--- go-lastrelease.obo 2026-03-29 06:04:49.072761008 +0000
+++ go.obo 2026-03-29 06:14:02.661498919 +0000
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2026-01-23
+data-version: releases/2026-03-29
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
@@ -44,7 +44,7 @@
property_value: has_ontology_root_term GO:0003674
property_value: has_ontology_root_term GO:0005575
property_value: has_ontology_root_term GO:0008150
-property_value: owl:versionInfo "2026-01-23" xsd:string
+property_value: owl:versionInfo "2026-03-29" xsd:string
property_value: terms:license http://creativecommons.org/licenses/by/4.0/
[Term]
@@ -69,7 +69,7 @@
id: GO:0000003
name: obsolete reproduction
namespace: biological_process
-def: "OBSOLETE. The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
+def: "OBSOLETE. The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:curators, GOC:isa_complete, GOC:jl, ISBN:0198506732]
comment: The reason for obsoletion is that this term is equivalent to reproductive process.
synonym: "reproductive physiological process" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27054" xsd:anyURI
@@ -167,14 +167,16 @@
[Term]
id: GO:0000014
-name: single-stranded DNA endodeoxyribonuclease activity
+name: single-stranded DNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks." [GOC:mah]
+synonym: "single-stranded DNA endodeoxyribonuclease activity" EXACT []
synonym: "single-stranded DNA specific endodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific endodeoxyribonuclease activity" RELATED [GOC:mah]
is_a: GO:0004520 ! DNA endonuclease activity
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31721" xsd:anyURI
[Term]
id: GO:0000015
@@ -197,9 +199,11 @@
xref: Reactome:R-HSA-189062 "lactose + H2O => D-glucose + D-galactose"
xref: Reactome:R-HSA-5658001 "Defective LCT does not hydrolyze Lac"
xref: RHEA:10076
+xref: RHEA:28659
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
property_value: skos:exactMatch EC:3.2.1.108
property_value: skos:exactMatch RHEA:10076
+property_value: skos:narrowMatch RHEA:28659
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -213,7 +217,7 @@
id: GO:0000018
name: regulation of DNA recombination
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732]
+def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:curators, ISBN:0198506732]
is_a: GO:0051052 ! regulation of DNA metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006310 ! DNA recombination
@@ -223,7 +227,7 @@
id: GO:0000019
name: regulation of mitotic recombination
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of DNA recombination during mitosis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of DNA recombination during mitosis." [GOC:curators]
synonym: "regulation of recombination within rDNA repeats" NARROW []
is_a: GO:0000018 ! regulation of DNA recombination
intersection_of: GO:0065007 ! biological regulation
@@ -234,7 +238,7 @@
id: GO:0000020
name: obsolete negative regulation of recombination within rDNA repeats
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:curators, ISBN:0198506732]
comment: This term was made obsolete because it describes a substrate-specific process.
synonym: "negative regulation of recombination within rDNA repeats" EXACT []
is_obsolete: true
@@ -490,7 +494,7 @@
id: GO:0000048
name: peptidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2). This reaction is catalyzed by a ribozyme." [PMID:11433365, PMID:9242921]
+def: "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2). This reaction is catalyzed by a ribozyme." [EC:2.3.2.12, PMID:11433365, PMID:9242921]
xref: EC:2.3.2.12
xref: MetaCyc:PEPTIDYLTRANSFERASE-RXN
xref: Reactome:R-HSA-156912 "Peptide transfer from P-site tRNA to the A-site tRNA"
@@ -509,6 +513,7 @@
alt_id: GO:0000946
def: "Binding to a transfer RNA." [GOC:ai]
synonym: "base pairing with tRNA" NARROW []
+xref: Reactome:R-HSA-2408509 "Sec-tRNA(Sec) binds to EEFSEC:GTP"
is_a: GO:0003723 ! RNA binding
[Term]
@@ -547,14 +552,14 @@
[Term]
id: GO:0000053
-name: argininosuccinate metabolic process
+name: obsolete argininosuccinate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate." [ISBN:0198506732]
+comment: This term was obsoleted because it represents a pathway intermediate.
synonym: "argininosuccinate metabolism" EXACT []
-is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0072350 ! tricarboxylic acid metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0000050
[Term]
id: GO:0000054
@@ -661,6 +666,7 @@
synonym: "histidine/arginine/lysine/ornithine porter activity" RELATED []
synonym: "L-ornithine transporter activity" BROAD []
xref: Reactome:R-HSA-70634 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic)"
+xref: Reactome:R-HSA-9956519 "SLC25A15 variants don't translocate ornithine and citrulline"
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
relationship: part_of GO:1903352 ! L-ornithine transmembrane transport
@@ -784,7 +790,7 @@
id: GO:0000079
name: regulation of cyclin-dependent protein serine/threonine kinase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity." [GOC:go_curators, GOC:pr]
+def: "Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity." [GOC:curators, GOC:pr]
subset: gocheck_obsoletion_candidate
synonym: "regulation of CDK activity" EXACT []
synonym: "regulation of cyclin-dependent protein kinase activity" BROAD []
@@ -939,7 +945,7 @@
id: GO:0000094
name: obsolete septin assembly and septum formation
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was not defined and the string name implied two separate processes.
synonym: "septin assembly and septum formation" EXACT []
is_obsolete: true
@@ -967,19 +973,20 @@
id: GO:0000096
name: sulfur amino acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine." [GOC:ai]
+def: "The chemical reactions and pathways involving amino acids containing sulfur." [GOC:curators]
synonym: "sulfur amino acid metabolism" EXACT []
synonym: "sulphur amino acid metabolic process" EXACT []
synonym: "sulphur amino acid metabolism" EXACT []
xref: Reactome:R-HSA-1614635 "Sulfur amino acid metabolism"
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31500" xsd:anyURI
[Term]
id: GO:0000097
name: sulfur amino acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the formation of amino acids containing sulfur." [GOC:curators]
synonym: "sulfur amino acid anabolism" EXACT []
synonym: "sulfur amino acid biosynthesis" EXACT []
synonym: "sulfur amino acid formation" EXACT []
@@ -989,12 +996,13 @@
is_a: GO:0000096 ! sulfur amino acid metabolic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31500" xsd:anyURI
[Term]
id: GO:0000098
name: sulfur amino acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur." [GOC:curators]
synonym: "sulfur amino acid breakdown" EXACT []
synonym: "sulfur amino acid catabolism" EXACT []
synonym: "sulfur amino acid degradation" EXACT []
@@ -1004,6 +1012,7 @@
is_a: GO:0000096 ! sulfur amino acid metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31500" xsd:anyURI
[Term]
id: GO:0000099
@@ -1074,8 +1083,10 @@
synonym: "succinyl dehydrogenase activity" EXACT []
xref: KEGG_REACTION:R00412
xref: RHEA:16357
+xref: RHEA:51848
is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
property_value: skos:exactMatch RHEA:16357
+property_value: skos:narrowMatch RHEA:51848
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17091" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -1083,17 +1094,21 @@
id: GO:0000105
name: L-histidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:curators]
synonym: "histidine anabolism" EXACT []
synonym: "histidine biosynthesis" EXACT []
synonym: "histidine biosynthetic process" BROAD []
synonym: "histidine formation" EXACT []
synonym: "histidine synthesis" EXACT []
xref: MetaCyc:HISTSYN-PWY
-is_a: GO:0006547 ! L-histidine metabolic process
+xref: MetaCyc:PWY-5029
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
+is_a: GO:0052803 ! imidazole-containing compound metabolic process
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:HISTSYN-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5029
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0000107
@@ -1269,7 +1284,7 @@
namespace: biological_process
alt_id: GO:0010553
alt_id: GO:0045816
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:go_curators, GOC:txnOH]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:curators, GOC:txnOH]
synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT []
synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED []
@@ -1770,7 +1785,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the hydroxylation of sphingolipid long chain bases." [PMID:9556590]
comment: The reason for obsoletion is that this term is equivalent to sphingolipid C4-monooxygenase activity.
-xref: Reactome:R-HSA-428260 "DEGS2 oxygenates dihydroceramide"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29717" xsd:anyURI
is_obsolete: true
replaced_by: GO:0102772
@@ -1816,12 +1830,14 @@
synonym: "3'-5'-exoribonuclease activity" EXACT []
xref: Reactome:R-HSA-430028 "Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion"
xref: Reactome:R-HSA-6791222 "21S pre-rRNA is nucleolytically processed at site E (site2a) to yield 18SE pre-rRNA"
-xref: Reactome:R-HSA-6791227 "47S pre-rRNA is nucleolytically processed at A' (01,A1), site A0, and site 02 (site 6) to yield 45S pre-rRNA"
xref: Reactome:R-HSA-9682603 "nsp14 acts as a 3'-to-5' exonuclease to remove misincorporated nucleotides from nascent RNA"
xref: Reactome:R-HSA-9694632 "nsp14 acts as a 3'-to-5' exonuclease to remove misincorporated nucleotides from nascent RNA"
xref: Reactome:R-HSA-9822437 "DIS3L2 hydrolyzes uridylated mRNA"
xref: Reactome:R-HSA-9836585 "SUPV3L1:PNPT1 hydrolyzes mitochondrial RNA to yield 4-5 nucleotide oligoribonucleotides"
xref: Reactome:R-HSA-9836822 "REXO2 hydrolyzes 4-5 nucleotide RNAs to ribonucleotides"
+xref: Reactome:R-HSA-9933585 "RNA exosome in PAXT:PAPOLG:TENT4A,B:ZC3H3:CBCA:polyadenylated m7GpppN-RNA:PABPN1 hydrolyzes RNA"
+xref: Reactome:R-HSA-9934763 "The RNA exosome in RNA exosome:NEXT:ZC3H18:CBCA:m7GpppN-RNA hydrolyzes RNA"
+xref: Reactome:R-HSA-9935824 "TRAMP:RNA exosome hydrolyzes oligoadenylated pre-rRNA 5' external transcribed spacer (5'ETS)"
is_a: GO:0008408 ! 3'-5' exonuclease activity
is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28062" xsd:anyURI
@@ -2269,7 +2285,7 @@
name: meiotic spindle organization
namespace: biological_process
alt_id: GO:0043147
-def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle." [GOC:go_curators, GOC:mah]
+def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle." [GOC:curators, GOC:mah]
synonym: "meiotic spindle organisation" EXACT []
synonym: "meiotic spindle organization and biogenesis" RELATED [GOC:mah]
synonym: "meiotic spindle stabilization" RELATED []
@@ -2348,7 +2364,7 @@
id: GO:0000219
name: obsolete vacuolar hydrogen-transporting ATPase
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "V-ATPase" EXACT []
synonym: "vacuolar hydrogen-transporting ATPase" EXACT []
@@ -2798,6 +2814,8 @@
xref: EC:1.1.1.170
xref: Reactome:R-HSA-194642 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one"
xref: Reactome:R-HSA-194718 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone)"
+xref: Reactome:R-HSA-9945787 "NSDHL decarboxylates 4a-carboxy-5a-cholest-8-ene-3b-ol to 5a-cholest-8-en-3-one"
+xref: Reactome:R-HSA-9945822 "NSDHL decarboxylates 4a-carboxy-4b-methyl-5a-cholest-8-en-3b-ol to 4a-methyl-5a-cholest-8-en-3b-ol"
xref: RHEA:34771
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.170
@@ -2818,14 +2836,36 @@
xref: MetaCyc:RXN-13686
xref: Reactome:R-HSA-194632 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol)"
xref: Reactome:R-HSA-194689 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol"
+xref: Reactome:R-HSA-9945784 "HSD17B7 reduces 4a-methyl-5a-cholest-8-en-3-one to 4a-methyl-5a-cholest-8-en-3b-ol"
+xref: Reactome:R-HSA-9945804 "HSD17B7 reduces 5a-cholest-8-en-3-one to ZYMSTNL"
xref: RHEA:18409
+xref: RHEA:33459
xref: RHEA:34787
xref: RHEA:36379
+xref: RHEA:46216
+xref: RHEA:46832
+xref: RHEA:46852
+xref: RHEA:56880
+xref: RHEA:56916
+xref: RHEA:69012
+xref: RHEA:69036
+xref: RHEA:85555
+xref: RHEA:85563
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.270
property_value: skos:exactMatch RHEA:34787
property_value: skos:narrowMatch RHEA:18409
+property_value: skos:narrowMatch RHEA:33459
property_value: skos:narrowMatch RHEA:36379
+property_value: skos:narrowMatch RHEA:46216
+property_value: skos:narrowMatch RHEA:46832
+property_value: skos:narrowMatch RHEA:46852
+property_value: skos:narrowMatch RHEA:56880
+property_value: skos:narrowMatch RHEA:56916
+property_value: skos:narrowMatch RHEA:69012
+property_value: skos:narrowMatch RHEA:69036
+property_value: skos:narrowMatch RHEA:85555
+property_value: skos:narrowMatch RHEA:85563
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29311" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -2841,6 +2881,8 @@
xref: MetaCyc:RXN-13188
xref: Reactome:R-HSA-194641 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol"
xref: Reactome:R-HSA-194669 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol"
+xref: Reactome:R-HSA-9947203 "MSMO1 oxidizes 4,4-diMe-5-cholest-8-en-3-ol to 4a-carboxy-4b-me-5a-cholest-8-en-3b-ol"
+xref: Reactome:R-HSA-9947207 "MSMO1 oxidizes 4a-me-5a-cholest-8-en-3b-ol to 4a-carboxy-5a-cholest-8-ene-3b-ol"
xref: RHEA:55220
is_a: GO:0016716 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.18.9
@@ -2872,7 +2914,7 @@
id: GO:0000257
name: nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH3. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides." [EC:3.5.5.1, GOC:kd]
+def: "Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH4+. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides." [RHEA:21724]
synonym: "acetonitrilase activity" RELATED [EC:3.5.5.1]
synonym: "benzonitrilase activity" RELATED [EC:3.5.5.1]
synonym: "nitrile aminohydrolase activity" RELATED [EC:3.5.5.1]
@@ -2880,11 +2922,15 @@
xref: KEGG_REACTION:R00540
xref: MetaCyc:3.5.5.1-RXN
xref: RHEA:21724
+xref: RHEA:40775
+xref: RHEA:45784
xref: UM-BBD_reactionID:r0377
xref: UM-BBD_reactionID:r0701
is_a: GO:0016815 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles
property_value: skos:exactMatch EC:3.5.5.1
property_value: skos:exactMatch RHEA:21724
+property_value: skos:narrowMatch RHEA:40775
+property_value: skos:narrowMatch RHEA:45784
[Term]
id: GO:0000258
@@ -3031,7 +3077,7 @@
id: GO:0000271
name: polysaccharide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:curators]
synonym: "glycan biosynthesis" EXACT []
synonym: "glycan biosynthetic process" EXACT []
synonym: "polysaccharide anabolism" EXACT []
@@ -3199,9 +3245,11 @@
xref: Reactome:R-HSA-1676134 "PI3P is phosphorylated to PI(3,5)P2 by PIP5K1A/B at the plasma membrane"
xref: Reactome:R-HSA-1676168 "PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the early endosome membrane"
xref: RHEA:13609
+xref: RHEA:42348
is_a: GO:0052742 ! phosphatidylinositol kinase activity
property_value: skos:exactMatch EC:2.7.1.150
property_value: skos:exactMatch RHEA:13609
+property_value: skos:narrowMatch RHEA:42348
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28336" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -4113,6 +4161,7 @@
namespace: molecular_function
def: "Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon." [GOC:krc, ISBN:0879695897, PMID:19239890]
synonym: "lariat formation, 5'-splice site cleavage" RELATED []
+xref: Reactome:R-HSA-9794542 "Formation of the Spliceosomal C complex containing intron lariat"
is_a: GO:0140098 ! catalytic activity, acting on RNA
relationship: part_of GO:0000375 ! RNA splicing, via transesterification reactions
@@ -4337,7 +4386,7 @@
id: GO:0000409
name: regulation of transcription by galactose
namespace: biological_process
-def: "Any process involving galactose that modulates the frequency, rate or extent or transcription." [GOC:go_curators]
+def: "Any process involving galactose that modulates the frequency, rate or extent or transcription." [GOC:curators]
is_a: GO:0006355 ! regulation of DNA-templated transcription
[Term]
@@ -4356,7 +4405,7 @@
id: GO:0000411
name: positive regulation of transcription by galactose
namespace: biological_process
-def: "Any process involving galactose that activates or increases the rate of transcription." [GOC:go_curators]
+def: "Any process involving galactose that activates or increases the rate of transcription." [GOC:curators]
synonym: "activation of transcription by galactose" NARROW []
synonym: "stimulation of transcription by galactose" NARROW []
synonym: "up regulation of transcription by galactose" EXACT []
@@ -5245,7 +5294,7 @@
id: GO:0000578
name: embryonic axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." [GOC:dph, GOC:go_curators, GOC:sdb_2009, GOC:tb]
+def: "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." [GOC:curators, GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "embryonic axis determination" RELATED []
is_a: GO:0009798 ! axis specification
is_a: GO:0009880 ! embryonic pattern specification
@@ -5288,7 +5337,7 @@
synonym: "endodeoxyribonuclease III" RELATED []
synonym: "endonuclease III" RELATED []
synonym: "endonuclease VIII activity" RELATED []
-synonym: "oxidized pyrimidine base lesion DNA N-glycosylase activity" EXACT [GOC:go_curators]
+synonym: "oxidized pyrimidine base lesion DNA N-glycosylase activity" EXACT [GOC:curators]
synonym: "pyrimidine-specific oxidized base lesion DNA N-glycosylase activity" RELATED []
xref: Reactome:R-HSA-110224 "Cleavage of thymine glycol by NTHL1 glycosylase"
xref: Reactome:R-HSA-110226 "Cleavage of cytosine glycol by NTHL1 glycosylase"
@@ -5835,10 +5884,13 @@
namespace: biological_process
alt_id: GO:0000218
alt_id: GO:0030462
-def: "During conjugation with cellular fusion, the process resulting in creating a single cell from complementary mating types. The localized remodeling and dissolution of external protective structures allow the fusion of the plasma membranes and cytoplasmic mixing. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh]
+def: "A reproductive process in a single-celled organism in which the cytoplasm of two mating cells fuse, resulting in the formation of a single cell containing the combined cellular contents." [GOC:vw]
+comment: Cytogamy follows cell recognition and mating projection formation (when present) and precedes or accompanies nuclear fusion (karyogamy).
synonym: "zygote formation" RELATED []
is_a: GO:0022413 ! reproductive process in single-celled organism
+is_a: GO:0140253 ! cell-cell fusion
relationship: part_of GO:0000747 ! conjugation with cellular fusion
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
[Term]
id: GO:0000756
@@ -5961,14 +6013,12 @@
[Term]
id: GO:0000768
-name: syncytium formation by plasma membrane fusion
+name: syncytium formation by cell-cell fusion
namespace: biological_process
def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb]
-synonym: "cell fusion" BROAD []
-is_a: GO:0006949 ! syncytium formation
+synonym: "syncytium formation by plasma membrane fusion" EXACT []
is_a: GO:0140253 ! cell-cell fusion
-intersection_of: GO:0006949 ! syncytium formation
-intersection_of: has_part GO:0045026 ! plasma membrane fusion
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
[Term]
id: GO:0000769
@@ -5976,10 +6026,8 @@
namespace: biological_process
def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by one or more rounds of nuclear division without cytokinesis." [GOC:mah, GOC:tb]
synonym: "syncytium formation by mitosis without cell division" RELATED [GOC:mah]
-is_a: GO:0006949 ! syncytium formation
-intersection_of: GO:0006949 ! syncytium formation
-intersection_of: has_part GO:0033301 ! cell cycle comprising mitosis without cytokinesis
-relationship: has_part GO:0033301 ! cell cycle comprising mitosis without cytokinesis
+is_a: GO:0033301 ! cell cycle comprising mitosis without cytokinesis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
[Term]
id: GO:0000770
@@ -6349,9 +6397,13 @@
xref: EC:3.6.1.75
xref: MetaCyc:RXN-11277
xref: RHEA:27449
+xref: RHEA:42856
+xref: RHEA:62092
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.75
property_value: skos:exactMatch RHEA:27449
+property_value: skos:narrowMatch RHEA:42856
+property_value: skos:narrowMatch RHEA:62092
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24052" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -6428,7 +6480,7 @@
id: GO:0000820
name: obsolete regulation of glutamine family amino acid metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:curators]
comment: The reason for obsoletion is that this is an unnecessary grouping term.
synonym: "regulation of glutamine family amino acid metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
@@ -6438,7 +6490,7 @@
id: GO:0000821
name: obsolete regulation of arginine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "regulation of arginine metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30570" xsd:anyURI
@@ -6448,7 +6500,7 @@
id: GO:0000822
name: inositol hexakisphosphate binding
namespace: molecular_function
-def: "Binding to inositol hexakisphosphate." [GOC:go_curators]
+def: "Binding to inositol hexakisphosphate." [GOC:curators]
synonym: "InsP6 binding" EXACT []
synonym: "IP6 binding" EXACT []
is_a: GO:0043168 ! anion binding
@@ -6679,7 +6731,7 @@
alt_id: GO:0007148
alt_id: GO:0045790
alt_id: GO:0045791
-def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb]
+def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:curators, GOC:dph, GOC:tb]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_yeast
@@ -6691,7 +6743,7 @@
name: obsolete regulation of cell shape during vegetative growth phase
namespace: biological_process
alt_id: GO:0090061
-def: "OBSOLETE. Any process that modulates the surface configuration of a cell during the vegetative growth phase. The vegetative growth phase is the growth phase during which single celled organisms reproduce by budding or other asexual methods." [GOC:clt, GOC:go_curators, GOC:vw]
+def: "OBSOLETE. Any process that modulates the surface configuration of a cell during the vegetative growth phase. The vegetative growth phase is the growth phase during which single celled organisms reproduce by budding or other asexual methods." [GOC:clt, GOC:curators, GOC:vw]
comment: The reason for obsoletion is that biological phases should be captured as extensions.
synonym: "cell morphogenesis during vegetative growth phase" RELATED [GOC:vw]
synonym: "cellular morphogenesis during vegetative growth" RELATED [GOC:dph, GOC:tb]
@@ -6702,7 +6754,7 @@
id: GO:0000904
name: obsolete cell morphogenesis involved in differentiation
namespace: biological_process
-def: "OBSOLETE. The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:go_curators]
+def: "OBSOLETE. The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:curators]
comment: This term is equivalent to cell morphogenesis.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24299" xsd:anyURI
is_obsolete: true
@@ -7448,6 +7500,7 @@
synonym: "RNA polymerase II promoter proximal region sequence-specific DNA binding" RELATED []
synonym: "RNA polymerase II proximal promoter sequence-specific DNA binding" RELATED []
synonym: "RNA polymerase II upstream activating sequence (UAS) sequence-specific DNA binding" RELATED []
+xref: Reactome:R-HSA-400204 "PPARA binds RXRA"
is_a: GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding
is_a: GO:0000987 ! cis-regulatory region sequence-specific DNA binding
created_by: krc
@@ -7612,7 +7665,6 @@
def: "Binding to an RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits." [GOC:txnOH]
synonym: "RNA polymerase II core binding" EXACT []
synonym: "RNAP II core binding" EXACT []
-is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding
is_a: GO:0043175 ! RNA polymerase core enzyme binding
created_by: krc
creation_date: 2010-08-11T03:57:27Z
@@ -7631,7 +7683,7 @@
name: RNA polymerase III general transcription initiation factor activity
namespace: molecular_function
alt_id: GO:0001034
-def: "A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. RNA polymerase III transcribes genes encoding short RNAs, including tRNAs, 5S rRNA, U6 snRNA, the short ncRNA component of RNases P, the mitochondrial RNA processing (MRP) RNA, the signal recognition particle SRP RNA, and in higher eukaryotes a number of micro and other small RNAs, though there is some variability across species as to whether a given small noncoding RNA is transcribed by RNA polymerase II or RNA polymerase III." [GOC:txnOH-2018, PMID:12381659, PMID:17977614, PMID:20413673, PMID:27068803, Wikipedia:RNA_polymerase_III]
+def: "A general transcription initiation factor activity that contributes to transcription start site selection and transcription initiation of genes transcribed by RNA polymerase III. Factors required for RNA polymerase III transcription initiation include TFIIIA, TFIIIB and TFIIIC. RNA polymerase III transcribes genes encoding short RNAs, including tRNAs, 5S rRNA, U6 snRNA, the short ncRNA component of RNases P, the mitochondrial RNA processing (MRP) RNA, the signal recognition particle SRP RNA, and in higher eukaryotes a number of micro and other small RNAs, though there is some variability across species as to whether a given small noncoding RNA is transcribed by RNA polymerase II or RNA polymerase III." [GOC:txnOH-2018, PMID:12381659, PMID:17977614, PMID:20413673, PMID:27068803, PMID:40762516, Wikipedia:RNA_polymerase_III]
synonym: "core RNA polymerase III binding transcription factor activity" NARROW []
synonym: "RNA polymerase III general initiation factor activity" EXACT []
synonym: "RNA polymerase III transcription factor activity, sequence-specific DNA binding" NARROW []
@@ -7640,6 +7692,7 @@
is_a: GO:0140223 ! general transcription initiation factor activity
relationship: part_of GO:0006383 ! transcription by RNA polymerase III
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15789" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15862" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22622" xsd:anyURI
created_by: krc
@@ -7747,14 +7800,17 @@
[Term]
id: GO:0001010
-name: RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity
+name: obsolete RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity
namespace: molecular_function
-def: "The function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions." [GOC:txnOH]
+def: "OBSOLETE. The function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions." [GOC:txnOH]
+comment: This term was obsoleted because it was not clearly defined.
synonym: "sequence-specific DNA binding transcription factor recruiting transcription factor activity" EXACT []
synonym: "transcription factor activity, sequence-specific DNA binding transcription factor recruiting" EXACT []
synonym: "transcription factor activity, sequence-specific DNA-binding transcription factor recruiting" RELATED []
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
-relationship: has_part GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31456" xsd:anyURI
+is_obsolete: true
+consider: GO:0003712
+consider: GO:0140463
created_by: krc
creation_date: 2010-08-18T06:46:33Z
@@ -8014,8 +8070,6 @@
def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH]
comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity.
synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase II promoter" EXACT []
-xref: Reactome:R-HSA-6814549 "Pre-snRNA transcript initiation, Integrator binding, LEC binding"
-xref: Reactome:R-HSA-6814559 "Pre-snRNA is elongated and capped with 7-methylguanosine"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI
is_obsolete: true
@@ -8030,7 +8084,6 @@
def: "OBSOLETE. Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH]
comment: The reason for obsoletion is that this term is equivalent to DNA-directed 5'-3' RNA polymerase activity.
synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT []
-xref: Reactome:R-HSA-1964482 "RNA polymerase III transcribes microbial dsDNA to dsRNA"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23779" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI
is_obsolete: true
@@ -8393,7 +8446,7 @@
namespace: molecular_function
def: "Binding to a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:txnOH, PMID:16858867]
synonym: "RNA polymerase II basal transcription factor binding" EXACT []
-is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding
+is_a: GO:0000993 ! RNA polymerase II complex binding
is_a: GO:0140296 ! general transcription initiation factor binding
created_by: krc
creation_date: 2010-10-28T02:30:02Z
@@ -8405,7 +8458,6 @@
def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIA complex, one of the complexes involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867]
synonym: "TFIIA-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
-is_a: GO:0044877 ! protein-containing complex binding
created_by: krc
creation_date: 2010-10-28T02:37:19Z
@@ -8425,7 +8477,6 @@
def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIID complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIID-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
-is_a: GO:0044877 ! protein-containing complex binding
created_by: krc
creation_date: 2010-10-28T02:48:33Z
@@ -8436,7 +8487,6 @@
def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIE complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIE-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
-is_a: GO:0044877 ! protein-containing complex binding
created_by: krc
creation_date: 2010-10-28T02:49:20Z
@@ -8447,7 +8497,6 @@
def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIF-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
-is_a: GO:0044877 ! protein-containing complex binding
created_by: krc
creation_date: 2010-10-28T02:51:20Z
@@ -8458,28 +8507,30 @@
def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIH complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIH-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
-is_a: GO:0044877 ! protein-containing complex binding
created_by: krc
creation_date: 2010-10-28T02:51:41Z
[Term]
id: GO:0001098
-name: basal transcription machinery binding
+name: obsolete basal transcription machinery binding
namespace: molecular_function
-def: "Binding to a component of the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
-comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors.
-is_a: GO:0005515 ! protein binding
+def: "OBSOLETE. Binding to a component of the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16062" xsd:anyURI
+is_obsolete: true
created_by: krc
creation_date: 2010-11-24T12:50:49Z
[Term]
id: GO:0001099
-name: basal RNA polymerase II transcription machinery binding
+name: obsolete basal RNA polymerase II transcription machinery binding
namespace: molecular_function
-def: "Binding to a component of the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
-comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors.
+def: "OBSOLETE. Binding to a component of the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
+comment: This term was obsoleted because it is equivalent to RNA polymerase II complex binding ; GO:0000993.
synonym: "basal RNAP II transcription machinery binding" EXACT []
-is_a: GO:0001098 ! basal transcription machinery binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16062" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0000993
created_by: krc
creation_date: 2010-11-24T12:54:33Z
@@ -8502,7 +8553,7 @@
id: GO:0001101
name: response to acid chemical
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:go_curators, GOC:rn]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:curators, GOC:rn]
comment: This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
subset: gocheck_do_not_annotate
synonym: "response to acid" BROAD []
@@ -8516,7 +8567,7 @@
namespace: molecular_function
def: "Binding to a component of the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase." [GOC:txnOH]
synonym: "basal bacterial-type RNA polymerase transcription machinery binding" EXACT []
-is_a: GO:0001098 ! basal transcription machinery binding
+is_a: GO:0070063 ! RNA polymerase binding
created_by: krc
creation_date: 2010-11-30T04:26:04Z
@@ -8742,14 +8793,15 @@
[Term]
id: GO:0001139
-name: RNA polymerase II complex recruiting activity
+name: obsolete RNA polymerase II complex recruiting activity
namespace: molecular_function
-def: "Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
+def: "OBSOLETE. Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
+comment: This term was obsoleted because it is now represented by transcription coactivator activity ; GO:0003713.
synonym: "core RNA polymerase II recruiting transcription factor activity" EXACT []
synonym: "transcription factor activity, core RNA polymerase II recruiting" RELATED []
-is_a: GO:0000993 ! RNA polymerase II complex binding
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
-relationship: part_of GO:0051123 ! RNA polymerase II preinitiation complex assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31456" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0003713
created_by: krc
creation_date: 2011-01-20T05:55:01Z
@@ -9365,6 +9417,7 @@
synonym: "transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding" NARROW []
synonym: "transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding" NARROW []
synonym: "transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding" EXACT []
+xref: Reactome:R-HSA-8936851 "AHRR binds ARNT"
is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific
is_a: GO:0001217 ! DNA-binding transcription repressor activity
intersection_of: GO:0140110 ! transcription regulator activity
@@ -9410,6 +9463,7 @@
synonym: "transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding" NARROW []
synonym: "transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding" EXACT []
synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" NARROW []
+xref: Reactome:R-HSA-8937177 "AHR:TCDD binds ARNT"
xref: Reactome:R-HSA-9856539 "MLXIPL:MLX binds PKLR gene promoter"
xref: Reactome:R-HSA-9856546 "MLXIPL:MLX binds FASN gene promoter"
xref: Reactome:R-HSA-9856548 "MLXIPL:MLX binds ACACB gene promoter"
@@ -9923,7 +9977,7 @@
id: GO:0001506
name: obsolete neurotransmitter biosynthetic process and storage
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of neurotransmitters and the storage of the synthesized molecules." [GOC:go_curators, ISBN:0123668387]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of neurotransmitters and the storage of the synthesized molecules." [GOC:curators, ISBN:0123668387]
comment: This term was made obsolete because it is an amalgamation of its two children.
synonym: "neurotransmitter anabolism and storage" EXACT []
synonym: "neurotransmitter biosynthetic process and storage" EXACT []
@@ -9948,7 +10002,7 @@
id: GO:0001508
name: action potential
namespace: biological_process
-def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8]
+def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:curators, GOC:dph, GOC:tb, ISBN:978-0-07-139011-8]
comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so.
