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Issue 28553 #29391

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merged 2 commits into from
Dec 9, 2024
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Issue 28553 #29391

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ebcbb84
fixed tryptophan to L-tryptophan fixes #28553
pgaudet Dec 9, 2024
ffd95ba
fixed tryptophan to L-tryptophan fixes #28553
pgaudet Dec 9, 2024
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68 changes: 38 additions & 30 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand All @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -407231,23 +407237,25 @@ 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 ! tryptophan metabolic process
intersection_of: regulates GO:0006568 ! L-tryptophan metabolic process
created_by: tb
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 ! tryptophan metabolic process
intersection_of: positively_regulates GO:0006568 ! L-tryptophan metabolic process
created_by: tb
creation_date: 2010-06-29T02:38:48Z

Expand Down
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