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Updating input and output chemicals in LD. Fixes #28966 #29339

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Nov 30, 2024
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Updating input and output chemicals in LD. Fixes #28966 #29339

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147 changes: 36 additions & 111 deletions src/ontology/go-edit.obo
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Expand Up @@ -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 []
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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 []
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 []
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down
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