is_a: GO:0042391 ! regulation of membrane potential
@@ -9975,8 +10029,10 @@
name: RNA methylation
namespace: biological_process
def: "Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor." [GOC:hjd, PMID:21823225]
+subset: gocheck_obsoletion_candidate
is_a: GO:0009451 ! RNA modification
is_a: GO:0043414 ! macromolecule methylation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27423" xsd:anyURI
[Term]
id: GO:0001511
@@ -10046,7 +10102,7 @@
def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + N-acetyl-D-glucosamine = adenosine 3',5'-bisphosphate + N-acetyl-D-glucosamine 6-sulfate." [GOC:ai, GOC:hjd]
subset: goslim_chembl
synonym: "N-acetylglucosamine 6-O-sulphotransferase activity" EXACT []
-xref: Reactome:R-HSA-2046222 "CHST2,5,6 transfer SO4(2-) to GlcNAc residues on keratan-PG to form KSPG"
+xref: Reactome:R-HSA-2046222 "CHST2,3,5,6 transfer sulfate to GlcNAc on keratan chain"
xref: Reactome:R-HSA-3656269 "Defective CHST6 does not transfer SO4(2-) to GlcNAc residues on keratan-PG"
xref: Reactome:R-HSA-6786012 "CHST4 transfers SO4(2-) from PAPS to Core 2 mucins"
is_a: GO:0008146 ! sulfotransferase activity
@@ -10137,12 +10193,13 @@
id: GO:0001527
name: microfibril
namespace: cellular_component
-def: "Extracellular matrix components occurring independently or along with elastin. Thought to have force-bearing functions in tendon. In addition to fibrillins, microfibrils may contain other associated proteins." [PMID:27026396, PMID:31226403]
+def: "Extracellular matrix components occurring independently or along with elastin. Thought to have force-bearing functions in tendon. In addition to fibrillins, microfibrils may contain microfibrillar-Associated Proteins (MFAPs): MFAP1, MFAP2 (also known as MAGP-1), MFAP3, MFAP4, and MFAP5 (also known as MAGP-2)." [PMID:27026396, PMID:31226403]
synonym: "extended fibrils" EXACT []
synonym: "fibrillin" RELATED []
is_a: GO:0099512 ! supramolecular fiber
relationship: part_of GO:0071953 ! elastic fiber
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31132" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31712" xsd:anyURI
[Term]
id: GO:0001528
@@ -10438,7 +10495,7 @@
id: GO:0001558
name: regulation of cell growth
namespace: biological_process
-def: "Any process that modulates the frequency, rate, extent or direction of cell growth." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate, extent or direction of cell growth." [GOC:curators]
is_a: GO:0040008 ! regulation of growth
is_a: GO:0051128 ! regulation of cellular component organization
intersection_of: GO:0065007 ! biological regulation
@@ -10512,7 +10569,7 @@
id: GO:0001564
name: obsolete resistance to pathogenic protozoa
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "resistance to pathogenic protozoa" EXACT []
is_obsolete: true
@@ -10543,10 +10600,12 @@
xref: KEGG_REACTION:R07218
xref: MetaCyc:1.14.99.38-RXN
xref: RHEA:21104
+xref: RHEA:46132
is_a: GO:0008395 ! steroid hydroxylase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: skos:exactMatch EC:1.14.99.38
property_value: skos:exactMatch RHEA:21104
+property_value: skos:narrowMatch RHEA:46132
[Term]
id: GO:0001568
@@ -10683,7 +10742,7 @@
id: GO:0001580
name: detection of chemical stimulus involved in sensory perception of bitter taste
namespace: biological_process
-def: "The series of events required for a bitter taste stimulus to be received and converted to a molecular signal." [GOC:go_curators]
+def: "The series of events required for a bitter taste stimulus to be received and converted to a molecular signal." [GOC:curators]
synonym: "bitter taste detection" EXACT []
synonym: "perception of bitter taste, detection of chemical stimulus" EXACT []
synonym: "perception of bitter taste, sensory transduction of chemical stimulus" EXACT []
@@ -10700,7 +10759,7 @@
id: GO:0001581
name: detection of chemical stimulus involved in sensory perception of sour taste
namespace: biological_process
-def: "The series of events required for a sour taste stimulus to be received and converted to a molecular signal." [GOC:go_curators]
+def: "The series of events required for a sour taste stimulus to be received and converted to a molecular signal." [GOC:curators]
synonym: "perception of sour taste, detection of chemical stimulus" EXACT []
synonym: "perception of sour taste, sensory transduction of chemical stimulus" EXACT []
synonym: "sensory detection of chemical stimulus during perception of sour taste" EXACT []
@@ -10717,7 +10776,7 @@
id: GO:0001582
name: detection of chemical stimulus involved in sensory perception of sweet taste
namespace: biological_process
-def: "The series of events required for a sweet taste stimulus to be received and converted to a molecular signal." [GOC:go_curators]
+def: "The series of events required for a sweet taste stimulus to be received and converted to a molecular signal." [GOC:curators]
synonym: "perception of sweet taste, detection of chemical stimulus" EXACT []
synonym: "perception of sweet taste, sensory transduction of chemical stimulus" EXACT []
synonym: "sensory detection of chemical stimulus during perception of sweet taste" EXACT []
@@ -10734,7 +10793,7 @@
id: GO:0001583
name: obsolete detection of chemical stimulus involved in sensory perception of salty taste
namespace: biological_process
-def: "OBSOLETE. The series of events required for a salty taste stimulus to be received and converted to a molecular signal." [GOC:go_curators]
+def: "OBSOLETE. The series of events required for a salty taste stimulus to be received and converted to a molecular signal." [GOC:curators]
comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
synonym: "perception of salty taste, detection of chemical stimulus" EXACT []
synonym: "perception of salty taste, sensory transduction of chemical stimulus" EXACT []
@@ -10999,6 +11058,7 @@
subset: goslim_chembl
subset: goslim_generic
synonym: "viral receptor activity" EXACT []
+xref: Reactome:R-HSA-9922480 "Dengue virion gets internalized"
is_a: GO:0140272 ! exogenous protein binding
relationship: part_of GO:0046718 ! symbiont entry into host cell
@@ -11288,7 +11348,7 @@
id: GO:0001655
name: urogenital system development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048731 ! system development
relationship: has_part GO:0072001 ! renal system development
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22178" xsd:anyURI
@@ -11304,7 +11364,7 @@
id: GO:0001657
name: ureteric bud development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0072164 ! mesonephric tubule development
[Term]
@@ -11355,6 +11415,7 @@
synonym: "behavioural fear response" EXACT []
is_a: GO:0002209 ! behavioral defense response
is_a: GO:0042596 ! fear response
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31407" xsd:anyURI
[Term]
id: GO:0001664
@@ -11380,9 +11441,13 @@
xref: Reactome:R-HSA-9603991 "ST6GALNAC6 transfers Neu5Ac to Type 1 MSGG to form Type 1 DSGG"
xref: Reactome:R-HSA-9846305 "ST6GALNAC5,6 transfer Neu5Ac to GM1b"
xref: RHEA:11136
+xref: RHEA:81651
+xref: RHEA:81655
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.3
property_value: skos:exactMatch RHEA:11136
+property_value: skos:narrowMatch RHEA:81651
+property_value: skos:narrowMatch RHEA:81655
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -11427,7 +11492,6 @@
synonym: "ATPase stimulator activity" EXACT []
xref: Reactome:R-HSA-5251955 "HSP40s activate intrinsic ATPase activity of HSP70s in the nucleoplasm"
xref: Reactome:R-HSA-5251959 "HSP40s activate intrinsic ATPase activity of HSP70s in the cytosol"
-is_a: GO:0060590 ! ATPase regulator activity
is_a: GO:0140677 ! molecular function activator activity
relationship: positively_regulates GO:0140657 ! ATP-dependent activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20955" xsd:anyURI
@@ -11486,7 +11550,7 @@
id: GO:0001678
name: intracellular glucose homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of a steady state level of glucose within a cell." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "A homeostatic process involved in the maintenance of a steady state level of glucose within a cell." [GOC:curators, GOC:dph, GOC:tb]
synonym: "cell glucose homeostasis" EXACT [GOC:dph, GOC:tb]
synonym: "cellular glucose homeostasis" EXACT []
is_a: GO:0042593 ! glucose homeostasis
@@ -11496,7 +11560,7 @@
id: GO:0001680
name: tRNA 3'-terminal CCA addition
namespace: biological_process
-def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [GOC:go_curators, PMID:2247609]
+def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [GOC:curators, PMID:2247609]
is_a: GO:0042780 ! tRNA 3'-end processing
relationship: has_part GO:0004810 ! CCA tRNA nucleotidyltransferase activity
relationship: has_part GO:0052927 ! CC tRNA cytidylyltransferase activity
@@ -11682,14 +11746,14 @@
id: GO:0001700
name: embryonic development via the syncytial blastoderm
namespace: biological_process
-def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0009792 ! embryo development ending in birth or egg hatching
[Term]
id: GO:0001701
name: in utero embryonic development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0043009 ! chordate embryonic development
[Term]
@@ -11698,7 +11762,7 @@
namespace: biological_process
alt_id: GO:0010003
alt_id: GO:0048276
-def: "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." [GOC:go_curators, GOC:mtg_sensu]
+def: "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." [GOC:curators, GOC:mtg_sensu]
synonym: "deuterostomic gastrulation" EXACT [GOC:dph]
is_a: GO:0007369 ! gastrulation
@@ -11706,7 +11770,7 @@
id: GO:0001703
name: gastrulation with mouth forming first
namespace: biological_process
-def: "A gastrulation process in which the initial invagination becomes the mouth and the anus forms second." [GOC:go_curators, GOC:mtg_sensu]
+def: "A gastrulation process in which the initial invagination becomes the mouth and the anus forms second." [GOC:curators, GOC:mtg_sensu]
synonym: "protostomic gastrulation" NARROW [GOC:dph]
is_a: GO:0007369 ! gastrulation
@@ -11714,7 +11778,7 @@
id: GO:0001704
name: formation of primary germ layer
namespace: biological_process
-def: "The formation of the ectoderm, mesoderm and endoderm during gastrulation." [GOC:go_curators]
+def: "The formation of the ectoderm, mesoderm and endoderm during gastrulation." [GOC:curators]
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0007369 ! gastrulation
@@ -11722,7 +11786,7 @@
id: GO:0001705
name: ectoderm formation
namespace: biological_process
-def: "The formation of ectoderm during gastrulation." [GOC:go_curators]
+def: "The formation of ectoderm during gastrulation." [GOC:curators]
is_a: GO:0001704 ! formation of primary germ layer
relationship: part_of GO:0007398 ! ectoderm development
@@ -11730,7 +11794,7 @@
id: GO:0001706
name: endoderm formation
namespace: biological_process
-def: "The formation of the endoderm during gastrulation." [GOC:go_curators]
+def: "The formation of the endoderm during gastrulation." [GOC:curators]
synonym: "endoblast formation" NARROW [GOC:dph, GOC:sdb_2009, GOC:tb]
xref: Reactome:R-HSA-9823730 "Formation of definitive endoderm"
is_a: GO:0001704 ! formation of primary germ layer
@@ -11740,7 +11804,7 @@
id: GO:0001707
name: mesoderm formation
namespace: biological_process
-def: "The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts." [GOC:go_curators]
+def: "The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts." [GOC:curators]
is_a: GO:0001704 ! formation of primary germ layer
relationship: part_of GO:0048332 ! mesoderm morphogenesis
@@ -11748,7 +11812,7 @@
id: GO:0001708
name: cell fate specification
namespace: biological_process
-def: "The cellular developmental process involved in cell fate commitment in which the cell is designated to follow a developmental path, unless they receive extrinsic cues that direct an alternative fate." [GOC:go_curators]
+def: "The cellular developmental process involved in cell fate commitment in which the cell is designated to follow a developmental path, unless they receive extrinsic cues that direct an alternative fate." [GOC:curators]
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0045165 ! cell fate commitment
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24390" xsd:anyURI
@@ -11767,7 +11831,7 @@
id: GO:0001710
name: mesodermal cell fate commitment
namespace: biological_process
-def: "The cell differentiation process that results in commitment of a cell to become part of the mesoderm." [GOC:go_curators, ISBN:0878932437]
+def: "The cell differentiation process that results in commitment of a cell to become part of the mesoderm." [GOC:curators, ISBN:0878932437]
synonym: "mesoderm cell fate commitment" EXACT []
is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer
relationship: part_of GO:0048333 ! mesodermal cell differentiation
@@ -11776,7 +11840,7 @@
id: GO:0001711
name: endodermal cell fate commitment
namespace: biological_process
-def: "The cell differentiation process that results in commitment of a cell to become part of the endoderm." [GOC:go_curators, ISBN:0878932437]
+def: "The cell differentiation process that results in commitment of a cell to become part of the endoderm." [GOC:curators, ISBN:0878932437]
synonym: "endoderm cell fate commitment" EXACT []
is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer
relationship: part_of GO:0035987 ! endodermal cell differentiation
@@ -11785,7 +11849,7 @@
id: GO:0001712
name: ectodermal cell fate commitment
namespace: biological_process
-def: "The cell differentiation process that results in commitment of a cell to become part of the ectoderm." [GOC:go_curators, ISBN:0878932437]
+def: "The cell differentiation process that results in commitment of a cell to become part of the ectoderm." [GOC:curators, ISBN:0878932437]
synonym: "ectoderm cell fate commitment" EXACT []
is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer
relationship: part_of GO:0001705 ! ectoderm formation
@@ -11795,7 +11859,7 @@
id: GO:0001713
name: ectodermal cell fate determination
namespace: biological_process
-def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an ectoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, ISBN:0878932437]
+def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an ectoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators, ISBN:0878932437]
synonym: "ectoderm cell fate determination" EXACT []
is_a: GO:0001709 ! cell fate determination
relationship: part_of GO:0001712 ! ectodermal cell fate commitment
@@ -11804,7 +11868,7 @@
id: GO:0001714
name: endodermal cell fate specification
namespace: biological_process
-def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators]
+def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:curators]
synonym: "endoderm cell fate specification" EXACT []
is_a: GO:0001708 ! cell fate specification
relationship: part_of GO:0001711 ! endodermal cell fate commitment
@@ -11813,7 +11877,7 @@
id: GO:0001715
name: ectodermal cell fate specification
namespace: biological_process
-def: "The cell fate determination process that results in a cell becoming becomes capable of differentiating autonomously into an ectoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators]
+def: "The cell fate determination process that results in a cell becoming becomes capable of differentiating autonomously into an ectoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:curators]
synonym: "ectoderm cell fate specification" EXACT []
is_a: GO:0001708 ! cell fate specification
relationship: part_of GO:0001712 ! ectodermal cell fate commitment
@@ -11829,9 +11893,45 @@
xref: MetaCyc:L-AMINO-ACID-OXIDASE-RXN
xref: Reactome:R-HSA-2160492 "IL4I1:FAD oxidises L-Phe to kPPV"
xref: RHEA:13781
+xref: RHEA:19025
+xref: RHEA:51404
+xref: RHEA:60996
+xref: RHEA:61224
+xref: RHEA:61228
+xref: RHEA:61232
+xref: RHEA:61236
+xref: RHEA:61244
+xref: RHEA:61248
+xref: RHEA:61252
+xref: RHEA:61256
+xref: RHEA:61260
+xref: RHEA:61264
+xref: RHEA:61268
+xref: RHEA:61272
+xref: RHEA:61276
+xref: RHEA:61284
+xref: RHEA:61344
is_a: GO:0008131 ! primary methylamine oxidase activity
property_value: skos:exactMatch EC:1.4.3.2
property_value: skos:exactMatch RHEA:13781
+property_value: skos:narrowMatch RHEA:19025
+property_value: skos:narrowMatch RHEA:51404
+property_value: skos:narrowMatch RHEA:60996
+property_value: skos:narrowMatch RHEA:61224
+property_value: skos:narrowMatch RHEA:61228
+property_value: skos:narrowMatch RHEA:61232
+property_value: skos:narrowMatch RHEA:61236
+property_value: skos:narrowMatch RHEA:61244
+property_value: skos:narrowMatch RHEA:61248
+property_value: skos:narrowMatch RHEA:61252
+property_value: skos:narrowMatch RHEA:61256
+property_value: skos:narrowMatch RHEA:61260
+property_value: skos:narrowMatch RHEA:61264
+property_value: skos:narrowMatch RHEA:61268
+property_value: skos:narrowMatch RHEA:61272
+property_value: skos:narrowMatch RHEA:61276
+property_value: skos:narrowMatch RHEA:61284
+property_value: skos:narrowMatch RHEA:61344
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -11928,9 +12028,15 @@
xref: MetaCyc:CERAMIDE-KINASE-RXN
xref: Reactome:R-HSA-1638845 "CERK phosphorylates CERA to form C1P"
xref: RHEA:17929
+xref: RHEA:43312
+xref: RHEA:46340
+xref: RHEA:47904
is_a: GO:0001727 ! lipid kinase activity
property_value: skos:exactMatch EC:2.7.1.138
property_value: skos:exactMatch RHEA:17929
+property_value: skos:narrowMatch RHEA:43312
+property_value: skos:narrowMatch RHEA:46340
+property_value: skos:narrowMatch RHEA:47904
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -12029,9 +12135,11 @@
xref: EC:1.8.3.5
xref: MetaCyc:RXN-18932
xref: RHEA:53892
+xref: RHEA:70407
is_a: GO:0016670 ! oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.8.3.5
property_value: skos:exactMatch RHEA:53892
+property_value: skos:narrowMatch RHEA:70407
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -12094,7 +12202,7 @@
id: GO:0001742
name: oenocyte differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires the specialized features of an oenocyte. Oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments." [GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires the specialized features of an oenocyte. Oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments." [GOC:curators]
synonym: "oenocyte cell differentiation" EXACT []
is_a: GO:0030154 ! cell differentiation
@@ -12158,7 +12266,7 @@
id: GO:0001751
name: compound eye photoreceptor cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell." [GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell." [GOC:curators]
is_a: GO:0001754 ! eye photoreceptor cell differentiation
relationship: part_of GO:0001745 ! compound eye morphogenesis
@@ -12175,7 +12283,7 @@
id: GO:0001753
name: obsolete adult eye photoreceptor development (sensu Drosophila)
namespace: biological_process
-def: "OBSOLETE. Development of a photoreceptor, a receptor that responds to light, in the adult Drosophila eye." [GOC:go_curators]
+def: "OBSOLETE. Development of a photoreceptor, a receptor that responds to light, in the adult Drosophila eye." [GOC:curators]
comment: This term was made obsolete because eye photoreceptors have completed their development by the time the adult phase begins.
synonym: "adult eye photoreceptor development (sensu Drosophila)" EXACT []
is_obsolete: true
@@ -12185,7 +12293,7 @@
id: GO:0001754
name: eye photoreceptor cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms." [GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms." [GOC:curators]
is_a: GO:0046530 ! photoreceptor cell differentiation
relationship: part_of GO:0048592 ! eye morphogenesis
@@ -12233,9 +12341,17 @@
xref: Reactome:R-HSA-5362522 "ALDHs oxidise atRAL to atRA"
xref: Reactome:R-HSA-5696101 "ALDH8A1 oxidises 9cRAL to 9cRA"
xref: RHEA:16177
+xref: RHEA:42080
+xref: RHEA:42084
+xref: RHEA:47132
+xref: RHEA:67332
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.2.1.36
property_value: skos:exactMatch RHEA:16177
+property_value: skos:narrowMatch RHEA:42080
+property_value: skos:narrowMatch RHEA:42084
+property_value: skos:narrowMatch RHEA:47132
+property_value: skos:narrowMatch RHEA:67332
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30270" xsd:anyURI
@@ -12304,7 +12420,7 @@
id: GO:0001764
name: neuron migration
namespace: biological_process
-def: "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." [CL:0000540, GOC:go_curators]
+def: "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." [CL:0000540, GOC:curators]
synonym: "neuron chemotaxis" EXACT []
synonym: "neuron guidance" RELATED []
synonym: "neuronal migration" EXACT []
@@ -13697,6 +13813,7 @@
synonym: "UDP-N-acetyl-D-glucosamine:beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan 4IV-alpha-N-acetyl-D-glucosaminyltransferase activity" RELATED [EC:2.4.1.223]
xref: EC:2.4.1.223
xref: MetaCyc:2.4.1.223-RXN
+xref: Reactome:R-HSA-9953259 "EXTL3 dimer transfers GlcNAc to the GAG linker"
xref: RHEA:16221
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.223
@@ -15626,7 +15743,7 @@
name: purine nucleobase binding
namespace: molecular_function
def: "Binding to a purine nucleobase, an organic nitrogenous base with a purine skeleton." [GOC:hjd]
-synonym: "purine base binding" EXACT [GOC:go_curators]
+synonym: "purine base binding" EXACT [GOC:curators]
synonym: "purine binding" RELATED []
is_a: GO:0002054 ! nucleobase binding
@@ -15636,7 +15753,7 @@
namespace: molecular_function
def: "Binding to a pyrimidine nucleobase, an organic nitrogenous base with a pyrimidine skeleton." [GOC:hjd]
synonym: "1,3-diazine binding" NARROW []
-synonym: "pyrimidine base binding" EXACT [GOC:go_curators]
+synonym: "pyrimidine base binding" EXACT [GOC:curators]
synonym: "pyrimidine binding" RELATED []
is_a: GO:0002054 ! nucleobase binding
@@ -15814,7 +15931,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: all-trans-decaprenyl diphosphate + 4-hydroxybenzoate = 3-decaprenyl-4-hydroxybenzoate + diphosphate." [GOC:curators]
comment: This term was obsoleted because it represents a specific substrate of 4-hydroxybenzoate polyprenyltransferase activity ; GO:0008412.
-xref: Reactome:R-HSA-2162192 "COQ2 ligates all-E-10PrP2 to PHB"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26830" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008412
@@ -16123,7 +16239,7 @@
namespace: cellular_component
def: "A stable binary complex of a semaphorin and a plexin, together forming a functional semaphorin receptor." [GOC:hjd, PMID:10934324, PMID:12367632, PMID:12613544]
synonym: "plexin-neurophilin complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
[Term]
id: GO:0002117
@@ -25742,7 +25858,7 @@
namespace: cellular_component
def: "A receptor complex that contains one or more members of the tumor necrosis factor (TNF) receptor superfamily." [GOC:krc]
synonym: "TNF receptor superfamily complex" RELATED []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: hjd
creation_date: 2012-12-20T13:26:39Z
@@ -25837,10 +25953,22 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-deoxyribonucleoside + phosphate." [RHEA:36167]
xref: EC:3.1.3.89
+xref: RHEA:11080
+xref: RHEA:29355
+xref: RHEA:29363
+xref: RHEA:29371
+xref: RHEA:29379
+xref: RHEA:29383
xref: RHEA:36167
is_a: GO:0016791 ! phosphatase activity
property_value: skos:exactMatch EC:3.1.3.89
property_value: skos:exactMatch RHEA:36167
+property_value: skos:narrowMatch RHEA:11080
+property_value: skos:narrowMatch RHEA:29355
+property_value: skos:narrowMatch RHEA:29363
+property_value: skos:narrowMatch RHEA:29371
+property_value: skos:narrowMatch RHEA:29379
+property_value: skos:narrowMatch RHEA:29383
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27990" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -29274,7 +29402,7 @@
name: keratinocyte development
namespace: biological_process
def: "The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure." [GOC:dph]
-xref: Reactome:R-HSA-9725554 "Differentiation of keratinocytes in interfollicular epidermis in mammalian skin"
+xref: Reactome:R-HSA-9725554 "Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin"
is_a: GO:0002064 ! epithelial cell development
relationship: part_of GO:0030216 ! keratinocyte differentiation
created_by: dph
@@ -30480,7 +30608,7 @@
id: GO:0003673
name: obsolete Gene_Ontology
namespace: biological_process
-def: "OBSOLETE. A controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes." [GOC:go_curators]
+def: "OBSOLETE. A controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. GO provides three structured networks of defined terms to describe gene product attributes." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "Gene_Ontology" EXACT []
is_obsolete: true
@@ -30686,7 +30814,7 @@
namespace: molecular_function
def: "Binding to double-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
is_a: GO:0003690 ! double-stranded DNA binding
-is_a: GO:0042162 ! telomeric DNA binding
+is_a: GO:0042162 ! telomeric repeat DNA binding
[Term]
id: GO:0003692
@@ -30844,6 +30972,7 @@
namespace: molecular_function
def: "A nuclear receptor activity regulated by steroid binding and modulating the transcription of specific gene sets transcribed by RNA polymerase II." [GOC:signaling, PMID:14708019]
synonym: "steroid hormone receptor activity" BROAD []
+xref: Reactome:R-HSA-8963915 "1,25(OH)2D binds VDR"
is_a: GO:0004879 ! nuclear receptor activity
relationship: part_of GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
@@ -30886,7 +31015,7 @@
synonym: "transcription cofactor activity" EXACT []
synonym: "transcription coreceptor activity" EXACT []
synonym: "transcriptional co-regulator" EXACT []
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
+xref: Reactome:R-HSA-5340251 "NR1H4:DCA,CDCA,LCHA binds RXRA and NCOA1,2"
is_a: GO:0140110 ! transcription regulator activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15536" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15665" xsd:anyURI
@@ -30897,6 +31026,7 @@
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20962" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26489" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28926" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31471" xsd:anyURI
created_by: krc
creation_date: 2010-11-24T03:02:15Z
@@ -30931,6 +31061,7 @@
synonym: "RNA polymerase II transcription co-repressor activity" RELATED []
synonym: "RNA polymerase II transcription corepressor activity" RELATED []
synonym: "transcription co-repressor activity" EXACT []
+xref: Reactome:R-HSA-400183 "PPARA:RXRA binds Corepressors of PPARA"
is_a: GO:0003712 ! transcription coregulator activity
relationship: part_of GO:0045892 ! negative regulation of DNA-templated transcription
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15665" xsd:anyURI
@@ -31080,7 +31211,7 @@
name: double-stranded RNA adenosine deaminase activity
namespace: molecular_function
alt_id: GO:0003971
-def: "Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a double-stranded RNA molecule." [GOC:mah, RHEA:10120]
+def: "Catalysis of the reaction: adenosine + H2O = inosine + NH4+, in a double-stranded RNA molecule." [GOC:mah, RHEA:10120]
synonym: "double-stranded RNA specific editase activity" RELATED []
xref: EC:3.5.4.37
xref: Reactome:R-HSA-77614 "Deamination at C6 position of adenosine in Editosome (ADAR1)"
@@ -31298,6 +31429,7 @@
xref: Reactome:R-HSA-8950113 "IL12A binds IL12B"
xref: Reactome:R-HSA-8950183 "IL12B binds IL23A"
xref: Reactome:R-HSA-8950456 "IL12B dimerizes"
+xref: Reactome:R-HSA-9760559 "DsbA catalyzes disulfide crosslink formation on STa"
is_a: GO:0016864 ! intramolecular oxidoreductase activity, transposing S-S bonds
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:5.3.4.1
@@ -31598,7 +31730,7 @@
id: GO:0003793
name: obsolete defense/immunity protein activity
namespace: molecular_function
-def: "OBSOLETE. Any activity that plays a role in the defense/immune response of an organism against infection and disease." [GOC:go_curators]
+def: "OBSOLETE. Any activity that plays a role in the defense/immune response of an organism against infection and disease." [GOC:curators]
comment: This term was made obsolete because it refers to involvement in a biological process.
synonym: "defence/immunity protein activity" EXACT []
synonym: "defense/immunity protein activity" EXACT []
@@ -31619,7 +31751,7 @@
id: GO:0003795
name: obsolete antimicrobial peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, microbial cells." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, microbial cells." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "antimicrobial peptide activity" EXACT []
is_obsolete: true
@@ -31653,7 +31785,7 @@
id: GO:0003797
name: obsolete antibacterial peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, bacterial cells." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, bacterial cells." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "antibacterial peptide activity" EXACT []
is_obsolete: true
@@ -31663,7 +31795,7 @@
id: GO:0003798
name: obsolete male-specific antibacterial peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, bacterial cells, but which is only expressed in males." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, bacterial cells, but which is only expressed in males." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "male-specific antibacterial peptide activity" EXACT []
is_obsolete: true
@@ -31673,7 +31805,7 @@
id: GO:0003799
name: obsolete antifungal peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, fungal cells." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, fungal cells." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "antifungal peptide activity" EXACT []
is_obsolete: true
@@ -31875,7 +32007,6 @@
xref: MetaCyc:2.3.2.13-RXN
xref: Reactome:R-HSA-140851 "fibrin multimer -> fibrin multimer, crosslinked + NH4+"
xref: Reactome:R-HSA-6810894 "Envoplakin, periplakin, involucrin, SPR binding mediated by TGM1 crosslinking"
-xref: RESID:AA0124
xref: RHEA:54816
is_a: GO:0016755 ! aminoacyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -32152,9 +32283,19 @@
xref: Reactome:R-HSA-422454 "Polysialylation of NCAM1"
xref: Reactome:R-HSA-9845587 "ST8SIA5 transfers Neu5Ac to gangliosides"
xref: RHEA:19313
+xref: RHEA:48288
+xref: RHEA:48912
+xref: RHEA:48924
+xref: RHEA:48932
+xref: RHEA:77387
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.8
property_value: skos:exactMatch RHEA:19313
+property_value: skos:narrowMatch RHEA:48288
+property_value: skos:narrowMatch RHEA:48912
+property_value: skos:narrowMatch RHEA:48924
+property_value: skos:narrowMatch RHEA:48932
+property_value: skos:narrowMatch RHEA:77387
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32173,12 +32314,16 @@
xref: EC:2.4.1.102
xref: MetaCyc:2.4.1.102-RXN
xref: Reactome:R-HSA-914012 "GCNTs transfer GlcNAc from UDP-GlcNAc to Core 1 mucins"
-xref: Reactome:R-HSA-914018 "Addition of GlcNAc to Core 3 forms a Core 4 glycoprotein"
+xref: Reactome:R-HSA-914018 "GCNT3 transfers GlcNAc to Core 3 mucin"
xref: RHEA:18705
+xref: RHEA:56212
+xref: RHEA:56216
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
property_value: skos:exactMatch EC:2.4.1.102
property_value: skos:exactMatch RHEA:18705
+property_value: skos:narrowMatch RHEA:56212
+property_value: skos:narrowMatch RHEA:56216
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21793" xsd:anyURI
[Term]
@@ -32234,9 +32379,17 @@
xref: Reactome:R-HSA-9035950 "Defective B4GALT1 does not transfer Gal to a branch of keratan"
xref: Reactome:R-HSA-975919 "Addition of galactose by beta 4-galactosyltransferases"
xref: RHEA:22932
+xref: RHEA:56260
+xref: RHEA:82127
+xref: RHEA:82967
+xref: RHEA:84999
is_a: GO:0035250 ! UDP-galactosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.38
property_value: skos:exactMatch RHEA:22932
+property_value: skos:narrowMatch RHEA:56260
+property_value: skos:narrowMatch RHEA:82127
+property_value: skos:narrowMatch RHEA:82967
+property_value: skos:narrowMatch RHEA:84999
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32300,10 +32453,20 @@
xref: Reactome:R-HSA-4085033 "ST6GAL1,2 transfer Neu5Ac to terminal Gal (alpha-2,6 link)"
xref: Reactome:R-HSA-975902 "ST6GAL1 transfers Neu5Ac to terminal Gal of N-glycans"
xref: Reactome:R-HSA-977071 "ST6GAL1 transfers sialic acid to Tn antigens to form sTn antigens"
+xref: RHEA:11836
+xref: RHEA:21552
xref: RHEA:52104
+xref: RHEA:56268
+xref: RHEA:82903
+xref: RHEA:82947
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.1
property_value: skos:exactMatch RHEA:52104
+property_value: skos:narrowMatch RHEA:11836
+property_value: skos:narrowMatch RHEA:21552
+property_value: skos:narrowMatch RHEA:56268
+property_value: skos:narrowMatch RHEA:82903
+property_value: skos:narrowMatch RHEA:82947
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32315,25 +32478,28 @@
xref: MetaCyc:2.4.99.4-RXN
xref: Reactome:R-HSA-1022129 "ST3GAL4 transfers Neu5Ac to terminal Gal of N-glycans"
xref: Reactome:R-HSA-1912378 "Sialylation of Pre-NOTCH"
-xref: Reactome:R-HSA-2046285 "The keratan chain can be capped by N-acetylneuraminic acid"
+xref: Reactome:R-HSA-2046285 "ST3GAL1-4,6 optionally cap keratan chain"
xref: Reactome:R-HSA-3656258 "Defective ST3GAL3 does not transfer SA to keratan"
xref: Reactome:R-HSA-4084984 "ST3GAL1-6 transfer Neu5Ac to terminal Gal (alpha-2,3 link)"
xref: Reactome:R-HSA-9603987 "ST3GAL3 transfers Neu5Ac to Type 1 chain to form Type 1 MSGG"
xref: Reactome:R-HSA-9605600 "ST3GAL3,4,6 transfer Neu5Ac to Type 2 chain to form Type 2 MSGG"
-xref: Reactome:R-HSA-981497 "ST3GAL1-4 transfers sialic acid to the T antigen at the alpha 3 position"
xref: Reactome:R-HSA-9844860 "ST3GAL5 transfers NeuNAc to ceramides"
xref: Reactome:R-HSA-9845538 "ST3GAL2,3 transfer Neu5Ac to gangliosides"
xref: RHEA:21616
+xref: RHEA:56204
+xref: RHEA:56208
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.4
property_value: skos:exactMatch RHEA:21616
+property_value: skos:narrowMatch RHEA:56204
+property_value: skos:narrowMatch RHEA:56208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0003837
name: beta-ureidopropionase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-carbamoyl-beta-alanine + H2O = beta-alanine + CO2 + NH3." [EC:3.5.1.6]
+def: "Catalysis of the reaction: N-carbamoyl-beta-alanine + H2O = beta-alanine + CO2 + NH4+." [EC:3.5.1.6]
synonym: "N-carbamoyl-beta-alanine amidohydrolase activity" RELATED [EC:3.5.1.6]
xref: EC:3.5.1.6
xref: MetaCyc:BETA-UREIDOPROPIONASE-RXN
@@ -32389,7 +32555,6 @@
xref: EC:4.3.2.9
xref: MetaCyc:GAMMA-GLUTAMYLCYCLOTRANSFERASE-RXN
xref: Reactome:R-HSA-1247922 "GGCT transforms gGluCys to OPRO"
-xref: Reactome:R-HSA-6785928 "CHAC1,2 cleaves GSH to OPRO and CysGly"
xref: RHEA:20505
is_a: GO:0016842 ! amidine-lyase activity
property_value: skos:exactMatch EC:4.3.2.9
@@ -32434,10 +32599,58 @@
xref: Reactome:R-HSA-75885 "1-acyl LPA is acylated to PA by AGPAT (LPAAT)"
xref: Reactome:R-HSA-8849345 "LPAAT3 acylates lysophosphatidylcholine to yield phosphatidylcholine"
xref: RHEA:19709
+xref: RHEA:33187
+xref: RHEA:33315
+xref: RHEA:33319
+xref: RHEA:35911
+xref: RHEA:35915
+xref: RHEA:37135
+xref: RHEA:37139
+xref: RHEA:37151
+xref: RHEA:37155
+xref: RHEA:37159
+xref: RHEA:37163
+xref: RHEA:37171
+xref: RHEA:37175
+xref: RHEA:37179
+xref: RHEA:37183
+xref: RHEA:37187
+xref: RHEA:37223
+xref: RHEA:37427
+xref: RHEA:37435
+xref: RHEA:37439
+xref: RHEA:37451
+xref: RHEA:37595
+xref: RHEA:37603
+xref: RHEA:37607
is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
is_a: GO:0042171 ! lysophosphatidic acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.51
property_value: skos:exactMatch RHEA:19709
+property_value: skos:narrowMatch RHEA:33187
+property_value: skos:narrowMatch RHEA:33315
+property_value: skos:narrowMatch RHEA:33319
+property_value: skos:narrowMatch RHEA:35911
+property_value: skos:narrowMatch RHEA:35915
+property_value: skos:narrowMatch RHEA:37135
+property_value: skos:narrowMatch RHEA:37139
+property_value: skos:narrowMatch RHEA:37151
+property_value: skos:narrowMatch RHEA:37155
+property_value: skos:narrowMatch RHEA:37159
+property_value: skos:narrowMatch RHEA:37163
+property_value: skos:narrowMatch RHEA:37171
