @@ creation_date: 2015-12-18T11:28:34Z

[Term]
id: GO:1904875
name: regulation of DNA ligase activity
name: obsolete regulation of DNA ligase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of DNA ligase activity." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:rl, GOC:TermGenie, PMID:17389648]
subset: gocheck_obsoletion_candidate
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0003909 ! DNA ligase activity
relationship: regulates GO:0006266 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/13926"} ! DNA ligation
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of DNA ligase activity." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:rl, GOC:TermGenie, PMID:17389648]
comment: The reason for obsoletion is that the term represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: rl
creation_date: 2015-12-18T18:35:30Z

Expand All @@ -554235,17 +554247,16 @@ creation_date: 2015-12-18T18:35:37Z

[Term]
id: GO:1904877
name: positive regulation of DNA ligase activity
name: obsolete positive regulation of DNA ligase activity
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of DNA ligase activity." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:rl, GOC:TermGenie, PMID:17389648]
subset: gocheck_obsoletion_candidate
def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of DNA ligase activity." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:rl, GOC:TermGenie, PMID:17389648]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "activation of DNA ligase activity" NARROW [GOC:TermGenie]
synonym: "up regulation of DNA ligase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of DNA ligase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of DNA ligase activity" EXACT [GOC:TermGenie]
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0003909 ! DNA ligase activity
relationship: positively_regulates GO:0006266 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/13926"} ! DNA ligation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29219" xsd:anyURI
is_obsolete: true
created_by: rl
creation_date: 2015-12-18T18:35:44Z

Expand Down
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