From cb65e1eec53731721b87ac82ff60085b657d899b Mon Sep 17 00:00:00 2001 From: sjm41 Date: Sat, 30 Nov 2024 10:07:49 +0000 Subject: [PATCH] Updating input and output chemicals in LD. Fixes #28966 --- src/ontology/go-edit.obo | 147 ++++++++++----------------------------- 1 file changed, 36 insertions(+), 111 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index d9412d032f..835e8828fd 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -2674,7 +2674,7 @@ id: GO:0000253 name: 3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity namespace: molecular_function alt_id: GO:0050576 -def: "Catalysis of the reaction: a 3-beta-hydroxysteroid + NADP+ = a 3-oxosterol + NADPH + H+." [EC:1.1.1.270, GOC:mah, PMID:9811880] +def: "Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H+." [EC:1.1.1.270, GOC:mah, PMID:9811880] comment: Note that zymosterol is cholesta-8,24-dien-3-ol. synonym: "3-keto sterol reductase activity" EXACT [] synonym: "3-keto-steroid reductase activity" EXACT [] @@ -78449,9 +78449,9 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008397 name: sterol 12-alpha-hydroxylase activity namespace: molecular_function -def: "Catalysis of the reaction: a steroid + reduced [NADPH--hemoprotein reductase] + O2 = a 12-alpha-hydroxysteroid + oxidized [NADPH--hemoprotein reductase]- H2O +H+." [EC:1.14.14.139] +def: "Catalysis of the reaction: a steroid + donor-H2 + O2 = 12-alpha-hydroxysteroid + H2O." [GOC:mah] synonym: "cytochrome P450 CYP8B1" NARROW [] -xref: EC:1.14.14.139 {source="skos:exactMatch"} +xref: EC:1.14.14.139 is_a: GO:0008395 ! steroid hydroxylase activity is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24843" xsd:anyURI @@ -160583,12 +160583,11 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030343 name: vitamin D3 25-hydroxylase activity namespace: molecular_function -def: "Catalysis of the reaction: calciol (vitamin D3) + reduced [NADPH--hemoprotein reductase] + O2 = calcidiol + oxidized [NADPH--hemoprotein reductase]+ + H2O +H2." [RHEA:32903] +def: "Catalysis of the reaction: vitamin D3 + NADPH + H+ + O2 = calcidiol + NADP+ + H2O." [ISBN:0471331309, MetaCyc:RXN-9829] synonym: "cholecalciferol 25-hydroxylase activity" EXACT [] -xref: EC:1.14.14.24 {source="skos:exactMatch"} xref: MetaCyc:RXN-9829 -xref: RHEA:32903 {source="skos:exactMatch"} -is_a: GO:0008395 ! steroid hydroxylase activity +xref: RHEA:32903 +is_a: GO:0070643 ! vitamin D 25-hydroxylase activity relationship: part_of GO:0036378 ! calcitriol biosynthetic process from calciol [Term] @@ -163668,7 +163667,7 @@ relationship: part_of GO:0044304 ! main axon id: GO:0030674 name: protein-macromolecule adaptor activity namespace: molecular_function -def: "An adaptor activity that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw] +def: "The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw] subset: goslim_chembl subset: goslim_yeast synonym: "protein binding, bridging" EXACT [] @@ -190595,26 +190594,20 @@ intersection_of: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0033207 -name: obsolete beta-1,4-N-acetylgalactosaminyltransferase activity +name: beta-1,4-N-acetylgalactosaminyltransferase activity namespace: molecular_function -def: "OBSOLETE. Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage." [GOC:mah] -comment: This term was obsoleted because it represents the same reaction as N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity ; GO:0033842. +def: "Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming a beta-1,4 linkage." [GOC:mah] synonym: "beta-1,4-GalNAc transferase activity" EXACT [] -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18752" xsd:anyURI -is_obsolete: true -replaced_by: GO:0033842 +is_a: GO:0008376 ! acetylgalactosaminyltransferase activity [Term] id: GO:0033208 -name: obsolete UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity +name: UDP-N-acetylgalactosamine:N-acetylneuraminyl-alpha-2,3-galactosyl-beta-R 1,4-N-acetylgalactosaminyltransferase activity namespace: molecular_function -def: "OBSOLETE. Catalysis of the reaction: UDP-N-acetylgalactosamine + N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide = UDP + N-acetylgalactosaminyl-N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide." [GOC:mah, PMID:12678917, PMID:16024623] -comment: This term was obsoleted because it represents a specific substrate of N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity ; GO:0033842. +def: "Catalysis of the reaction: UDP-N-acetylgalactosamine + N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide = UDP + N-acetylgalactosaminyl-N-acetylneuraminyl-alpha-2,3-galactosyl-beta-oligosaccharide." [GOC:mah, PMID:12678917, PMID:16024623] synonym: "Sda beta 1,4GalNAc transferase" RELATED [] synonym: "UDP-GalNAc:Neu5Ac-alpha-2-Gal-beta-1-R beta-1,4-N-acetylgalactosaminyltransferase activity" EXACT [] -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18752" xsd:anyURI -is_obsolete: true -replaced_by: GO:0033842 +is_a: GO:0033207 ! beta-1,4-N-acetylgalactosaminyltransferase activity [Term] id: GO:0033209 @@ -196847,12 +196840,12 @@ id: GO:0033778 name: 7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase activity namespace: molecular_function def: "Catalysis of the reaction: 7alpha-hydroxycholest-4-en-3-one + H+ + NADPH + O2 = 7alpha,12alpha-dihydroxycholest-4-en-3-one + H2O + NADP+." [PMID:10051404, PMID:1400444, RHEA:46752] +synonym: "7alpha-hydroxy-4-cholesten-3-one 12alpha-monooxygenase activity" RELATED [EC:1.14.14.139] xref: KEGG_REACTION:R04826 xref: MetaCyc:1.14.13.95-RXN xref: RHEA:46752 is_a: GO:0008397 ! sterol 12-alpha-hydroxylase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24843" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29331" xsd:anyURI [Term] id: GO:0033779 @@ -196866,7 +196859,6 @@ xref: MetaCyc:1.14.13.96-RXN xref: RHEA:15261 is_a: GO:0008397 ! sterol 12-alpha-hydroxylase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24843" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29331" xsd:anyURI [Term] id: GO:0033780 @@ -224447,12 +224439,10 @@ synonym: "annealing helicase activity" RELATED [PMID:22888405] synonym: "ATP-dependent DNA annealing activity" RELATED [GOC:sp] synonym: "DNA rewinding activity" RELATED [PMID:22888405] synonym: "nucleoside-triphosphatase activity involved in DNA annealing" EXACT [GOC:bf] -is_a: GO:0008094 ! ATP-dependent activity, acting on DNA is_a: GO:1990814 ! DNA/DNA annealing activity relationship: has_part GO:0016887 ! ATP hydrolysis activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12465" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19669" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29334" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/9815" xsd:anyURI created_by: bf creation_date: 2012-08-14T15:24:29Z @@ -359626,9 +359616,10 @@ def: "The chemical reactions and pathways resulting in the breakdown of fructose intersection_of: GO:0009056 ! catabolic process intersection_of: has_part GO:0050354 ! triokinase activity intersection_of: has_part GO:0061609 ! fructose-1-phosphate aldolase activity -intersection_of: has_primary_input CHEBI:28757 ! fructose -intersection_of: has_primary_output CHEBI:58027 ! glyceraldehyde 3-phosphate(2-) +intersection_of: has_primary_input CHEBI:28645 ! beta-D-fructofuranose +intersection_of: has_primary_output CHEBI:59776 ! D-glyceraldehyde 3-phosphate(2-) intersection_of: starts_with GO:0004454 ! ketohexokinase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28966" xsd:anyURI created_by: dph creation_date: 2014-04-29T12:58:28Z @@ -359678,14 +359669,11 @@ creation_date: 2014-05-14T14:32:02Z [Term] id: GO:0061628 -name: H3K27me3 histone reader activity +name: H3K27me3 modified histone binding namespace: molecular_function -def: "A histone reader that recognizes a histone H3 trimethylated at lysine 27." [GOC:dph, PMID:23948251] -synonym: "H3-K27me3 modified histone binding" NARROW [] -synonym: "H3K27me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI +def: "Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation." [GOC:dph, PMID:23948251] +synonym: "H3-K27me3 modified histone binding" EXACT [GOC:dph] +is_a: GO:0035064 ! methylated histone binding created_by: dph creation_date: 2014-05-14T15:36:53Z @@ -359895,7 +359883,7 @@ creation_date: 2014-10-02T15:26:53Z id: GO:0061649 name: ubiquitin-modified histone reader activity namespace: molecular_function -def: "A histone reader that recognizes a histone that bears a ubiquinated lysine residue." [GOC:dph, PMID:24526689] +def: "A molecular adaptor that recognizes and binds a histone protein containing a ubiquitination modification and that brings the target protein into contact with another protein to allow those proteins to function in a coordinated way." [GOC:dph, PMID:24526689] synonym: "ubiquitin modification-dependent histone binding" EXACT [] synonym: "ubiquitinated histone binding" RELATED [] is_a: GO:0140036 ! ubiquitin-modified protein reader activity @@ -364108,13 +364096,10 @@ creation_date: 2018-09-04T13:40:52Z [Term] id: GO:0062072 -name: H3K9me3 histone reader activity +name: H3K9me3 modified histone binding namespace: molecular_function -def: "A histone reader that recognizes a histone H3 trimethylated at lysine 9." [PMID:30110338] -synonym: "H3K9me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI +def: "Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation." [PMID:30110338] +is_a: GO:0035064 ! methylated histone binding created_by: dph creation_date: 2018-09-05T12:58:43Z @@ -372612,17 +372597,14 @@ creation_date: 2009-05-08T02:47:41Z [Term] id: GO:0070643 -name: obsolete vitamin D 25-hydroxylase activity +name: vitamin D 25-hydroxylase activity namespace: molecular_function -def: "OBSOLETE. Catalysis of the hydroxylation of C-25 of any form of vitamin D." [GOC:BHF, GOC:mah] -comment: This term was obsoleted because it was an