+property_value: skos:narrowMatch RHEA:37175
+property_value: skos:narrowMatch RHEA:37179
+property_value: skos:narrowMatch RHEA:37183
+property_value: skos:narrowMatch RHEA:37187
+property_value: skos:narrowMatch RHEA:37223
+property_value: skos:narrowMatch RHEA:37427
+property_value: skos:narrowMatch RHEA:37435
+property_value: skos:narrowMatch RHEA:37439
+property_value: skos:narrowMatch RHEA:37451
+property_value: skos:narrowMatch RHEA:37595
+property_value: skos:narrowMatch RHEA:37603
+property_value: skos:narrowMatch RHEA:37607
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32455,8 +32668,9 @@
synonym: "pyrroline-5-carboxylic acid dehydrogenase activity" RELATED [EC:1.2.1.88]
xref: EC:1.2.1.88
xref: MetaCyc:RXN-14116
-xref: Reactome:R-HSA-6784399 "ALDH4A1 dimer dehydrogenates 4-OH-L-glutamate semialdehyde to 4-OH-L-glutamate"
+xref: Reactome:R-HSA-6784402 "ALDH4A1 converts 1PYR-3OH-5COOH to 4-OH-L-glutamate"
xref: Reactome:R-HSA-70679 "ALDH4A1 oxidises L-GluSS to Glu"
+xref: Reactome:R-HSA-9929439 "ALDH4A1 oxidizes 1PYR-3OH-5COOH"
xref: RHEA:30235
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.2.1.88
@@ -32543,7 +32757,6 @@
synonym: "beta-hydroxysteroid dehydrogenase" BROAD []
synonym: "corticosteroid 11-reductase" RELATED []
synonym: "corticosteroid 11beta-dehydrogenase" RELATED []
-xref: Reactome:R-HSA-194023 "HSD11B2,HSD11B1 dimer oxidise CORT to COR"
xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21915" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28173" xsd:anyURI
@@ -32568,10 +32781,32 @@
xref: Reactome:R-HSA-6800334 "MOGAT1,2,3 transfer acyl group from acyl-CoA to 2-acylglycerol to form DAG"
xref: RHEA:16741
xref: RHEA:32947
+xref: RHEA:38467
+xref: RHEA:39951
+xref: RHEA:77271
+xref: RHEA:77275
+xref: RHEA:77279
+xref: RHEA:77283
+xref: RHEA:77287
+xref: RHEA:77291
+xref: RHEA:77539
+xref: RHEA:77543
+xref: RHEA:77547
is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.22
property_value: skos:exactMatch RHEA:16741
property_value: skos:narrowMatch RHEA:32947
+property_value: skos:narrowMatch RHEA:38467
+property_value: skos:narrowMatch RHEA:39951
+property_value: skos:narrowMatch RHEA:77271
+property_value: skos:narrowMatch RHEA:77275
+property_value: skos:narrowMatch RHEA:77279
+property_value: skos:narrowMatch RHEA:77283
+property_value: skos:narrowMatch RHEA:77287
+property_value: skos:narrowMatch RHEA:77291
+property_value: skos:narrowMatch RHEA:77539
+property_value: skos:narrowMatch RHEA:77543
+property_value: skos:narrowMatch RHEA:77547
[Term]
id: GO:0003847
@@ -32594,9 +32829,19 @@
xref: MetaCyc:3.1.1.47-RXN
xref: Reactome:R-HSA-8869206 "PAFAH2 hydrolyses PAF to lyso-PAF and acetate"
xref: RHEA:17777
+xref: RHEA:40479
+xref: RHEA:41183
+xref: RHEA:41368
+xref: RHEA:41372
+xref: RHEA:41376
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.47
property_value: skos:exactMatch RHEA:17777
+property_value: skos:narrowMatch RHEA:40479
+property_value: skos:narrowMatch RHEA:41183
+property_value: skos:narrowMatch RHEA:41368
+property_value: skos:narrowMatch RHEA:41372
+property_value: skos:narrowMatch RHEA:41376
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32688,10 +32933,14 @@
xref: EC:2.4.1.47
xref: MetaCyc:2.4.1.47-RXN
xref: Reactome:R-HSA-6785933 "UGT8 transfers Gal from UDP-Gal to CERA"
+xref: RHEA:10856
xref: RHEA:13093
+xref: RHEA:44896
is_a: GO:0035250 ! UDP-galactosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.47
property_value: skos:exactMatch RHEA:13093
+property_value: skos:narrowMatch RHEA:10856
+property_value: skos:narrowMatch RHEA:44896
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27679" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28173" xsd:anyURI
@@ -32851,11 +33100,20 @@
xref: Reactome:R-HSA-77331 "(S)-Hydroxyoctanoyl-CoA+NAD<=>3-Oxooctanoyl-CoA+NADH+H"
xref: Reactome:R-HSA-77342 "(S)-Hydroxydecanoyl-CoA+NAD<=>3-Oxodecanoyl-CoA+NADH+H"
xref: RHEA:22432
+xref: RHEA:34851
+xref: RHEA:40211
+xref: RHEA:78919
+xref: RHEA:78923
xref: UM-BBD_reactionID:r1063
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.35
property_value: skos:exactMatch RHEA:22432
+property_value: skos:narrowMatch RHEA:34851
+property_value: skos:narrowMatch RHEA:40211
+property_value: skos:narrowMatch RHEA:78919
+property_value: skos:narrowMatch RHEA:78923
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30577" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
[Term]
id: GO:0003858
@@ -32984,12 +33242,16 @@
xref: EC:1.2.4.4
xref: MetaCyc:1.2.4.4-RXN
xref: RHEA:13457
+xref: RHEA:84639
+xref: RHEA:84643
is_a: GO:0016624 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
property_value: skos:broadMatch EC:1.2.1.25
property_value: skos:broadMatch MetaCyc:1.2.1.25-RXN
property_value: skos:exactMatch EC:1.2.4.4
property_value: skos:exactMatch MetaCyc:1.2.4.4-RXN
property_value: skos:narrowMatch RHEA:13457
+property_value: skos:narrowMatch RHEA:84639
+property_value: skos:narrowMatch RHEA:84643
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21144" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29951" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30031" xsd:anyURI
@@ -33042,9 +33304,13 @@
xref: Reactome:R-HSA-9705713 "SRD5A2 dehydrogenates TEST to DHTEST"
xref: Reactome:R-HSA-9705714 "SRD5A3 dehydrogenates TEST to DHTEST"
xref: RHEA:13805
+xref: RHEA:51048
+xref: RHEA:51060
is_a: GO:0033765 ! steroid dehydrogenase activity, acting on the CH-CH group of donors
property_value: skos:exactMatch EC:1.3.99.5
property_value: skos:exactMatch RHEA:13805
+property_value: skos:narrowMatch RHEA:51048
+property_value: skos:narrowMatch RHEA:51060
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26703" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -33089,7 +33355,6 @@
synonym: "gamma-aminobutyric acid transaminase activity" EXACT []
synonym: "gamma-aminobutyric transaminase activity" EXACT []
synonym: "glutamate-succinic semialdehyde transaminase activity" EXACT []
-xref: Reactome:R-HSA-916855 "PXLP-K357-ABAT dimer:2Fe-2S transforms GABA to SUCCSA"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28183" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28802" xsd:anyURI
is_obsolete: true
@@ -33198,7 +33463,7 @@
synonym: "phosphohexokinase activity" BROAD [EC:2.7.1.11]
xref: EC:2.7.1.11
xref: MetaCyc:6PFRUCTPHOS-RXN
-xref: Reactome:R-HSA-70467 "D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP"
+xref: Reactome:R-HSA-70467 "PFK tetramer phosphorylates Fru(6)P"
xref: RHEA:16109
is_a: GO:0008443 ! phosphofructokinase activity
relationship: part_of GO:0061615 ! glycolytic process through fructose-6-phosphate
@@ -33220,7 +33485,7 @@
xref: EC:2.7.1.105
xref: KEGG_REACTION:R02732
xref: MetaCyc:6-PHOSPHOFRUCTO-2-KINASE-RXN
-xref: Reactome:R-HSA-71802 "D-fructose 6-phosphate + ATP => D-fructose 2,6-bisphosphate + ADP"
+xref: Reactome:R-HSA-71802 "PFKFKB dimer phosphorylates Fru(6)P"
xref: RHEA:15653
is_a: GO:0008443 ! phosphofructokinase activity
property_value: skos:exactMatch EC:2.7.1.105
@@ -33277,7 +33542,7 @@
id: GO:0003876
name: AMP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AMP + H2O = IMP + NH3." [EC:3.5.4.6]
+def: "Catalysis of the reaction: AMP + H2O = IMP + NH4+." [RHEA:14777]
synonym: "5-adenylate deaminase activity" RELATED [EC:3.5.4.6]
synonym: "5-adenylic acid deaminase activity" RELATED [EC:3.5.4.6]
synonym: "5-AMP deaminase activity" RELATED [EC:3.5.4.6]
@@ -33357,8 +33622,8 @@
property_value: skos:exactMatch KEGG_REACTION:R00352
property_value: skos:exactMatch MetaCyc:ATP-CITRATE-PRO-S--LYASE-RXN
property_value: skos:exactMatch RHEA:21160
-property_value: skos:relatedMatch MetaCyc:PWY-5172
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0003879
@@ -33479,9 +33744,47 @@
xref: MetaCyc:D-AMINO-ACID-OXIDASE-RXN
xref: Reactome:R-HSA-389821 "glycine + O2 => glyoxylate + H2O2 + NH4+"
xref: RHEA:21816
+xref: RHEA:37583
+xref: RHEA:70951
+xref: RHEA:70959
+xref: RHEA:70963
+xref: RHEA:70971
+xref: RHEA:78203
+xref: RHEA:78207
+xref: RHEA:78211
+xref: RHEA:78215
+xref: RHEA:78219
+xref: RHEA:78223
+xref: RHEA:78227
+xref: RHEA:78235
+xref: RHEA:78239
+xref: RHEA:78243
+xref: RHEA:78247
+xref: RHEA:78251
+xref: RHEA:78255
+xref: RHEA:78791
is_a: GO:0008131 ! primary methylamine oxidase activity
property_value: skos:exactMatch EC:1.4.3.3
property_value: skos:exactMatch RHEA:21816
+property_value: skos:narrowMatch RHEA:37583
+property_value: skos:narrowMatch RHEA:70951
+property_value: skos:narrowMatch RHEA:70959
+property_value: skos:narrowMatch RHEA:70963
+property_value: skos:narrowMatch RHEA:70971
+property_value: skos:narrowMatch RHEA:78203
+property_value: skos:narrowMatch RHEA:78207
+property_value: skos:narrowMatch RHEA:78211
+property_value: skos:narrowMatch RHEA:78215
+property_value: skos:narrowMatch RHEA:78219
+property_value: skos:narrowMatch RHEA:78223
+property_value: skos:narrowMatch RHEA:78227
+property_value: skos:narrowMatch RHEA:78235
+property_value: skos:narrowMatch RHEA:78239
+property_value: skos:narrowMatch RHEA:78243
+property_value: skos:narrowMatch RHEA:78247
+property_value: skos:narrowMatch RHEA:78251
+property_value: skos:narrowMatch RHEA:78255
+property_value: skos:narrowMatch RHEA:78791
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -33619,6 +33922,8 @@
xref: Reactome:R-HSA-69116 "Formation of Okazaki fragments"
xref: Reactome:R-HSA-73932 "Resynthesis of excised residue by POLB"
xref: Reactome:R-HSA-9710480 "Decitabine triphosphate incorporates into DNA"
+xref: Reactome:R-HSA-9914364 "POLG in the replisome polymerizes the H strand"
+xref: Reactome:R-HSA-9914498 "POLG in the replisome polymerizes the L strand"
is_a: GO:0034061 ! DNA polymerase activity
property_value: skos:exactMatch EC:2.7.7.7
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28442" xsd:anyURI
@@ -33680,10 +33985,13 @@
xref: Reactome:R-HSA-167121 "Addition of the third nucleotide on the nascent HIV-1 transcript"
xref: Reactome:R-HSA-167136 "Addition of nucleotides 5 through 9 on the growing HIV-1 transcript"
xref: Reactome:R-HSA-174425 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere"
+xref: Reactome:R-HSA-1964482 "RNA polymerase III transcribes microbial dsDNA to dsRNA"
xref: Reactome:R-HSA-203901 "Pol II mediated transcription of microRNA genes"
xref: Reactome:R-HSA-427366 "Transcription of intergenic spacer of the rRNA gene"
xref: Reactome:R-HSA-5601926 "RNA polymerase II polymerizes primary piRNA transcript"
xref: Reactome:R-HSA-6781824 "Active RNA Pol II complex transcribes lesion-containing DNA template"
+xref: Reactome:R-HSA-6814549 "Pre-snRNA transcript initiation, Integrator binding, LEC binding"
+xref: Reactome:R-HSA-6814559 "Pre-snRNA is elongated and capped with 7-methylguanosine"
xref: Reactome:R-HSA-68913 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin"
xref: Reactome:R-HSA-74986 "Elongation of pre-rRNA transcript"
xref: Reactome:R-HSA-75850 "Addition of the third nucleotide on the nascent transcript"
@@ -33693,6 +34001,8 @@
xref: Reactome:R-HSA-9670149 "TERRA transcription"
xref: Reactome:R-HSA-9697084 "Defective RpoB in Mtb RNAP transcribes RNA polyanion"
xref: Reactome:R-HSA-9697085 "RNAP transcribes Mtb RNA polyanion"
+xref: Reactome:R-HSA-9914409 "POLRMT polymerizes RNA primer for mitochondrial L strand replication"
+xref: Reactome:R-HSA-9915448 "POLRMT polymerizes R-loop RNA"
is_a: GO:0034062 ! 5'-3' RNA polymerase activity
relationship: part_of GO:0032774 ! RNA biosynthetic process
property_value: skos:exactMatch EC:2.7.7.6
@@ -33869,6 +34179,7 @@
synonym: "sealase activity" RELATED [EC:6.5.1.1]
xref: EC:6.5.1.1
xref: MetaCyc:DNA-LIGASE-ATP-RXN
+xref: Reactome:R-HSA-9914903 "LIG3 (Ligase III) ligates nascent mitochondrial DNA strands"
is_a: GO:0003909 ! DNA ligase activity
property_value: skos:exactMatch EC:6.5.1.1
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -33979,6 +34290,7 @@
synonym: "untwisting enzyme activity" RELATED [EC:5.6.2.1]
xref: EC:5.6.2.1
xref: MetaCyc:5.99.1.2-RXN
+xref: Reactome:R-HSA-9914922 "TOP3A (Topoisomerase 3a) decatenates mitochondrial DNA"
is_a: GO:0003916 ! DNA topoisomerase activity
property_value: skos:exactMatch EC:5.6.2.1
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15575" xsd:anyURI
@@ -34063,7 +34375,7 @@
id: GO:0003921
name: GMP synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + XMP + NH4(+) = AMP + diphosphate + GMP + 2H+." [RHEA:18301]
+def: "Catalysis of the reaction: ATP + XMP + NH4+ = AMP + diphosphate + GMP + 2H+." [RHEA:18301]
xref: MetaCyc:GMP-SYN-NH3-RXN
xref: RHEA:18301
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -34195,6 +34507,8 @@
xref: Reactome:R-HSA-9645598 "RRAGC,D hydrolyzes GTP"
xref: Reactome:R-HSA-9649736 "RAS intrinsic GTPase activity hydrolyzes GTP to GDP"
xref: Reactome:R-HSA-983422 "Disassembly of COPII coated vesicle"
+xref: Reactome:R-HSA-9947842 "GBP1 hydrolyzes GTP forming GBP1 oligomers"
+xref: Reactome:R-HSA-9954919 "ABCE1:ATP binds PELO:HBS1L-1:GTP:80S ribosome:non-stop mRNA:peptidyl-tRNA with nascent peptide and HBS1L-1:GDP is released"
xref: RHEA:19669
is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
property_value: skos:exactMatch RHEA:19669
@@ -34223,7 +34537,6 @@
xref: EC:3.6.5.1
xref: EC:3.6.5.2
xref: Reactome:R-HSA-400027 "Gq alpha:G beta:G gamma dissociates to Gq alpha:GTP and G beta:G gamma"
-xref: Reactome:R-HSA-400037 "Gi,Go Heterotrimeric G-protein complex dissociates"
xref: Reactome:R-HSA-422320 "Heterotrimeric G(s) complex dissociates"
is_a: GO:0003924 ! GTPase activity
is_a: GO:0098772 ! molecular function regulator activity
@@ -34429,8 +34742,8 @@
synonym: "glycosaminoglycan alpha-L-iduronohydrolase activity" RELATED [EC:3.2.1.76]
xref: EC:3.2.1.76
xref: MetaCyc:3.2.1.76-RXN
-xref: Reactome:R-HSA-1678716 "IDUA hydrolyses Heparan sulfate chain(1)"
-xref: Reactome:R-HSA-1793186 "IDUA) hydrolyses the unsulfated alpha-L-iduronosidic link in DS"
+xref: Reactome:R-HSA-1678716 "IDUA cleaves iduronate from HS chain"
+xref: Reactome:R-HSA-1793186 "IDUA hydrolyses the unsulfated alpha-L-iduronosidic link in DS"
xref: Reactome:R-HSA-2090037 "IDUA hydrolyses Heparan sulfate chain(6)"
xref: Reactome:R-HSA-2206299 "Defective IDUA does not hydrolyse Heparan sulfate chain(6)"
xref: Reactome:R-HSA-9036037 "Defective IDUA does not hydrolyse Heparan sulfate chain(1)"
@@ -34444,7 +34757,7 @@
id: GO:0003941
name: L-serine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine = pyruvate + NH3." [EC:4.3.1.17]
+def: "Catalysis of the reaction: L-serine = pyruvate + NH4+." [RHEA:19169]
synonym: "L-hydroxyaminoacid dehydratase activity" BROAD []
synonym: "L-serine ammonia-lyase (pyruvate-forming) activity" RELATED [EC:4.3.1.17]
synonym: "L-serine deaminase activity" EXACT []
@@ -34454,6 +34767,7 @@
synonym: "serine deaminase activity" BROAD [EC:4.3.1.17]
xref: EC:4.3.1.17
xref: MetaCyc:4.3.1.17-RXN
+xref: Reactome:R-HSA-9929460 "SDS dimers:PXLP convert L-Ser to PYR and NH4+"
xref: RHEA:19169
is_a: GO:0016841 ! ammonia-lyase activity
property_value: skos:exactMatch EC:4.3.1.17
@@ -34759,8 +35073,12 @@
synonym: "type 1 dehydrogenase activity" RELATED []
synonym: "type I dehydrogenase activity" RELATED []
xref: RHEA:11356
+xref: RHEA:30147
+xref: RHEA:47524
is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H
property_value: skos:exactMatch RHEA:11356
+property_value: skos:narrowMatch RHEA:30147
+property_value: skos:narrowMatch RHEA:47524
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -34906,9 +35224,11 @@
xref: Reactome:R-HSA-9018867 "5-HEDH dehydrogenates 5(S)-Hp-18(S)-HpEPE to 18(S)-RvE2"
xref: Reactome:R-HSA-9018901 "5-HEDH dehydrogenates 5(S)-Hp-18(R)-HEPE to 18(R)-RvE2"
xref: RHEA:13149
+xref: RHEA:30151
is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H
property_value: skos:exactMatch EC:1.6.99.1
property_value: skos:exactMatch RHEA:13149
+property_value: skos:narrowMatch RHEA:30151
[Term]
id: GO:0003960
@@ -35091,6 +35411,8 @@
xref: Reactome:R-HSA-9834719 "Synthesis of negative sense genomic RNA of respiratory syncytial virus"
xref: Reactome:R-HSA-9834736 "Synthesis of antigenomic RNA of human respiratory syncytial virus"
xref: Reactome:R-HSA-9837511 "Abortive replication of hRSV A"
+xref: Reactome:R-HSA-9922955 "NS5 synthesizes minus strand genome"
+xref: Reactome:R-HSA-9923068 "NS5 synthesizes plus strand genome"
is_a: GO:0034062 ! 5'-3' RNA polymerase activity
relationship: part_of GO:0001172 ! RNA-templated transcription
property_value: skos:exactMatch EC:2.7.7.48
@@ -35130,7 +35452,7 @@
alt_id: GO:0052852
alt_id: GO:0052853
alt_id: GO:0052854
-def: "Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + hydrogen peroxide." [RHEA:16789]
+def: "Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + H2O2." [RHEA:16789]
synonym: "glycolate oxidase activity" RELATED []
synonym: "hydroxy-acid oxidase A activity" NARROW [EC:1.1.3.15]
synonym: "hydroxy-acid oxidase B activity" NARROW [EC:1.1.3.15]
@@ -35146,11 +35468,15 @@
xref: Reactome:R-HSA-389842 "HAO1 tetramer oxidizes glycolate to glyoxylate"
xref: Reactome:R-HSA-6787811 "HAO2 tetramer oxidises 2OH-PALM"
xref: RHEA:16789
+xref: RHEA:27662
+xref: RHEA:41227
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.1.3.15
property_value: skos:exactMatch MetaCyc:S-2-HYDROXY-ACID-OXIDASE-RXN
property_value: skos:exactMatch RHEA:16789
property_value: skos:narrowMatch MetaCyc:RXN-969
+property_value: skos:narrowMatch RHEA:27662
+property_value: skos:narrowMatch RHEA:41227
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21795" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -35159,7 +35485,6 @@
name: UDP-N-acetylglucosamine 4-epimerase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-galactosamine." [EC:5.1.3.7]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "UDP acetylglucosamine epimerase activity" RELATED [EC:5.1.3.7]
synonym: "UDP-GlcNAc 4-epimerase activity" RELATED [EC:5.1.3.7]
synonym: "UDP-N-acetyl-D-glucosamine 4-epimerase activity" RELATED [EC:5.1.3.7]
@@ -35172,9 +35497,9 @@
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
property_value: skos:exactMatch EC:5.1.3.7
property_value: skos:exactMatch RHEA:20517
-property_value: skos:relatedMatch MetaCyc:PWY-5512
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0003975
@@ -35327,7 +35652,7 @@
xref: EC:2.7.7.9
xref: KEGG_REACTION:R00289
xref: MetaCyc:GLUC1PURIDYLTRANS-RXN
-xref: Reactome:R-HSA-70286 "UTP + D-glucose 1-phosphate <=> pyrophosphate + UDP-glucose"
+xref: Reactome:R-HSA-70286 "UTP + D-glucose 1-phosphate => pyrophosphate + UDP-glucose"
xref: RHEA:19889
is_a: GO:0051748 ! UTP-monosaccharide-1-phosphate uridylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.9
@@ -35369,7 +35694,7 @@
synonym: "acetyl coenzyme A thiolase activity" RELATED []
xref: EC:2.3.1.9
xref: MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN
-xref: Reactome:R-HSA-70844 "alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA"
+xref: Reactome:R-HSA-70844 "alpha-methylacetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA"
xref: Reactome:R-HSA-73916 "2 acetyl-CoA <=> acetoacetyl-CoA + CoA"
xref: Reactome:R-HSA-74181 "acetoacetyl-CoA + CoA <=> 2 acetyl-CoA"
xref: Reactome:R-HSA-8848215 "ACAT2 condenses 2 Ac-CoA to form ACA-CoA"
@@ -35406,11 +35731,12 @@
[Term]
id: GO:0003987
-name: acetate-CoA ligase activity
+name: acetyl-CoA synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA." [EC:6.2.1.1]
+def: "Catalysis of the reaction: acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate." [RHEA:23176]
synonym: "acetate thiokinase activity" BROAD [EC:6.2.1.1]
synonym: "acetate to acetyl-CoA" RELATED []
+synonym: "acetate-CoA ligase activity" EXACT []
synonym: "acetate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.1]
synonym: "acetic thiokinase activity" RELATED [EC:6.2.1.1]
synonym: "acetyl activating enzyme" RELATED [EC:6.2.1.1]
@@ -35419,8 +35745,8 @@
synonym: "acetyl coenzyme A synthetase activity" RELATED [EC:6.2.1.1]
synonym: "acetyl-activating enzyme activity" RELATED [EC:6.2.1.1]
synonym: "acetyl-CoA synthase activity" RELATED [EC:6.2.1.1]
-synonym: "acetyl-CoA synthetase activity" RELATED [EC:6.2.1.1]
synonym: "acetyl-coenzyme A synthase activity" RELATED [EC:6.2.1.1]
+synonym: "acetyl-coenzyme A synthetase activity" EXACT []
synonym: "ACS" RELATED [EC:6.2.1.1]
synonym: "acyl-activating enzyme activity" BROAD [EC:6.2.1.1]
synonym: "short chain fatty acyl-CoA synthetase activity" RELATED [EC:6.2.1.1]
@@ -35432,7 +35758,6 @@
xref: Reactome:R-HSA-8875071 "ACSS3 ligates CoA to CH3COO-"
xref: RHEA:23176
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.1
property_value: skos:exactMatch RHEA:23176
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -35461,10 +35786,24 @@
xref: Reactome:R-HSA-77340 "3-Oxodecanoyl-CoA+CoA-SH<=>Octanoyl-CoA"
xref: Reactome:R-HSA-8874745 "ACAA2 tetramer transfers acyl group from Ac-CoA to acyl-CoA forming 3OA-CoA and CoA-SH"
xref: RHEA:21564
+xref: RHEA:34799
+xref: RHEA:46312
+xref: RHEA:67224
+xref: RHEA:78895
+xref: RHEA:78899
+xref: RHEA:78903
+xref: RHEA:78907
xref: UM-BBD_reactionID:r1051
is_a: GO:0016408 ! C-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.16
property_value: skos:exactMatch RHEA:21564
+property_value: skos:narrowMatch RHEA:34799
+property_value: skos:narrowMatch RHEA:46312
+property_value: skos:narrowMatch RHEA:67224
+property_value: skos:narrowMatch RHEA:78895
+property_value: skos:narrowMatch RHEA:78899
+property_value: skos:narrowMatch RHEA:78903
+property_value: skos:narrowMatch RHEA:78907
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -35529,10 +35868,10 @@
[Term]
id: GO:0003992
-name: N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
+name: N2-acetyl-L-ornithine:2-oxoglutarate 5-transaminase activity
namespace: molecular_function
alt_id: GO:0047318
-def: "Catalysis of the reaction: 2-oxoglutarate + N(2)-acetyl-L-ornithine = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate." [EC:2.6.1.11, RHEA:18049]
+def: "Catalysis of the reaction: N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate." [RHEA:18049]
synonym: "2-N-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity" RELATED [EC:2.6.1.11]
synonym: "acetylornithine 5-aminotransferase activity" RELATED [EC:2.6.1.11]
synonym: "acetylornithine aminotransferase activity" BROAD []
@@ -35542,6 +35881,7 @@
synonym: "N(2)-acetylornithine 5-transaminase activity" RELATED [EC:2.6.1.11]
synonym: "N-acetylornithine aminotransferase activity" RELATED [EC:2.6.1.11]
synonym: "N-acetylornithine-delta-transaminase activity" RELATED [EC:2.6.1.11]
+synonym: "N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity" EXACT []
synonym: "N2-acetyl-L-ornithine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.11]
synonym: "N2-acetylornithine 5-aminotransferase activity" EXACT []
synonym: "N2-acetylornithine 5-transaminase activity" RELATED [EC:2.6.1.11]
@@ -35554,6 +35894,7 @@
property_value: skos:exactMatch EC:2.6.1.11
property_value: skos:exactMatch RHEA:18049
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0003993
@@ -35647,10 +35988,42 @@
xref: Reactome:R-HSA-193369 "25(S) DHCA-CoA is dehydrogenated to 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA"
xref: Reactome:R-HSA-2066787 "Oxidation of tetracosapentaenoyl-CoA to delta2-tetracosaheptaenoyl-CoA"
xref: Reactome:R-HSA-390256 "ACOX1 oxidizes C26:0 CoA"
+xref: RHEA:22952
xref: RHEA:38959
+xref: RHEA:39071
+xref: RHEA:39087
+xref: RHEA:40271
+xref: RHEA:40275
+xref: RHEA:40315
+xref: RHEA:40471
+xref: RHEA:66208
+xref: RHEA:66212
+xref: RHEA:66216
+xref: RHEA:66220
+xref: RHEA:66224
+xref: RHEA:66228
+xref: RHEA:66232
+xref: RHEA:66236
+xref: RHEA:67212
is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.3.3.6
property_value: skos:exactMatch RHEA:38959
+property_value: skos:narrowMatch RHEA:22952
+property_value: skos:narrowMatch RHEA:39071
+property_value: skos:narrowMatch RHEA:39087
+property_value: skos:narrowMatch RHEA:40271
+property_value: skos:narrowMatch RHEA:40275
+property_value: skos:narrowMatch RHEA:40315
+property_value: skos:narrowMatch RHEA:40471
+property_value: skos:narrowMatch RHEA:66208
+property_value: skos:narrowMatch RHEA:66212
+property_value: skos:narrowMatch RHEA:66216
+property_value: skos:narrowMatch RHEA:66220
+property_value: skos:narrowMatch RHEA:66224
+property_value: skos:narrowMatch RHEA:66228
+property_value: skos:narrowMatch RHEA:66232
+property_value: skos:narrowMatch RHEA:66236
+property_value: skos:narrowMatch RHEA:67212
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28733" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -35702,7 +36075,7 @@
id: GO:0004000
name: adenosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine + H2O = inosine + NH3." [RHEA:24408]
+def: "Catalysis of the reaction: adenosine + H2O = inosine + NH4+." [RHEA:24408]
synonym: "adenosine aminohydrolase activity" RELATED [EC:3.5.4.4]
synonym: "adenosine deaminase reaction" EXACT []
xref: MetaCyc:ADENODEAMIN-RXN
@@ -35811,9 +36184,9 @@
[Term]
id: GO:0004015
-name: adenosylmethionine-8-amino-7-oxononanoate transaminase activity
+name: S-adenosyl-L-methionine:8-amino-7-oxononanoate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate." [EC:2.6.1.62, RHEA:16861]
+def: "Catalysis of the reaction: (8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = S-adenosyl-4-methylsulfanyl-2-oxobutanoate + (7R,8S)-7,8-diammoniononanoate." [RHEA:16861]
synonym: "7,8-diamino-pelargonic acid aminotransferase activity" RELATED [EC:2.6.1.62]
synonym: "7,8-diaminonanoate transaminase activity" RELATED [EC:2.6.1.62]
synonym: "7,8-diaminononanoate aminotransferase activity" RELATED [EC:2.6.1.62]
@@ -35824,6 +36197,7 @@
synonym: "adenosyl methionine-8-amino-7-oxononanoate transaminase activity" EXACT []
synonym: "adenosylmethionine--8-amino-7-oxononanoate aminotransferase activity" RELATED [EC:2.6.1.62]
synonym: "adenosylmethionine-8-amino-7-oxononanoate aminotransferase activity" EXACT []
+synonym: "adenosylmethionine-8-amino-7-oxononanoate transaminase activity" EXACT []
synonym: "DAPA aminotransferase activity" RELATED [EC:2.6.1.62]
synonym: "DAPA transaminase activity" RELATED [EC:2.6.1.62]
synonym: "diaminopelargonate synthase activity" RELATED [EC:2.6.1.62]
@@ -35836,6 +36210,7 @@
property_value: skos:exactMatch EC:2.6.1.62
property_value: skos:exactMatch RHEA:16861
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004016
@@ -35959,10 +36334,9 @@
[Term]
id: GO:0004021
-name: L-alanine:2-oxoglutarate aminotransferase activity
+name: L-alanine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate." [RHEA:19453]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: L-alanine + 2-oxoglutarate = pyruvate + L-glutamate." [RHEA:19453]
synonym: "alanine aminotransferase activity" BROAD []
synonym: "alanine transaminase activity" BROAD [EC:2.6.1.2]
synonym: "alanine-alpha-ketoglutarate aminotransferase activity" RELATED [EC:2.6.1.2]
@@ -35977,6 +36351,7 @@
synonym: "L-alanine aminotransferase activity" BROAD [EC:2.6.1.2]
synonym: "L-alanine transaminase activity" BROAD [EC:2.6.1.2]
synonym: "L-alanine-alpha-ketoglutarate aminotransferase activity" RELATED [EC:2.6.1.2]
+synonym: "L-alanine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "pyruvate transaminase activity" BROAD [EC:2.6.1.2]
synonym: "pyruvate-alanine aminotransferase activity" RELATED [EC:2.6.1.2]
synonym: "pyruvate-glutamate transaminase activity" RELATED [EC:2.6.1.2]
@@ -35988,13 +36363,14 @@
xref: Reactome:R-HSA-70523 "PXLP-K314-GPT transaminates L-Ala to form PYR"
xref: Reactome:R-HSA-70524 "PXLP-K314-GPT transaminates PYR to form L-Ala"
xref: RHEA:19453
-is_a: GO:0047635 ! alanine-oxo-acid transaminase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.2
property_value: skos:exactMatch KEGG_REACTION:R00258
property_value: skos:exactMatch MetaCyc:ALANINE-AMINOTRANSFERASE-RXN
property_value: skos:exactMatch RHEA:19453
-property_value: skos:relatedMatch MetaCyc:ALANINE-SYN2-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004022
@@ -36076,10 +36452,28 @@
xref: EC:2.3.1.84
xref: MetaCyc:ALCOHOL-O-ACETYLTRANSFERASE-RXN
xref: RHEA:17229
+xref: RHEA:55972
+xref: RHEA:64624
+xref: RHEA:64628
+xref: RHEA:64632
+xref: RHEA:64676
+xref: RHEA:65236
+xref: RHEA:65456
+xref: RHEA:65460
+xref: RHEA:65468
is_a: GO:0016413 ! O-acetyltransferase activity
is_a: GO:0034318 ! alcohol O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.84
property_value: skos:exactMatch RHEA:17229
+property_value: skos:narrowMatch RHEA:55972
+property_value: skos:narrowMatch RHEA:64624
+property_value: skos:narrowMatch RHEA:64628
+property_value: skos:narrowMatch RHEA:64632
+property_value: skos:narrowMatch RHEA:64676
+property_value: skos:narrowMatch RHEA:65236
+property_value: skos:narrowMatch RHEA:65456
+property_value: skos:narrowMatch RHEA:65460
+property_value: skos:narrowMatch RHEA:65468
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36110,9 +36504,13 @@
xref: Reactome:R-HSA-176494 "SULTs transfer (SO4)2- group to 27HCHOL"
xref: Reactome:R-HSA-176609 "cholesterol + PAPS => cholesterol sulfate + PAP"
xref: RHEA:22552
+xref: RHEA:59300
+xref: RHEA:59304
is_a: GO:0008146 ! sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.2
property_value: skos:exactMatch RHEA:22552
+property_value: skos:narrowMatch RHEA:59300
+property_value: skos:narrowMatch RHEA:59304
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36149,6 +36547,40 @@
xref: Reactome:R-HSA-71691 "acetaldehyde + NAD+ => acetate + NADH + H+ [cytosolic]"
xref: Reactome:R-HSA-71723 "acetaldehyde + NAD+ => acetate + NADH + H+ [mitochondrial]"
xref: RHEA:16185
+xref: RHEA:30867
+xref: RHEA:30879
+xref: RHEA:31043
+xref: RHEA:31059
+xref: RHEA:31215
+xref: RHEA:31231
+xref: RHEA:31243
+xref: RHEA:31259
+xref: RHEA:31299
+xref: RHEA:31515
+xref: RHEA:33803
+xref: RHEA:34219
+xref: RHEA:39039
+xref: RHEA:42340
+xref: RHEA:42384
+xref: RHEA:45764
+xref: RHEA:47152
+xref: RHEA:47932
+xref: RHEA:59432
+xref: RHEA:60688
+xref: RHEA:60708
+xref: RHEA:61632
+xref: RHEA:67252
+xref: RHEA:67256
+xref: RHEA:69080
+xref: RHEA:69084
+xref: RHEA:69088
+xref: RHEA:69164
+xref: RHEA:69168
+xref: RHEA:75119
+xref: RHEA:76655
+xref: RHEA:76667
+xref: RHEA:81191
+xref: RHEA:81419
xref: UM-BBD_reactionID:r0003
xref: UM-BBD_reactionID:r0023
xref: UM-BBD_reactionID:r0605
@@ -36156,6 +36588,40 @@
is_a: GO:0004030 ! aldehyde dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.2.1.3
property_value: skos:exactMatch RHEA:16185
+property_value: skos:narrowMatch RHEA:30867
+property_value: skos:narrowMatch RHEA:30879
+property_value: skos:narrowMatch RHEA:31043
+property_value: skos:narrowMatch RHEA:31059
+property_value: skos:narrowMatch RHEA:31215
+property_value: skos:narrowMatch RHEA:31231
+property_value: skos:narrowMatch RHEA:31243
+property_value: skos:narrowMatch RHEA:31259
+property_value: skos:narrowMatch RHEA:31299
+property_value: skos:narrowMatch RHEA:31515
+property_value: skos:narrowMatch RHEA:33803
+property_value: skos:narrowMatch RHEA:34219
+property_value: skos:narrowMatch RHEA:39039
+property_value: skos:narrowMatch RHEA:42340
+property_value: skos:narrowMatch RHEA:42384
+property_value: skos:narrowMatch RHEA:45764
+property_value: skos:narrowMatch RHEA:47152
+property_value: skos:narrowMatch RHEA:47932
+property_value: skos:narrowMatch RHEA:59432
+property_value: skos:narrowMatch RHEA:60688
+property_value: skos:narrowMatch RHEA:60708
+property_value: skos:narrowMatch RHEA:61632
+property_value: skos:narrowMatch RHEA:67252
+property_value: skos:narrowMatch RHEA:67256
+property_value: skos:narrowMatch RHEA:69080
+property_value: skos:narrowMatch RHEA:69084
+property_value: skos:narrowMatch RHEA:69088
+property_value: skos:narrowMatch RHEA:69164
+property_value: skos:narrowMatch RHEA:69168
+property_value: skos:narrowMatch RHEA:75119
+property_value: skos:narrowMatch RHEA:76655
+property_value: skos:narrowMatch RHEA:76667
+property_value: skos:narrowMatch RHEA:81191
+property_value: skos:narrowMatch RHEA:81419
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28144" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29544" xsd:anyURI
@@ -36183,7 +36649,7 @@
name: aldehyde oxidase activity
namespace: molecular_function
alt_id: GO:0050250
-def: "Catalysis of the reaction: an aldehyde + H2O + O2 = a carboxylic acid + hydrogen peroxide." [EC:1.2.3.1]
+def: "Catalysis of the reaction: an aldehyde + O2 + H2O = a carboxylate + H2O2 + H+." [RHEA:16829]
synonym: "aldehyde:oxygen oxidoreductase activity" RELATED [EC:1.2.3.1]
synonym: "quinoline oxidase activity" RELATED [EC:1.2.3.1]
synonym: "retinal oxidase activity" NARROW []
@@ -36195,6 +36661,16 @@
xref: Reactome:R-HSA-3204311 "AOX1 oxidises PXL to PDXate"
xref: RHEA:16829
xref: RHEA:22520
+xref: RHEA:33439
+xref: RHEA:49636
+xref: RHEA:56736
+xref: RHEA:58964
+xref: RHEA:58976
+xref: RHEA:58980
+xref: RHEA:58984
+xref: RHEA:58988
+xref: RHEA:59000
+xref: RHEA:59004
is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.2.3.1
property_value: skos:exactMatch MetaCyc:ALDEHYDE-OXIDASE-RXN
@@ -36203,6 +36679,16 @@
property_value: skos:narrowMatch MetaCyc:RXN-8093
property_value: skos:narrowMatch MetaCyc:RXN-8094
property_value: skos:narrowMatch RHEA:22520
+property_value: skos:narrowMatch RHEA:33439
+property_value: skos:narrowMatch RHEA:49636
+property_value: skos:narrowMatch RHEA:56736
+property_value: skos:narrowMatch RHEA:58964
+property_value: skos:narrowMatch RHEA:58976
+property_value: skos:narrowMatch RHEA:58980
+property_value: skos:narrowMatch RHEA:58984
+property_value: skos:narrowMatch RHEA:58988
+property_value: skos:narrowMatch RHEA:59000
+property_value: skos:narrowMatch RHEA:59004
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22680" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -36218,12 +36704,15 @@
xref: KEGG_REACTION:R02820
xref: Reactome:R-HSA-196060 "Reduction of isocaproaldehyde to 4-methylpentan-1-ol"
xref: Reactome:R-HSA-5652172 "AKR1B1 reduces Glc to D-sorbitol"
+xref: Reactome:R-HSA-9931850 "AKR1B1 reduces galactose to galactitol"
xref: RHEA:12789
+xref: RHEA:59924
is_a: GO:0008106 ! alcohol dehydrogenase (NADP+) activity
property_value: skos:broadMatch EC:1.1.1.21
property_value: skos:broadMatch MetaCyc:ALDEHYDE-REDUCTASE-RXN
property_value: skos:exactMatch KEGG_REACTION:R02820
property_value: skos:exactMatch RHEA:12789
+property_value: skos:narrowMatch RHEA:59924
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27136" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27881" xsd:anyURI
@@ -36238,26 +36727,6 @@
synonym: "aldo-keto reductase (NADP+) activity" EXACT []
synonym: "aldo-keto reductase activity" EXACT []
synonym: "NADPH-dependent aldo-keto reductase activity" EXACT [GOC:vw]
-xref: Reactome:R-HSA-192033 "4-cholesten-7alpha-ol-3-one is reduced to 5beta-cholestan-7alpha-ol-3-one"
-xref: Reactome:R-HSA-192036 "5Beta-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha, 12alpha-triol"
-xref: Reactome:R-HSA-192067 "4-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholesten-7alpha, 12alpha-diol-3-one"
-xref: Reactome:R-HSA-192160 "5beta-cholestan-7alpha-ol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha-diol"
-xref: Reactome:R-HSA-193746 "4-cholesten-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-7alpha,24(S)-diol-3-one"
-xref: Reactome:R-HSA-193755 "4-cholesten-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,24(S)-triol-3-one"
-xref: Reactome:R-HSA-193758 "5beta-cholestan-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,24(S)-triol"
-xref: Reactome:R-HSA-193781 "5Beta-cholestan-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol"
-xref: Reactome:R-HSA-193800 "5Beta-cholestan-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,27-tetrol"
-xref: Reactome:R-HSA-193821 "4-cholesten-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,27-triol-3-one"
-xref: Reactome:R-HSA-193824 "4-cholesten-7alpha,27-diol-3-one is reduced to 5beta-cholestan-7alpha,27-diol-3-one"
-xref: Reactome:R-HSA-193841 "5beta-cholestan-7alpha,27-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,27-triol"
-xref: Reactome:R-HSA-198845 "CYB5A:heme reduces Asc.- to AscH-"
-xref: Reactome:R-HSA-2855252 "AKRs reduce RBP2:atRAL to RBP2:atROL"
-xref: Reactome:R-HSA-5423637 "AKR dimers reduce AFBDHO to AFBDOH"
