From ebcbb8446f9c0962356c432b988ec894ab2e7914 Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Mon, 9 Dec 2024 10:50:41 +0100 Subject: [PATCH 1/2] fixed tryptophan to L-tryptophan fixes #28553 --- src/ontology/go-edit.obo | 62 ++++++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 28 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 04b58733a9..72ada90719 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -1632,18 +1632,19 @@ replaced_by: GO:0038066 [Term] id: GO:0000162 -name: tryptophan biosynthetic process +name: L-tryptophan biosynthetic process namespace: biological_process alt_id: GO:0009096 -def: "The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate." [GOC:mah, ISBN:0471331309, MetaCyc:TRPSYN-PWY] +def: "The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate." [GOC:mah, ISBN:0471331309, MetaCyc:TRPSYN-PWY] synonym: "aromatic amino acid family biosynthetic process, anthranilate pathway" EXACT [] -synonym: "tryptophan anabolism" EXACT [] -synonym: "tryptophan biosynthesis" EXACT [] +synonym: "L-tryptophan anabolism" EXACT [] +synonym: "L-tryptophan biosynthesis" EXACT [] +synonym: "tryptophan biosynthetic process" RELATED [] synonym: "tryptophan formation" EXACT [] -synonym: "tryptophan synthesis" EXACT [] +synonym: "tryptophan synthesis" RELATED [] xref: MetaCyc:TRPSYN-PWY intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:64554 ! tryptophan zwitterion +intersection_of: has_primary_output CHEBI:57912 ! L-tryptophan zwitterion [Term] id: GO:0000164 @@ -46850,7 +46851,7 @@ xref: KEGG_REACTION:R02722 xref: MetaCyc:TRYPSYN-RXN xref: RHEA:10532 is_a: GO:0016836 ! hydro-lyase activity -relationship: part_of GO:0000162 ! tryptophan biosynthetic process +relationship: part_of GO:0000162 ! L-tryptophan biosynthetic process [Term] id: GO:0004835 @@ -63510,26 +63511,28 @@ intersection_of: has_primary_input CHEBI:32832 ! threoninate [Term] id: GO:0006568 -name: tryptophan metabolic process +name: L-tryptophan metabolic process namespace: biological_process def: "The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [ISBN:0198547684] -synonym: "tryptophan metabolism" EXACT [] +synonym: "tryptophan metabolic process" RELATED [] +synonym: "tryptophan metabolism" RELATED [] xref: Wikipedia:Tryptophan intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:57912 ! L-tryptophan zwitterion [Term] id: GO:0006569 -name: tryptophan catabolic process +name: L-tryptophan catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [ISBN:0198547684] +def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [ISBN:0198547684] synonym: "tryptophan breakdown" EXACT [] +synonym: "tryptophan catabolic process" RELATED [] synonym: "tryptophan catabolic process, using tryptophanase" NARROW [] synonym: "tryptophan catabolism" EXACT [] synonym: "tryptophan catabolism, using tryptophanase" NARROW [] synonym: "tryptophan degradation" EXACT [] intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64554 ! tryptophan zwitterion +intersection_of: has_primary_input CHEBI:57912 ! L-tryptophan zwitterion [Term] id: GO:0006570 @@ -86706,7 +86709,7 @@ xref: MetaCyc:TRYPDEG-PWY {source="skos:relatedMatch"} xref: MetaCyc:TRYPTOPHAN-RXN {source="skos:exactMatch"} xref: RHEA:19553 {source="skos:exactMatch"} is_a: GO:0016830 ! carbon-carbon lyase activity -relationship: part_of GO:0006569 ! tryptophan catabolic process +relationship: part_of GO:0006569 ! L-tryptophan catabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI [Term] @@ -95172,7 +95175,7 @@ synonym: "indoleacetic acid anabolism via tryptophan" EXACT [] synonym: "indoleacetic acid formation via tryptophan" EXACT [] synonym: "indoleacetic acid synthesis via tryptophan" EXACT [] xref: MetaCyc:PWY-581 -is_a: GO:0006568 ! tryptophan metabolic process +is_a: GO:0006568 ! L-tryptophan metabolic process is_a: GO:0009684 ! indoleacetic acid biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_intermediate CHEBI:57912 ! L-tryptophan zwitterion @@ -143683,41 +143686,44 @@ replaced_by: GO:0009056 [Term] id: GO:0019440 -name: tryptophan catabolic process to indole-3-acetate +name: L-tryptophan catabolic process to indole-3-acetate namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including indole-3-acetate." [GOC:go_curators] +def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including indole-3-acetate." [GOC:go_curators] synonym: "tryptophan breakdown to indole-3-acetate" EXACT [] synonym: "tryptophan catabolic process to IAA" EXACT [] +synonym: "tryptophan catabolic process to indole-3-acetate" EXACT [] synonym: "tryptophan catabolic process to indoleacetic acid" EXACT [] synonym: "tryptophan catabolism to indoleacetic acid" EXACT [] synonym: "tryptophan degradation to indole-3-acetate" EXACT [] xref: MetaCyc:TRPIAACAT-PWY intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64554 ! tryptophan