diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 49445c238c..d99c9df6cb 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 [] @@ -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 [] @@ -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 @@ -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 [] @@ -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] @@ -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 [] @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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