-xref: Reactome:R-HSA-5692232 "AKR1A1 oxidises BaPtDHD to BaP-7,8-dione"
-xref: Reactome:R-HSA-9027531 "Dehydrogenase dehydrogenates 13-HDHA to 13-oxo-DHA"
-xref: Reactome:R-HSA-9027562 "Dehydrogenase dehydrogenates 17-HDHA to 17-oxo-DHA"
-xref: Reactome:R-HSA-9027598 "Dehydrogenase dehydrogenates 13(R)-HDPAn-3 to 13-oxo-DPAn-3"
-xref: Reactome:R-HSA-9027600 "Dehydrogenase dehydrogenates 17-HDPAn-3 to 17-oxo-DPAn-3"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28532" xsd:anyURI
is_obsolete: true
@@ -36272,6 +36741,8 @@
synonym: "mutarotase activity" RELATED [EC:5.1.3.3]
xref: EC:5.1.3.3
xref: MetaCyc:ALDOSE-1-EPIMERASE-RXN
+xref: Reactome:R-HSA-9931853 "GALM converts beta-D-GAL to alpha-D-GAL"
+xref: Reactome:R-HSA-9931926 "Defective GALM doesn't convert beta-D-GAL to alpha-D-GAL"
xref: RHEA:10264
xref: RHEA:28675
xref: RHEA:63332
@@ -36367,17 +36838,31 @@
xref: EC:3.5.1.4
xref: MetaCyc:AMIDASE-RXN
xref: RHEA:12020
+xref: RHEA:34367
+xref: RHEA:34375
+xref: RHEA:35063
+xref: RHEA:45048
+xref: RHEA:64820
+xref: RHEA:64824
+xref: RHEA:68112
xref: UM-BBD_reactionID:r0084
xref: UM-BBD_reactionID:r0375
xref: UM-BBD_reactionID:r1440
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.4
property_value: skos:exactMatch RHEA:12020
+property_value: skos:narrowMatch RHEA:34367
+property_value: skos:narrowMatch RHEA:34375
+property_value: skos:narrowMatch RHEA:35063
+property_value: skos:narrowMatch RHEA:45048
+property_value: skos:narrowMatch RHEA:64820
+property_value: skos:narrowMatch RHEA:64824
+property_value: skos:narrowMatch RHEA:68112
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
id: GO:0004042
-name: L-glutamate N-acetyltransferase activity
+name: L-glutamate N-acetyltransferase activity, acting on acetyl-CoA as donor
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamate + acetyl-CoA = N-acetyl-L-glutamate + CoA + H+." [RHEA:24292]
synonym: "acetyl-CoA:L-glutamate N-acetyltransferase activity" EXACT []
@@ -36385,14 +36870,17 @@
synonym: "AGAS" RELATED [EC:2.3.1.1]
synonym: "amino acid acetyltransferase activity" RELATED [EC:2.3.1.1]
synonym: "amino-acid N-acetyltransferase activity" BROAD [EC:2.3.1.1]
+synonym: "L-glutamate N-acetyltransferase activity" BROAD []
synonym: "N-acetylglutamate synthase activity" BROAD [EC:2.3.1.1]
xref: KEGG_REACTION:R00259
xref: MetaCyc:N-ACETYLTRANSFER-RXN
xref: Reactome:R-HSA-70542 "glutamate + acetyl CoA => N-acetyl glutamate + CoA"
+xref: Reactome:R-HSA-9955697 "NAGS variants don't synthesize N-acetylglutamate"
xref: RHEA:24292
is_a: GO:0140085 ! L-amino-acid N-acetyltransferase activity
property_value: skos:broadMatch EC:2.3.1.1
property_value: skos:exactMatch RHEA:24292
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31438" xsd:anyURI
[Term]
id: GO:0004043
@@ -36464,11 +36952,15 @@
synonym: "N-substituted aminoacyl transfer RNA hydrolase activity" RELATED [EC:3.1.1.29]
xref: EC:3.1.1.29
xref: MetaCyc:AMINOCYL-TRNA-HYDROLASE-RXN
+xref: Reactome:R-HSA-9937374 "MTRFR:MTRES1:39S ribosomal subunit:mRNA:peptidyl-tRNA:MALSU1:MIEF1:NDUFAB1 dissociates"
+xref: Reactome:R-HSA-9937719 "ICT1 hydrolyzes the peptidyl-tRNA bond of the nascent polypeptide"
xref: RHEA:54448
+xref: RHEA:81979
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: skos:exactMatch EC:3.1.1.29
property_value: skos:exactMatch RHEA:54448
+property_value: skos:narrowMatch RHEA:81979
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29746" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -36497,9 +36989,27 @@
xref: Reactome:R-HSA-9638046 "ACY3:Zn2+ dimer hydrolyses mercapturic acids"
xref: Reactome:R-HSA-9753944 "ACY1:Zn2+ dimer deacetylates NAC to L-Cys"
xref: RHEA:15565
+xref: RHEA:36855
+xref: RHEA:52628
+xref: RHEA:54184
+xref: RHEA:67368
+xref: RHEA:67440
+xref: RHEA:75515
+xref: RHEA:81115
+xref: RHEA:81119
+xref: RHEA:81123
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.14
property_value: skos:exactMatch RHEA:15565
+property_value: skos:narrowMatch RHEA:36855
+property_value: skos:narrowMatch RHEA:52628
+property_value: skos:narrowMatch RHEA:54184
+property_value: skos:narrowMatch RHEA:67368
+property_value: skos:narrowMatch RHEA:67440
+property_value: skos:narrowMatch RHEA:75515
+property_value: skos:narrowMatch RHEA:81115
+property_value: skos:narrowMatch RHEA:81119
+property_value: skos:narrowMatch RHEA:81123
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36573,10 +37083,20 @@
def: "Catalysis of the reaction: a ribonucleoside 5'-triphosphate + 2 H2O = a ribonucleoside 5'-phosphate + 2 phosphate. This reaction consists of two distinct successive phosphate-releasing steps, with NDPs as intermediates. Apyrases are active against both di- and triphosphate nucleotides (NDPs and NTPs) and hydrolyze NTPs to nucleotide monophosphates (NMPs)." [EC:3.6.1.5]
xref: EC:3.6.1.5
xref: MetaCyc:RXN-14024
+xref: RHEA:20988
xref: RHEA:36795
+xref: RHEA:64896
+xref: RHEA:64904
+xref: RHEA:64908
+xref: RHEA:77735
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.5
property_value: skos:exactMatch RHEA:36795
+property_value: skos:narrowMatch RHEA:20988
+property_value: skos:narrowMatch RHEA:64896
+property_value: skos:narrowMatch RHEA:64904
+property_value: skos:narrowMatch RHEA:64908
+property_value: skos:narrowMatch RHEA:77735
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/2473" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -36658,6 +37178,7 @@
xref: MetaCyc:ARGINASE-RXN
xref: Reactome:R-HSA-452036 "arginine + H2O => ornithine + urea [ARG2]"
xref: Reactome:R-HSA-70569 "arginine + H2O => ornithine + urea [ARG1]"
+xref: Reactome:R-HSA-9956512 "ARG1 variants don't synthesize urea and ornithine"
xref: RHEA:20569
is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
property_value: skos:exactMatch EC:3.5.3.1
@@ -36697,6 +37218,7 @@
xref: EC:6.3.4.5
xref: MetaCyc:ARGSUCCINSYN-RXN
xref: Reactome:R-HSA-70577 "ASS1 tetramer:NMRAL1 dimer:NADPH transforms L-Asp and L-Cit to ARSUA"
+xref: Reactome:R-HSA-9956517 "ASS1 variants don't synthesize arginosuccinate"
xref: RHEA:10932
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
property_value: skos:exactMatch EC:6.3.4.5
@@ -36718,6 +37240,7 @@
xref: EC:4.3.2.1
xref: MetaCyc:ARGSUCCINLYA-RXN
xref: Reactome:R-HSA-70573 "argininosuccinate <=> fumarate + arginine"
+xref: Reactome:R-HSA-9956524 "ASL variants don't synthesize fumarate and arginine"
xref: RHEA:24020
is_a: GO:0016842 ! amidine-lyase activity
property_value: skos:exactMatch EC:4.3.2.1
@@ -36783,9 +37306,25 @@
xref: MetaCyc:ARALKYLAMINE-N-ACETYLTRANSFERASE-RXN
xref: Reactome:R-HSA-209792 "N-acetylation of serotonin"
xref: RHEA:20497
+xref: RHEA:25217
+xref: RHEA:51388
+xref: RHEA:66136
+xref: RHEA:66140
+xref: RHEA:66144
+xref: RHEA:66148
+xref: RHEA:66152
+xref: RHEA:66196
is_a: GO:0008080 ! N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.87
property_value: skos:exactMatch RHEA:20497
+property_value: skos:narrowMatch RHEA:25217
+property_value: skos:narrowMatch RHEA:51388
+property_value: skos:narrowMatch RHEA:66136
+property_value: skos:narrowMatch RHEA:66140
+property_value: skos:narrowMatch RHEA:66144
+property_value: skos:narrowMatch RHEA:66148
+property_value: skos:narrowMatch RHEA:66152
+property_value: skos:narrowMatch RHEA:66196
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31077" xsd:anyURI
@@ -36808,12 +37347,16 @@
xref: Reactome:R-HSA-174963 "NAT1 acetylation"
xref: Reactome:R-HSA-174967 "NAT2 acetylation"
xref: Reactome:R-HSA-9753676 "NAT1,2 acetylate APAP-Cys to APAP-Mer"
+xref: RHEA:14241
xref: RHEA:16613
+xref: RHEA:56316
xref: UM-BBD_reactionID:r1333
xref: UM-BBD_reactionID:r1626
is_a: GO:0008080 ! N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.5
property_value: skos:exactMatch RHEA:16613
+property_value: skos:narrowMatch RHEA:14241
+property_value: skos:narrowMatch RHEA:56316
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36866,9 +37409,29 @@
xref: Reactome:R-HSA-176585 "3,5,3'-triiodothyronine + PAPS => 3,5,3'-triiodothyronine 4-sulfate + PAP"
xref: Reactome:R-HSA-176646 "p-nitrophenol + PAPS => p-nitrophenol sulfate + PAP"
xref: RHEA:12164
+xref: RHEA:66548
+xref: RHEA:66572
+xref: RHEA:66576
+xref: RHEA:66580
+xref: RHEA:67876
+xref: RHEA:67888
+xref: RHEA:67892
+xref: RHEA:83343
+xref: RHEA:83351
+xref: RHEA:83575
is_a: GO:0008146 ! sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.1
property_value: skos:exactMatch RHEA:12164
+property_value: skos:narrowMatch RHEA:66548
+property_value: skos:narrowMatch RHEA:66572
+property_value: skos:narrowMatch RHEA:66576
+property_value: skos:narrowMatch RHEA:66580
+property_value: skos:narrowMatch RHEA:67876
+property_value: skos:narrowMatch RHEA:67888
+property_value: skos:narrowMatch RHEA:67892
+property_value: skos:narrowMatch RHEA:83343
+property_value: skos:narrowMatch RHEA:83351
+property_value: skos:narrowMatch RHEA:83575
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36996,7 +37559,6 @@
name: aspartate 1-decarboxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-aspartate = beta-alanine + CO2." [EC:4.1.1.11]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "aspartate alpha-decarboxylase activity" RELATED [EC:4.1.1.11]
synonym: "aspartic alpha-decarboxylase" BROAD [EC:4.1.1.11]
synonym: "L-aspartate 1-carboxy-lyase (beta-alanine-forming)" RELATED [EC:4.1.1.11]
@@ -37009,15 +37571,14 @@
property_value: skos:exactMatch EC:4.1.1.11
property_value: skos:exactMatch MetaCyc:ASPDECARBOX-RXN
property_value: skos:exactMatch RHEA:19497
-property_value: skos:relatedMatch MetaCyc:PWY-5155
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004069
-name: L-aspartate:2-oxoglutarate aminotransferase activity
+name: L-aspartate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate." [EC:2.6.1.1]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate." [RHEA:21824]
synonym: "2-oxoglutarate-glutamate aminotransferase activity" RELATED [EC:2.6.1.1]
synonym: "AAT" RELATED [EC:2.6.1.1]
synonym: "aspartate alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.1]
@@ -37043,6 +37604,7 @@
synonym: "L-aspartate-2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.1]
synonym: "L-aspartate-2-oxoglutarate-transaminase activity" RELATED [EC:2.6.1.1]
synonym: "L-aspartate-alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.1]
+synonym: "L-aspartate:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "L-aspartic aminotransferase activity" BROAD [EC:2.6.1.1]
synonym: "oxaloacetate transferase activity" RELATED [EC:2.6.1.1]
synonym: "oxaloacetate-aspartate aminotransferase activity" RELATED [EC:2.6.1.1]
@@ -37052,16 +37614,16 @@
xref: MetaCyc:ASPAMINOTRANS-RXN
xref: Reactome:R-HSA-70581 "oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]"
xref: Reactome:R-HSA-70592 "PXLP-K259-GOT1 transaminates 2-OG and L-Asp"
-xref: Reactome:R-HSA-70596 "GOT2 dimer deaminates L-Asp"
+xref: Reactome:R-HSA-70596 "GOT2 dimer transaminates L-Asp"
xref: Reactome:R-HSA-70613 "GOT2 transaminates OA and L-Glu"
xref: RHEA:21824
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.1
property_value: skos:exactMatch RHEA:21824
-property_value: skos:relatedMatch MetaCyc:ASPARTATE-DEG1-PWY
-property_value: skos:relatedMatch MetaCyc:ASPARTATESYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004070
@@ -37094,7 +37656,7 @@
id: GO:0004071
name: aspartate-ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + L-aspartate + NH3 = AMP + diphosphate + L-asparagine." [EC:6.3.1.1]
+def: "Catalysis of the reaction: ATP + L-aspartate + NH4+ = AMP + diphosphate + L-asparagine." [RHEA:11372]
synonym: "asparagine synthetase activity" RELATED [EC:6.3.1.1]
synonym: "L-asparagine synthetase activity" RELATED [EC:6.3.1.1]
synonym: "L-aspartate:ammonia ligase (AMP-forming)" RELATED [EC:6.3.1.1]
@@ -37220,6 +37782,15 @@
xref: MetaCyc:6.3.4.11-RXN
xref: MetaCyc:6.3.4.9-RXN
xref: MetaCyc:BIOTINLIG-RXN
+xref: Reactome:R-HSA-2993447 "HLCS biotinylates 6x(PCCA:PCCB)"
+xref: Reactome:R-HSA-2993799 "HLCS biotinylates 6xMCCC1:6xMCCC2"
+xref: Reactome:R-HSA-2993802 "HLCS biotinylates PC:Mn2+"
+xref: Reactome:R-HSA-2993814 "HLCS biotinylates ACACA:Mn2+"
+xref: Reactome:R-HSA-3323184 "Defective HLCS does not biotinylate ACACA:Mn2+"
+xref: Reactome:R-HSA-4167511 "HLCS biotinylates ACACB"
+xref: Reactome:R-HSA-9035987 "Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2"
+xref: Reactome:R-HSA-9035988 "Defective HLCS does not biotinylate PC:Mn2+"
+xref: Reactome:R-HSA-9035990 "Defective HLCS does not biotinylate 6x(PCCA:PCCB)"
xref: RHEA:11204
xref: RHEA:11756
xref: RHEA:23668
@@ -37341,12 +37912,13 @@
[Term]
id: GO:0004084
-name: branched-chain-amino-acid transaminase activity
+name: branched-chain-amino-acid:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: a branched-chain amino acid (L-leucine, L-isoleucine and L-valine) + 2-oxoglutarate = L-glutamate + a 2-oxocarboxylate derived from the branched-chain amino acid." [EC:2.6.1.42]
synonym: "branched-chain amino acid aminotransferase activity" EXACT []
synonym: "branched-chain amino acid-glutamate transaminase activity" RELATED [EC:2.6.1.42]
synonym: "branched-chain aminotransferase activity" RELATED [EC:2.6.1.42]
+synonym: "branched-chain-amino-acid transaminase activity" EXACT []
synonym: "branched-chain-amino-acid:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.42]
synonym: "glutamate-branched-chain amino acid transaminase activity" RELATED [EC:2.6.1.42]
synonym: "L-branched chain amino acid aminotransferase activity" RELATED [EC:2.6.1.42]
@@ -37356,9 +37928,10 @@
xref: Reactome:R-HSA-508189 "a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT1]"
xref: Reactome:R-HSA-70723 "leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT1]"
xref: Reactome:R-HSA-70724 "leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT2]"
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.42
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004085
@@ -37406,6 +37979,7 @@
xref: KEGG_REACTION:R00149
xref: MetaCyc:RXN-13202
xref: Reactome:R-HSA-70555 "2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]"
+xref: Reactome:R-HSA-9955543 "CPS1 variants don't synthesize carbamoyl phosphate"
xref: RHEA:18029
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
property_value: skos:exactMatch EC:6.3.4.16
@@ -37493,11 +38067,93 @@
xref: EC:1.1.1.184
xref: MetaCyc:CARBONYL-REDUCTASE-NADPH-RXN
xref: Reactome:R-HSA-8937419 "CBR3 reduces DOX to DOXOL"
+xref: RHEA:10724
+xref: RHEA:12212
+xref: RHEA:13829
+xref: RHEA:16321
+xref: RHEA:16817
+xref: RHEA:18941
xref: RHEA:19257
+xref: RHEA:25960
+xref: RHEA:31891
+xref: RHEA:32339
+xref: RHEA:32619
+xref: RHEA:35607
+xref: RHEA:36587
+xref: RHEA:42500
+xref: RHEA:42768
+xref: RHEA:45116
+xref: RHEA:47540
+xref: RHEA:53820
+xref: RHEA:62068
+xref: RHEA:62216
+xref: RHEA:62268
+xref: RHEA:63476
+xref: RHEA:63480
+xref: RHEA:63504
+xref: RHEA:64416
+xref: RHEA:65056
+xref: RHEA:65060
+xref: RHEA:65496
+xref: RHEA:68136
+xref: RHEA:68140
+xref: RHEA:68144
+xref: RHEA:68148
+xref: RHEA:70215
+xref: RHEA:70219
+xref: RHEA:74707
+xref: RHEA:81575
+xref: RHEA:81583
+xref: RHEA:81719
+xref: RHEA:82231
+xref: RHEA:84223
+xref: RHEA:85047
+xref: RHEA:85103
is_a: GO:0008106 ! alcohol dehydrogenase (NADP+) activity
property_value: skos:exactMatch EC:1.1.1.184
property_value: skos:exactMatch MetaCyc:CARBONYL-REDUCTASE-NADPH-RXN
property_value: skos:exactMatch RHEA:19257
+property_value: skos:narrowMatch RHEA:10724
+property_value: skos:narrowMatch RHEA:12212
+property_value: skos:narrowMatch RHEA:13829
+property_value: skos:narrowMatch RHEA:16321
+property_value: skos:narrowMatch RHEA:16817
+property_value: skos:narrowMatch RHEA:18941
+property_value: skos:narrowMatch RHEA:25960
+property_value: skos:narrowMatch RHEA:31891
+property_value: skos:narrowMatch RHEA:32339
+property_value: skos:narrowMatch RHEA:32619
+property_value: skos:narrowMatch RHEA:35607
+property_value: skos:narrowMatch RHEA:36587
+property_value: skos:narrowMatch RHEA:42500
+property_value: skos:narrowMatch RHEA:42768
+property_value: skos:narrowMatch RHEA:45116
+property_value: skos:narrowMatch RHEA:47540
+property_value: skos:narrowMatch RHEA:53820
+property_value: skos:narrowMatch RHEA:62068
+property_value: skos:narrowMatch RHEA:62216
+property_value: skos:narrowMatch RHEA:62268
+property_value: skos:narrowMatch RHEA:63476
+property_value: skos:narrowMatch RHEA:63480
+property_value: skos:narrowMatch RHEA:63504
+property_value: skos:narrowMatch RHEA:64416
+property_value: skos:narrowMatch RHEA:65056
+property_value: skos:narrowMatch RHEA:65060
+property_value: skos:narrowMatch RHEA:65496
+property_value: skos:narrowMatch RHEA:68136
+property_value: skos:narrowMatch RHEA:68140
+property_value: skos:narrowMatch RHEA:68144
+property_value: skos:narrowMatch RHEA:68148
+property_value: skos:narrowMatch RHEA:70215
+property_value: skos:narrowMatch RHEA:70219
+property_value: skos:narrowMatch RHEA:74707
+property_value: skos:narrowMatch RHEA:81575
+property_value: skos:narrowMatch RHEA:81583
+property_value: skos:narrowMatch RHEA:81719
+property_value: skos:narrowMatch RHEA:82231
+property_value: skos:narrowMatch RHEA:84223
+property_value: skos:narrowMatch RHEA:85047
+property_value: skos:narrowMatch RHEA:85103
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28530" xsd:anyURI
[Term]
@@ -37552,7 +38208,6 @@
xref: EC:2.3.1.21
xref: MetaCyc:CARNITINE-O-PALMITOYLTRANSFERASE-RXN
xref: Reactome:R-HSA-200406 "CPT1A transfers PALM to CAR"
-xref: Reactome:R-HSA-200410 "CPT2 converts palmitoyl carnitine to palmitoyl-CoA"
xref: Reactome:R-HSA-9911362 "CPT1B transfers PALM to CAR"
xref: RHEA:12661
is_a: GO:0016406 ! carnitine O-acyltransferase activity
@@ -37567,7 +38222,7 @@
namespace: molecular_function
alt_id: GO:0016952
alt_id: GO:0016953
-def: "Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O." [EC:1.11.1.6]
+def: "Catalysis of the reaction: 2 H2O2 = O2 + 2 H2O." [EC:1.11.1.6]
synonym: "bacterial catalase-peroxidase activity" NARROW []
synonym: "caperase activity" RELATED [EC:1.11.1.6]
synonym: "CAT" RELATED [EC:1.11.1.6]
@@ -37613,6 +38268,10 @@
xref: EC:1.10.3.1
xref: MetaCyc:CATECHOL-OXIDASE-RXN
xref: MetaCyc:RXN-13061
+xref: Reactome:R-HSA-5662662 "Tyrosinase oxidises tyrosine to dopaquinone"
+xref: Reactome:R-HSA-5662692 "Dopa is oxidized to dopaquinone by TYR"
+xref: Reactome:R-HSA-5663050 "DHI and DHICA polymerize forming eumelanin"
+xref: Reactome:R-HSA-8878581 "TYRP1 oxidises DHICA to IQCA"
xref: RHEA:21632
is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016682 ! oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
@@ -37867,7 +38526,6 @@
name: creatine kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H+." [EC:2.7.3.2, RHEA:17157]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "adenosine triphosphate-creatine transphosphorylase activity" RELATED [EC:2.7.3.2]
synonym: "ATP:creatine N-phosphotransferase activity" RELATED [EC:2.7.3.2]
synonym: "ATP:creatine phosphotransferase activity" RELATED [EC:2.7.3.2]
@@ -37894,9 +38552,9 @@
is_a: GO:0016775 ! phosphotransferase activity, nitrogenous group as acceptor
property_value: skos:exactMatch EC:2.7.3.2
property_value: skos:exactMatch RHEA:17157
-property_value: skos:relatedMatch MetaCyc:PWY-6158
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004112
@@ -37925,9 +38583,17 @@
xref: EC:3.1.4.37
xref: MetaCyc:3.1.4.37-RXN
xref: RHEA:14489
+xref: RHEA:37191
+xref: RHEA:37211
+xref: RHEA:37239
+xref: RHEA:41956
is_a: GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
property_value: skos:exactMatch EC:3.1.4.37
property_value: skos:exactMatch RHEA:14489
+property_value: skos:narrowMatch RHEA:37191
+property_value: skos:narrowMatch RHEA:37211
+property_value: skos:narrowMatch RHEA:37239
+property_value: skos:narrowMatch RHEA:41956
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -37956,9 +38622,13 @@
xref: MetaCyc:3.1.4.17-RXN
xref: Reactome:R-HSA-162425 "p-S295-PDE3B hydrolyses cAMP to AMP"
xref: RHEA:14653
+xref: RHEA:70575
+xref: RHEA:72675
is_a: GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
property_value: skos:exactMatch EC:3.1.4.17
property_value: skos:exactMatch RHEA:14653
+property_value: skos:narrowMatch RHEA:70575
+property_value: skos:narrowMatch RHEA:72675
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -38210,19 +38880,20 @@
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
+is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
property_value: skos:exactMatch EC:7.1.1.9
property_value: skos:exactMatch RHEA:11436
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20924" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
[Term]
id: GO:0004130
name: cytochrome-c peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 ferrocytochrome c + hydrogen peroxide = 2 ferricytochrome c + 2 H2O." [EC:1.11.1.5]
+def: "Catalysis of the reaction: 2 ferrocytochrome c + H2O2 = 2 ferricytochrome c + 2 H2O." [EC:1.11.1.5]
synonym: "apocytochrome c peroxidase activity" RELATED [EC:1.11.1.5]
synonym: "cytochrome c peroxidase activity" RELATED [EC:1.11.1.5]
synonym: "cytochrome c-551 peroxidase activity" RELATED [EC:1.11.1.5]
@@ -38244,7 +38915,7 @@
id: GO:0004131
name: cytosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cytosine + H2O = uracil + NH3." [EC:3.5.4.1]
+def: "Catalysis of the reaction: cytosine + H2O = uracil + NH4+." [RHEA:20605]
synonym: "cytosine aminohydrolase activity" RELATED [EC:3.5.4.1]
synonym: "isocytosine deaminase activity" RELATED [EC:3.5.4.1]
xref: EC:3.5.4.1
@@ -38260,7 +38931,7 @@
id: GO:0004132
name: dCMP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dCMP + H2O = dUMP + NH3." [EC:3.5.4.12]
+def: "Catalysis of the reaction: dCMP + H2O = dUMP + NH4+." [RHEA:22924]
synonym: "dCMP aminohydrolase activity" RELATED [EC:3.5.4.12]
synonym: "deoxy-CMP-deaminase activity" RELATED [EC:3.5.4.12]
synonym: "deoxycytidine monophosphate deaminase activity" RELATED [EC:3.5.4.12]
@@ -38364,9 +39035,13 @@
xref: EC:2.7.1.74
xref: MetaCyc:DEOXYCYTIDINE-KINASE-RXN
xref: RHEA:20061
+xref: RHEA:46036
+xref: RHEA:46040
is_a: GO:0019136 ! deoxynucleoside kinase activity
property_value: skos:exactMatch EC:2.7.1.74
property_value: skos:exactMatch RHEA:20061
+property_value: skos:narrowMatch RHEA:46036
+property_value: skos:narrowMatch RHEA:46040
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -38472,10 +39147,24 @@
xref: Reactome:R-HSA-1482961 "CDP-Cho and DAG are converted to PC by CEPT1 at the ER membrane"
xref: Reactome:R-HSA-1482973 "CDP-Cho and DAG are converted to PC by CHPT1 at the Golgi membrane"
xref: RHEA:32939
+xref: RHEA:54232
+xref: RHEA:54236
+xref: RHEA:54240
+xref: RHEA:54244
+xref: RHEA:54332
+xref: RHEA:54336
+xref: RHEA:54344
is_a: GO:0017169 ! CDP-alcohol phosphatidyltransferase activity
relationship: part_of GO:0006657 ! CDP-choline pathway
property_value: skos:exactMatch EC:2.7.8.2
property_value: skos:exactMatch RHEA:32939
+property_value: skos:narrowMatch RHEA:54232
+property_value: skos:narrowMatch RHEA:54236
+property_value: skos:narrowMatch RHEA:54240
+property_value: skos:narrowMatch RHEA:54244
+property_value: skos:narrowMatch RHEA:54332
+property_value: skos:narrowMatch RHEA:54336
+property_value: skos:narrowMatch RHEA:54344
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -38491,10 +39180,26 @@
xref: MetaCyc:DIACYLGLYKIN-RXN
xref: Reactome:R-HSA-426240 "DAG kinase produces phosphatidic acid from DAG"
xref: RHEA:10272
+xref: RHEA:40323
+xref: RHEA:40327
+xref: RHEA:40335
+xref: RHEA:40359
+xref: RHEA:43416
+xref: RHEA:43424
+xref: RHEA:43428
+xref: RHEA:63324
is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.107
property_value: skos:exactMatch RHEA:10272
+property_value: skos:narrowMatch RHEA:40323
+property_value: skos:narrowMatch RHEA:40327
+property_value: skos:narrowMatch RHEA:40335
+property_value: skos:narrowMatch RHEA:40359
+property_value: skos:narrowMatch RHEA:43416
+property_value: skos:narrowMatch RHEA:43424
+property_value: skos:narrowMatch RHEA:43428
+property_value: skos:narrowMatch RHEA:63324
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25280" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -38516,9 +39221,19 @@
xref: Reactome:R-HSA-75900 "1,2-diacyl-glycerol + acyl-CoA => triacylglycerol + CoASH [DGAT1]"
xref: Reactome:R-HSA-8848580 "DGAT2L6,L7P transfer acyl group from acyl-CoA to DAG, forming TAG"
xref: RHEA:10868
+xref: RHEA:38163
+xref: RHEA:38219
+xref: RHEA:38299
+xref: RHEA:38307
+xref: RHEA:56536
is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.20
property_value: skos:exactMatch RHEA:10868
+property_value: skos:narrowMatch RHEA:38163
+property_value: skos:narrowMatch RHEA:38219
+property_value: skos:narrowMatch RHEA:38299
+property_value: skos:narrowMatch RHEA:38307
+property_value: skos:narrowMatch RHEA:56536
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -38545,9 +39260,19 @@
xref: Reactome:R-HSA-351207 "Spermine => N-acetylated spermine"
xref: Reactome:R-HSA-351208 "Spermidine => N-acetylated spermidine"
xref: RHEA:11116
+xref: RHEA:25181
+xref: RHEA:28150
+xref: RHEA:28270
+xref: RHEA:79547
+xref: RHEA:79551
is_a: GO:0008080 ! N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.57
property_value: skos:exactMatch RHEA:11116
+property_value: skos:narrowMatch RHEA:25181
+property_value: skos:narrowMatch RHEA:28150
+property_value: skos:narrowMatch RHEA:28270
+property_value: skos:narrowMatch RHEA:79547
+property_value: skos:narrowMatch RHEA:79551
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30342" xsd:anyURI
[Term]
@@ -38654,7 +39379,6 @@
synonym: "succinyl-CoA:enzyme-N6-(dihydrolipoyl)lysine S-succinyltransferase activity" RELATED [EC:2.3.1.61]
xref: EC:2.3.1.61
xref: Reactome:R-HSA-9853512 "DLST transfers succinyl to CoA"
-xref: Reactome:R-HSA-9858590 "DLST transfers glutaryl to CoA"
xref: RHEA:15213
is_a: GO:0016751 ! S-succinyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -38718,7 +39442,7 @@
id: GO:0004153
name: dihydropterin deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydropterin + H2O = 7,8-dihydrolumazine + NH3." [GOC:jl, PMID:19567870, PMID:38786926]
+def: "Catalysis of the reaction: 7,8-dihydropterin + H2O = 7,8-dihydrolumazine + NH4+." [GOC:jl, PMID:19567870, PMID:38786926]
xref: MetaCyc:RXN-15261
is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
@@ -38975,8 +39699,12 @@
xref: Reactome:R-HSA-109338 "Isomerization of cis,cis-3,6-Dodecadienoyl-CoA to form trans,cis-Lauro-2,6-dienoyl-CoA"
xref: Reactome:R-HSA-6809808 "ECI2 isomerizes 3Z-enoyl-CoA to 2E-enoyl-CoA"
xref: RHEA:23716
+xref: RHEA:29847
xref: RHEA:45228
+xref: RHEA:45748
xref: RHEA:45900
+xref: RHEA:46044
+xref: RHEA:77195
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
property_value: skos:exactMatch EC:5.3.3.8
property_value: skos:exactMatch RHEA:45900
@@ -38984,7 +39712,11 @@
property_value: skos:narrowMatch MetaCyc:RXN-7836
property_value: skos:narrowMatch MetaCyc:RXN-7931
property_value: skos:narrowMatch RHEA:23716
+property_value: skos:narrowMatch RHEA:29847
property_value: skos:narrowMatch RHEA:45228
+property_value: skos:narrowMatch RHEA:45748
+property_value: skos:narrowMatch RHEA:46044
+property_value: skos:narrowMatch RHEA:77195
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21637" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -39039,6 +39771,7 @@
xref: EC:5.3.3.12
xref: KEGG_REACTION:R03673
xref: MetaCyc:DOPACHROME-DELTA-ISOMERASE-RXN
+xref: Reactome:R-HSA-5662660 "Dopachrome is transformed to DHICA by DCT"
xref: RHEA:13041
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
property_value: skos:exactMatch EC:5.3.3.12
@@ -39080,6 +39813,7 @@
xref: Reactome:R-HSA-5615556 "Defective POMT2 does not transfer Man from Dol-P-Man to DAG1"
xref: Reactome:R-HSA-5615604 "Defective POMT1 does not transfer Man from Dol-P-Man to DAG1"
xref: Reactome:R-HSA-5615637 "POMT1:POMT2 transfers Man from Dol-P-Man to DAG1(30-653)"
+xref: Reactome:R-HSA-9816277 "CDH1 is O-manosylated"
is_a: GO:0000030 ! mannosyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
relationship: part_of GO:0035269 ! protein O-linked glycosylation via mannose
@@ -39207,7 +39941,7 @@
xref: Reactome:R-HSA-353125 "26S proteosome degrades ODC holoenzyme complex"
xref: Reactome:R-HSA-3640874 "Ub-RibC-AXIN is degraded by the proteasome"
xref: Reactome:R-HSA-3928656 "gamma-secretase cleaves EPHB2"
-xref: Reactome:R-HSA-450466 "AUF1:mRNA complex is destroyed"
+xref: Reactome:R-HSA-450466 "AUF1:mRNA complex is degraded"
xref: Reactome:R-HSA-4608855 "PRICKLE1 is degraded by the proteasome"
xref: Reactome:R-HSA-4641256 "Ubiquitinated AXIN is degraded by the proteasome"
xref: Reactome:R-HSA-4641260 "Ubiquitinated DVL1 is degraded by the proteasome"
@@ -39256,7 +39990,9 @@
xref: Reactome:R-HSA-9614271 "Autocleavage of ADGRG6"
xref: Reactome:R-HSA-9755303 "26S proteasome degrades HIFalpha"
xref: Reactome:R-HSA-9755306 "ub UBXN7 is degraded by the 26S proteasome"
+xref: Reactome:R-HSA-9760521 "Unknown peptidase cleaves pro-STa"
xref: Reactome:R-HSA-9762096 "Ub,pS335,S338,T NFE2L2 is degraded"
+xref: Reactome:R-HSA-9766223 "Proteasome-dependent degradation of ubiquitinated CDH1"
xref: Reactome:R-HSA-983150 "Proteasomal cleavage of substrate"
xref: Reactome:R-HSA-983158 "Trimming of peptides in ER"
xref: Reactome:R-HSA-9839376 "TGFBR3(784-851) degradation"
@@ -39265,6 +40001,18 @@
xref: Reactome:R-HSA-9908105 "Maturation of the 20S immunoproteasome core particle"
xref: Reactome:R-HSA-9908108 "Maturation of the 20S thymoproteasome core particle"
xref: Reactome:R-HSA-9908780 "Maturation of the preholospermatoproteasome"
+xref: Reactome:R-HSA-9912636 "Proteasomal cleavage of intracellular substrate (PA28-alpha-beta-20S proteasome catalyst)"
+xref: Reactome:R-HSA-9912655 "Proteasomal cleavage of intracellular substrate (immunoproteasome catalyst)"
+xref: Reactome:R-HSA-9912747 "Proteasomal clevage of exogenous antigen (immunoproteasome catalyst)"
+xref: Reactome:R-HSA-9912751 "Proteasomal cleavage of partially digested antigen (immunoproteasome catalyst)"
+xref: Reactome:R-HSA-9929352 "Ubiquitinated CD274 is degraded by the 26S proteasome"
+xref: Reactome:R-HSA-9929486 "SPOP-mediated degradation of CD274 by 26S Proteosome"
+xref: Reactome:R-HSA-9931314 "Proteasomal degradation of polyUb-p-S195-CD274"
+xref: Reactome:R-HSA-9934884 "Proteolysis of K48polyUb,p-S-CRY1,2"
+xref: Reactome:R-HSA-9934887 "Proteolysis of K48polyUb-K107,p-S-CRY1,K48polyUb-K126,p-S-CRY2"
+xref: Reactome:R-HSA-9934893 "Proteolysis of K48polyUb-K,p-S-PER1,2,3"
+xref: Reactome:R-HSA-9949676 "The proteasome degrades the alanine-tailed K48-polyUb nascent peptide bound to LTN1:NEMF:TCF25:VCP hexamer"
+xref: Reactome:R-HSA-9954728 "The proteasome degrades the K48-polyubiquitinated alanine-tailed nascent peptide"
is_a: GO:0008233 ! peptidase activity
property_value: skos:narrowMatch EC:3.4.99.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25813" xsd:anyURI
@@ -39384,14 +40132,15 @@
xref: MetaCyc:CARBOXYPEPTIDASE-A-RXN
xref: MetaCyc:GLY-X-CARBOXYPEPTIDASE-RXN
xref: MetaCyc:LYSINEARGININE-CARBOXYPEPTIDASE-RXN
-xref: Reactome:R-HSA-2022378 "ACE2(18-805):Zn2+ hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-9)"
-xref: Reactome:R-HSA-2022379 "ACE2(18-805):Zn2+ hydrolyzes Angiotensin-(1-8) to Angiotensin-(1-7)"
-xref: Reactome:R-HSA-2028294 "Mast Cell Carboxypeptidase hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-9)"
+xref: Reactome:R-HSA-2022378 "ACE2(18-805):Zn2+ hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-33) (Angiotensin-(1-9))"
+xref: Reactome:R-HSA-2022379 "ACE2(18-805):Zn2+ hydrolyzes AGT(25-32) (Angiotensin-(1-8)) to AGT(25-31) (Angiotensin-(1-7))"
+xref: Reactome:R-HSA-2028294 "Mast Cell Carboxypeptidase hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-33) (Angiotensin-(1-9))"
xref: Reactome:R-HSA-8852809 "CPN, CPB2 cleave C3a, C5a"
xref: Reactome:R-HSA-8866105 "CCPs deglutamylate tubulin"
xref: Reactome:R-HSA-8955712 "SVBP:VASH1,VASH2 hydrolyzes the terminal L-Tyr residue from alphaY-beta tubulin dimer"
xref: Reactome:R-HSA-9023159 "Carboxypeptidase E hydrolyzes Insulin(57-89) to yield C-peptide (Insulin(57-87))"
xref: Reactome:R-HSA-9023163 "Carboxypeptidase E cleaves Insulin(25-56) to yield Insulin(25-54)"
+xref: Reactome:R-HSA-9944488 "ACE2:Zn2+ cleaves 1-Ala-AGT(25-32) to yield Alamandine (1-Ala-AGT(25-31)"
is_a: GO:0004180 ! carboxypeptidase activity
is_a: GO:0008235 ! metalloexopeptidase activity
property_value: skos:exactMatch EC:3.4.17.-
@@ -39606,9 +40355,9 @@
xref: MetaCyc:3.4.23.5-RXN
xref: Reactome:R-HSA-157353 "NEXT1 is cleaved to produce NICD1"
xref: Reactome:R-HSA-157640 "NEXT2 is cleaved to produce NICD2"
-xref: Reactome:R-HSA-2022403 "Renin:Prorenin Receptor hydrolyzes Angiotensinogen to Angiotensin-(1-10)"
-xref: Reactome:R-HSA-2022412 "Renin hydrolyzes Angiotensinogen to Angiotensin-(1-10)"
-xref: Reactome:R-HSA-2065357 "Prorenin:Prorenin Receptor hydrolyzes Angiotensinogen to Angiotensin-(1-10)"
+xref: Reactome:R-HSA-2022403 "Renin:Prorenin Receptor hydrolyzes Angiotensinogen to AGT(25-34) (Angiotensin-(1-10))"
+xref: Reactome:R-HSA-2022412 "Renin hydrolyzes Angiotensinogen to AGT(25-34) (Angiotensin-(1-10))"
+xref: Reactome:R-HSA-2065357 "Prorenin:Prorenin Receptor hydrolyzes Angiotensinogen to AGT(25-35) (Angiotensin-(1-10))"
xref: Reactome:R-HSA-2220988 "NEXT1 PEST domain mutants are cleaved to produce NICD1 PEST domain mutants"
xref: Reactome:R-HSA-373705 "Caspase cleavage of DCC"
xref: Reactome:R-HSA-9013361 "NEXT3 is cleaved to produce NICD3"
@@ -39807,7 +40556,7 @@
xref: Reactome:R-HSA-264865 "Caspase-mediated cleavage of Lamin A"
xref: Reactome:R-HSA-264871 "Caspase-mediated cleavage of Lamin B1"
xref: Reactome:R-HSA-3465448 "Caspase-8 and FLIP(L) processing at DISC"
-xref: Reactome:R-HSA-350158 "LGMN degrades GC"
+xref: Reactome:R-HSA-350158 "LGMN hydrolyzes GC, releasing CUBN and 25(OH)D"
xref: Reactome:R-HSA-350318 "Caspase-mediated cleavage of vimentin at TNLD (429)"
xref: Reactome:R-HSA-350319 "Caspase mediated cleavage of vimentin at IDVD (259)"
xref: Reactome:R-HSA-350651 "Caspase-mediated cleavage of MASK"
@@ -39829,6 +40578,7 @@
xref: Reactome:R-HSA-5660663 "Caspase-8 cleaves IL1B precursor"
xref: Reactome:R-HSA-5681987 "LC3 is cleaved by ATG4"
xref: Reactome:R-HSA-5682377 "LC3 de-lipidation by ATG4"
+xref: Reactome:R-HSA-6800797 "The PIDDosome activates CASP2"
xref: Reactome:R-HSA-6814387 "CASP14 cleaves filaggrin"
xref: Reactome:R-HSA-9012556 "IL37:2x(CASP1(120-197):CASP1(317-404)) cleaves IL37"
xref: Reactome:R-HSA-9013895 "Caspase-8 processing within TLR3 complex"
@@ -39855,10 +40605,21 @@
xref: Reactome:R-HSA-9694625 "nsp3 cleaves nsp1-4"
xref: Reactome:R-HSA-9694732 "3CLp cleaves pp1ab"
xref: Reactome:R-HSA-9697750 "RIPK1 is cleaved by CASP8:FLIP(L)"
-xref: Reactome:R-HSA-9710101 "CASP4, CASP5 cleave GSDMD"
xref: Reactome:R-HSA-9729704 "SARS-CoV-2 3CLpro dimer cleaves TAB1"
xref: Reactome:R-HSA-9729730 "SARS-CoV-2 nsp3 cleaves IRF3"
xref: Reactome:R-HSA-9729741 "SARS-CoV-2 3CLpro dimer cleaves NLRP12"
+xref: Reactome:R-HSA-9792568 "CTSL1 cleaves proHPSE"
+xref: Reactome:R-HSA-9947849 "CASP5 autocatalysis on LPS micelles"
+xref: Reactome:R-HSA-9947861 "CASP4 autocatalysis on LPS micelles"
+xref: Reactome:R-HSA-9947908 "CASP4 autocatalysis on the bacterial surface"
+xref: Reactome:R-HSA-9947978 "CASP5 cleaves IL18 at D36"
+xref: Reactome:R-HSA-9947987 "CASP4 cleaves IL18 at D36"
+xref: Reactome:R-HSA-9947997 "CASP5 cleaves GSDMD"
+xref: Reactome:R-HSA-9948146 "CASP4 cleaves GSDMD"
+xref: Reactome:R-HSA-9956714 "CASP1 cleaves GBP1"
+xref: Reactome:R-HSA-9958657 "CASP4 cleaves IL1B at D27"
+xref: Reactome:R-HSA-9960522 "CASP5 cleaves IL1B at D27"
+xref: Reactome:R-HSA-9960526 "CASP4 cleaves IL1B at D116"
is_a: GO:0004175 ! endopeptidase activity
is_a: GO:0008234 ! cysteine-type peptidase activity
property_value: skos:exactMatch EC:3.4.22.-
@@ -40113,7 +40874,7 @@
id: GO:0004219
name: obsolete pyroglutamyl-peptidase I activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: pyroglutamyl-peptide + H2O = pyroglutamate + peptide." [GOC:curator]
+def: "OBSOLETE. Catalysis of the reaction: pyroglutamyl-peptide + H2O = pyroglutamate + peptide." [GOC:curators]
comment: This term was made obsolete because it represents a gene product.
