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Merge pull request #29216 from geneontology/issue-29215
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obsoleted term fixes #29215
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pgaudet authored Nov 14, 2024
2 parents efa7e29 + 80b5c4b commit b68a9e4
Showing 1 changed file with 58 additions and 43 deletions.
101 changes: 58 additions & 43 deletions src/ontology/go-edit.obo
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Expand Up @@ -93523,15 +93523,17 @@ intersection_of: has_primary_output CHEBI:62071 ! 2-cis-abscisate

[Term]
id: GO:0009689
name: induction of phytoalexin biosynthetic process
name: obsolete induction of phytoalexin biosynthetic process
namespace: biological_process
def: "The activation of the chemical reactions and pathways resulting in the formation of phytoalexins, low-molecular mass, lipophilic antimicrobial compounds that accumulate rapidly at sites of incompatible pathogen infection." [ISBN:0943088399]
def: "OBSOLETE. The activation of the chemical reactions and pathways resulting in the formation of phytoalexins, low-molecular mass, lipophilic antimicrobial compounds that accumulate rapidly at sites of incompatible pathogen infection." [ISBN:0943088399]
comment: This term was obsoleted because it represents the same process as positive regulation of phytoalexin biosynthetic process ; GO:0052322.
synonym: "induction of phytoalexin anabolism" EXACT []
synonym: "induction of phytoalexin biosynthesis" EXACT []
synonym: "induction of phytoalexin formation" EXACT []
synonym: "induction of phytoalexin synthesis" EXACT []
is_a: GO:0052322 ! positive regulation of phytoalexin biosynthetic process
is_a: GO:0098542 ! defense response to other organism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true
replaced_by: GO:0052322

[Term]
id: GO:0009690
Expand Down Expand Up @@ -97838,8 +97840,6 @@ synonym: "regulation of abscisic acid anabolism" EXACT []
synonym: "regulation of abscisic acid biosynthesis" EXACT []
synonym: "regulation of abscisic acid formation" EXACT []
synonym: "regulation of abscisic acid synthesis" EXACT []
is_a: GO:0010565 ! regulation of ketone metabolic process
is_a: GO:0043455 ! regulation of secondary metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009688 ! abscisic acid biosynthetic process

Expand Down Expand Up @@ -258307,12 +258307,16 @@ creation_date: 2012-02-01T02:40:50Z

[Term]
id: GO:0044501
name: perturbation of signal transduction in another organism
name: obsolete perturbation of signal transduction in another organism
namespace: biological_process
def: "The process in which an organism effects a change in a signal transduction process - a cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell - in a second organism." [GOC:fj, GOC:jl]
def: "OBSOLETE. The process in which an organism effects a change in a signal transduction process - a cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell - in a second organism." [GOC:fj, GOC:jl]
comment: This term was obsoleted because it is too general.
synonym: "modulation of signal transduction in another organism" EXACT []
synonym: "modulation of signal transduction in other organism" EXACT []
is_a: GO:0035821 ! modulation of process of another organism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29215" xsd:anyURI
is_obsolete: true
consider: GO:0044509
consider: GO:0052027
created_by: jl
creation_date: 2012-02-23T03:48:19Z

Expand Down Expand Up @@ -258390,7 +258394,6 @@ namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of signal transduction in the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
synonym: "envenomation resulting in modulation of signal transduction in other organismm" EXACT []
is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
relationship: has_part GO:0044501 ! perturbation of signal transduction in another organism
created_by: jl
creation_date: 2012-02-23T04:58:10Z

Expand Down Expand Up @@ -325640,7 +325643,7 @@ intersection_of: has_primary_input CHEBI:61293 ! adenyl nucleotide

[Term]
id: GO:0051504
name: diterpene phytoalexin precursor biosynthetic process pathway
name: diterpene phytoalexin precursor biosynthetic process
namespace: biological_process
def: "A branched pathway that produces the precursors to four structurally distinct types of polycyclic diterpenes. The pathway starts with the cyclization of geranylgeranyl diphosphate into ent-copalyl diphosphate and syn-copalyl diphosphate. The catalytic conversion by diterpene cyclases of these two compounds produces the four diterpene hydrocarbons which are precursors to the four structurally distinct classes of diterpene phytoalexins." [MetaCyc:PWY-2981]
synonym: "diterpene phytoalexin precursor anabolism pathway" EXACT []
Expand Down Expand Up @@ -332007,7 +332010,7 @@ id: GO:0052081
name: symbiont-mediated perturbation of host salicylic acid-mediated signal transduction pathway
namespace: biological_process
alt_id: GO:0052445
def: "A process in which a symbiont alters or subverts a salicylic acid-mediated signal transduction pathway in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
def: "A process in which a symbiont alters or subverts a salicylic acid-mediated signal transduction pathway in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, PMID:35698792]
synonym: "modulation by organism of defense-related salicylic acid-mediated signal transduction pathway in other organism involved in symbiotic interaction" BROAD []
synonym: "modulation by symbiont of defense-related host salicylic acid-mediated signal transduction pathway" EXACT []
synonym: "modulation of defense-related host SA-mediated signal transduction pathway by organism" EXACT []
Expand Down Expand Up @@ -332081,7 +332084,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i