unnecessary grouping term. +def: "Catalysis of the hydroxylation of C-25 of any form of vitamin D." [GOC:BHF, GOC:mah] synonym: "calciferol 25-hydroxylase activity" NARROW [GOC:mah] synonym: "cholecalciferol 25-hydroxylase activity" NARROW [GOC:mah] synonym: "ergocalciferol 25-hydroxylase activity" NARROW [GOC:mah] synonym: "vitamin D2 25-hydroxylase activity" NARROW [GOC:mah] -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29330" xsd:anyURI -is_obsolete: true -consider: GO:0030343 +is_a: GO:0008395 ! steroid hydroxylase activity created_by: mah creation_date: 2009-05-08T03:42:29Z @@ -394168,14 +394150,11 @@ creation_date: 2011-01-25T05:19:30Z [Term] id: GO:0072555 -name: obsolete 17-beta-ketosteroid reductase (NADPH) activity +name: 17-beta-ketosteroid reductase (NADPH) activity namespace: molecular_function -def: "OBSOLETE. Catalysis of the reaction: a 17-beta-ketosteroid + NADPH + H+ = a 17-beta-hydroxysteroid + NADP+." [GOC:kad, PMID:17074428] -comment: This term was obsoleted because it was an unnecessary grouoing term. +def: "Catalysis of the reaction: a 17-beta-ketosteroid + NADPH + H+ = a 17-beta-hydroxysteroid + NADP+." [GOC:kad, PMID:17074428] synonym: "7beta-ketosteroid reductase activity" EXACT [GOC:kad] -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29329" xsd:anyURI -is_obsolete: true -consider: GO:0072582 +is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor created_by: mah creation_date: 2011-01-27T11:36:14Z @@ -450102,57 +450081,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2024-11-12T09:29:56Z -[Term] -id: GO:0140002 -name: H3K4me3 histone reader activity -namespace: molecular_function -def: "A histone reader that recognizes a histone H3 trimethylated at lysine 4." [PMID:15647753, PMID:23318260] -synonym: "H3-K4me3 modified histone binding" NARROW [] -synonym: "H3K4me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI -created_by: pg -creation_date: 2024-11-29T14:13:16Z - -[Term] -id: GO:0140003 -name: H3K36me3 histone reader activity -namespace: molecular_function -def: "A histone reader that recognizes a histone H3 trimethylated at lysine 36." [PMID:15489290, PMID:16364921] -synonym: "H3-K36me3 modified histone binding" NARROW [] -synonym: "H3K36me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI -created_by: pg -creation_date: 2024-11-29T14:20:22Z - -[Term] -id: GO:0140004 -name: H3Q5ser histone reader activity -namespace: molecular_function -def: "A histone reader that recognizes a histone H3 serotonylated at glutamine 5." [PMID:34144982] -synonym: "H3Q5-serotonin histone reader activity" EXACT [] -synonym: "H3Q5-serotonin modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI -created_by: pg -creation_date: 2024-11-29T14:37:52Z - -[Term] -id: GO:0140005 -name: H4K20me2 histone reader activity -namespace: molecular_function -def: "A histone reader that recognizes a histone H4 dimethylated at lysine 20." [PMID:22150589] -synonym: "H4K20me2 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24912" xsd:anyURI -created_by: pg -creation_date: 2024-11-29T15:16:39Z - [Term] id: GO:0140007 name: KICSTOR complex @@ -454017,7 +453945,7 @@ creation_date: 2020-05-06T07:47:09Z id: GO:0140463 name: chromatin-protein adaptor activity namespace: molecular_function -def: "An adaptor activity that brings together a protein and a region of the chromatin, such as a nucleosome, to establish or maintain the chromatin localization of the protein, or the complex to which it belongs." [PMID:32277274] +def: "The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex." [PMID:32277274] synonym: "chromatin adaptor" EXACT [] synonym: "chromatin adaptor activity" EXACT [] synonym: "chromatin receptor" EXACT [] @@ -454997,7 +454925,7 @@ creation_date: 2020-11-25T16:07:58Z id: GO:0140566 name: histone reader activity namespace: molecular_function -def: "A chromatin adaptor activity that brings together a protein and a specific form of histone, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351] +def: "A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351] synonym: "epigenetic reader" BROAD [] synonym: "histone reader" EXACT [] is_a: GO:0140463 ! chromatin-protein adaptor activity @@ -584128,13 +584056,10 @@ creation_date: 2015-10-28T22:31:13Z [Term] id: GO:1990889 -name: H4K20me3 histone reader activity +name: H4K20me3 modified histone binding namespace: molecular_function -def: "A histone reader that recognizes a histone H4 trimethylated at lysine 20." [PMID:22150589] -synonym: "H4K20me3 modified histone binding" NARROW [] -is_a: GO:0140566 ! histone reader activity -relationship: has_part GO:0035064 ! methylated histone binding -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI +def: "Binding to a histone H4 in which the lysine residue at position 20 has been modified by trimethylation." [PMID:22150589] +is_a: GO:0035064 ! methylated histone binding created_by: al creation_date: 2015-10-30T15:43:09Z