synonym: "pyroglutamyl-peptidase I activity" EXACT []
is_obsolete: true
@@ -40283,6 +41044,7 @@
xref: Reactome:R-HSA-8949649 "PMPCA:PMPCB cleaves the transit peptide of proSMDT1 (proEMRE)"
xref: Reactome:R-HSA-8949659 "AFG3L2 (m-AAA protease) degrades SMDT1 that is not assembled in MCU"
xref: Reactome:R-HSA-8949668 "YME1L1 proteolyzes unassembled proSMDT1"
+xref: Reactome:R-HSA-9010034 "ADAM10:Zn2+:TSPANs cleaves APP(18-770)"
xref: Reactome:R-HSA-9624272 "MMPs cleave HB-EGF"
xref: Reactome:R-HSA-9822532 "ADAMTS13 cleaves VWF multimer"
xref: Reactome:R-HSA-9824402 "ADAMTS13 variant does not cleave VWF multimer"
@@ -40604,7 +41366,7 @@
id: GO:0004245
name: obsolete neprilysin activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the preferential cleavage at the amino group of hydrophobic residues in insulin, casein, hemoglobin, and a number of other proteins and polypeptides." [GOC:curator]
+def: "OBSOLETE. Catalysis of the preferential cleavage at the amino group of hydrophobic residues in insulin, casein, hemoglobin, and a number of other proteins and polypeptides." [GOC:curators]
comment: This term was made obsolete because it represents a gene product.
synonym: "acute lymphoblastic leukemia antigen" RELATED []
synonym: "CALLA" RELATED []
@@ -40765,7 +41527,7 @@
xref: Reactome:R-HSA-139893 "Granzyme-B activates BID by cleavage"
xref: Reactome:R-HSA-140599 "factor XIII -> factor XIII cleaved tetramer + 2 factor XIII A activation peptides"
xref: Reactome:R-HSA-140664 "prothrombin -> activated thrombin (factor IIa) + thrombin activation peptide (prothrombinase catalyst)"
-xref: Reactome:R-HSA-140696 "factor V -> factor Va + factor V activation peptide"
+xref: Reactome:R-HSA-140696 "factor V -> factor Va + factor V activation peptide (thrombin catalyst)"
xref: Reactome:R-HSA-140700 "prothrombin -> activated thrombin (factor IIa) + thrombin activation peptide (Xa catalyst)"
xref: Reactome:R-HSA-140736 "factor X -> factor Xa + factor X activation peptide (TF:F7a catalyst)"
xref: Reactome:R-HSA-140769 "factor VII -> factor VIIa"
@@ -40845,7 +41607,7 @@
xref: Reactome:R-HSA-187020 "Part of pro-beta-NGF is processed to mature beta-NGF"
xref: Reactome:R-HSA-1912369 "NOTCH precursor cleaved to form mature NOTCH"
xref: Reactome:R-HSA-1912372 "Fringe-modified Pre-NOTCH is cleaved by FURIN"
-xref: Reactome:R-HSA-2022411 "Cathepsin G hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
+xref: Reactome:R-HSA-2022411 "Cathepsin G hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-32) (Angiotensin-(1-8))"
xref: Reactome:R-HSA-2129357 "Fibrillin C-terminal processing"
xref: Reactome:R-HSA-2168923 "Collagen type XVIII endostatin release"
xref: Reactome:R-HSA-2168960 "Collagen type XVII ectodomain shedding"
@@ -40860,6 +41622,7 @@
xref: Reactome:R-HSA-2534206 "E-cadherin degradation by PS1:NCSTN (Gamma-secretase)"
xref: Reactome:R-HSA-2534260 "E-cadherin degradation by caspase-3 and calpain-1"
xref: Reactome:R-HSA-265301 "Corticotropin cleavage from POMC"
+xref: Reactome:R-HSA-3244626 "DENV protease NS2B3 cleaves STING"
xref: Reactome:R-HSA-3266557 "Factor I cleaves iC3b"
xref: Reactome:R-HSA-3785684 "Fibronectin degradation by CTSG"
xref: Reactome:R-HSA-3788061 "Fibronectin degradation by ADAM8"
@@ -40936,11 +41699,34 @@
xref: Reactome:R-HSA-9770187 "S2 Cleavage by TMPRSS2 Exposes S2' Initiating Cell-Cell Fusion"
xref: Reactome:R-HSA-977371 "Factor I inactivates Factor H-boundC3b"
xref: Reactome:R-HSA-977615 "Factor I inactivates MCP/CR1-bound C4b/C3b"
+xref: Reactome:R-HSA-9816275 "CDH1 is proteolytically cleaved in Golgi"
xref: Reactome:R-HSA-9829030 "Nascent F signal peptide is cleaved at ER membrane"
xref: Reactome:R-HSA-9829200 "F0 is cleaved, releasing F1, F2, F(110-136)"
xref: Reactome:R-HSA-9830805 "Nascent sG localizes to ER lumen, gets glycosylated"
xref: Reactome:R-HSA-9830882 "Nascent G signal peptide is cleaved at ER membrane"
xref: Reactome:R-HSA-9839367 "TGFBR3_mem cleavage by MMPs"
+xref: Reactome:R-HSA-9911236 "ELANE cleaves NOTCH2NLA"
+xref: Reactome:R-HSA-9911383 "LepB cleaves prepro-STa"
+xref: Reactome:R-HSA-9912368 "LepB cleaves pre-EltA"
+xref: Reactome:R-HSA-9912371 "LepB cleaves pre-EltB"
+xref: Reactome:R-HSA-9913329 "Autoproteolysis of DAG1 to alpha and beta chains"
+xref: Reactome:R-HSA-9918772 "Dengue polyprotein cis-auto-cleaves"
+xref: Reactome:R-HSA-9918780 "Unknown peptidase cleaves NS1-NS2A"
+xref: Reactome:R-HSA-9918787 "NS2B3 cleaves C-prM-E-NS1-NS2A"
+xref: Reactome:R-HSA-9918795 "Signalase cleaves prM-E-NS1-NS2A"
+xref: Reactome:R-HSA-9918813 "NS2B3 cleaves NS4AB"
+xref: Reactome:R-HSA-9918817 "NS2B3 cleaves polyprotein"
+xref: Reactome:R-HSA-9918823 "NS345:NS2B cleaves NS345"
+xref: Reactome:R-HSA-9918871 "Signalase cleaves prepro-NS4B"
+xref: Reactome:R-HSA-9918876 "NS2B3 cleaves prepro-C at the C-prM junction"
+xref: Reactome:R-HSA-9919050 "Furin cleaves prM:E"
+xref: Reactome:R-HSA-9921595 "NS2B3 cleaves FAM134B"
+xref: Reactome:R-HSA-9921689 "NS3 cleaves GrpEL1"
+xref: Reactome:R-HSA-9926936 "EspC(54-1018) cleaves hemoglobin"
+xref: Reactome:R-HSA-9926963 "Hbp cis-autocleaves"
+xref: Reactome:R-HSA-9927009 "Hbp(53-1100) cleaves hemoglobin"
+xref: Reactome:R-HSA-9932162 "Removal of CDH1 signal peptide"
+xref: Reactome:R-HSA-9947496 "ACOT2 cleaves NS345"
is_a: GO:0004175 ! endopeptidase activity
is_a: GO:0008236 ! serine-type peptidase activity
property_value: skos:exactMatch EC:3.4.21.-
@@ -41494,9 +42280,39 @@
xref: Reactome:R-HSA-9915986 "11,12-EET is hydrolysed to 11,12-DHET by EPHX2"
xref: Reactome:R-HSA-9915994 "14,15-EET is hydrolysed to 14,15-DHET by EPHX2"
xref: RHEA:19037
+xref: RHEA:44032
+xref: RHEA:44036
+xref: RHEA:44040
+xref: RHEA:44044
+xref: RHEA:44048
+xref: RHEA:45352
+xref: RHEA:56584
+xref: RHEA:80591
+xref: RHEA:80779
+xref: RHEA:80783
+xref: RHEA:80787
+xref: RHEA:80791
+xref: RHEA:80795
+xref: RHEA:80799
+xref: RHEA:81855
is_a: GO:0016803 ! ether hydrolase activity
property_value: skos:exactMatch EC:3.3.2.10
property_value: skos:exactMatch RHEA:19037
+property_value: skos:narrowMatch RHEA:44032
+property_value: skos:narrowMatch RHEA:44036
+property_value: skos:narrowMatch RHEA:44040
+property_value: skos:narrowMatch RHEA:44044
+property_value: skos:narrowMatch RHEA:44048
+property_value: skos:narrowMatch RHEA:45352
+property_value: skos:narrowMatch RHEA:56584
+property_value: skos:narrowMatch RHEA:80591
+property_value: skos:narrowMatch RHEA:80779
+property_value: skos:narrowMatch RHEA:80783
+property_value: skos:narrowMatch RHEA:80787
+property_value: skos:narrowMatch RHEA:80791
+property_value: skos:narrowMatch RHEA:80795
+property_value: skos:narrowMatch RHEA:80799
+property_value: skos:narrowMatch RHEA:81855
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27074" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -41522,9 +42338,9 @@
xref: MetaCyc:ESTRADIOL-17-BETA-DEHYDROGENASE-RXN
xref: Reactome:R-HSA-5693390 "HSD17B11 dehydrogenates EST17b to E1"
xref: Reactome:R-HSA-5696822 "AKR1B15 reduces EST17b to E1"
-xref: Reactome:R-HSA-6810594 "HSD17B14 tetramer oxidises estradiol (E2) to estrone (E1)"
+xref: Reactome:R-HSA-6810594 "HSD17B14 tetramer oxidises estradiol (EST17b) to estrone (E1)"
xref: Reactome:R-HSA-804969 "HSD17B1 hydrogenates E1 to EST17b"
-xref: Reactome:R-HSA-8862137 "HSD17B2 oxidises estradiol (E2) to estrone (E1)"
+xref: Reactome:R-HSA-8862137 "HSD17B2 oxidises estradiol (EST17b) to estrone (E1)"
xref: RHEA:24612
xref: RHEA:24616
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -41610,9 +42426,17 @@
xref: MetaCyc:ETHANOLAMINEPHOSPHOTRANSFERASE-RXN
xref: Reactome:R-HSA-1482962 "CDP-ETA and DAG are converted to PE by CEPT1/EPT1"
xref: RHEA:32943
+xref: RHEA:54248
+xref: RHEA:54252
+xref: RHEA:54340
+xref: RHEA:80247
is_a: GO:0017169 ! CDP-alcohol phosphatidyltransferase activity
property_value: skos:exactMatch EC:2.7.8.1
property_value: skos:exactMatch RHEA:32943
+property_value: skos:narrowMatch RHEA:54248
+property_value: skos:narrowMatch RHEA:54252
+property_value: skos:narrowMatch RHEA:54340
+property_value: skos:narrowMatch RHEA:80247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -41665,8 +42489,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: 2 farnesyl diphosphate = diphosphate + presqualene diphosphate." [GOC:curators]
comment: This term was obsoleted because it represents a subreaction of squalene synthase activity ; GO:0051996.
-xref: Reactome:R-HSA-191402 "Reduction of presqualene diphosphate to form squalene"
-xref: Reactome:R-HSA-191405 "Two FPP molecules dimerize to form presqualene diphosphate"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28819" xsd:anyURI
is_obsolete: true
replaced_by: GO:0051996
@@ -41676,7 +42498,7 @@
name: geranylgeranyl diphosphate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = (2E,6E,10E)-geranylgeranyl diphosphate + diphosphate." [RHEA:17653]
-comment: The catalyzed reaction forms (free) geranylgeranyl diphosphate. There is no relationship between this activity and protein farnesyltransferase activity, GO:0004660, where the catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein. Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+comment: The catalyzed reaction forms (free) geranylgeranyl diphosphate. There is no relationship between this activity and protein farnesyltransferase activity, GO:0004660, where the catalyzed reaction transfers a farnesyl group from farnesyl diphosphate to a target protein.
synonym: "farnesyltranstransferase activity" EXACT [EC:2.5.1.29]
synonym: "geranylgeranyl pyrophosphate synthase activity" EXACT [EC:2.5.1.29]
synonym: "geranylgeranyl pyrophosphate synthetase activity" EXACT [EC:2.5.1.29]
@@ -41690,12 +42512,12 @@
is_a: GO:0120531 ! prenyl diphosphate synthase activity
property_value: skos:exactMatch EC:2.5.1.29
property_value: skos:exactMatch RHEA:17653
-property_value: skos:relatedMatch MetaCyc:PWY-5120
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20661" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28430" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29264" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004312
@@ -41798,13 +42620,55 @@
xref: EC:2.3.1.41
xref: MetaCyc:2.3.1.179-RXN
xref: MetaCyc:3-OXOACYL-ACP-SYNTH-RXN
+xref: RHEA:14565
xref: RHEA:22836
+xref: RHEA:41800
+xref: RHEA:41820
+xref: RHEA:41836
+xref: RHEA:41852
+xref: RHEA:41868
+xref: RHEA:41884
+xref: RHEA:41900
+xref: RHEA:41916
+xref: RHEA:42248
+xref: RHEA:42252
+xref: RHEA:42260
+xref: RHEA:42268
+xref: RHEA:42272
+xref: RHEA:42276
+xref: RHEA:47824
+xref: RHEA:54924
+xref: RHEA:54940
+xref: RHEA:55040
+xref: RHEA:65308
+xref: RHEA:65312
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.41
property_value: skos:exactMatch MetaCyc:3-OXOACYL-ACP-SYNTH-RXN
property_value: skos:exactMatch RHEA:22836
property_value: skos:narrowMatch EC:2.3.1.179
property_value: skos:narrowMatch MetaCyc:2.3.1.179-RXN
+property_value: skos:narrowMatch RHEA:14565
+property_value: skos:narrowMatch RHEA:41800
+property_value: skos:narrowMatch RHEA:41820
+property_value: skos:narrowMatch RHEA:41836
+property_value: skos:narrowMatch RHEA:41852
+property_value: skos:narrowMatch RHEA:41868
+property_value: skos:narrowMatch RHEA:41884
+property_value: skos:narrowMatch RHEA:41900
+property_value: skos:narrowMatch RHEA:41916
+property_value: skos:narrowMatch RHEA:42248
+property_value: skos:narrowMatch RHEA:42252
+property_value: skos:narrowMatch RHEA:42260
+property_value: skos:narrowMatch RHEA:42268
+property_value: skos:narrowMatch RHEA:42272
+property_value: skos:narrowMatch RHEA:42276
+property_value: skos:narrowMatch RHEA:47824
+property_value: skos:narrowMatch RHEA:54924
+property_value: skos:narrowMatch RHEA:54940
+property_value: skos:narrowMatch RHEA:55040
+property_value: skos:narrowMatch RHEA:65308
+property_value: skos:narrowMatch RHEA:65312
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21801" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26423" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -41989,6 +42853,8 @@
synonym: "TPNH-ferredoxin reductase activity" RELATED [EC:1.18.1.2]
xref: EC:1.18.1.2
xref: MetaCyc:1.18.1.2-RXN
+xref: Reactome:R-HSA-2395512 "FDXR transfers electrons to FDX1,2 (FDX1L)"
+xref: Reactome:R-HSA-2395517 "NADPH transfers electrons to FDXR"
xref: RHEA:20125
is_a: GO:0008937 ! ferredoxin-[NAD(P)H] reductase activity
property_value: skos:exactMatch EC:1.18.1.2
@@ -41998,10 +42864,11 @@
[Term]
id: GO:0004325
-name: ferrochelatase activity
+name: protoporphyrin ferrochelatase activity
namespace: molecular_function
def: "Catalysis of the reaction: heme B (protoheme) + H+ = Fe(2+) + protoporphyrin IX." [RHEA:22584]
synonym: "ferro-protoporphyrin chelatase activity" EXACT []
+synonym: "ferrochelatase activity" BROAD []
synonym: "heme synthase activity" BROAD []
synonym: "heme synthetase activity" BROAD [EC:4.98.1.1]
synonym: "iron chelatase activity" BROAD [EC:4.98.1.1]
@@ -42018,6 +42885,7 @@
property_value: skos:exactMatch RHEA:22584
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23371" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31620" xsd:anyURI
[Term]
id: GO:0004326
@@ -42114,7 +42982,7 @@
xref: EC:3.1.3.46
xref: MetaCyc:3.1.3.46-RXN
xref: Reactome:R-HSA-5628905 "TIGAR converts D-fructose-2,6-bisphosphate to D-fructose 6-phosphate"
-xref: Reactome:R-HSA-70262 "Fructose 2,6-bisphosphate is hydrolyzed to form fructose-6-phosphate and orthophosphate"
+xref: Reactome:R-HSA-70262 "PFKFKB dimer dephosphorylates fructose 2,6-bisphosphate"
xref: RHEA:17289
is_a: GO:0050308 ! sugar-phosphatase activity
property_value: skos:exactMatch EC:3.1.3.46
@@ -42144,7 +43012,7 @@
xref: EC:4.1.2.13
xref: MetaCyc:F16ALDOLASE-RXN
xref: Reactome:R-HSA-71495 "Aldolase tetramers convert GA3P and DHAP to F1,6PP"
-xref: Reactome:R-HSA-71496 "D-fructose 1,6-bisphosphate <=> dihydroxyacetone phosphate + D-glyceraldehyde 3-phosphate"
+xref: Reactome:R-HSA-71496 "Aldolase tetramer cleaves F1,6PP"
xref: RHEA:14729
is_a: GO:0016832 ! aldehyde-lyase activity
property_value: skos:exactMatch EC:4.1.2.13
@@ -42328,10 +43196,12 @@
xref: Reactome:R-HSA-5621918 "Defective GCK does not phosphorylate Glc to form G6P"
xref: Reactome:R-HSA-70420 "HK1,2,3,GCK,HKDC1 phosphorylate Glc to form G6P"
xref: RHEA:17825
+xref: RHEA:36495
is_a: GO:0004396 ! hexokinase activity
relationship: part_of GO:0051156 ! glucose 6-phosphate metabolic process
property_value: skos:exactMatch EC:2.7.1.2
property_value: skos:exactMatch RHEA:17825
+property_value: skos:narrowMatch RHEA:36495
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -42436,7 +43306,7 @@
synonym: "Zwischenferment" RELATED [EC:1.1.1.49]
xref: EC:1.1.1.49
xref: MetaCyc:GLU6PDEHYDROG-RXN
-xref: Reactome:R-HSA-70377 "alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+"
+xref: Reactome:R-HSA-70377 "G6PD multimers dehydrogenate G6P"
xref: RHEA:15841
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.49
@@ -42459,9 +43329,11 @@
xref: Reactome:R-HSA-3282876 "Defective G6PC3 does not hydrolyze glucose 6-phosphate"
xref: Reactome:R-HSA-71825 "G6PC hydrolyzes G6P to Glc and Pi (liver)"
xref: RHEA:16689
+xref: RHEA:44904
is_a: GO:0050309 ! sugar-terminal-phosphatase activity
property_value: skos:exactMatch EC:3.1.3.9
property_value: skos:exactMatch RHEA:16689
+property_value: skos:narrowMatch RHEA:44904
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -42484,7 +43356,7 @@
synonym: "phosphosaccharomutase activity" BROAD [EC:5.3.1.9]
xref: EC:5.3.1.9
xref: MetaCyc:PGLUCISOM-RXN
-xref: Reactome:R-HSA-70471 "alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate"
+xref: Reactome:R-HSA-70471 "GPI dimer isomerizes G6P"
xref: Reactome:R-HSA-70475 "GPI dimer isomerizes Fru(6)P to G6P"
xref: RHEA:11816
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
@@ -42517,10 +43389,12 @@
xref: Reactome:R-HSA-1861788 "GBA2 hydrolyzes GlcCer (plasma membrane)"
xref: Reactome:R-HSA-1861789 "GBA3 hydrolyzes GlcCer (cytosol)"
xref: RHEA:13269
+xref: RHEA:59284
is_a: GO:0017042 ! glycosylceramidase activity
property_value: skos:exactMatch EC:3.2.1.45
property_value: skos:exactMatch MetaCyc:GLUCOSYLCERAMIDASE-RXN
property_value: skos:exactMatch RHEA:13269
+property_value: skos:narrowMatch RHEA:59284
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25793" xsd:anyURI
[Term]
@@ -42597,7 +43471,6 @@
name: L-glutamate dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamate + NAD+ + H2O = 2-oxoglutarate + NH4+ + NADH + H+." [RHEA:15133]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "glutamate dehydrogenase (NAD)" BROAD [EC:1.4.1.2]
synonym: "glutamate dehydrogenase (NAD+) activity" BROAD []
synonym: "glutamate oxidoreductase activity" RELATED [EC:1.4.1.2]
@@ -42620,39 +43493,36 @@
is_a: GO:0004353 ! L-glutamate dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.4.1.2
property_value: skos:exactMatch RHEA:15133
-property_value: skos:relatedMatch MetaCyc:GLUTAMATE-DEG1-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004353
name: L-glutamate dehydrogenase [NAD(P)+] activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamate + NAD(P)+ + H2O = 2-oxoglutarate + NH4+ + NAD(P)H + H+." [EC:1.4.1.3]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "glutamate dehydrogenase (NAD+) activity" RELATED []
synonym: "glutamic dehydrogenase activity" BROAD [EC:1.4.1.3]
synonym: "L-glutamate:NAD(P)+ oxidoreductase (deaminating)" EXACT [EC:1.4.1.3]
xref: EC:1.4.1.3
xref: MetaCyc:GLUTAMATE-DEHYDROGENASE-NADP+-RXN
-xref: Reactome:R-HSA-70589 "alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]"
-xref: Reactome:R-HSA-70600 "glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]"
+xref: Reactome:R-HSA-70589 "alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ (GLUD1,2)"
+xref: Reactome:R-HSA-70600 "glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ (GLUD1,2)"
is_a: GO:0050018 ! amino-acid dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.4.1.3
property_value: skos:exactMatch MetaCyc:GLUTAMATE-DEHYDROGENASE-NADP+-RXN
-property_value: skos:relatedMatch MetaCyc:GLUTAMATE-SYN2-PWY
-property_value: skos:relatedMatch MetaCyc:PWY-5766
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004354
name: L-glutamate dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamate + NADP+ + H2O = 2-oxoglutarate + NH4+ + NADPH + H+." [RHEA:11612]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate))" RELATED [EC:1.4.1.4]
synonym: "glutamic acid dehydrogenase" BROAD [EC:1.4.1.4]
synonym: "glutamic dehydrogenase activity" BROAD [EC:1.4.1.4]
@@ -42668,16 +43538,15 @@
property_value: skos:exactMatch EC:1.4.1.4
property_value: skos:exactMatch MetaCyc:GLUTDEHYD-RXN
property_value: skos:exactMatch RHEA:11612
-property_value: skos:relatedMatch MetaCyc:GLUTSYNIII-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004355
name: glutamate synthase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamate + NADP+ = 2-oxoglutarate + L-glutamine + H+ + NADPH. This is a two-step reaction: (a) L-glutamate + NH3 = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH3 + 2-oxoglutarate + NADPH + H+." [EC:1.4.1.13, RHEA:15501]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: 2 L-glutamate + NADP+ = 2-oxoglutarate + L-glutamine + H+ + NADPH. This is a two-step reaction: (a) L-glutamate + NH4+ = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH4+ + 2-oxoglutarate + NADPH + H+." [RHEA:15501]
synonym: "glutamate (reduced nicotinamide adenine dinucleotide phosphate) synthase activity" RELATED [EC:1.4.1.13]
synonym: "glutamate synthetase (NADP) activity" RELATED [EC:1.4.1.13]
synonym: "glutamine amide-2-oxoglutarate aminotransferase (oxidoreductase, NADP) activity" RELATED [EC:1.4.1.13]
@@ -42699,8 +43568,8 @@
property_value: skos:exactMatch EC:1.4.1.13
property_value: skos:exactMatch MetaCyc:GLUTAMATESYN-RXN
property_value: skos:exactMatch RHEA:15501
-property_value: skos:relatedMatch MetaCyc:GLUTSYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004356
@@ -42745,24 +43614,24 @@
name: L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donor
namespace: molecular_function
def: "Catalysis of the reaction: N2-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine." [RHEA:15349]
-synonym: "2-N-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" RELATED [EC:2.3.1.35]
+synonym: "2-N-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" EXACT [EC:2.3.1.35]
synonym: "acetyl-L-glutamate:acetyl-L-ornithine transacetylase activity" EXACT []
-synonym: "acetylglutamate synthetase activity" RELATED [EC:2.3.1.35]
-synonym: "acetylglutamate-acetylornithine transacetylase activity" RELATED [EC:2.3.1.35]
-synonym: "acetylglutamic synthetase activity" RELATED [EC:2.3.1.35]
-synonym: "acetylglutamic-acetylornithine transacetylase activity" RELATED [EC:2.3.1.35]
+synonym: "acetylglutamate synthetase activity" BROAD [EC:2.3.1.35]
+synonym: "acetylglutamate-acetylornithine transacetylase activity" EXACT [EC:2.3.1.35]
+synonym: "acetylglutamic synthetase activity" BROAD [EC:2.3.1.35]
+synonym: "acetylglutamic-acetylornithine transacetylase activity" EXACT [EC:2.3.1.35]
synonym: "acetylornithinase activity" BROAD [EC:2.3.1.35]
-synonym: "acetylornithine glutamate acetyltransferase activity" RELATED [EC:2.3.1.35]
-synonym: "alpha-N-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" RELATED [EC:2.3.1.35]
-synonym: "glutamate acetyltransferase activity" RELATED [EC:2.3.1.35]
+synonym: "acetylornithine glutamate acetyltransferase activity" EXACT [EC:2.3.1.35]
+synonym: "alpha-N-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" EXACT [EC:2.3.1.35]
+synonym: "glutamate acetyltransferase activity" BROAD [EC:2.3.1.35]
synonym: "glutamate N-acetyltransferase activity" BROAD []
synonym: "L-glutamate N-acetyltransferase activity" BROAD []
synonym: "N-acetyl-L-glutamate synthetase activity" BROAD [EC:2.3.1.35]
synonym: "N-acetylglutamate synthase activity" BROAD [EC:2.3.1.35]
synonym: "N-acetylglutamate synthetase activity" BROAD [EC:2.3.1.35]
-synonym: "N2-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" RELATED [EC:2.3.1.35]
-synonym: "ornithine acetyltransferase activity" RELATED [EC:2.3.1.35]
-synonym: "ornithine transacetylase activity" RELATED [EC:2.3.1.35]
+synonym: "N2-acetyl-L-ornithine:L-glutamate N-acetyltransferase activity" EXACT [EC:2.3.1.35]
+synonym: "ornithine acetyltransferase activity" BROAD [EC:2.3.1.35]
+synonym: "ornithine transacetylase activity" BROAD [EC:2.3.1.35]
xref: EC:2.3.1.35
xref: KEGG_REACTION:R02282
xref: MetaCyc:GLUTAMATE-N-ACETYLTRANSFERASE-RXN
@@ -42784,7 +43653,7 @@
synonym: "L-glutaminase activity" RELATED [EC:3.5.1.2]
synonym: "L-glutamine amidohydrolase activity" RELATED [EC:3.5.1.2]
xref: EC:3.5.1.2
-xref: Reactome:R-HSA-70609 "glutamine + H2O => glutamate + NH4+ [GLS]"
+xref: Reactome:R-HSA-70609 "glutamine + H2O => glutamate + NH4+ (GLS)"
xref: RHEA:15889
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:broadMatch MetaCyc:GLUTAMIN-RXN
@@ -42795,9 +43664,9 @@
[Term]
id: GO:0004360
-name: glutamine-fructose-6-phosphate transaminase (isomerizing) activity
+name: L-glutamine:D-fructose-6-phosphate transaminase (isomerizing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate." [EC:2.6.1.16, RHEA:13237]
+def: "Catalysis of the reaction: D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate." [RHEA:13237]
synonym: "D-fructose-6-phosphate amidotransferase activity" RELATED [EC:2.6.1.16]
synonym: "GlcN6P synthase activity" RELATED [EC:2.6.1.16]
synonym: "glucosamine 6-phosphate synthase activity" RELATED [EC:2.6.1.16]
@@ -42805,6 +43674,7 @@
synonym: "glucosamine-6-phosphate isomerase (glutamine-forming) activity" EXACT []
synonym: "glucosamine-6-phosphate synthase activity" RELATED [EC:2.6.1.16]
synonym: "glucosaminephosphate isomerase" BROAD [EC:2.6.1.16]
+synonym: "glutamine-fructose-6-phosphate transaminase (isomerizing) activity" EXACT []
synonym: "hexosephosphate aminotransferase activity" RELATED [EC:2.6.1.16]
synonym: "L-glutamine-D-fructose-6-phosphate amidotransferase activity" RELATED [EC:2.6.1.16]
synonym: "L-glutamine:D-fructose-6-phosphate isomerase (deaminating)" RELATED [EC:2.6.1.16]
@@ -42814,10 +43684,11 @@
xref: Reactome:R-HSA-4085027 "Defective GFPT1 does not transfer an amino group from L-Gln to F6P to form GlcN6P"
xref: Reactome:R-HSA-449715 "GFPT1,2 transfer an amino group from L-Gln to F6P to form GlcN6P"
xref: RHEA:13237
-is_a: GO:0070548 ! L-glutamine aminotransferase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.16
property_value: skos:exactMatch RHEA:13237
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004361
@@ -42917,9 +43788,11 @@
xref: Reactome:R-HSA-9748996 "GST dimers cleave AZA to 6MP"
xref: Reactome:R-HSA-9753280 "GSTs transfer GSH to NAPQI to form APAP-SG"
xref: RHEA:16437
+xref: RHEA:51220
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
property_value: skos:exactMatch EC:2.5.1.18
property_value: skos:exactMatch RHEA:16437
+property_value: skos:narrowMatch RHEA:51220
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31085" xsd:anyURI
@@ -42941,7 +43814,7 @@
synonym: "triosephosphate dehydrogenase activity" BROAD [EC:1.2.1.12]
xref: EC:1.2.1.12
xref: MetaCyc:GAPOXNPHOSPHN-RXN
-xref: Reactome:R-HSA-70449 "D-glyceraldehyde 3-phosphate + orthophosphate + NAD+ <=> 1,3-bisphospho-D-glycerate + NADH + H+"
+xref: Reactome:R-HSA-70449 "GADPH tetramer dehydrogenates GA3P"
xref: Reactome:R-HSA-70482 "GAPDH tetramers reduce 1,3BPG to GA3P"
xref: RHEA:10300
is_a: GO:0043891 ! glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity
@@ -42971,9 +43844,23 @@
xref: Reactome:R-HSA-549112 "G3P is acylated to 1-acyl LPA by AGPAT6"
xref: Reactome:R-HSA-75886 "glycerol 3-phosphate + acyl-CoA => 1-acylglycerol 3-phosphate + CoASH [mitochondrial membrane-associated]"
xref: RHEA:15325
+xref: RHEA:35723
+xref: RHEA:35727
+xref: RHEA:35731
+xref: RHEA:37195
+xref: RHEA:37199
+xref: RHEA:37203
+xref: RHEA:37463
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.15
property_value: skos:exactMatch RHEA:15325
+property_value: skos:narrowMatch RHEA:35723
+property_value: skos:narrowMatch RHEA:35727
+property_value: skos:narrowMatch RHEA:35731
+property_value: skos:narrowMatch RHEA:37195
+property_value: skos:narrowMatch RHEA:37199
+property_value: skos:narrowMatch RHEA:37203
+property_value: skos:narrowMatch RHEA:37463
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -42991,9 +43878,13 @@
xref: MetaCyc:RXN-15745
xref: Reactome:R-HSA-188467 "Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)"
xref: RHEA:18977
+xref: RHEA:28755
+xref: RHEA:29219
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.1.5.3
property_value: skos:exactMatch RHEA:18977
+property_value: skos:narrowMatch RHEA:28755
+property_value: skos:narrowMatch RHEA:29219
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25984" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -43252,10 +44143,20 @@
xref: Reactome:R-HSA-9033959 "ABO-A:Mn2+ transfers GalNAc to H antigen-RBC to form A antigen-RBC"
xref: Reactome:R-HSA-9034042 "sABO-A:Mn2+ transfers GalNAc to H antigen-sec to form A antigen-sec"
xref: RHEA:19021
+xref: RHEA:84499
+xref: RHEA:84507
+xref: RHEA:84511
+xref: RHEA:84535
+xref: RHEA:84539
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
property_value: skos:exactMatch EC:2.4.1.40
property_value: skos:exactMatch RHEA:19021
+property_value: skos:narrowMatch RHEA:84499
+property_value: skos:narrowMatch RHEA:84507
+property_value: skos:narrowMatch RHEA:84511
+property_value: skos:narrowMatch RHEA:84535
+property_value: skos:narrowMatch RHEA:84539
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -43284,9 +44185,19 @@
xref: Reactome:R-HSA-9033961 "ABO-B:Mn2+ transfers Gal to H antigen-RBC to form B antigen-RBC"
xref: Reactome:R-HSA-9034053 "sABO-B:Mn2+ transfers Gal to H antigen-sec to form B antigen"
xref: RHEA:14349
+xref: RHEA:84519
+xref: RHEA:84523
+xref: RHEA:84527
+xref: RHEA:84739
+xref: RHEA:84743
is_a: GO:0035250 ! UDP-galactosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.37
property_value: skos:exactMatch RHEA:14349
+property_value: skos:narrowMatch RHEA:84519
+property_value: skos:narrowMatch RHEA:84523
+property_value: skos:narrowMatch RHEA:84527
+property_value: skos:narrowMatch RHEA:84739
+property_value: skos:narrowMatch RHEA:84743
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -43302,6 +44213,7 @@
synonym: "guanosine-diphosphatase activity" EXACT []
xref: EC:3.6.1.42
xref: MetaCyc:GUANOSINE-DIPHOSPHATASE-RXN
+xref: Reactome:R-HSA-9947887 "GBP1 hydrolyzes GDP"
xref: RHEA:22156
is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
property_value: skos:exactMatch EC:3.6.1.42
@@ -43388,6 +44300,8 @@
xref: Reactome:R-HSA-169468 "MCM2-7 mediated fork unwinding"
xref: Reactome:R-HSA-5686410 "BLM mediates dissolution of double Holliday junction"
xref: Reactome:R-HSA-5690996 "ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA"
+xref: Reactome:R-HSA-9922957 "NS3 melts (+)-RNA secondary structures"
+xref: Reactome:R-HSA-9923073 "NS3 unwinds dsRNA secondary structures"
is_a: GO:0120545 ! nucleic acid conformation isomerase activity
is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
is_a: GO:0140657 ! ATP-dependent activity
@@ -43426,7 +44340,7 @@