[Term]
id: GO:0052088
name: symbiont defense to host-produced jasmonic acid
name: symbiont-mediated perturbation of host jasmonic acid signaling
namespace: biological_process
alt_id: GO:0052068
alt_id: GO:0052069
Expand All @@ -332092,7 +332095,7 @@ alt_id: GO:0052267
alt_id: GO:0052271
alt_id: GO:0052283
alt_id: GO:0052443
def: "Any process in which a symbiont modulates the frequency, rate or extent of the jasmonic acid-mediated defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
def: "A process in which a symbiont alters or subverts a jasmonic acid-mediated signal transduction pathway in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, PMID:29222513, PMID:35698792]
synonym: "activation by organism of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
synonym: "activation by organism of defense-related host SA-mediated signal transduction pathway" NARROW []
synonym: "activation by symbiont of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
Expand All @@ -332117,12 +332120,14 @@ synonym: "positive regulation by symbiont of defense-related host jasmonic acid-
synonym: "stimulation by symbiont of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
synonym: "suppression by organism of host JA-mediated defense response" EXACT []
synonym: "suppression by symbiont of host jasmonic acid-mediated defense response" RELATED []
synonym: "symbiont defense to host-produced jasmonic acid" EXACT []
synonym: "up regulation by symbiont of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
synonym: "up-regulation by symbiont of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
synonym: "upregulation by organism of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
synonym: "upregulation by organism of defense-related host SA-mediated signal transduction pathway" NARROW []
synonym: "upregulation by symbiont of defense-related host jasmonic acid-mediated signal transduction pathway" NARROW []
is_a: GO:0042783 ! evasion of host immune response
is_a: GO:0052027 ! symbiont-mediated perturbation of host signal transduction pathway
is_a: GO:0052167 ! symbiont-mediated perturbation of host innate immune response
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18798" xsd:anyURI

[Term]
Expand Down Expand Up @@ -332981,7 +332986,7 @@ alt_id: GO:0052304
alt_id: GO:0052378
alt_id: GO:0052549
alt_id: GO:0052566
def: "Any process in which a symbiont modulates the frequency, rate or extent of production of phytoalexins as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
def: "Any process in which a symbiont modulates the frequency, rate or extent of production of phytoalexins as part of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, PMID:6870275]
synonym: "evasion or tolerance by symbiont of host-produced phytoalexins" EXACT []
synonym: "evasion or tolerance of phytoalexins" EXACT []
synonym: "evasion or tolerance of phytoalexins produced by host in response to organism" EXACT []
Expand All @@ -332991,6 +332996,7 @@ synonym: "modulation by symbiont of host phytoalexin production" NARROW []
synonym: "phytoalexin detoxification" NARROW []
synonym: "response to host phytoalexin production" BROAD []
synonym: "response to phytoalexin production by other organism involved in symbiotic interaction" BROAD []
xref: PMID:28805743
is_a: GO:0042783 ! evasion of host immune response
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18798" xsd:anyURI

Expand Down Expand Up @@ -333914,7 +333920,7 @@ intersection_of: has_primary_input_or_output GOCHE:26115 ! substance with phytoa
id: GO:0052315
name: phytoalexin biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of phytoalexins, any of a range of substances produced by plants as part of their defense response." [Wikipedia:Phytoalexin]
def: "The chemical reactions and pathways resulting in the formation of phytoalexins, any of a range of substances produced by plants as part of their defense response." [PMID:22209038, PMID:3882051, Wikipedia:Phytoalexin]
synonym: "phytoalexin biosynthesis" EXACT []
intersection_of: GO:0009058 ! biosynthetic process
intersection_of: has_primary_output GOCHE:26115 ! substance with phytoalexin role
Expand All @@ -333939,48 +333945,52 @@ intersection_of: has_primary_input_or_output CHEBI:22990 ! camalexin

