From 17f755287e9382e6df4de833a1343cf2f35e5d98 Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Thu, 30 Jan 2025 13:24:30 +0100 Subject: [PATCH 1/3] removed do not annotate fixes #29584 --- src/ontology/go-edit.obo | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index d36593848..b2aba852e 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -286787,7 +286787,7 @@ is_a: GO:0016413 ! O-acetyltransferase activity id: GO:0047186 name: N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity namespace: molecular_function -def: "Catalysis of the reaction: N-acetylneuraminate + acetyl-CoA = N-acetyl-7-O(or 9-O)-acetylneuraminate + CoA." [EC:2.3.1.45, MetaCyc:2.3.1.45-RXN] +def: "Catalysis of the reaction: N-acetylneuraminate + acetyl-CoA = N-acetyl-7-O(or 9-O)-acetylneuraminate + CoA." [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate 7-O(or 9-O)-acetyltransferase activity" RELATED [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate-7- and/or 8-O-acetyltransferase activity" RELATED [EC:2.3.1.45] synonym: "acetyl-CoA:N-acetylneuraminate-7- or 8-O-acetyltransferase activity" RELATED [EC:2.3.1.45] @@ -451601,7 +451601,6 @@ name: molecular carrier activity namespace: molecular_function def: "Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location." [GOC:molecular_function_refactoring, GOC:pdt] comment: Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization. -subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_generic subset: goslim_plant_ribbon @@ -451611,6 +451610,7 @@ is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005488 ! binding property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14221" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20848" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29584" xsd:anyURI created_by: pg creation_date: 2017-09-19T13:10:18Z From 700e6f6979fd77dc174e5098263914ab15483efc Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Thu, 30 Jan 2025 13:55:13 +0100 Subject: [PATCH 2/3] fixed parents for #27678 --- src/ontology/go-edit.obo | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index b2aba852e..de6d1e9aa 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -33331,7 +33331,7 @@ synonym: "reduced nicotinamide-adenine dinucleotide (phosphate) dehydrogenase ac synonym: "viologen accepting pyridine nucleotide oxidoreductase activity" NARROW [EC:1.6.5.2] synonym: "vitamin K reductase activity" NARROW [EC:1.6.5.2] synonym: "vitamin-K reductase activity" NARROW [EC:1.6.5.2] -xref: EC:1.6.5.2 +xref: EC:1.6.5.2 {source="skos:exactMatch"} xref: MetaCyc:NQOR-RXN xref: UM-BBD_reactionID:r0227 is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor @@ -33427,9 +33427,9 @@ synonym: "TPNH dehydrogenase activity" RELATED [EC:1.6.99.1] synonym: "TPNH-diaphorase activity" RELATED [EC:1.6.99.1] synonym: "triphosphopyridine diaphorase activity" RELATED [EC:1.6.99.1] synonym: "triphosphopyridine nucleotide diaphorase activity" RELATED [EC:1.6.99.1] -xref: EC:1.6.99.1 +xref: EC:1.6.99.1 {source="skos:exactMatch"} xref: MetaCyc:NADPH-DEHYDROGENASE-RXN -xref: RHEA:13149 +xref: RHEA:13149 {source="skos:exactMatch"} is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H [Term] @@ -33442,7 +33442,8 @@ synonym: "quinone oxidoreductase activity" BROAD [EC:1.6.5.5] synonym: "zeta-crystallin activity" NARROW [EC:1.6.5.5] xref: EC:1.6.5.5 xref: MetaCyc:QOR-RXN -xref: RHEA:14269 +xref: RHEA:14269 {source="skos:exactMatch"} +is_a: GO:0003959 ! NADPH dehydrogenase activity is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor [Term] @@ -75832,6 +75833,7 @@ synonym: "ubiquinone reductase activity" EXACT [] xref: EC:7.1.1.2 xref: MetaCyc:NADH-DEHYDROG-A-RXN xref: RHEA:29091 +is_a: GO:0003954 ! NADH dehydrogenase activity is_a: GO:0009055 ! electron transfer activity is_a: GO:0015078 ! proton transmembrane transporter activity is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity @@ -82674,6 +82676,7 @@ xref: MetaCyc:RXN0-271 {source="skos:narrowMatch"} xref: MetaCyc:RXN0-7385 {source="skos:exactMatch"} xref: RHEA:46164 {source="skos:exactMatch"} is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity +is_a: GO:0003959 ! NADPH dehydrogenase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI [Term] @@ -123822,7 +123825,7 @@ is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H id: GO:0016656 name: monodehydroascorbate reductase (NADH) activity namespace: molecular_function -def: "Catalysis of the reaction: NADH + H+ + 2 monodehydroascorbate = NAD+ + 2 ascorbate." [EC:1.6.5.4] +def: "Catalysis of the reaction: 2 monodehydro-L-ascorbate radical + NADH + H+ = 2 L-ascorbate + NAD+." [RHEA:14581] synonym: "AFR" RELATED [EC:1.6.5.4] synonym: "AFR-reductase activity" RELATED [EC:1.6.5.4] synonym: "ascorbate free radical reductase activity" RELATED [EC:1.6.5.4] @@ -123838,9 +123841,9 @@ synonym: "NADH:monodehydroascorbate oxidoreductase activity" RELATED [EC:1.6.5.4 synonym: "NADH:semidehydroascorbic acid oxidoreductase activity" RELATED [EC:1.6.5.4] synonym: "SDA reductase activity" RELATED [EC:1.6.5.4] synonym: "semidehydroascorbate reductase activity" RELATED [EC:1.6.5.4] -xref: EC:1.6.5.4 +xref: EC:1.6.5.4 {source="skos:exactMatch"} xref: MetaCyc:1.6.5.4-RXN -xref: RHEA:14581 +xref: RHEA:14581 {source="skos:exactMatch"} is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor [Term] @@ -134076,7 +134079,7 @@ synonym: "NADPH:p-benzoquinone oxidoreductase activity" RELATED [EC:1.6.5.6] xref: EC:1.6.5.6 xref: KEGG_REACTION:R05244 xref: MetaCyc:1.6.5.6-RXN -xref: RHEA:23488 +xref: RHEA:23488 {source="skos:exactMatch"} is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor [Term] @@ -309194,11 +309197,11 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0050136 name: NADH:ubiquinone reductase (non-electrogenic) activity namespace: molecular_function -def: "Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol." [EC:1.6.5.9, GOC:mah, RHEA:46160] +def: "Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol." [RHEA:46160] synonym: "NADH dehydrogenase (quinone) activity" RELATED [] -xref: EC:1.6.5.9 +xref: EC:1.6.5.9 {source="skos:exactMatch"} xref: MetaCyc:1.6.99.5-RXN -xref: RHEA:46160 +xref: RHEA:46160 {source="skos:exactMatch"} is_a: GO:0003954 ! NADH dehydrogenase activity is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25784" xsd:anyURI @@ -316029,16 +316032,16 @@ id: GO:0050625 name: 2-hydroxy-1,4-benzoquinone reductase activity namespace: molecular_function alt_id: GO:0018540 -def: "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H+ + NADH = benzene-1,2,4-triol + NAD+." [EC:1.6.5.7, RHEA:12428] +def: "Catalysis of the reaction: 2-hydroxy-1,4-benzoquinone + 2 H+ + NADH = benzene-1,2,4-triol + NAD+." [RHEA:12428] synonym: "1,2,4-trihydroxybenzene:NAD oxidoreductase activity" RELATED [EC:1.6.5.7] synonym: "1,2,4-trihydroxybenzene:NAD+ oxidoreductase activity" RELATED [EC:1.6.5.7] synonym: "2-hydroxy-1,4-benzoquinone:NADH oxidoreductase activity" RELATED [EC:1.6.5.7] synonym: "hydroxybenzoquinone reductase activity" RELATED [EC:1.6.5.-] synonym: "NADH:2-hydroxy-1,4-benzoquinone oxidoreductase activity" RELATED [EC:1.6.5.7] -xref: EC:1.6.5.7 +xref: EC:1.6.5.7 {source="skos:exactMatch"} xref: KEGG_REACTION:R05399 xref: MetaCyc:1.6.5.7-RXN -xref: RHEA:12428 +xref: RHEA:12428 {source="skos:exactMatch"} xref: UM-BBD_reactionID:r0667 is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor @@ -439060,8 +439063,10 @@ replaced_by: GO:0008753 id: GO:0103036 name: NADH:menaquinone oxidoreductase activity namespace: molecular_function -def: "Catalysis of the reaction: 5 H+ + NADH + a menaquinone = 4 H+ + NAD + a menaquinol." [GOC:pz] +def: "Catalysis of the reaction: 5 H+ + NADH + a menaquinone = 4 H+ + NAD + a menaquinol." [GOC:pz, RHEA:29099] xref: MetaCyc:RXN0-5388 +xref: RHEA:29099 +is_a: GO:0003954 ! NADH dehydrogenase activity is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor [Term] From 7a3c9de0fc3013bdcbabcd62813fa26b5fe385ac Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Thu, 30 Jan 2025 14:04:19 +0100 Subject: [PATCH 3/3] obsoleted term fixes #20017 --- src/ontology/go-edit.obo | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index de6d1e9aa..1e44131f6 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -407469,11 +407469,13 @@ creation_date: 2010-07-12T10:32:27Z [Term] id: GO:0090363 -name: regulation of proteasome core complex assembly +name: obsolete regulation of proteasome core complex assembly namespace: biological_process -def: "Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of a mature, active 20S proteasome core particle complex that does not contain any regulatory particles." [GOC:dph, GOC:elh, GOC:tb] -intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0080129 ! proteasome core complex assembly +def: "OBSOLETE. Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of a mature, active 20S proteasome core particle complex that does not contain any regulatory particles." [GOC:dph, GOC:elh, GOC:tb] +comment: This term was obsoleted because was too specific. +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20017" xsd:anyURI +is_obsolete: true +consider: GO:0043248 created_by: tb creation_date: 2010-07-12T10:48:57Z