synonym: "heparin 2-sulfotransferase activity" RELATED []
synonym: "heparin-sulphate 2-sulphotransferase activity" RELATED []
xref: MetaCyc:RXN-11558
-xref: Reactome:R-HSA-2076508 "HS2ST1 sulfates IdoA at C2 in heparan sulfate"
+xref: Reactome:R-HSA-2076508 "HS2ST1 trimer sulfates IdoA at C2 in heparan sulfate"
is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24749" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28380" xsd:anyURI
@@ -43470,7 +44384,7 @@
id: GO:0004397
name: histidine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidine = urocanate + NH3." [EC:4.3.1.3]
+def: "Catalysis of the reaction: L-histidine = trans-urocanate + NH4+." [RHEA:21232]
synonym: "histidase activity" RELATED [GOC:hjd]
synonym: "histidinase activity" RELATED [GOC:hjd]
synonym: "histidine alpha-deaminase activity" RELATED [GOC:hjd]
@@ -43518,13 +44432,14 @@
[Term]
id: GO:0004400
-name: histidinol-phosphate transaminase activity
+name: L-histidinol-phosphate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidinol-phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate." [EC:2.6.1.9]
+def: "Catalysis of the reaction: L-histidinol-phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate." [RHEA:23744]
synonym: "glutamic-imidazoleacetol phosphate transaminase activity" RELATED [EC:2.6.1.9]
synonym: "histidine:imidazoleacetol phosphate transaminase activity" RELATED [EC:2.6.1.9]
synonym: "histidinol phosphate aminotransferase activity" RELATED [EC:2.6.1.9]
synonym: "histidinol-phosphate aminotransferase activity" EXACT []
+synonym: "histidinol-phosphate transaminase activity" EXACT []
synonym: "IAP transaminase activity" RELATED [EC:2.6.1.9]
synonym: "imidazole acetol-phosphate transaminase activity" RELATED [EC:2.6.1.9]
synonym: "imidazoleacetol phosphate transaminase activity" RELATED [EC:2.6.1.9]
@@ -43535,10 +44450,11 @@
xref: EC:2.6.1.9
xref: MetaCyc:HISTAMINOTRANS-RXN
xref: RHEA:23744
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.9
property_value: skos:exactMatch RHEA:23744
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004401
@@ -43597,6 +44513,7 @@
xref: Reactome:R-HSA-3697920 "CLOCK acetylates lysine-10 of histone H3, H4"
xref: Reactome:R-HSA-5144542 "CLOCK acetylates lysine-15 of histone H3, H4"
xref: Reactome:R-HSA-5250938 "B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9"
+xref: Reactome:R-HSA-9926482 "CREBBP, EP300 acetylate MITF-M"
xref: RHEA:21992
is_a: GO:0061733 ! protein-lysine-acetyltransferase activity
is_a: GO:0140993 ! histone modifying activity
@@ -43774,12 +44691,13 @@
synonym: "hyaluronoglucosidase activity" RELATED [EC:3.2.1.35]
xref: EC:3.2.1.35
xref: MetaCyc:3.2.1.35-RXN
-xref: Reactome:R-HSA-1793209 "HYAL1 hydrolyses Chondroitin chains"
+xref: Reactome:R-HSA-1793209 "HYAL1-4 hydrolyze chondroitin chains"
xref: Reactome:R-HSA-2160874 "HYAL1 hydrolyses (HA)50"
-xref: Reactome:R-HSA-2160892 "Hyaluronidase 2 (HYAL2) hydrolyses HA into 20kDa fragments"
+xref: Reactome:R-HSA-2160892 "HYAL2 hydrolyses HA into 20kDa fragments"
xref: Reactome:R-HSA-2318585 "Defective HYAL1 does not hydrolyse Chondroitin chains"
-xref: Reactome:R-HSA-5693356 "CEMIP hydrolyses HA"
+xref: Reactome:R-HSA-5693356 "CEMIP hydrolyzes HA"
xref: Reactome:R-HSA-9036077 "Defective HYAL1 does not hydrolyse (HA)50"
+xref: Reactome:R-HSA-9941055 "SPAM1 randomly cleaves HA"
is_a: GO:0015929 ! hexosaminidase activity
property_value: skos:exactMatch EC:3.2.1.35
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -43797,9 +44715,11 @@
xref: MetaCyc:RXN-7919
xref: Reactome:R-HSA-6783221 "HAGH hydrolyses (R)-S-LGSH to GSH and LACT"
xref: RHEA:21864
+xref: RHEA:25245
is_a: GO:0016790 ! thiolester hydrolase activity
property_value: skos:exactMatch EC:3.1.2.6
property_value: skos:exactMatch RHEA:21864
+property_value: skos:narrowMatch RHEA:25245
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30176" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -44193,9 +45113,11 @@
xref: Reactome:R-HSA-6809777 "PI3P is dephosphorylated to PI by MTMR2:SBF1"
xref: Reactome:R-HSA-6809975 "PI3P is dephosphorylated to PI by the MTMR2:SBF2 tetramer at the plasma membrane"
xref: RHEA:12316
+xref: RHEA:42328
is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
property_value: skos:exactMatch EC:3.1.3.64
property_value: skos:exactMatch RHEA:12316
+property_value: skos:narrowMatch RHEA:42328
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24252" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -44220,10 +45142,12 @@
xref: Reactome:R-HSA-1676177 "PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane"
xref: Reactome:R-HSA-8868648 "SYNJ hydrolyze PI(4,5)P2 to PI(4)P"
xref: RHEA:22764
+xref: RHEA:43576
is_a: GO:0034595 ! phosphatidylinositol phosphate 5-phosphatase activity
is_a: GO:0106019 ! phosphatidylinositol-4,5-bisphosphate phosphatase activity
property_value: skos:exactMatch EC:3.1.3.36
property_value: skos:exactMatch RHEA:22764
+property_value: skos:narrowMatch RHEA:43576
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -44247,7 +45171,7 @@
id: GO:0004442
name: obsolete inositol-1,4,-bisphosphate 3-phosphatase
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: D-myo-inositol 1,3-bisphosphate + H2O = D-myo-inositol 1-monophosphate + phosphate." [EC:3.1.3.65, GOC:go_curators]
+def: "OBSOLETE. Catalysis of the reaction: D-myo-inositol 1,3-bisphosphate + H2O = D-myo-inositol 1-monophosphate + phosphate." [EC:3.1.3.65, GOC:curators]
synonym: "inositol-1,4,-bisphosphate 3-phosphatase" EXACT []
is_obsolete: true
consider: GO:0004438
@@ -44256,7 +45180,7 @@
id: GO:0004443
name: obsolete inositol-1,4,-bisphosphate 4-phosphatase
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: D-myo-inositol 3,4-bisphosphate + H2O = D-myo-inositol 3-monophosphate + phosphate." [EC:3.1.3.66, GOC:go_curators]
+def: "OBSOLETE. Catalysis of the reaction: D-myo-inositol 3,4-bisphosphate + H2O = D-myo-inositol 3-monophosphate + phosphate." [EC:3.1.3.66, GOC:curators]
synonym: "inositol-1,4,-bisphosphate 4-phosphatase" EXACT []
is_obsolete: true
consider: GO:0016316
@@ -44317,7 +45241,7 @@
id: GO:0004447
name: iodide peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: iodide + H2O2 = iodine + 2 H2O." [RHEA:23336]
+def: "Catalysis of the reactions: (1) 2 iodide + H2O2 + 2 H+ = diiodine + 2 H2O; (2) [thyroglobulin]-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3-iodo-L-tyrosine + 2 H2O; (3) [thyroglobulin]-3-iodo-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3,5-diiodo-L-tyrosine + 2 H2O; (4) 2 [thyroglobulin]-3,5-diiodo-L-tyrosine + H2O2 = [thyroglobulin]-L-thyroxine + [thyroglobulin]-dehydroalanine + 2 H2O; (5) [thyroglobulin]-3-iodo-L-tyrosine + [thyroglobulin]-3,5-diiodo-L-tyrosine + H2O2 = [thyroglobulin]-3,3',5-triiodo-L-thyronine + [thyroglobulin]-dehydroalanine + 2 H2O." [EC:1.11.1.8, PMID:8651700]
synonym: "iodinase activity" RELATED [EC:1.11.1.8]
synonym: "thyroid peroxidase activity" RELATED [EC:1.11.1.8]
synonym: "thyroperoxidase activity" RELATED [EC:1.11.1.8]
@@ -44325,12 +45249,21 @@
xref: EC:1.11.1.8
xref: MetaCyc:IODIDE-PEROXIDASE-RXN
xref: RHEA:23336
+xref: RHEA:48956
+xref: RHEA:48960
+xref: RHEA:48964
+xref: RHEA:48968
is_a: GO:0140905 ! haloperoxidase activity
property_value: skos:exactMatch EC:1.11.1.8
-property_value: skos:exactMatch RHEA:23336
+property_value: skos:narrowMatch RHEA:23336
+property_value: skos:narrowMatch RHEA:48956
+property_value: skos:narrowMatch RHEA:48960
+property_value: skos:narrowMatch RHEA:48964
+property_value: skos:narrowMatch RHEA:48968
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21027" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23587" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30597" xsd:anyURI
[Term]
id: GO:0004448
@@ -44690,6 +45623,7 @@
xref: EC:4.4.1.20
xref: KEGG_REACTION:R03059
xref: MetaCyc:LEUKOTRIENE-C4-SYNTHASE-RXN
+xref: Reactome:R-HSA-2162019 "LTA4 is converted to EXA4 by ALOX15"
xref: Reactome:R-HSA-266050 "LTA4 is converted to LTC4 by LTC4S"
xref: RHEA:17617
is_a: GO:0016846 ! carbon-sulfur lyase activity
@@ -44736,9 +45670,67 @@
xref: EC:1.3.8.8
xref: MetaCyc:LONG-CHAIN-ACYL-COA-DEHYDROGENASE-RXN
xref: RHEA:17721
+xref: RHEA:43448
+xref: RHEA:47228
+xref: RHEA:47236
+xref: RHEA:47240
+xref: RHEA:47300
+xref: RHEA:47304
+xref: RHEA:47316
+xref: RHEA:47432
+xref: RHEA:47448
+xref: RHEA:48188
+xref: RHEA:82939
+xref: RHEA:83023
+xref: RHEA:83055
+xref: RHEA:83155
+xref: RHEA:83159
+xref: RHEA:83207
+xref: RHEA:83223
+xref: RHEA:83335
+xref: RHEA:83371
+xref: RHEA:83387
+xref: RHEA:84463
+xref: RHEA:84467
+xref: RHEA:84595
+xref: RHEA:84599
+xref: RHEA:84603
+xref: RHEA:84619
+xref: RHEA:84623
+xref: RHEA:85107
+xref: RHEA:85123
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
property_value: skos:exactMatch EC:1.3.8.8
property_value: skos:exactMatch RHEA:17721
+property_value: skos:narrowMatch RHEA:43448
+property_value: skos:narrowMatch RHEA:47228
+property_value: skos:narrowMatch RHEA:47236
+property_value: skos:narrowMatch RHEA:47240
+property_value: skos:narrowMatch RHEA:47300
+property_value: skos:narrowMatch RHEA:47304
+property_value: skos:narrowMatch RHEA:47316
+property_value: skos:narrowMatch RHEA:47432
+property_value: skos:narrowMatch RHEA:47448
+property_value: skos:narrowMatch RHEA:48188
+property_value: skos:narrowMatch RHEA:82939
+property_value: skos:narrowMatch RHEA:83023
+property_value: skos:narrowMatch RHEA:83055
+property_value: skos:narrowMatch RHEA:83155
+property_value: skos:narrowMatch RHEA:83159
+property_value: skos:narrowMatch RHEA:83207
+property_value: skos:narrowMatch RHEA:83223
+property_value: skos:narrowMatch RHEA:83335
+property_value: skos:narrowMatch RHEA:83371
+property_value: skos:narrowMatch RHEA:83387
+property_value: skos:narrowMatch RHEA:84463
+property_value: skos:narrowMatch RHEA:84467
+property_value: skos:narrowMatch RHEA:84595
+property_value: skos:narrowMatch RHEA:84599
+property_value: skos:narrowMatch RHEA:84603
+property_value: skos:narrowMatch RHEA:84619
+property_value: skos:narrowMatch RHEA:84623
+property_value: skos:narrowMatch RHEA:85107
+property_value: skos:narrowMatch RHEA:85123
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -44748,7 +45740,7 @@
namespace: molecular_function
alt_id: GO:0003996
def: "Catalysis of the reaction: a long-chain fatty acid + ATP + CoA = a long-chain fatty acyl-CoA + AMP + diphosphate. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons." [RHEA:15421]
-comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283). Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
synonym: "acyl-activating enzyme activity" BROAD []
synonym: "acyl-CoA ligase activity" RELATED []
synonym: "acyl-CoA synthetase activity" RELATED [EC:6.2.1.3]
@@ -44784,21 +45776,95 @@
xref: Reactome:R-HSA-5696004 "ACSF2 ligates CoA-SH to MCFA"
xref: Reactome:R-HSA-9734535 "SLC27A2 ligates CoA to bempedoic acid to form ETC-1002-CoA"
xref: RHEA:15421
+xref: RHEA:30751
+xref: RHEA:33607
+xref: RHEA:33615
+xref: RHEA:33619
+xref: RHEA:33635
+xref: RHEA:33643
+xref: RHEA:33647
+xref: RHEA:33651
+xref: RHEA:36139
+xref: RHEA:44076
+xref: RHEA:44084
+xref: RHEA:44092
+xref: RHEA:44192
+xref: RHEA:44200
+xref: RHEA:44204
+xref: RHEA:44208
+xref: RHEA:44212
+xref: RHEA:44216
+xref: RHEA:44220
+xref: RHEA:44224
+xref: RHEA:44932
+xref: RHEA:44936
+xref: RHEA:46208
+xref: RHEA:52008
+xref: RHEA:52012
+xref: RHEA:52016
+xref: RHEA:52088
+xref: RHEA:52108
+xref: RHEA:52112
+xref: RHEA:52116
+xref: RHEA:67848
+xref: RHEA:83019
+xref: RHEA:83035
+xref: RHEA:83199
+xref: RHEA:83203
+xref: RHEA:83347
+xref: RHEA:85307
is_a: GO:0120515 ! fatty acid-CoA ligase activity
relationship: part_of GO:0001676 ! long-chain fatty acid metabolic process
property_value: skos:exactMatch EC:6.2.1.3
property_value: skos:exactMatch MetaCyc:RXN-7904
property_value: skos:exactMatch RHEA:15421
-property_value: skos:relatedMatch MetaCyc:PWY-5143
+property_value: skos:narrowMatch RHEA:30751
+property_value: skos:narrowMatch RHEA:33607
+property_value: skos:narrowMatch RHEA:33615
+property_value: skos:narrowMatch RHEA:33619
+property_value: skos:narrowMatch RHEA:33635
+property_value: skos:narrowMatch RHEA:33643
+property_value: skos:narrowMatch RHEA:33647
+property_value: skos:narrowMatch RHEA:33651
+property_value: skos:narrowMatch RHEA:36139
+property_value: skos:narrowMatch RHEA:44076
+property_value: skos:narrowMatch RHEA:44084
+property_value: skos:narrowMatch RHEA:44092
+property_value: skos:narrowMatch RHEA:44192
+property_value: skos:narrowMatch RHEA:44200
+property_value: skos:narrowMatch RHEA:44204
+property_value: skos:narrowMatch RHEA:44208
+property_value: skos:narrowMatch RHEA:44212
+property_value: skos:narrowMatch RHEA:44216
+property_value: skos:narrowMatch RHEA:44220
+property_value: skos:narrowMatch RHEA:44224
+property_value: skos:narrowMatch RHEA:44932
+property_value: skos:narrowMatch RHEA:44936
+property_value: skos:narrowMatch RHEA:46208
+property_value: skos:narrowMatch RHEA:52008
+property_value: skos:narrowMatch RHEA:52012
+property_value: skos:narrowMatch RHEA:52016
+property_value: skos:narrowMatch RHEA:52088
+property_value: skos:narrowMatch RHEA:52108
+property_value: skos:narrowMatch RHEA:52112
+property_value: skos:narrowMatch RHEA:52116
+property_value: skos:narrowMatch RHEA:67848
+property_value: skos:narrowMatch RHEA:83019
+property_value: skos:narrowMatch RHEA:83035
+property_value: skos:narrowMatch RHEA:83199
+property_value: skos:narrowMatch RHEA:83203
+property_value: skos:narrowMatch RHEA:83347
+property_value: skos:narrowMatch RHEA:85307
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18967" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20462" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25799" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004468
-name: L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor
+name: L-lysine N6-acetyltransferase activity, acting on acetyl phosphate as donor
namespace: molecular_function
def: "Catalysis of the reaction: acetyl phosphate + L-lysine = phosphate + N6-acetyl-L-lysine." [RHEA:14417]
synonym: "acetyl-phosphate:L-lysine 6-N-acetyltransferase activity" RELATED [EC:2.3.1.32]
@@ -45008,8 +46074,8 @@
alt_id: GO:0070128
def: "Catalysis of the reaction: 10-formyltetrahydrofolate + L-methionyl-tRNA + H2O = tetrahydrofolate + N-formylmethionyl-tRNA." [EC:2.1.2.9]
synonym: "10-formyltetrahydrofolate:L-methionyl-tRNA N-formyltransferase activity" RELATED [EC:2.1.2.9]
-synonym: "conversion of met-tRNAf to fmet-tRNA" RELATED [GO:curators]
-synonym: "conversion of mitochondrial met-tRNAf to fmet-tRNA" RELATED [GO:curators]
+synonym: "conversion of met-tRNAf to fmet-tRNA" RELATED [GOC:curators]
+synonym: "conversion of mitochondrial met-tRNAf to fmet-tRNA" RELATED [GOC:curators]
synonym: "formylmethionyl-transfer ribonucleic synthetase activity" RELATED [EC:2.1.2.9]
synonym: "methionyl ribonucleic formyltransferase activity" RELATED [EC:2.1.2.9]
synonym: "methionyl-transfer ribonucleate methyltransferase activity" RELATED [EC:2.1.2.9]
@@ -45017,9 +46083,9 @@
synonym: "methionyl-transfer RNA transformylase activity" RELATED [EC:2.1.2.9]
synonym: "methionyl-tRNA Met formyltransferase activity" RELATED [EC:2.1.2.9]
synonym: "methionyl-tRNA transformylase activity" RELATED [EC:2.1.2.9]
-synonym: "mitochondrial N-terminal peptidyl-methionine N-formylation" RELATED [GO:curators]
+synonym: "mitochondrial N-terminal peptidyl-methionine N-formylation" RELATED [GOC:curators]
synonym: "N(10)-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase activity" RELATED [EC:2.1.2.9]
-synonym: "N-terminal peptidyl-methionine N-formylation" RELATED [GO:curators]
+synonym: "N-terminal peptidyl-methionine N-formylation" RELATED [GOC:curators]
synonym: "N10-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase activity" RELATED [EC:2.1.2.9]
xref: EC:2.1.2.9
xref: MetaCyc:METHIONYL-TRNA-FORMYLTRANSFERASE-RXN
@@ -45069,6 +46135,7 @@
xref: Reactome:R-HSA-9694492 "nsp14 acts as a cap N7 methyltransferase to modify SARS-CoV-2 gRNA complement (minus strand)"
xref: Reactome:R-HSA-9694737 "nsp14 acts as a cap N7 methyltransferase to modify SARS-CoV-2 gRNA (plus strand)"
xref: Reactome:R-HSA-9830848 "L protein acts as a cap N7 methyltransferase to modify RSV mRNAs"
+xref: Reactome:R-HSA-9923104 "NS5 acts as a cap N7 methyltransferase to methylate 5 G pppA of DENV genomic +ssRNA"
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008174 ! mRNA methyltransferase activity
relationship: part_of GO:0006370 ! 7-methylguanosine mRNA capping
@@ -45096,6 +46163,7 @@
xref: Reactome:R-HSA-9694521 "nsp16 acts as a cap 2'-O-methyltransferase to modify SARS-CoV-2 gRNA complement (minus strand)"
xref: Reactome:R-HSA-9694721 "nsp16 acts as a cap 2'-O-methyltransferase to modify SARS-CoV-2 gRNA (plus strand)"
xref: Reactome:R-HSA-9834003 "L protein acts as a cap 2'-O-methyltransferase to modify RSV mRNAs"
+xref: Reactome:R-HSA-9923097 "NS5 acts as a cap 2'-O-methyltransferase to methylate 5 m7GpppA of DENV genomic +ssRNA"
xref: RHEA:67020
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
@@ -45118,10 +46186,15 @@
xref: Reactome:R-HSA-77081 "Formation of the CE:GMP intermediate complex"
xref: Reactome:R-HSA-77083 "Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA"
xref: Reactome:R-HSA-9815529 "nsp12 transfers guanylyl onto SARS-CoV-2 plus strand subgenomic RNAs"
+xref: Reactome:R-HSA-9923071 "NS5 transfers guanylyl onto DENV genomic 5'-ppRNA"
xref: RHEA:54592
+xref: RHEA:60836
+xref: RHEA:60844
is_a: GO:0008192 ! RNA guanylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.50
property_value: skos:exactMatch RHEA:54592
+property_value: skos:narrowMatch RHEA:60836
+property_value: skos:narrowMatch RHEA:60844
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -45139,8 +46212,8 @@
xref: EC:6.4.1.4
xref: KEGG_REACTION:R04138
xref: MetaCyc:METHYLCROTONYL-COA-CARBOXYLASE-RXN
-xref: Reactome:R-HSA-508308 "beta-methylglutaconyl-CoA + ADP + orthophosphate <=> beta-methylcrotonyl-CoA + ATP + CO2 (MCCA)"
-xref: Reactome:R-HSA-70773 "beta-methylcrotonyl-CoA + ATP + CO2 <=> beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O [MCCA]"
+xref: Reactome:R-HSA-508308 "beta-methylglutaconyl-CoA + ADP + orthophosphate <=> beta-methylcrotonyl-CoA + ATP + HCO3- (MCCA)"
+xref: Reactome:R-HSA-70773 "beta-methylcrotonyl-CoA + ATP + HCO3- <=> beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O (MCCA)"
xref: Reactome:R-HSA-9909466 "MCCC mutants don't synthesize beta-methylglutaconyl-CoA"
xref: RHEA:13589
is_a: GO:0016421 ! CoA carboxylase activity
@@ -45156,8 +46229,6 @@
comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "5,10-methylene-THF dehydrogenase activity" EXACT [GOC:vw]
synonym: "N5,N10-methylenetetrahydrofolate dehydrogenase activity" RELATED []
-xref: Reactome:R-HSA-200644 "5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+"
-xref: Reactome:R-HSA-200718 "MTHFD1 dimer dehydrogenates 5,10-methenyl-THFPG to 5,10-methylene-THFPG"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30105" xsd:anyURI
is_obsolete: true
@@ -45191,6 +46262,8 @@
xref: EC:1.5.1.5
xref: KEGG_REACTION:R01220
xref: MetaCyc:METHYLENETHFDEHYDROG-NADP-RXN
+xref: Reactome:R-HSA-200644 "5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+"
+xref: Reactome:R-HSA-200718 "MTHFD1 dimer dehydrogenates 5,10-methenyl-THFPG to 5,10-methylene-THFPG"
xref: RHEA:22812
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.5.1.5
@@ -45272,7 +46345,7 @@
synonym: "MSDH activity" RELATED [EC:1.2.1.27]
xref: EC:1.2.1.27
xref: MetaCyc:1.2.1.27-RXN
-xref: Reactome:R-HSA-70893 "methylmalonate semialdehyde + NAD+ + CoA => propionyl-CoA + CO2 + NADH + H+"
+xref: Reactome:R-HSA-70893 "methylmalonate semialdehyde + NAD+ + CoA + H2O => propionyl-CoA + HCO3- + NADH + H+"
xref: RHEA:20804
xref: RHEA:76615
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
@@ -45426,9 +46499,6 @@
xref: Reactome:R-HSA-5602272 "Defective CYP4F22 does not 20-hydroxylate TrXA3"
xref: Reactome:R-HSA-5602295 "CYP4F22 20-hydroxylates TrXA3"
xref: Reactome:R-HSA-5605147 "Defective CYP1B1 does not 4-hydroxylate EST17b"
-xref: Reactome:R-HSA-5662662 "Tyrosinase oxidises tyrosine to dopaquinone"
-xref: Reactome:R-HSA-5662692 "Dopa is oxidized to dopaquinone by TYR"
-xref: Reactome:R-HSA-5663050 "DHI and DHICA polymerize forming eumelanin"
xref: Reactome:R-HSA-76354 "Vinyl chloride is oxidized to 2-Chloroethylene oxide"
xref: Reactome:R-HSA-76373 "N-hydroxylation of 4-aminobiphenyl"
xref: Reactome:R-HSA-76386 "CYP1A2 S-demethylates 6MMP"
@@ -45437,7 +46507,7 @@
xref: Reactome:R-HSA-76426 "N-atom dealkylation of caffeine"
xref: Reactome:R-HSA-76434 "Dehalogenation of carbon tetrachloride to form a free radical"
xref: Reactome:R-HSA-76456 "O-atom dealkylation of dextromethorphan"
-xref: Reactome:R-HSA-76466 "CYP4A11 12-hydroxylates DDCX"
+xref: Reactome:R-HSA-76466 "CYP4A11 omega-hydroxylates DDCX"
xref: Reactome:R-HSA-76472 "Ethylene is oxidized to Ethylene oxide by CYP1A1"
xref: Reactome:R-HSA-76475 "Dehalogenation of the poly-halogenated hydrocarbon Halothane to form the acylhalide Trifluoroacetlychloride and hydrogen bromide"
xref: Reactome:R-HSA-8865107 "MICAL1 produces NADP+, H2O2"
@@ -45667,7 +46737,7 @@
xref: Reactome:R-HSA-71118 "PAH:Fe2+ tetramer hydroxylates L-Phe to L-Tyr"
xref: RHEA:20273
is_a: GO:0016714 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen
-relationship: part_of GO:0019293 ! L-tyrosine biosynthetic process, by oxidation of phenylalanine
+relationship: part_of GO:0006571 ! L-tyrosine biosynthetic process
property_value: skos:exactMatch EC:1.14.16.1
property_value: skos:exactMatch RHEA:20273
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20583" xsd:anyURI
@@ -45717,10 +46787,18 @@
xref: Reactome:R-HSA-5580292 "Defective CYP11B1 does not oxidise 11DCORT"
xref: Reactome:R-HSA-5600598 "Defective CYP11B2 does not oxidise 11DCORST"
xref: RHEA:15629
+xref: RHEA:46100
+xref: RHEA:46104
+xref: RHEA:84067
+xref: RHEA:84071
is_a: GO:0008395 ! steroid hydroxylase activity
is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.15.4
property_value: skos:exactMatch RHEA:15629
+property_value: skos:narrowMatch RHEA:46100
+property_value: skos:narrowMatch RHEA:46104
+property_value: skos:narrowMatch RHEA:84067
+property_value: skos:narrowMatch RHEA:84071
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -45751,7 +46829,12 @@
xref: Reactome:R-HSA-5601843 "Defective CYP17A1 does not 17-hydroxylate PREG"
xref: Reactome:R-HSA-9035954 "Defective CYP17A1 does not 17-hydroxylate P4"
xref: Reactome:R-HSA-9035956 "Defective CYP17A1 does not cleave 17aHPROG"
+xref: RHEA:14753
+xref: RHEA:46308
+xref: RHEA:50236
+xref: RHEA:50244
xref: RHEA:65760
+xref: RHEA:84243
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: skos:exactMatch EC:1.14.14.19
@@ -45759,6 +46842,11 @@
property_value: skos:exactMatch RHEA:65760
property_value: skos:narrowMatch EC:1.14.14.32
property_value: skos:narrowMatch MetaCyc:4.1.2.30-RXN
+property_value: skos:narrowMatch RHEA:14753
+property_value: skos:narrowMatch RHEA:46308
+property_value: skos:narrowMatch RHEA:50236
+property_value: skos:narrowMatch RHEA:50244
+property_value: skos:narrowMatch RHEA:84243
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27671" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29041" xsd:anyURI
@@ -45971,6 +47059,9 @@
xref: Reactome:R-HSA-5690990 "5'- incision of DNA by ERCC1:ERCC4 in GG-NER"
xref: Reactome:R-HSA-5693533 "DCLRE1C (ARTEMIS) processes DNA DSB ends"
xref: Reactome:R-HSA-72180 "Cleavage of mRNA at the 3'-end"
+xref: Reactome:R-HSA-9970193 "CPSF3 cleaves pre-mRNA at distal 3'UTR PAS"
+xref: Reactome:R-HSA-9970282 "U1 snRNP suppresses CPSF3-mediated pre-mRNA cleavage at intronic PAS"
+xref: Reactome:R-HSA-9970294 "CPSF3 cleaves pre-mRNA at proximal 3'UTR PAS"
is_a: GO:0004518 ! nuclease activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
@@ -46016,6 +47107,7 @@
xref: Reactome:R-HSA-927836 "SMG6 hydrolyzes mRNA with premature termination codon"
xref: Reactome:R-HSA-9708327 "ANG cleaves tRNA to yield tRNA halves"
xref: Reactome:R-HSA-9708812 "ELAC2 cleaves pre-tRNA to yield 3' trailer (type II tRF or tRF-1)"
+xref: Reactome:R-HSA-9948427 "ANKZF1 cleaves the peptidyl-tRNA in VCP hexamer:LTN1:NEMF:60S ribosome subunit:peptidyl-tRNA with K48polyUb-nascent peptide"
is_a: GO:0004519 ! endonuclease activity
is_a: GO:0004540 ! RNA nuclease activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
@@ -46084,6 +47176,9 @@
xref: Reactome:R-HSA-173769 "RNase H-mediated digestion of tRNA, 3'PPT and cPPT RNA primers"
xref: Reactome:R-HSA-182795 "RNase H-mediated degradation of the template strand"
xref: Reactome:R-HSA-182859 "RNase H-mediated degradation of the RNA strand of the -sssDNA:RNA duplex"
+xref: Reactome:R-HSA-9913637 "RNASEH1 cleaves R-loop RNA to yield RNA primer for H strand polymerization"
+xref: Reactome:R-HSA-9914858 "RNASEH1 cleaves RNA primer from nascent H strand, leaving RNA dinucleotides"
+xref: Reactome:R-HSA-9915449 "RNASEH1 cleaves RNA primer from nascent L strand, leaving RNA dinucleotides"
is_a: GO:0016891 ! RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism
property_value: skos:exactMatch EC:3.1.26.4
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -46250,6 +47345,12 @@
def: "Catalysis of the sequential cleavage of mononucleotides from a free 5' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684]
synonym: "5'-3' exoribonuclease activity" EXACT []
xref: Reactome:R-HSA-429845 "5' to 3' exoribonuclease hydrolyzes decapped mRNA"
+xref: Reactome:R-HSA-6791227 "47S pre-rRNA is nucleolytically processed at A' (01,A1), site A0, and site 02 (site 6) to yield 45S pre-rRNA"
+xref: Reactome:R-HSA-9915442 "EXOG cleaves RNA dinucleotide from nascent mitochondrial DNA"
+xref: Reactome:R-HSA-9935265 "DXO hydrolyzes uncapped RNA"
+xref: Reactome:R-HSA-9935299 "XRN2 5'-3' exonucleolytically hydrolyzes uncapped RNA"
+xref: Reactome:R-HSA-9946917 "XRN1 incompletely hydrolyzes DENV decapped mRNA"
+xref: Reactome:R-HSA-9971054 "XRN2 degrades downstream RNA fragment, promoting transcription termination"
is_a: GO:0008409 ! 5'-3' exonuclease activity
is_a: GO:0016896 ! RNA exonuclease activity, producing 5'-phosphomonoesters
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28062" xsd:anyURI
@@ -46267,6 +47368,8 @@
xref: Reactome:R-HSA-429955 "CCR4-NOT complex deadenylates mRNA"
xref: Reactome:R-HSA-429992 "PARN deadenylates mRNA"
xref: Reactome:R-HSA-430021 "PAN2-PAN3 complex partially deadenylates mRNA"
+xref: Reactome:R-HSA-9009950 "PDE12 cleaves 2'-5' oligoadenylates"
+xref: Reactome:R-HSA-9615042 "Viral 2',5'-PDE cleaves 2'-5' oligoadenylates"
xref: Reactome:R-HSA-9822311 "CCR4-NOT deadenylates mRNA in CCR4-NOT:BTG4:PABPN1L:mRNP"
xref: Reactome:R-HSA-9822335 "CCR4-NOT(CNOT6L) deadenylates mRNA in CCR4-NOT(CNOT6L):ZFP36L2:mRNA"
is_a: GO:0000175 ! 3'-5'-RNA exonuclease activity
@@ -46563,18 +47666,14 @@
xref: MetaCyc:3.2.1.52-RXN
xref: Reactome:R-HSA-1605595 "bHEXA hydrolyzes GM2A:GM2 to GM2A:GM3"
xref: Reactome:R-HSA-1605632 "bHEXA,bHEXB hydrolyze PSAP(195-273):Gb4Cer:PE"
-xref: Reactome:R-HSA-1638053 "HEXA cleaves the terminal GalNAc from keratan sulfate"
+xref: Reactome:R-HSA-1638053 "HEXA cleaves the terminal GlcNAc from keratan sulfate"
xref: Reactome:R-HSA-2105001 "HEXA cleaves the terminal GalNAc from DS"
-xref: Reactome:R-HSA-2162225 "HEXA cleaves the terminal GalNAc from small HA fragments"
-xref: Reactome:R-HSA-3656259 "Defective HEXA does not cleave the terminal GalNAc from DS"
-xref: Reactome:R-HSA-3662344 "Defective HEXB does not cleave the terminal GalNAc from DS"
+xref: Reactome:R-HSA-2162225 "HEXA cleaves the terminal GlcNAc from small HA fragments"
xref: Reactome:R-HSA-9035976 "Defective HEXA does not cleave the terminall GalNAc from small HA fragments"
-xref: Reactome:R-HSA-9035978 "Defective HEXA does not cleave the terminal GalNAc from keratan sulfate"
xref: Reactome:R-HSA-9035982 "Defective HEXB does not cleave the terminal GalNAc from HA fragments"
-xref: Reactome:R-HSA-9035983 "Defective HEXB does not cleave the terminal GalNAc from keratan sulfate"
xref: Reactome:R-HSA-9638075 "HEXB cleaves the terminal GalNAc from DS"
-xref: Reactome:R-HSA-9638076 "HEXB cleaves the terminal GalNAc from small HA fragments"
-xref: Reactome:R-HSA-9638078 "HEXB cleaves the terminal GalNAc from keratan sulfate"
+xref: Reactome:R-HSA-9638076 "HEXB cleaves the terminal GlcNAc from small HA fragments"
+xref: Reactome:R-HSA-9638078 "HEXB cleaves the terminal GlcNAc from keratan sulfate"
xref: Reactome:R-HSA-9840833 "bHEXA,bHEXB hydrolyze GM2A:GA2 to GM2A:LacCer"
xref: Reactome:R-HSA-9840884 "bHEXA,bHEXS hydrolyze GM2A:SM2"
is_a: GO:0015929 ! hexosaminidase activity
@@ -46609,7 +47708,6 @@
name: beta-galactosidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides." [EC:3.2.1.23]
-comment: Note that the inclusion of 'MetaCyc:BGALACT-PWY' is exceptional: normally MetaCyc pathway entries are database references for biological process terms, not molecular function terms. An exception was made in this case because the MetaCyc entry 'BGALACT-PWY' describes only one reaction, that catalyzed by beta-galactosidase.