zwitterion +intersection_of: has_primary_input CHEBI:57912 ! L-tryptophan zwitterion intersection_of: has_primary_output CHEBI:30854 ! indole-3-acetate [Term] id: GO:0019441 -name: tryptophan catabolic process to kynurenine +name: L-tryptophan catabolic process to kynurenine namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including kynurenine." [GOC:go_curators] +def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including kynurenine." [GOC:go_curators] synonym: "tryptophan breakdown to kynurenine" EXACT [] +synonym: "tryptophan catabolic process to kynurenine" EXACT [] synonym: "tryptophan degradation to kynurenine" EXACT [] xref: MetaCyc:TRPKYNCAT-PWY intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64554 ! tryptophan zwitterion +intersection_of: has_primary_input CHEBI:57912 ! L-tryptophan zwitterion intersection_of: has_primary_output CHEBI:28683 ! kynurenine [Term] id: GO:0019442 -name: tryptophan catabolic process to acetyl-CoA +name: L-tryptophan catabolic process to acetyl-CoA namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including acetyl-CoA." [GOC:go_curators] +def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including acetyl-CoA." [GOC:go_curators] synonym: "tryptophan breakdown to acetyl-CoA" EXACT [] +synonym: "tryptophan catabolic process to acetyl-CoA" EXACT [] synonym: "tryptophan degradation to acetyl-CoA" EXACT [] xref: MetaCyc:TRYPTOPHAN-DEGRADATION-1 intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:64554 ! tryptophan zwitterion +intersection_of: has_primary_input CHEBI:57912 ! L-tryptophan zwitterion intersection_of: has_primary_output CHEBI:57288 ! acetyl-CoA(4-) [Term] @@ -143735,10 +143741,11 @@ consider: GO:0009034 [Term] id: GO:0019444 -name: tryptophan catabolic process to catechol +name: L-tryptophan catabolic process to catechol namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of tryptophan into other compounds, including catechol." [GOC:go_curators] +def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including catechol." [GOC:go_curators] synonym: "tryptophan breakdown to catechol" EXACT [] +synonym: "tryptophan catabolic process to catechol" EXACT [] synonym: "tryptophan degradation to catechol" EXACT [] xref: MetaCyc:TRPCAT-PWY intersection_of: GO:0009056 ! catabolic process @@ -203594,7 +203601,6 @@ name: 'de novo' NAD biosynthetic process from tryptophan namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of tryptophan from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH." [PMID:17161604] synonym: "de novo NAD biosynthetic process from tryptophan" RELATED [] -is_a: GO:0006568 ! tryptophan metabolic process is_a: GO:0034627 ! 'de novo' NAD biosynthetic process [Term] @@ -407236,7 +407242,7 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:tb] synonym: "regulation of tryptophan metabolism" EXACT [GOC:tb] intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0006568 ! tryptophan metabolic process +intersection_of: regulates GO:0006568 ! L-tryptophan metabolic process created_by: tb creation_date: 2010-06-29T02:38:48Z @@ -407247,7 +407253,7 @@ namespace: biological_process def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:tb] synonym: "positive regulation of tryptophan metabolism" EXACT [GOC:tb] intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0006568 ! tryptophan metabolic process +intersection_of: positively_regulates GO:0006568 ! L-tryptophan metabolic process created_by: tb creation_date: 2010-06-29T02:38:48Z From ffd95ba4a16d546a76f6a986223a25c88d62766e Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Mon, 9 Dec 2024 10:53:25 +0100 Subject: [PATCH 2/2] fixed tryptophan to L-tryptophan fixes #28553 --- src/ontology/go-edit.obo | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 72ada90719..24b0e313fe 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -407237,9 +407237,10 @@ creation_date: 2010-06-29T01:51:18Z [Term] id: GO:0090357 -name: regulation of tryptophan metabolic process +name: regulation of L-tryptophan metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:tb] +synonym: "regulation of tryptophan metabolic process" RELATED [] synonym: "regulation of tryptophan metabolism" EXACT [GOC:tb] intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006568 ! L-tryptophan metabolic process @@ -407248,9 +407249,10 @@ creation_date: 2010-06-29T02:38:48Z [Term] id: GO:0090358 -name: positive regulation of tryptophan metabolic process +name: positive regulation of L-tryptophan metabolic process namespace: biological_process def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:tb] +synonym: "positive regulation of tryptophan metabolic process" RELATED [] synonym: "positive regulation of tryptophan metabolism" EXACT [GOC:tb] intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006568 ! L-tryptophan metabolic process