[Term]
id: GO:0052318
name: regulation of phytoalexin metabolic process
name: obsolete regulation of phytoalexin metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response." [GOC:ai]
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins, any of a range of substances produced by plants as part of their defense response." [GOC:ai]
comment: This term was obsoleted because it was an unnecessary grouping class.
synonym: "regulation of phytoalexin metabolism" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0052314 ! phytoalexin metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0052319
name: regulation of phytoalexin biosynthetic process
name: obsolete regulation of phytoalexin biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of phytoalexin biosynthesis, the chemical reactions and pathways resulting in the formation of phytoalexins." [GOC:ai]
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of phytoalexin biosynthesis, the chemical reactions and pathways resulting in the formation of phytoalexins." [GOC:ai]
comment: This term was obsoleted because it was an unnecessary grouping class.
synonym: "regulation of phytoalexin biosynthesis" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0052315 ! phytoalexin biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0052320
name: positive regulation of phytoalexin metabolic process
name: obsolete positive regulation of phytoalexin metabolic process
namespace: biological_process
def: "Any process that activates, maintains or increases the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins." [GOC:mtg_pamgo_17jul06]
def: "OBSOLETE. Any process that activates, maintains or increases the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins." [GOC:mtg_pamgo_17jul06]
comment: This term was obsoleted because it was an unnecessary grouping class.
synonym: "activation of phytoalexin metabolism" NARROW []
synonym: "positive regulation of phytoalexin metabolism" RELATED []
synonym: "stimulation of phytoalexin metabolism" NARROW []
synonym: "up regulation of phytoalexin metabolism" EXACT []
synonym: "up-regulation of phytoalexin metabolism" EXACT []
synonym: "upregulation of phytoalexin metabolism" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0052314 ! phytoalexin metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0052321
name: negative regulation of phytoalexin metabolic process
name: obsolete negative regulation of phytoalexin metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins." [GOC:ai]
def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of phytoalexin metabolism, the chemical reactions and pathways involving phytoalexins." [GOC:ai]
comment: This term was obsoleted because it was an unnecessary grouping class.
synonym: "down regulation of phytoalexin metabolism" EXACT []
synonym: "down-regulation of phytoalexin metabolism" EXACT []
synonym: "downregulation of phytoalexin metabolism" EXACT []
synonym: "inhibition of phytoalexin metabolism" NARROW []
synonym: "negative regulation of phytoalexin metabolism" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0052314 ! phytoalexin metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true

[Term]
id: GO:0052322
Expand All @@ -333993,21 +334003,24 @@ synonym: "stimulation of phytoalexin biosynthesis" NARROW []
synonym: "up regulation of phytoalexin biosynthesis" EXACT []
synonym: "up-regulation of phytoalexin biosynthesis" EXACT []
synonym: "upregulation of phytoalexin biosynthesis" EXACT []
is_a: GO:0140546 ! defense response to symbiont
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0052315 ! phytoalexin biosynthetic process

[Term]
id: GO:0052323
name: negative regulation of phytoalexin biosynthetic process
name: obsolete negative regulation of phytoalexin biosynthetic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phytoalexin biosynthesis, the chemical reactions and pathways resulting in the formation of phytoalexins." [GOC:ai]
def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of phytoalexin biosynthesis, the chemical reactions and pathways resulting in the formation of phytoalexins." [GOC:ai]
comment: This term was obsoleted because it represents the same process as symbiont-mediated suppression of host phytoalexin production ; GO:1990217.
synonym: "down regulation of phytoalexin biosynthesis" EXACT []
synonym: "down-regulation of phytoalexin biosynthesis" EXACT []
synonym: "downregulation of phytoalexin biosynthesis" EXACT []
synonym: "inhibition of phytoalexin biosynthesis" NARROW []
synonym: "negative regulation of phytoalexin biosynthesis" EXACT []
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0052315 ! phytoalexin biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true
replaced_by: GO:1990217

[Term]
id: GO:0052324
Expand Down Expand Up @@ -489042,15 +489055,16 @@ creation_date: 2012-07-19T04:11:46Z

[Term]
id: GO:1901182
name: regulation of camalexin biosynthetic process
name: obsolete regulation of camalexin biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of camalexin biosynthetic process." [GOC:TermGenie]
def: "OBSOLETE. Any process that modulates the frequency, rate or extent of camalexin biosynthetic process." [GOC:TermGenie]
comment: This term was obsoleted because it was an unnecessary grouping class.
synonym: "regulation of camalexin anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of camalexin biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of camalexin formation" EXACT [GOC:TermGenie]
synonym: "regulation of camalexin synthesis" EXACT [GOC:TermGenie]
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0010120 ! camalexin biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29218" xsd:anyURI
is_obsolete: true
created_by: tb
creation_date: 2012-07-23T02:16:52Z

Expand Down Expand Up @@ -576353,10 +576367,11 @@ creation_date: 2013-10-10T15:45:17Z

[Term]
id: GO:1990217
name: suppression by symbiont of host phytoalexin production
name: symbiont-mediated suppression of host phytoalexin production
namespace: biological_process
def: "Any process in which a symbiont stops, prevents, or reduces the frequency, rate or extent of phytoalexin production in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:21402357]
def: "A process in which a symbiont inhibits or disrupts the production of phytoalexins in the host organism. Phytoalexins are produced by plants to fight against pathogens. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:21402357]
synonym: "negative regulation by symbiont of host phytoalexin production" EXACT []
synonym: "suppression by symbiont of host phytoalexin production" EXACT []
is_a: GO:0052165 ! symbiont defense to host-produced phytoalexin
created_by: ml
creation_date: 2013-10-10T15:49:33Z
Expand Down

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