synonym: "beta-D-galactanase activity" RELATED []
synonym: "beta-D-galactoside galactohydrolase activity" RELATED []
synonym: "beta-D-lactosidase activity" RELATED []
@@ -46621,7 +47719,7 @@
xref: Reactome:R-HSA-1605624 "Beta-galactosidases hydrolyse mobilized GM1 to mobilized GM2"
xref: Reactome:R-HSA-1606312 "GLB1 hydrolyzes SapB/C:LacCer"
xref: Reactome:R-HSA-1630306 "GLB1 hydrolyses a glycosaminoglycan"
-xref: Reactome:R-HSA-1793217 "Keratan sulfate is cleaved from its proteoglycan by an unknown galactosidase"
+xref: Reactome:R-HSA-1793217 "Unknown endo--galactosidase cleaves keratan chain"
xref: Reactome:R-HSA-2090079 "GLB1 hydrolyses linker chain(2)"
xref: Reactome:R-HSA-2265534 "Defective GLB1 does not hydrolyse a glycosaminoglycan"
xref: Reactome:R-HSA-9036061 "Defective GLB1 does not hydrolyse linker chain(2)"
@@ -46629,8 +47727,8 @@
is_a: GO:0015925 ! galactosidase activity
property_value: skos:exactMatch EC:3.2.1.23
property_value: skos:exactMatch MetaCyc:3.2.1.23-RXN
-property_value: skos:relatedMatch MetaCyc:BGALACT-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004566
@@ -46645,15 +47743,21 @@
xref: EC:3.2.1.31
xref: MetaCyc:BETA-GLUCURONID-RXN
xref: Reactome:R-HSA-1678854 "GUSB tetramer hydrolyses CS/HS precursor"
-xref: Reactome:R-HSA-2162226 "GUSB tetramer hydrolyses GlcA-1,3-GlcNAc"
+xref: Reactome:R-HSA-2162226 "GUSB tetramer hydrolyzes GlcA-1,3-GlcNAc"
xref: Reactome:R-HSA-2162227 "GUSB tetramer hydrolyses (HA)2"
xref: Reactome:R-HSA-2318373 "Defective GUSB does not hydrolyse (HA)2"
xref: Reactome:R-HSA-9036068 "Defective GUSB does not hydrolyse GlcA-1,3-GlcNAc"
xref: Reactome:R-HSA-9036070 "Defective GUSB does not hydrolyse CS/HS precursor"
xref: RHEA:17633
+xref: RHEA:28326
+xref: RHEA:30475
+xref: RHEA:76111
is_a: GO:0046574 ! glucuronidase activity
property_value: skos:exactMatch EC:3.2.1.31
property_value: skos:exactMatch RHEA:17633
+property_value: skos:narrowMatch RHEA:28326
+property_value: skos:narrowMatch RHEA:30475
+property_value: skos:narrowMatch RHEA:76111
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30698" xsd:anyURI
@@ -46787,6 +47891,7 @@
xref: Reactome:R-HSA-4793947 "Defective MOGS does not cleave glucose from an N-glycosylated protein"
xref: Reactome:R-HSA-532678 "Trimming of the first glucose by by mannosyl-oligosaccharide glucosidase"
xref: Reactome:R-HSA-9694364 "N-glycan glucose trimming of Spike"
+xref: Reactome:R-HSA-9932344 "MOGS removes terminal glucose from Glu3Man9GlcNAc2-CDH1"
xref: RHEA:55988
is_a: GO:0090599 ! alpha-glucosidase activity
property_value: skos:exactMatch EC:3.2.1.106
@@ -46910,10 +48015,17 @@
xref: MetaCyc:RXN-16761
xref: Reactome:R-HSA-446209 "Transfer of N-glycan to the protein"
xref: Reactome:R-HSA-9694793 "Spike protein gets N-glycosylated"
+xref: Reactome:R-HSA-9816276 "CDH1 is N-glycosylated on asparagine residues in endoplasmic reticulum"
+xref: Reactome:R-HSA-9918962 "E is N-glycosylated"
+xref: Reactome:R-HSA-9918988 "pre-M is N-glycosylated"
+xref: Reactome:R-HSA-9919011 "Pre-NS1 folds and is N-glycosylated"
+xref: Reactome:R-HSA-9931286 "CD274 N-linked glycosylation in ER"
xref: RHEA:22980
+xref: RHEA:50348
is_a: GO:0004576 ! oligosaccharyl transferase activity
property_value: skos:exactMatch EC:2.4.99.18
property_value: skos:exactMatch RHEA:22980
+property_value: skos:narrowMatch RHEA:50348
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26808" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -47021,6 +48133,7 @@
xref: EC:2.1.3.3
xref: MetaCyc:ORNCARBAMTRANSFER-RXN
xref: Reactome:R-HSA-70560 "carbamoyl phosphate + ornithine => citrulline + orthophosphate"
+xref: Reactome:R-HSA-9956527 "OTC variants don't synthesize L-citrulline"
xref: RHEA:19513
is_a: GO:0016743 ! carboxyl- or carbamoyltransferase activity
relationship: part_of GO:0006591 ! ornithine metabolic process
@@ -47048,9 +48161,9 @@
[Term]
id: GO:0004587
-name: ornithine aminotransferase activity
+name: L-ornithine transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 2-oxocarboxylate + L-ornithine = an L-alpha-amino acid + L-glutamate 5-semialdehyde." [EC:2.6.1.13]
+def: "Catalysis of the reaction: a 2-oxocarboxylate + L-ornithine = L-glutamate 5-semialdehyde + an L-alpha-amino acid." [RHEA:13877]
synonym: "GabT" RELATED [EC:2.6.1.13]
synonym: "L-ornithine 5-aminotransferase activity" RELATED [EC:2.6.1.13]
synonym: "L-ornithine aminotransferase activity" RELATED [EC:2.6.1.13]
@@ -47058,6 +48171,7 @@
synonym: "L-ornithine:alpha-ketoglutarate delta-aminotransferase activity" RELATED [EC:2.6.1.13]
synonym: "OAT" RELATED [EC:2.6.1.13]
synonym: "ornithine 5-aminotransferase activity" RELATED [EC:2.6.1.13]
+synonym: "ornithine aminotransferase activity" EXACT []
synonym: "ornithine delta-transaminase activity" RELATED [EC:2.6.1.13]
synonym: "ornithine ketoacid aminotransferase activity" RELATED [EC:2.6.1.13]
synonym: "ornithine transaminase activity" RELATED [EC:2.6.1.13]
@@ -47077,12 +48191,15 @@
xref: Reactome:R-HSA-70654 "ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]"
xref: Reactome:R-HSA-70666 "glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]"
xref: RHEA:13877
+xref: RHEA:25160
is_a: GO:0008483 ! transaminase activity
property_value: skos:exactMatch EC:2.6.1.13
property_value: skos:exactMatch MetaCyc:ORNITHINE--OXO-ACID-AMINOTRANSFERASE-RXN
property_value: skos:exactMatch RHEA:13877
+property_value: skos:narrowMatch RHEA:25160
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25975" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004588
@@ -47299,9 +48416,21 @@
xref: EC:2.3.1.255
xref: Reactome:R-HSA-6814090 "NatC acetylates ARFFRP1"
xref: RHEA:21028
+xref: RHEA:50508
+xref: RHEA:50512
+xref: RHEA:50516
+xref: RHEA:57320
+xref: RHEA:75243
+xref: RHEA:75247
is_a: GO:0034212 ! protein N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.255
property_value: skos:exactMatch RHEA:21028
+property_value: skos:narrowMatch RHEA:50508
+property_value: skos:narrowMatch RHEA:50512
+property_value: skos:narrowMatch RHEA:50516
+property_value: skos:narrowMatch RHEA:57320
+property_value: skos:narrowMatch RHEA:75243
+property_value: skos:narrowMatch RHEA:75247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24761" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27532" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29507" xsd:anyURI
@@ -47371,14 +48500,9 @@
xref: KEGG_REACTION:R03532
xref: Reactome:R-HSA-1222346 "AhpC reduces H2O2"
xref: Reactome:R-HSA-140359 "PGG2 is reduced to PGH2 by PTGS1"
-xref: Reactome:R-HSA-209815 "Tyrosine is monoiodinated"
-xref: Reactome:R-HSA-209840 "Two DITs combine to form thyroxine"
-xref: Reactome:R-HSA-209925 "DIT and MIT combine to form triiodothyronine"
-xref: Reactome:R-HSA-209973 "Tyrosine is diiodinated"
xref: Reactome:R-HSA-2309773 "PGG2 is reduced to PGH2 by PTGS2"
xref: Reactome:R-HSA-2559639 "Collagen type IV sulfilimine cross-linking by peroxidasin"
xref: Reactome:R-HSA-3341296 "GPX7,8 catalyze peroxidation of P4HB (PDI)"
-xref: Reactome:R-HSA-350901 "Iodide is organified"
xref: Reactome:R-HSA-5631885 "PRDX1 overoxidizes"
xref: Reactome:R-HSA-6789031 "Membrane-bound myeloperoxidase (MPO) produces hypochlorous acid (HOCl)"
xref: Reactome:R-HSA-6789126 "Myeloperoxidase (MPO) produces hypochlorous acid (HOCl)"
@@ -47398,7 +48522,7 @@
name: glutathione peroxidase activity
namespace: molecular_function
alt_id: GO:0016224
-def: "Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O." [EC:1.11.1.9, PMID:36771108]
+def: "Catalysis of the reaction: 2 glutathione + H2O2 = oxidized glutathione + 2 H2O." [EC:1.11.1.9, PMID:36771108]
synonym: "glutathione:hydrogen-peroxide oxidoreductase activity" RELATED [EC:1.11.1.9]
synonym: "GSH peroxidase activity" RELATED [EC:1.11.1.9]
synonym: "non-selenium glutathione peroxidase activity" NARROW []
@@ -47495,9 +48619,15 @@
xref: Reactome:R-HSA-1483121 "PA is converted to CDP-DAG by CDS1"
xref: Reactome:R-HSA-1483165 "PA is converted to CDP-DAG by CDS2"
xref: RHEA:16229
+xref: RHEA:45652
+xref: RHEA:45664
+xref: RHEA:45668
is_a: GO:0070567 ! cytidylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.41
property_value: skos:exactMatch RHEA:16229
+property_value: skos:narrowMatch RHEA:45652
+property_value: skos:narrowMatch RHEA:45664
+property_value: skos:narrowMatch RHEA:45668
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -47515,9 +48645,11 @@
xref: MetaCyc:2.3.1.43-RXN
xref: Reactome:R-HSA-264695 "cholesterol + phosphatidylcholine (lecithin) => cholesterol ester + 2-lysophosphatidylcholine (lysolecithin)"
xref: RHEA:21204
+xref: RHEA:34087
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.43
property_value: skos:exactMatch RHEA:21204
+property_value: skos:narrowMatch RHEA:34087
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -47537,10 +48669,18 @@
xref: MetaCyc:2.1.1.17-RXN
xref: Reactome:R-HSA-1483174 "PE is methylated to PC by PEMT"
xref: RHEA:11164
+xref: RHEA:70619
+xref: RHEA:70739
+xref: RHEA:70751
+xref: RHEA:70763
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.17
property_value: skos:exactMatch RHEA:11164
+property_value: skos:narrowMatch RHEA:70619
+property_value: skos:narrowMatch RHEA:70739
+property_value: skos:narrowMatch RHEA:70751
+property_value: skos:narrowMatch RHEA:70763
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -47693,7 +48833,7 @@
synonym: "phosphogluconic acid dehydrogenase activity" RELATED [EC:1.1.1.44]
xref: EC:1.1.1.44
xref: MetaCyc:RXN-9952
-xref: Reactome:R-HSA-71299 "6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+"
+xref: Reactome:R-HSA-71299 "PGD decarboxylates 6-phospho-D-gluconate"
xref: RHEA:10116
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.44
@@ -47757,7 +48897,7 @@
xref: KEGG_REACTION:R01512
xref: MetaCyc:PHOSGLYPHOS-RXN
xref: Reactome:R-HSA-70486 "PGK complexes (PGK1,2) phosphorylate 3PG to form 1,3BPG"
-xref: Reactome:R-HSA-71850 "1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ATP"
+xref: Reactome:R-HSA-71850 "PGK complexes dephosphorylate 1,3BPG"
xref: RHEA:14801
is_a: GO:0016301 ! kinase activity
is_a: GO:0016774 ! phosphotransferase activity, carboxyl group as acceptor
@@ -47783,8 +48923,8 @@
xref: KEGG_REACTION:R01516
xref: MetaCyc:3PGAREARR-RXN
xref: MetaCyc:RXN-15513
-xref: Reactome:R-HSA-71445 "PGAM dimers (PGAM1,2) isomerise 2PG to 3PG"
-xref: Reactome:R-HSA-71654 "3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate"
+xref: Reactome:R-HSA-71445 "PGAM dimers isomerise 2PG to 3PG"
+xref: Reactome:R-HSA-71654 "PGAM dimers isomerise 3PG to 2PG"
xref: RHEA:15901
is_a: GO:0016868 ! intramolecular phosphotransferase activity
property_value: skos:exactMatch RHEA:15901
@@ -47815,14 +48955,16 @@
id: GO:0004621
name: GPI anchor phospholipase D activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycoprotein phosphatidylinositol + H2O = phosphatidate + glycoprotein inositol, by cleavage of the second phosphodiester bond between the phosphate and phospholipid." [PMID:2760042]
+def: "Catalysis of the reaction: glycoprotein phosphatidylinositol + H2O = phosphatidate + glycoprotein inositol, by cleavage of the second phosphodiester bond between the phosphate and phospholipid." [PMID:2760042, RHEA:86263]
synonym: "glycoprotein phospholipase D activity" BROAD []
synonym: "glycoprotein-phosphatidylinositol phosphatidohydrolase activity" EXACT []
synonym: "glycosylphosphatidyl inositol-anchor protein phospholipase D activity" EXACT []
synonym: "GPI-PLD activity" EXACT []
xref: Reactome:R-HSA-8940388 "GPLD1 hydrolyses GPI-anchors from proteins"
+xref: RHEA:86263
is_a: GO:0004630 ! D-type glycerophospholipase activity
property_value: skos:broadMatch EC:3.1.4.50
+property_value: skos:exactMatch RHEA:86263
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28868" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31078" xsd:anyURI
@@ -48104,7 +49246,7 @@
xref: EC:4.2.1.11
xref: MetaCyc:2PGADEHYDRAT-RXN
xref: Reactome:R-HSA-70494 "Enolase dimers (ENO1,2,3) convert PEP to 2PG"
-xref: Reactome:R-HSA-71660 "2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O"
+xref: Reactome:R-HSA-71660 "Enolase dimers dehydrates 2PG"
xref: RHEA:10164
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.11
@@ -48364,15 +49506,16 @@
[Term]
id: GO:0004648
-name: O-phospho-L-serine:2-oxoglutarate aminotransferase activity
+name: O-phospho-L-serine:2-oxoglutarate transaminase activity
namespace: molecular_function
alt_id: GO:0004646
-def: "Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate." [EC:2.6.1.52]
+def: "Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate." [RHEA:14329]
synonym: "3-O-phospho-L-serine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.52]
synonym: "3-phosphoserine aminotransferase activity" RELATED [EC:2.6.1.52]
synonym: "3PHP transaminase activity" RELATED [EC:2.6.1.52]
synonym: "hydroxypyruvic phosphate--glutamic transaminase activity" RELATED [EC:2.6.1.52]
synonym: "L-phosphoserine aminotransferase activity" RELATED [EC:2.6.1.52]
+synonym: "O-phospho-L-serine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "PdxC" RELATED [EC:2.6.1.52]
synonym: "phosphohydroxypyruvate transaminase activity" RELATED [EC:2.6.1.52]
synonym: "phosphohydroxypyruvic--glutamic transaminase activity" RELATED [EC:2.6.1.52]
@@ -48388,6 +49531,7 @@
property_value: skos:exactMatch EC:2.6.1.52
property_value: skos:exactMatch RHEA:14329
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004649
@@ -48437,6 +49581,7 @@
xref: EC:3.1.3.33
xref: MetaCyc:RXN-21861
xref: Reactome:R-HSA-77078 "Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme"
+xref: Reactome:R-HSA-9923980 "NS3 cleaves triphosphate moiety of genomic +ssRNA"
xref: RHEA:67772
xref: RHEA:67776
is_a: GO:0016791 ! phosphatase activity
@@ -48594,8 +49739,7 @@
xref: EC:1.5.5.2
xref: MetaCyc:RXN-14903
xref: Reactome:R-HSA-6784224 "PRODH2:FAD dimer dehydrogenates HPRO to 1-pyrroline-3-hydroxy-5-carboxylate"
-xref: Reactome:R-HSA-70670 "PRODH oxidises L-Pro to 1PYR-5COOH"
-xref: Reactome:R-HSA-8955817 "PRODH2 oxidises HPRO to 1PYR-5COOH"
+xref: Reactome:R-HSA-8955817 "PRODH2 oxidises HPRO to 1PYR-3OH-5COOH"
xref: RHEA:23784
is_a: GO:0016649 ! oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.5.5.2
@@ -48645,6 +49789,7 @@
xref: MetaCyc:RXN-17573
xref: Reactome:R-HSA-2530501 "FNTA:FNTB transfers FARN to GNGT1"
xref: Reactome:R-HSA-9647978 "pro-RAS proteins are farnesylated"
+xref: Reactome:R-HSA-9948016 "FNTA:FNTB transfers farnesyl to GBP1"
xref: RHEA:13345
is_a: GO:0008318 ! protein prenyltransferase activity
property_value: skos:exactMatch EC:2.5.1.58
@@ -48676,6 +49821,8 @@
synonym: "type I protein geranyl-geranyltransferase activity" RELATED [EC:2.5.1.59]
xref: EC:2.5.1.59
xref: MetaCyc:RXN-3701
+xref: Reactome:R-HSA-9947999 "FNTA:PGGT1B geranylgeranylates GBP2"
+xref: Reactome:R-HSA-9954195 "FNTA:PGGT1B geranylgeranylates GBP5"
is_a: GO:0004661 ! protein geranylgeranyltransferase activity
property_value: skos:exactMatch EC:2.5.1.59
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25798" xsd:anyURI
@@ -48843,6 +49990,7 @@
subset: goslim_candida
synonym: "protamine kinase activity" NARROW []
xref: Reactome:R-HSA-156832 "INF-gamma induced phosphorylation of L13a"
+xref: Reactome:R-HSA-5693148 "BCKDK phosphorylates BCKDH"
xref: Reactome:R-HSA-937034 "IRAK1 phosphorylates Pellino"
xref: Reactome:R-HSA-9604606 "Unknown kinase phosphorylates NICD4"
xref: Reactome:R-HSA-9673284 "GTP-bound RAC1 contributes to MAPK8 activation"
@@ -48966,9 +50114,9 @@
xref: Reactome:R-HSA-168140 "Active IKK Complex phosphorylates NF-kappa-B inhibitor"
xref: Reactome:R-HSA-168184 "Activated TAK1 mediates phosphorylation of the IKK Complex"
xref: Reactome:R-HSA-170055 "Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes"
-xref: Reactome:R-HSA-170076 "CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes"
-xref: Reactome:R-HSA-170087 "CAK-mediated phosphorylation of Cyclin A:Cdc2 complexes"
-xref: Reactome:R-HSA-170116 "Myt-1 mediated phosphorylation of Cyclin A:Cdc2"
+xref: Reactome:R-HSA-170076 "CAK phosphorylates CDK1 bound to CCNB1"
+xref: Reactome:R-HSA-170087 "CAK phosphorylates CDK1 bound to CCNA"
+xref: Reactome:R-HSA-170116 "PKMYT1 phosphorylates CCNA:CDK1"
xref: Reactome:R-HSA-170126 "Phosphorylation of Cyclin B1 in the CRS domain"
xref: Reactome:R-HSA-170977 "FRS2 is phosphorylated by active TrkA receptor"
xref: Reactome:R-HSA-174119 "Free APC/C phosphorylated by Plk1"
@@ -48979,6 +50127,7 @@
xref: Reactome:R-HSA-187949 "CAK-mediated phosphorylation of Cyclin A:Cdk2"
xref: Reactome:R-HSA-188350 "CAK-mediated phosphorylation of Cyclin E:Cdk2"
xref: Reactome:R-HSA-193647 "IRAK is activated"
+xref: Reactome:R-HSA-193703 "IKKbeta is activated"
xref: Reactome:R-HSA-193705 "IKKbeta phosphorylates IkB causing NF-kB to dissociate"
xref: Reactome:R-HSA-195275 "Phosphorylation of APC component of the destruction complex"
xref: Reactome:R-HSA-195283 "Phosphorylation of phospho- (Ser45, Thr41) beta-catenin at Ser37 by GSK-3"
@@ -49117,7 +50266,6 @@
xref: Reactome:R-HSA-399951 "Phosphorylation of CRMPs by GSK3beta"
xref: Reactome:R-HSA-399952 "Phosphorylation of LIMK-1 by PAK"
xref: Reactome:R-HSA-399978 "Protein kinase C, alpha type phosphorylates MARCKS"
-xref: Reactome:R-HSA-400382 "CSNK1E,CSNK1D phosphorylate CRY and PER proteins"
xref: Reactome:R-HSA-4088134 "PLK1 phosphorylates FOXM1"
xref: Reactome:R-HSA-419083 "Myosin phosphatase inactivation by ROCK"
xref: Reactome:R-HSA-419087 "LIM kinase phosphorylation by ROCK"
@@ -49178,8 +50326,10 @@
xref: Reactome:R-HSA-5610722 "CK1 phosphorylates p-GLI3"
xref: Reactome:R-HSA-5610730 "GSK3 phosphorylates p-GLI2"
xref: Reactome:R-HSA-5610732 "GSK3 phosphorylates p-GLI3"
+xref: Reactome:R-HSA-5623667 "PDPK1 phosphorylates PKN1,2,3"
xref: Reactome:R-HSA-5624473 "Protein kinase A (PKA) and RPS6KA5 (MSK1) phosphorylates p65 (RELA) subunit"
xref: Reactome:R-HSA-5624492 "PAK phosphorylates p21 RAF1 on S338"
+xref: Reactome:R-HSA-5625784 "PKN1 phosphorylates histone 3 of nucleosomes associate with KLK2 and KLK3 promoters"
xref: Reactome:R-HSA-5627775 "Autophosphorylation of PAK1,2,3"
xref: Reactome:R-HSA-5632670 "CSNK1A1 phosphorylates SMO dimer"
xref: Reactome:R-HSA-5632672 "ADRBK1 phosphorylates SMO dimer"
@@ -49192,6 +50342,7 @@
xref: Reactome:R-HSA-5668947 "PAK1 phosphorylates myosin phosphatase"
xref: Reactome:R-HSA-5668984 "PAK1 or PAK2 phosphorylates MYLK"
xref: Reactome:R-HSA-5669250 "PAK1 phosphorylates FLNA"
+xref: Reactome:R-HSA-5671749 "p-T774-PKN1 phosphorylates CDC25C"
xref: Reactome:R-HSA-5671763 "p-T774-PKN1 phosphorylates PPP1R14A"
xref: Reactome:R-HSA-5671919 "Activated CIT phosphorylates MRLCs"
xref: Reactome:R-HSA-5672008 "Thr-180 of ULK1 is phosphorylated"
@@ -49274,8 +50425,8 @@
xref: Reactome:R-HSA-6810233 "CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter"
xref: Reactome:R-HSA-6811454 "MAPKs phosphorylate PP2A"
xref: Reactome:R-HSA-6814409 "CK2 phosphorylates PDCL"
-xref: Reactome:R-HSA-69604 "Phosphorylation of Cdc25A at Ser-123 by Chk1"
-xref: Reactome:R-HSA-69608 "Phosphorylation of Cdc25A at Ser-123 by Chk2"
+xref: Reactome:R-HSA-69604 "Phosphorylation of CDC25A by CHEK1"
+xref: Reactome:R-HSA-69608 "Phosphorylation of CDC25A by CHEK2"
xref: Reactome:R-HSA-69685 "CHEK2 phosphorylates TP53"
xref: Reactome:R-HSA-69891 "Phosphorylation and activation of CHEK2 by ATM"
xref: Reactome:R-HSA-75010 "Phosphorylation of Cdc25C at Ser 216 by Chk1"
@@ -49323,6 +50474,7 @@
xref: Reactome:R-HSA-9009208 "Activated ERKs phosphorylate RUNX2"
xref: Reactome:R-HSA-9012319 "p-TEFb phosphorylates serine 2 in RNA polymerase II CTD"
xref: Reactome:R-HSA-9013978 "Phosphorylation of IRF-3/IRF7 and their release from the activated TLR3 complex"
+xref: Reactome:R-HSA-9021357 "PRKCI phosphorylates ELF3"
xref: Reactome:R-HSA-9022314 "HIPK2 phosphorylates MECP2"
xref: Reactome:R-HSA-9023132 "AURKB phosphorylates MECP2 at S423"
xref: Reactome:R-HSA-9032751 "Estrogen-independent phosphorylation of ESR1 S118 by MAPK1 and MAPK3"
@@ -49330,6 +50482,7 @@
xref: Reactome:R-HSA-912470 "ATR phosphorylates Histone H2A.X at unsynapsed regions"
xref: Reactome:R-HSA-913996 "PKA/PKG phosphorylate Rap1GAP2"
xref: Reactome:R-HSA-918229 "Phosphorylation and release of IRF3/IRF7"
+xref: Reactome:R-HSA-927889 "SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)"
xref: Reactome:R-HSA-933525 "Phosphorylation and release of IRF7"
xref: Reactome:R-HSA-934559 "SPRY2 is phosphorylated by phosphorylated MNK1"
xref: Reactome:R-HSA-936951 "Activation of TAK1 complex bound to activated TLR4 complex"
@@ -49349,6 +50502,7 @@
xref: Reactome:R-HSA-9624526 "AKT phosphorylates FOXO3 downstream of ESR1 and EGFR"
xref: Reactome:R-HSA-9626880 "MAPK11 or MAPK14 phosphorylates NCF1 at Ser345"
xref: Reactome:R-HSA-9627089 "CASP9 is phosphorylated at T412"
+xref: Reactome:R-HSA-9632858 "PRKCZ autophosphorylates downstream of estrogen stimulation"
xref: Reactome:R-HSA-9632868 "CDKN1B is phosphorylated in response to estrogen"
xref: Reactome:R-HSA-9633008 "p-T899-EIF2AK4 (GCN2) phosphorylates EIF2AS1"
xref: Reactome:R-HSA-9633742 "EIF2AK4 (GCN2) dimer autophosphorylates"
@@ -49385,9 +50539,11 @@
xref: Reactome:R-HSA-975874 "Second phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR complex"
xref: Reactome:R-HSA-975878 "First phosphorylation of IRAK1 by IRAK4 bound to MyD88:activated TLR"
xref: Reactome:R-HSA-9762094 "GSK3B phosphorylates p-NFE2L2"
+xref: Reactome:R-HSA-9765960 "ERKs phosphorylate MCRIP1"
xref: Reactome:R-HSA-9766532 "SQSTM1 oligomer is phosphorylated"
xref: Reactome:R-HSA-9769115 "MAPK1,(MAPK3) phosphorylates NPAS4"
xref: Reactome:R-HSA-9773803 "Active IKBKB phosphorylates NF-kappa-B inhibitor"
+xref: Reactome:R-HSA-9796053 "PRKCI phosphorylates NFE2L2"
xref: Reactome:R-HSA-9796067 "PRKAA2 phosphorylates nuclear NFE2L2"
xref: Reactome:R-HSA-9796081 "EIF2AK3 phosphorylates NFE2L2"
xref: Reactome:R-HSA-9815501 "MAPKAPK2 phosphorylates RIPK1 at S320"
@@ -49411,10 +50567,31 @@
xref: Reactome:R-HSA-9851972 "PLK1 phosphorylates FIRRM at S43"
xref: Reactome:R-HSA-9853369 "PLK1 phosphorylates FIRMM at S744"
xref: Reactome:R-HSA-9855910 "USF1 is phosphorylated by p-MAPK14"
+xref: Reactome:R-HSA-9857661 "p-T308,S473-AKT1 (phospho-PKB) phosphorylates GJA1 (Connexin-43)"
+xref: Reactome:R-HSA-9857673 "p-T308,S473-AKT1 phosphorylates ITGA5 (Integrin alpha5) in ITGA5:ITGB1 (Integrin alpha5:Integrin beta1)"
xref: Reactome:R-HSA-9860292 "Activated IKBKB phosphorylates IRF5"
xref: Reactome:R-HSA-9860785 "PDPK1 (PDK1) phosphorylates PKN2 on threonine-816"
xref: Reactome:R-HSA-9860800 "mTORC2 phosphorylates AKT1 on serine-473"
xref: Reactome:R-HSA-9861642 "NEK1 phosphorylates ME1"
+xref: Reactome:R-HSA-9909369 "CSNK1E,CSNK1D phosphorylate CRY and PER proteins"
+xref: Reactome:R-HSA-9912396 "CDK5 phosphorylates CLOCK on serine-451 and serine-461"
+xref: Reactome:R-HSA-9912401 "CK2alpha phosphorylates BMAL1 (ARNTL) on serine-90"
+xref: Reactome:R-HSA-9920673 "CDK5 phosphorylates PER2 on serine-396"
+xref: Reactome:R-HSA-9922273 "CSNK1D,E phosphorylates CLOCK in p-S-CRY:p-S-PER:CSNK1D,E:p-S90,Ac-538-BMAL:p-2T,3S-CLOCK:target gene"
+xref: Reactome:R-HSA-9926483 "MARK3 phosphorylates MITF-M on S173"
+xref: Reactome:R-HSA-9929360 "GSK3B phosphorylates CD274"
+xref: Reactome:R-HSA-9931292 "AMPK phosphorylates CD274"
+xref: Reactome:R-HSA-9931409 "NEK2 phosphorylates CD274"
+xref: Reactome:R-HSA-9931418 "CK2 phosphorylates CD274"
+xref: Reactome:R-HSA-9933380 "Cytosolic tail of CDH1 is phosphorylated"
+xref: Reactome:R-HSA-9942578 "Phosphorylation of CDC25A by p38 MAPK"
+xref: Reactome:R-HSA-9943662 "CHEK1 phosphorylates NEK11"
+xref: Reactome:R-HSA-9943675 "GSK3B phosphorylates CDC25A"
+xref: Reactome:R-HSA-9943676 "NEK11 phosphorylates CDC25A"
+xref: Reactome:R-HSA-9943678 "CHEK1 phosphorylates CHEK2-phosphorylated CDC25A"
+xref: Reactome:R-HSA-9943687 "PLK3 phosphorylates CDC25A"
+xref: Reactome:R-HSA-9943736 "Casein kinase I phosphorylates CDC25A"
+xref: Reactome:R-HSA-9954237 "PIM1 phosphorylates GBP1"
is_a: GO:0004672 ! protein kinase activity
property_value: skos:exactMatch EC:2.7.11.-
property_value: skos:exactMatch MetaCyc:PROTEIN-KINASE-RXN
@@ -49685,7 +50862,7 @@
xref: EC:2.7.11.11
xref: Reactome:R-HSA-163672 "Phosphorylation of ChREBP at Thr(653) by PKA"
xref: Reactome:R-HSA-163676 "Phosphorylation of pChREBP (Thr 653) at Ser(196) by PKA"
-xref: Reactome:R-HSA-163773 "Phosphorylation of PF2K-Pase by PKA catalytic subunit"
+xref: Reactome:R-HSA-163773 "PKA tetramer:cAMP phosphorylates PF2K-Pase"
xref: Reactome:R-HSA-177275 "PKA phosphorylates DARPP-32 on Thr34"
xref: Reactome:R-HSA-177284 "PKA phosphorylates PDE4B"
xref: Reactome:R-HSA-432232 "Phosphorylation of Aquaporin-2 by Protein Kinase A (PKA)"
@@ -49722,6 +50899,7 @@
xref: Reactome:R-HSA-1497853 "Sepiapterin reductase (SPR) is phosphorylated by Ca2+/calmodulin-dependent protein kinase II"
xref: Reactome:R-HSA-418442 "PKG1 phosphorylates IRAG:IP3R1 inhibiting IP3-stimulated Ca2+ release"
xref: Reactome:R-HSA-418549 "PKG1 phosphorylates BK channels"
+xref: Reactome:R-HSA-9920025 "PKG phosphorylates NS5"
is_a: GO:0004690 ! cyclic nucleotide-dependent protein kinase activity
relationship: has_part GO:0030553 ! cGMP binding
property_value: skos:exactMatch EC:2.7.11.12
@@ -49779,7 +50957,7 @@
xref: Reactome:R-HSA-2990882 "CDK1 phosphorylates NUP98"
xref: Reactome:R-HSA-3788705 "CDKN1A (p21) prevents phosphorylation of Cdh1 by Cyclin A:Cdk2"
xref: Reactome:R-HSA-380278 "CCNB1:p-T160-CDK1 phosphorylates NUMA1"
-xref: Reactome:R-HSA-4086410 "CDK1 phosphorylates BORA"
+xref: Reactome:R-HSA-4086410 "CCNB:CDK1 phosphorylates BORA"
xref: Reactome:R-HSA-4088024 "CCNA:CDK1/2 complexes and CCNB1:CDK1 complexes phosphorylate FOXM1"
xref: Reactome:R-HSA-5195402 "CDK1 phosphorylates LPIN"
xref: Reactome:R-HSA-5244669 "CDK1 phosphorylates lamins and facilitates depolymerization of lamin filaments"
@@ -49790,12 +50968,21 @@
xref: Reactome:R-HSA-68944 "Orc1 is phosphorylated by cyclin A/CDK2"
xref: Reactome:R-HSA-69005 "Cdc6 protein is phosphorylated by CDK"
xref: Reactome:R-HSA-69227 "Cyclin D:CDK4/6 phosphorylates RB1 and prevents RB1 binding to E2F1/2/3:DP1/2 complexes"
-xref: Reactome:R-HSA-69754 "Phosphorylation of proteins involved in G2/M transition by active Cyclin A1:Cdc2 complexes"
-xref: Reactome:R-HSA-69756 "Phosphorylation of proteins involved in G2/M transition by active Cyclin A2:Cdc2 complexes"
xref: Reactome:R-HSA-9008412 "CDK4 phosphorylates RUNX2"
xref: Reactome:R-HSA-9009282 "CDK1 phosphorylates RUNX2"
xref: Reactome:R-HSA-9624800 "CDK1 phosphorylates LBR"
xref: Reactome:R-HSA-9686521 "CDK2:CCNA phosphorylates TERF2"
+xref: Reactome:R-HSA-9929482 "CDK4:CCND1 phosphorylates SPOP"
+xref: Reactome:R-HSA-9929514 "CDK1 phosphorylates CCNA"
+xref: Reactome:R-HSA-9929532 "CCNA:CDK1 phosphorylates BORA"
+xref: Reactome:R-HSA-9929535 "CCNA:CDK1 phosphorylates WEE1"
+xref: Reactome:R-HSA-9929717 "CCNA:CDK1 phosphorylates FZR1"
+xref: Reactome:R-HSA-9929719 "CCNA:CDK1 phosphorylates TICRR"
+xref: Reactome:R-HSA-9929720 "CCNA:CDK1 phosphorylates OBI1"
+xref: Reactome:R-HSA-9929721 "CCNA:CDK1 phosphorylates SGO1"
+xref: Reactome:R-HSA-9929884 "CCNA:CDK1 phosphorylates HJURP"
+xref: Reactome:R-HSA-9929904 "CCNA:CDK1 phosphorylates MIS18BP1"
+xref: Reactome:R-HSA-9929935 "CCNA:CDK1 phosphorylates CDC25B"
is_a: GO:0004674 ! protein serine/threonine kinase activity
is_a: GO:0097472 ! cyclin-dependent protein kinase activity
property_value: skos:exactMatch EC:2.7.11.22
@@ -49840,33 +51027,9 @@
synonym: "protein kinase Cepsilon activity" NARROW [EC:2.7.11.13]
synonym: "STK24" RELATED [EC:2.7.11.13]
xref: EC:2.7.11.13
-xref: Reactome:R-HSA-1433508 "PKC alpha interacts with and phosphorylates KIT"
-xref: Reactome:R-HSA-193703 "IKKbeta is activated"
-xref: Reactome:R-HSA-198314 "DAG stimulates protein kinase C-delta"
-xref: Reactome:R-HSA-2179413 "Activated PKC-alpha activate MMP3"
-xref: Reactome:R-HSA-2730863 "Phosphorylation of CARMA1 by PKC-theta"
-xref: Reactome:R-HSA-374664 "Phosphorylation and activation of Ezrin"
-xref: Reactome:R-HSA-429698 "PRKD1,2,3 phosphorylates CERT1-2"
-xref: Reactome:R-HSA-450533 "PKCdelta phosphorylates HuR"
-xref: Reactome:R-HSA-450550 "PKCalpha phosphorylates HuR"
-xref: Reactome:R-HSA-5138432 "DVL2 is phosphorylated by PKC"
xref: Reactome:R-HSA-5218805 "PKC autophosphorylates"
-xref: Reactome:R-HSA-5218823 "PKC phosphorylates sphingosine kinase 1"
-xref: Reactome:R-HSA-5229194 "Depolymerization of lamin filaments after PKC-mediated phosphorylation"
-xref: Reactome:R-HSA-5623667 "PDPK1 phosphorylates PKN1,2,3"
-xref: Reactome:R-HSA-5625784 "PKN1 phosphorylates histone 3 of nucleosomes associate with KLK2 and KLK3 promoters"
-xref: Reactome:R-HSA-5671749 "p-T774-PKN1 phosphorylates CDC25C"
-xref: Reactome:R-HSA-74615 "PRKCA/Q phosphorylate RGS9-1:GN5B:RGS9BP"
xref: Reactome:R-HSA-751040 "PKC phosphorylates G alpha (z)"
-xref: Reactome:R-HSA-8932284 "PKC phosphorylates NFE2L2"
-xref: Reactome:R-HSA-8934446 "Activated PKC phosphorylates SHC1"
-xref: Reactome:R-HSA-9010681 "PKC phosphorylates ROBO3.1"
-xref: Reactome:R-HSA-9021357 "PRKCI phosphorylates ELF3"
-xref: Reactome:R-HSA-909552 "Phosphorylation of STAT1 at Ser727"
-xref: Reactome:R-HSA-927889 "SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)"
xref: Reactome:R-HSA-9626817 "PKC phosphorylates NCF1"
-xref: Reactome:R-HSA-9632858 "PRKCZ autophosphorylates downstream of estrogen stimulation"
-xref: Reactome:R-HSA-9796053 "PRKCI phosphorylates NFE2L2"
is_a: GO:0004674 ! protein serine/threonine kinase activity
property_value: skos:exactMatch EC:2.7.11.13
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25457" xsd:anyURI
@@ -49881,10 +51044,19 @@
synonym: "conventional protein kinase C activity" EXACT [PMID:9601053]
xref: Reactome:R-HSA-114683 "Phosphorylation of Platelet Sec-1"
xref: Reactome:R-HSA-114684 "Phosphorylation of Syntaxin-4"
+xref: Reactome:R-HSA-1433508 "PKC alpha interacts with and phosphorylates KIT"
+xref: Reactome:R-HSA-2179413 "Activated PKC-alpha activate MMP3"
xref: Reactome:R-HSA-416639 "Trafficking of GluR2-containing AMPA receptors to extrasynaptic sites"
xref: Reactome:R-HSA-421007 "Endocytosis of Ca impermeable AMPA receptors"
+xref: Reactome:R-HSA-450550 "PKCalpha phosphorylates HuR"
+xref: Reactome:R-HSA-5138432 "DVL2 is phosphorylated by PKC"
+xref: Reactome:R-HSA-5218823 "PKC phosphorylates sphingosine kinase 1"
+xref: Reactome:R-HSA-5229194 "Depolymerization of lamin filaments after PKC-mediated phosphorylation"
+xref: Reactome:R-HSA-74615 "PRKCA/Q phosphorylate RGS9-1:GN5B:RGS9BP"
+xref: Reactome:R-HSA-8934446 "Activated PKC phosphorylates SHC1"
xref: Reactome:R-HSA-8986937 "MECP2 is phosphorylated at T308"
xref: Reactome:R-HSA-9005561 "Active PKA, CaMK IV do not phosphorylate MECP2 mutants R306C,(R306H) at T308"
+xref: Reactome:R-HSA-9010681 "PKC phosphorylates ROBO3.1"
is_a: GO:0004697 ! diacylglycerol-dependent serine/threonine kinase activity
is_a: GO:0009931 ! calcium-dependent protein serine/threonine kinase activity
property_value: skos:broadMatch EC:2.7.11.13
@@ -49899,7 +51071,14 @@
synonym: "atypical protein kinase C activity" RELATED []
synonym: "calcium-independent PKC activity" EXACT []
synonym: "novel protein kinase C activity" EXACT [PMID:9601053]
+xref: Reactome:R-HSA-198314 "DAG stimulates protein kinase C-delta"
+xref: Reactome:R-HSA-2730863 "Phosphorylation of CARMA1 by PKC-theta"
+xref: Reactome:R-HSA-374664 "Phosphorylation and activation of Ezrin"
+xref: Reactome:R-HSA-429698 "PRKD1,2,3 phosphorylates CERT1-2"
+xref: Reactome:R-HSA-450533 "PKCdelta phosphorylates HuR"
xref: Reactome:R-HSA-5607740 "PKC-delta phosphorylates CARD9"
+xref: Reactome:R-HSA-8932284 "PKC phosphorylates NFE2L2"
+xref: Reactome:R-HSA-909552 "Phosphorylation of STAT1 at Ser727"
is_a: GO:0004697 ! diacylglycerol-dependent serine/threonine kinase activity
property_value: skos:broadMatch EC:2.7.11.13
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25457" xsd:anyURI
@@ -50167,7 +51346,7 @@
xref: Reactome:R-HSA-1524186 "Phosphorylation of PLCgamma by PDGFR"
xref: Reactome:R-HSA-1671691 "PRLR-bound STAT5 is phosphorylated"
xref: Reactome:R-HSA-170070 "Wee1-mediated phosphorylation of Cyclin B1:phospho-Cdc2 complexes"
-xref: Reactome:R-HSA-170156 "Wee1-mediated phosphorylation of Cyclin A:phospho-Cdc2 complexes"
+xref: Reactome:R-HSA-170156 "WEE1 phosphorylates CCNA:CDK1"
xref: Reactome:R-HSA-170991 "SRC-1 autophosphorylates"
xref: Reactome:R-HSA-171011 "Binding and activation of MAP Kinase"
xref: Reactome:R-HSA-174164 "Phosphorylation of Cyclin A:Cdk2 at Tyr 15"
@@ -50526,6 +51705,8 @@
xref: Reactome:R-HSA-9860759 "p-T816-PKN2 phosphorylates AKT1 on serine-308"
xref: Reactome:R-HSA-9861469 "p-Y397-PTK2 (FAK) phosphorylates CHUK (IKKA)"
xref: Reactome:R-HSA-9865196 "p-Y393-ABL1 phosphorylates tyrosine-407 of YAP1"
+xref: Reactome:R-HSA-9931290 "IL6-activated JAK1 phosphorylates CD274"
+xref: Reactome:R-HSA-9934751 "CDH1 is phosphorylated on tyrosine residues"
xref: RHEA:10596
is_a: GO:0004672 ! protein kinase activity
property_value: skos:exactMatch EC:2.7.10.-
@@ -50678,7 +51859,7 @@
name: protein-lysine 6-oxidase activity
namespace: molecular_function
alt_id: GO:0018056
-def: "Catalysis of the reaction: peptidyl-L-lysyl-peptide + H2O + O2 = peptidyl-allysyl-peptide + NH3 + hydrogen peroxide." [EC:1.4.3.13]
+def: "Catalysis of the reaction: L-lysyl-[protein] + O2 + H2O = (S)-2-amino-6-oxohexanoyl-[protein] + H2O2 + NH4+." [RHEA:24544]
synonym: "lysyl oxidase activity" RELATED [EC:1.4.3.13]
synonym: "protein-L-lysine:oxygen 6-oxidoreductase (deaminating)" RELATED [EC:1.4.3.13]
xref: EC:1.4.3.13
@@ -50711,7 +51892,7 @@
xref: Reactome:R-HSA-1363276 "Dephosphorylation of p130 (RBL2) by PP2A"
xref: Reactome:R-HSA-167072 "Hypophosphorylation of RNA Pol II CTD by FCP1P protein"
xref: Reactome:R-HSA-170153 "Dephosphorylation of nuclear Cyclin B1:phospho-Cdc2 (Thr 14, Tyr15) complexes by Cdc25 phosphatases"
-xref: Reactome:R-HSA-170158 "Dephosphorylation of nuclear Cyclin A:phospho-Cdc2 complexes"
+xref: Reactome:R-HSA-170158 "CDC25A dephosphorylates CCNA:CDK1"
xref: Reactome:R-HSA-170161 "Dephosphorylation of cytoplasmic Cyclin B1/B2:phospho-Cdc2 (Thr 14, Tyr 15) complexes by CDC25B"
xref: Reactome:R-HSA-174110 "Cdc25A mediated dephosphorylation of Cyclin A:phospho-Cdk2"
xref: Reactome:R-HSA-174124 "Dephosphorylation of phospho-Cdh1"
@@ -50760,8 +51941,8 @@
xref: MetaCyc:3.1.3.16-RXN
xref: Reactome:R-HSA-1295632 "PPA2A dephosphorylates SPRY2"
xref: Reactome:R-HSA-163568 "phosphorylated perilipin + H2O -> perilipin + orthophosphate"
-xref: Reactome:R-HSA-163689 "Dephosphorylation of pChREBP (Ser 196) by PP2A"
-xref: Reactome:R-HSA-163750 "Dephosphorylation of phosphoPFKFB1 by PP2A complex"
+xref: Reactome:R-HSA-163689 "PP2A complex dephosphorylates pChREBP (MLXIPL)"
+xref: Reactome:R-HSA-163750 "PP2A complex dephosphorylates pPFKFB1"
xref: Reactome:R-HSA-1638821 "PP2A-B56 dephosphorylates centromeric cohesin"
xref: Reactome:R-HSA-199425 "PHLPP dephosphorylates S473 in AKT"
xref: Reactome:R-HSA-199959 "ERKs are inactivated by protein phosphatase 2A"
@@ -50784,7 +51965,6 @@
xref: Reactome:R-HSA-5683405 "PPP5C dephosphorylates TP53BP1"
xref: Reactome:R-HSA-5687758 "PPP4C:PPP4R2 dephosphorylates RPA2"
xref: Reactome:R-HSA-5692754 "CDC14A,B dephosphorylate p-3S,T MAPK6"
-xref: Reactome:R-HSA-5693153 "PPM1K dephosphorylates p-BCKDH"
xref: Reactome:R-HSA-5694421 "PP6 dephosphorylates SEC24"
xref: Reactome:R-HSA-6792863 "PP2A-PP2R5C dephosphorylates MDM2"
xref: Reactome:R-HSA-6811504 "AKT1 dephosphorylation by PP2A-B56-beta,gamma"
@@ -50803,6 +51983,7 @@
xref: Reactome:R-HSA-9865226 "PP2A dephosphorylates serine-127 of YAP1"
xref: Reactome:R-HSA-9865238 "PP2A dephosphorylates serine-715 of PDE4D5 in p-S715-PDE4D5:integrin alpha5:integrin beta1:fibronectin"
xref: Reactome:R-HSA-9912527 "H139Hfs13* PPM1K does not dephosphorylate BCKDH"
+xref: Reactome:R-HSA-9970190 "PP1 dephosphorylates RNA Pol II"
xref: RHEA:20629
xref: RHEA:47004
is_a: GO:0004721 ! phosphoprotein phosphatase activity
@@ -50997,9 +52178,15 @@
xref: Reactome:R-HSA-9735789 "Defective PNP does not convert (deoxy)guanosine to guanine and (deoxy)ribose"
xref: Reactome:R-HSA-9755044 "PNP trimer transforms RBV to T-CONH2"
xref: RHEA:19805
+xref: RHEA:27638
+xref: RHEA:27642
+xref: RHEA:27646
is_a: GO:0016763 ! pentosyltransferase activity
property_value: skos:exactMatch EC:2.4.2.1
property_value: skos:exactMatch RHEA:19805
+property_value: skos:narrowMatch RHEA:27638
+property_value: skos:narrowMatch RHEA:27642
+property_value: skos:narrowMatch RHEA:27646
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -51021,7 +52208,7 @@
id: GO:0004733
name: pyridoxamine phosphate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH4+ + hydrogen peroxide. This activity can also oxidize pyridoxine 5'-phosphate to pyridoxal 5'-phosphate + hydrogen peroxide." [PMID:11786019]
+def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH4+ + H2O2. This activity can also oxidize pyridoxine 5'-phosphate to pyridoxal 5'-phosphate + H2O2." [EC:1.4.3.5, PMID:11786019]
synonym: "PMP oxidase activity" RELATED [EC:1.4.3.5]
synonym: "pyridoxal 5'-phosphate synthase activity" RELATED [EC:1.4.3.5]
synonym: "pyridoxamine 5'-phosphate oxidase activity" RELATED [EC:1.4.3.5]
@@ -51034,11 +52221,13 @@
xref: MetaCyc:PMPOXI-RXN
xref: Reactome:R-HSA-965019 "2xPNPO:2xFMN oxidizes PDXP to PXLP"
xref: Reactome:R-HSA-965079 "2xPNPO:2xFMN oxidizes PXAP to PXLP"
+xref: RHEA:15149
xref: RHEA:15817
is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
-relationship: part_of GO:0042823 ! pyridoxal phosphate biosynthetic process
+relationship: part_of GO:0042823 ! pyridoxal 5'-phosphate biosynthetic process
property_value: skos:exactMatch EC:1.4.3.5
-property_value: skos:exactMatch RHEA:15817
+property_value: skos:narrowMatch RHEA:15149
+property_value: skos:narrowMatch RHEA:15817
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22748" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -51071,7 +52260,7 @@
xref: EC:1.5.1.2
xref: MetaCyc:PYRROLINECARBREDUCT-RXN
xref: Reactome:R-HSA-6783939 "PYCR2 decamer reduces (S)-1-pyrroline-5-carboxylate to L-Pro"
-xref: Reactome:R-HSA-6783955 "PYCRL decamer reduces (S)-1-pyrroline-5-carboxylate to L-Pro"
+xref: Reactome:R-HSA-6783955 "PYCR3 decamer reduces (S)-1-pyrroline-5-carboxylate to L-Pro"
xref: Reactome:R-HSA-70664 "PYCR1 decamer reduces (S)-1-pyrroline-5-carboxylate to L-Pro"
xref: RHEA:14109
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
@@ -51109,9 +52298,19 @@
xref: EC:4.1.1.1
xref: MetaCyc:PYRUVATE-DECARBOXYLASE-RXN
xref: RHEA:11628
+xref: RHEA:45484
+xref: RHEA:50312
+xref: RHEA:54356
+xref: RHEA:54360
+xref: RHEA:55072
is_a: GO:0016831 ! carboxy-lyase activity
property_value: skos:exactMatch EC:4.1.1.1
property_value: skos:exactMatch RHEA:11628
+property_value: skos:narrowMatch RHEA:45484
+property_value: skos:narrowMatch RHEA:50312
+property_value: skos:narrowMatch RHEA:54356
+property_value: skos:narrowMatch RHEA:54360
+property_value: skos:narrowMatch RHEA:55072
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -51230,7 +52429,7 @@
synonym: "phosphoenolpyruvate kinase activity" RELATED [EC:2.7.1.40]
xref: EC:2.7.1.40
xref: MetaCyc:PEPDEPHOS-RXN
-xref: Reactome:R-HSA-71670 "PKM dephosphorylates PEP to PYR"
+xref: Reactome:R-HSA-71670 "Pyruvate kinase dephosphorylates PEP to PYR"
xref: RHEA:18157
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
relationship: part_of GO:0006096 ! glycolytic process
@@ -51337,9 +52536,13 @@
xref: Reactome:R-HSA-111751 "RNR (M1M2) reduces nucleotide diphosphates to deoxynucleotide diphosphates (thioredoxin)"
xref: Reactome:R-HSA-111804 "RNR (M1M2B) reduces nucleotide diphosphates to deoxynucleotide diphosphates (thioredoxin)"
xref: RHEA:23252
+xref: RHEA:28030
+xref: RHEA:28038
is_a: GO:0061731 ! ribonucleoside-diphosphate reductase activity
property_value: skos:exactMatch EC:1.17.4.1
property_value: skos:exactMatch RHEA:23252
+property_value: skos:narrowMatch RHEA:28030
+property_value: skos:narrowMatch RHEA:28038
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -51347,7 +52550,6 @@
name: ribose phosphate diphosphokinase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H+." [RHEA:15609]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "5-phosphoribose pyrophosphorylase activity" RELATED [EC:2.7.6.1]
synonym: "5-phosphoribosyl-1-pyrophosphate synthetase activity" RELATED [EC:2.7.6.1]
synonym: "5-phosphoribosyl-alpha-1-pyrophosphate synthetase activity" RELATED [EC:2.7.6.1]
@@ -51368,16 +52570,16 @@
xref: EC:2.7.6.1
xref: KEGG_REACTION:R01049
xref: MetaCyc:PRPPSYN-RXN
-xref: Reactome:R-HSA-111215 "D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate"
-xref: Reactome:R-HSA-73580 "D-ribose 5-phosphate + ATP => 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + adenosine 5'-monophosphate"
+xref: Reactome:R-HSA-111215 "PRPS1 dimer pyrophosphorylates R5P using dATP"
+xref: Reactome:R-HSA-73580 "PRPS dimers pyrophosphorylate R5P using ATP"
xref: RHEA:15609
is_a: GO:0016778 ! diphosphotransferase activity
property_value: skos:exactMatch EC:2.7.6.1
property_value: skos:exactMatch KEGG_REACTION:R01049
property_value: skos:exactMatch MetaCyc:PRPPSYN-RXN
property_value: skos:exactMatch RHEA:15609
-property_value: skos:relatedMatch MetaCyc:PWY0-662
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0004750
@@ -51403,7 +52605,7 @@
xref: EC:5.1.3.1
xref: KEGG_REACTION:R01529
xref: MetaCyc:RIBULP3EPIM-RXN
-xref: Reactome:R-HSA-199803 "xylulose 5-phosphate <=> D-ribulose 5-phosphate"
+xref: Reactome:R-HSA-199803 "RPE dimers isomerize XY5P to RU5P"
xref: Reactome:R-HSA-71303 "RPE dimers isomerise RU5P to XY5P"
xref: RHEA:13677
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
@@ -51429,10 +52631,10 @@
xref: EC:5.3.1.6
xref: KEGG_REACTION:R01056
xref: MetaCyc:RIB5PISOM-RXN
-xref: Reactome:R-HSA-177784 "ribose 5-phosphate <=> D-ribulose 5-phosphate"
+xref: Reactome:R-HSA-177784 "RPIA isomerizes ribose 5-phosphate to D-ribulose 5-phosphate"
xref: Reactome:R-HSA-5660013 "Defective RPIA does not isomerize RU5P to R5P"
xref: Reactome:R-HSA-5660015 "Defective RPIA does not isomerize R5P to RU5P"
-xref: Reactome:R-HSA-71306 "D-ribulose 5-phosphate <=> ribose 5-phosphate"
+xref: Reactome:R-HSA-71306 "RPIA isomerizes D-ribulose 5-phosphate to ribose 5-phosphate"
xref: RHEA:14657
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
property_value: skos:exactMatch EC:5.3.1.6
@@ -51549,13 +52751,14 @@
[Term]
id: GO:0004760
-name: L-serine-pyruvate transaminase activity
+name: L-serine:pyruvate transaminase activity
namespace: molecular_function
alt_id: GO:0004761
alt_id: GO:0004762
alt_id: GO:0004763
-def: "Catalysis of the reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine." [EC:2.6.1.51, RHEA:22852]
+def: "Catalysis of the reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine." [RHEA:22852]
synonym: "hydroxypyruvate:L-alanine transaminase activity" RELATED [EC:2.6.1.51]
+synonym: "L-serine-pyruvate transaminase activity" EXACT []
synonym: "L-serine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.51]
synonym: "serine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.51]
synonym: "serine-pyruvate aminotransferase activity" EXACT []
@@ -51567,10 +52770,11 @@
xref: KEGG_REACTION:R00585
xref: MetaCyc:SERINE--PYRUVATE-AMINOTRANSFERASE-RXN
xref: RHEA:22852
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.51
property_value: skos:exactMatch RHEA:22852
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004764
@@ -51651,10 +52855,14 @@
xref: Reactome:R-HSA-1640164 "ENPP7 hydrolyzes sphingomyelin"
xref: Reactome:R-HSA-193706 "Production of ceramide which can activate JNK and other targets"
xref: RHEA:19253
+xref: RHEA:45324
+xref: RHEA:54284
is_a: GO:0008081 ! phosphoric diester hydrolase activity
is_a: GO:0120570 ! sphingophospholipase activity
property_value: skos:exactMatch EC:3.1.4.12
property_value: skos:exactMatch RHEA:19253
+property_value: skos:narrowMatch RHEA:45324
+property_value: skos:narrowMatch RHEA:54284
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31030" xsd:anyURI
@@ -51709,9 +52917,17 @@
xref: Reactome:R-HSA-195690 "Zymosterol is isomerized to cholesta-7,24-dien-3beta-ol"
xref: Reactome:R-HSA-6807052 "EBP isomerizes ZYMSTNL to LTHSOL"
xref: RHEA:14709
+xref: RHEA:32187
+xref: RHEA:43928
+xref: RHEA:43936
+xref: RHEA:56936
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
property_value: skos:exactMatch EC:5.3.3.1
property_value: skos:exactMatch RHEA:14709
+property_value: skos:narrowMatch RHEA:32187
+property_value: skos:narrowMatch RHEA:43928
+property_value: skos:narrowMatch RHEA:43936
+property_value: skos:narrowMatch RHEA:56936
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -51738,11 +52954,17 @@
xref: Reactome:R-HSA-6813720 "NCEH1 hydrolyzes cholesterol esters"
xref: Reactome:R-HSA-8865667 "LIPA hydrolyses sterol esters to sterols and fatty acids"
xref: RHEA:10100
+xref: RHEA:33543
+xref: RHEA:33547
+xref: RHEA:36403
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.13
property_value: skos:exactMatch MetaCyc:STEROL-ESTERASE-RXN
property_value: skos:exactMatch RHEA:10100
+property_value: skos:narrowMatch RHEA:33543
+property_value: skos:narrowMatch RHEA:33547
+property_value: skos:narrowMatch RHEA:36403
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
[Term]
@@ -51793,7 +53015,7 @@
name: succinate-CoA ligase activity
namespace: molecular_function
def: "Catalysis of the reaction: succinate + CoA + nucleotide triphosphate = nucleotide diphosphate + phosphate + succinyl-CoA." [GOC:ai]
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
[Term]
id: GO:0004775
@@ -51968,7 +53190,6 @@
xref: EC:1.8.1.2
xref: MetaCyc:SULFITE-REDUCT-RXN
xref: RHEA:13801
-is_a: GO:0016002 ! sulfite reductase activity
is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
property_value: skos:exactMatch EC:1.8.1.2
property_value: skos:exactMatch RHEA:13801
@@ -51982,7 +53203,7 @@
alt_id: GO:0008382
alt_id: GO:0008383
alt_id: GO:0016954
-def: "Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide." [EC:1.15.1.1, GOC:vw, PMID:15064408]
+def: "Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + H2O2." [EC:1.15.1.1, GOC:vw, PMID:15064408]
synonym: "copper, zinc superoxide dismutase activity" NARROW []
synonym: "Cu,Zn-SOD" RELATED [EC:1.15.1.1]
synonym: "Cu-Zn superoxide dismutase activity" NARROW [EC:1.15.1.1]
@@ -52032,7 +53253,7 @@
id: GO:0004786
name: obsolete Mn, Fe superoxide dismutase
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the function is covered by an existing term.
synonym: "Mn, Fe superoxide dismutase" EXACT []
is_obsolete: true
@@ -52207,6 +53428,7 @@
synonym: "threonine dehydratase activity" BROAD []
xref: EC:4.3.1.19
xref: MetaCyc:THREDEHYD-RXN
+xref: Reactome:R-HSA-9014627 "SDS dimers:PXLP convert L-Thr to 2OBUTA"
xref: RHEA:22108
xref: UM-BBD_reactionID:r0433
is_a: GO:0016841 ! ammonia-lyase activity
@@ -52331,7 +53553,6 @@
xref: EC:1.21.99.4
xref: MetaCyc:THYROXINE-DEIODINASE-RXN
xref: Reactome:R-HSA-209772 "Thyroxine is deiodinated to triiodothyronine"
-xref: Reactome:R-HSA-350869 "Thyroxine is deiodinated to reverse triiodothyronine (RT3)"
xref: RHEA:19745
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
property_value: skos:exactMatch EC:1.21.99.4
@@ -52470,12 +53691,30 @@
xref: Reactome:R-HSA-8848338 "PNPLA4 hydrolyzes TAG"
xref: Reactome:R-HSA-8848339 "PNPLA5 hydrolyzes TAG"
xref: RHEA:12044
+xref: RHEA:35667
+xref: RHEA:38495
+xref: RHEA:38575
+xref: RHEA:40475
+xref: RHEA:47864
+xref: RHEA:48024
+xref: RHEA:48028
+xref: RHEA:59020
+xref: RHEA:59024
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:broadMatch EC:3.1.1.79
property_value: skos:exactMatch EC:3.1.1.3
property_value: skos:exactMatch MetaCyc:RXN-19278
property_value: skos:exactMatch RHEA:12044
+property_value: skos:narrowMatch RHEA:35667
+property_value: skos:narrowMatch RHEA:38495
+property_value: skos:narrowMatch RHEA:38575
+property_value: skos:narrowMatch RHEA:40475
+property_value: skos:narrowMatch RHEA:47864
+property_value: skos:narrowMatch RHEA:48024
+property_value: skos:narrowMatch RHEA:48028
+property_value: skos:narrowMatch RHEA:59020
+property_value: skos:narrowMatch RHEA:59024
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
@@ -52494,8 +53733,8 @@
xref: EC:5.3.1.1
xref: KEGG_REACTION:R01015
xref: MetaCyc:TRIOSEPISOMERIZATION-RXN
-xref: Reactome:R-HSA-70454 "dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate"
-xref: Reactome:R-HSA-70481 "TPI1 isomerizes GA3P to DHAP"
+xref: Reactome:R-HSA-70454 "TPI1 dimer isomerizes DHAP to GA3P"
+xref: Reactome:R-HSA-70481 "TPI1 dimer isomerizes GA3P to DHAP"
xref: RHEA:18585
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
property_value: skos:exactMatch EC:5.3.1.1
@@ -53155,14 +54394,15 @@
[Term]
id: GO:0004838
-name: L-tyrosine-2-oxoglutarate transaminase activity
+name: L-tyrosine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate." [RHEA:15093]
+def: "Catalysis of the reaction: L-tyrosine + 2-oxoglutarate = 3-(4-hydroxyphenyl)pyruvate + L-glutamate." [RHEA:15093]
synonym: "glutamic phenylpyruvic aminotransferase activity" RELATED [EC:2.6.1.5]
synonym: "glutamic-hydroxyphenylpyruvic transaminase activity" RELATED [EC:2.6.1.5]
synonym: "L-phenylalanine 2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.5]
synonym: "L-tyrosine aminotransferase activity" BROAD [EC:2.6.1.5]
synonym: "L-tyrosine transaminase activity" BROAD []
+synonym: "L-tyrosine-2-oxoglutarate transaminase activity" EXACT []
synonym: "L-tyrosine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "phenylalanine aminotransferase activity" RELATED [EC:2.6.1.5]
synonym: "phenylalanine transaminase activity" RELATED [EC:2.6.1.5]
@@ -53180,10 +54420,11 @@
xref: Reactome:R-HSA-71155 "TAT deaminates tyrosine"
xref: RHEA:15093
xref: UM-BBD_reactionID:r0297
-is_a: GO:0008793 ! aromatic-amino-acid transaminase activity
+is_a: GO:0008793 ! aromatic-amino-acid:2-oxoglutarate transaminase activity
property_value: skos:broadMatch EC:2.6.1.5
property_value: skos:exactMatch RHEA:15093
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0004839
@@ -53219,13 +54460,6 @@
synonym: "ubiquitin protein-ligase activity" NARROW []
synonym: "ubiquitin-conjugating enzyme activity" NARROW []
xref: KEGG_REACTION:R03876
-xref: Reactome:R-HSA-1169394 "ISGylation of IRF3"
-xref: Reactome:R-HSA-1169395 "ISGylation of viral protein NS1"
-xref: Reactome:R-HSA-1169397 "Activation of ISG15 by UBA7 E1 ligase"
-xref: Reactome:R-HSA-1169398 "ISGylation of host protein filamin B"
-xref: Reactome:R-HSA-1169402 "ISGylation of E2 conjugating enzymes"
-xref: Reactome:R-HSA-1169405 "ISGylation of protein phosphatase 1 beta (PP2CB)"
-xref: Reactome:R-HSA-1169406 "ISGylation of host proteins"
xref: Reactome:R-HSA-1234163 "Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha"
xref: Reactome:R-HSA-1234172 "Nuclear VBC complex ubiquitinylates HIF-alpha"
xref: Reactome:R-HSA-1253282 "ERBB4 ubiquitination by WWP1/ITCH"
@@ -53286,7 +54520,6 @@
xref: Reactome:R-HSA-3781009 "NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1"
xref: Reactome:R-HSA-3788724 "Cdh1:APC/C ubiquitinates EHMT1 and EHMT2"
xref: Reactome:R-HSA-3797226 "Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)"
-xref: Reactome:R-HSA-400267 "BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins"
xref: Reactome:R-HSA-4332236 "CBL neddylates TGFBR2"
xref: Reactome:R-HSA-446877 "TRAF6 is K63 poly-ubiquitinated"
xref: Reactome:R-HSA-450358 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation"
@@ -53313,7 +54546,7 @@
xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2"
xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains"
xref: Reactome:R-HSA-68712 "The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1"
-xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A"
+xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated CDC25A"
xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO"
xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1"
xref: Reactome:R-HSA-870449 "TRIM33 monoubiquitinates SMAD4"
@@ -53335,6 +54568,7 @@
xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex"
xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane"
xref: Reactome:R-HSA-9758604 "Ubiquitination of IKBKG by TRAF6"
+xref: Reactome:R-HSA-9766227 "MDM2 mediates CDH1 ubiquitination"
xref: Reactome:R-HSA-9793444 "ITCH polyubiquitinates MLKL at K50"
xref: Reactome:R-HSA-9793485 "PRKN polyubiquitinates RIPK3"
xref: Reactome:R-HSA-9793679 "LUBAC ubiquitinates RIPK1 at K627"
@@ -53347,10 +54581,15 @@
xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation"
xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate"
xref: Reactome:R-HSA-9833155 "Ubiquitination of STAT2"
-xref: Reactome:R-HSA-9833973 "ISGylation of PKR"
xref: Reactome:R-HSA-9834070 "PRKN ubiquitinates MOM substrates"
xref: Reactome:R-HSA-9861563 "CTLH E3 ligase ubiquitinates LDHA"
xref: Reactome:R-HSA-9861640 "CTLH E3 ligase ubiquitinates PKM-1"
+xref: Reactome:R-HSA-9929350 "Ubiquitination of CD274 by BTRC-SCF E3-ligase complex"
+xref: Reactome:R-HSA-9934753 "CBLL1 ubiquitinates CDH1"
+xref: Reactome:R-HSA-9948301 "ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit"
+xref: Reactome:R-HSA-9954721 "NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide"
+xref: Reactome:R-HSA-9955146 "S.flexneri ipaH9.8 ubiquitinates GBPs"
+xref: Reactome:R-HSA-9970191 "RBBP6 activates CPSF complex"
is_a: GO:0019787 ! ubiquitin-like protein transferase activity
[Term]
@@ -53485,7 +54724,7 @@
id: GO:0004846
name: urate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: urate + O2 + H2O = 5-hydroxyisourate + hydrogen peroxide." [EC:1.7.3.3]
+def: "Catalysis of the reaction: urate + O2 + H2O = 5-hydroxyisourate + H2O2." [EC:1.7.3.3]
synonym: "urate:oxygen oxidoreductase activity" RELATED [EC:1.7.3.3]
synonym: "uric acid oxidase activity" RELATED [EC:1.7.3.3]
synonym: "uricase activity" RELATED [EC:1.7.3.3]
@@ -53581,7 +54820,7 @@
id: GO:0004851
name: uroporphyrin-III C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 S-adenosyl-L-methionine + uroporphyrin III = 2 S-adenosyl-L-homocysteine + precorrin-2." [EC:2.1.1.107]
+def: "Catalysis of the reaction: uroporphyrinogen III + 2 S-adenosyl-L-methionine = precorrin-2 + 2 S-adenosyl-L-homocysteine + H+." [RHEA:32459]
synonym: "adenosylmethionine-uroporphyrinogen III methyltransferase activity" RELATED [EC:2.1.1.107]
synonym: "CobA" RELATED [EC:2.1.1.107]
synonym: "CysG" RELATED [EC:2.1.1.107]
@@ -53671,7 +54910,7 @@
id: GO:0004855
name: xanthine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: xanthine + H2O + O2 = urate + hydrogen peroxide." [EC:1.17.3.2]
+def: "Catalysis of the reaction: xanthine + H2O + O2 = urate + H2O2." [EC:1.17.3.2]
synonym: "hypoxanthine-xanthine oxidase activity" BROAD [EC:1.17.3.2]
synonym: "schardinger enzyme" RELATED [EC:1.17.3.2]
synonym: "Schardinger enzyme activity" RELATED [EC:1.17.3.2]
@@ -53719,6 +54958,8 @@
def: "A molecular function regulator that reduces a catalytic activity." [GOC:ai, GOC:ebc]
comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
synonym: "metalloenzyme inhibitor activity" NARROW []
+xref: Reactome:R-HSA-1474158 "GCHFR binds to GCH1 and negatively regulates its activity"
+xref: Reactome:R-HSA-1614336 "SUMF2 binds SUMF1, inhibiting SUMF1-mediated activation of arylsulfatases"
is_a: GO:0030234 ! enzyme regulator activity
is_a: GO:0140678 ! molecular function inhibitor activity
relationship: negatively_regulates GO:0003824 ! catalytic activity
@@ -53854,7 +55095,7 @@
alt_id: GO:0005062
alt_id: GO:0009369
alt_id: GO:0009370
-def: "OBSOLETE. Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:go_curators]
+def: "OBSOLETE. Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." [GOC:curators]
comment: This term was obsoleted because it was not clearly defined and is not a useful grouping term.
synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor signal transducer activity" NARROW []
synonym: "quorum sensing response regulator activity" NARROW []
@@ -53961,6 +55202,10 @@
synonym: "vitamin A receptor activity" NARROW []
synonym: "vitamin D receptor activity" NARROW []
synonym: "vitamin D3 receptor activity" NARROW [GOC:bf, Wikipedia:Calcitriol_receptor]
+xref: Reactome:R-HSA-400143 "Fatty acid ligands activate PPARA"
+xref: Reactome:R-HSA-8936849 "AHR:2xHSP90:AIP:PTGES3 binds TCDD"
+xref: Reactome:R-HSA-8937169 "AHR:TCDD:2xHSP90AB1:AIP:PTGES3 translocates from cytosol to nucleoplasm"
+xref: Reactome:R-HSA-8937191 "AHR:TCDD:2xHSP90AB1:AIP:PTGES3 dissociates"
is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific
is_a: GO:0038023 ! signaling receptor activity
is_a: GO:0098531 ! ligand-modulated transcription factor activity
@@ -53986,7 +55231,7 @@
namespace: molecular_function
alt_id: GO:0004926
alt_id: GO:0099600
-def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [GOC:go_curators, Wikipedia:Transmembrane_receptor]
+def: "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." [GOC:curators, Wikipedia:Transmembrane_receptor]
comment: This term includes intracellular membrane receptors, e.g. IP3 triggered release of Ca2+ from intracellular stores.
synonym: "transmembrane receptor activity" BROAD [GOC:bf, GOC:signaling]
synonym: "transmembrane signalling receptor activity" EXACT [GOC:mah]
@@ -54348,7 +55593,7 @@
id: GO:0004928
name: obsolete frizzled receptor activity
namespace: molecular_function
-def: "OBSOLETE. Combining with a member of the Wnt-family of signaling molecules to initiate a change in cell activity." [GOC:go_curators]
+def: "OBSOLETE. Combining with a member of the Wnt-family of signaling molecules to initiate a change in cell activity." [GOC:curators]
comment: This term was made obsolete because it represents a gene product rather than an activity.
synonym: "frizzled receptor activity" EXACT []
is_obsolete: true
@@ -54358,7 +55603,7 @@
id: GO:0004929
name: obsolete frizzled-2 receptor activity
namespace: molecular_function
-def: "OBSOLETE. Combining with to a member of the Wnt-family of signaling molecules to initiate a change in cell activity." [GOC:go_curators]
+def: "OBSOLETE. Combining with to a member of the Wnt-family of signaling molecules to initiate a change in cell activity." [GOC:curators]
comment: This term was made obsolete because it represents a gene product rather than an activity.
synonym: "frizzled-2 receptor activity" EXACT []
is_obsolete: true
@@ -54411,6 +55656,7 @@
synonym: "purinoceptor" BROAD []
synonym: "purinoreceptor" BROAD []
xref: Reactome:R-HSA-877187 "P2X7 mediates loss of intracellular K+"
+xref: Reactome:R-HSA-9905964 "P2RX7 in ATP:P2RX7:PANX1 transports cations from the extracellular region to the cytosol"
is_a: GO:0005231 ! excitatory extracellular ligand-gated monoatomic ion channel activity
is_a: GO:0035381 ! ATP-gated ion channel activity
is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
@@ -54704,6 +55950,7 @@
name: glucagon receptor activity
namespace: molecular_function
def: "Combining with glucagon and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:mah, GOC:signaling, PMID:22438981]
+xref: Reactome:R-HSA-163625 "Glucagon binds to Glucagon receptor"
is_a: GO:0008528 ! G protein-coupled peptide receptor activity
relationship: part_of GO:0071377 ! cellular response to glucagon stimulus
@@ -54969,6 +56216,7 @@
synonym: "thyroid stimulating hormone receptor activity" EXACT []
synonym: "thyrotropin receptor" EXACT []
synonym: "TSH receptor activity" EXACT []
+xref: Reactome:R-HSA-391375 "TSHR binds TSH/Thyrostimulin"
xref: Wikipedia:Thyrotropin_receptor
is_a: GO:0004930 ! G protein-coupled receptor activity
is_a: GO:0016500 ! protein-hormone receptor activity
@@ -55145,7 +56393,7 @@
id: GO:0005012
name: obsolete Neu/ErbB-2 receptor activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a class of receptor rather than an activity.
synonym: "Neu/ErbB-2 receptor activity" EXACT []
is_obsolete: true
@@ -55542,7 +56790,7 @@
id: GO:0005050
name: obsolete peroxisome receptor
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes a cellular component.
synonym: "peroxisome receptor" EXACT []
is_obsolete: true
@@ -55579,7 +56827,7 @@
id: GO:0005054
name: obsolete peroxisome integral membrane receptor
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes a cellular component.
synonym: "Pas20p" RELATED []
synonym: "peroxisome integral membrane receptor" EXACT []
@@ -55627,7 +56875,7 @@
id: GO:0005065
name: obsolete heterotrimeric G-protein
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a cellular component and not a molecular function.
synonym: "heterotrimeric G-protein" EXACT []
is_obsolete: true
@@ -55637,7 +56885,7 @@
id: GO:0005066
name: obsolete transmembrane receptor protein tyrosine kinase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "transmembrane receptor protein tyrosine kinase signaling protein activity" EXACT []
synonym: "transmembrane receptor protein tyrosine kinase signalling protein activity" EXACT []
@@ -55670,7 +56918,7 @@
id: GO:0005071
name: obsolete transmembrane receptor protein serine/threonine kinase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "transmembrane receptor protein serine/threonine kinase signaling protein activity" EXACT []
synonym: "transmembrane receptor protein serine/threonine kinase signalling protein activity" EXACT []
@@ -55721,7 +56969,7 @@
id: GO:0005076
name: obsolete receptor signaling protein serine/threonine kinase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "receptor signaling protein serine/threonine kinase signaling protein activity" EXACT []
synonym: "receptor signalling protein serine/threonine kinase signalling protein activity" EXACT []
@@ -55742,11 +56990,12 @@
[Term]
id: GO:0005078
-name: MAP-kinase scaffold activity
+name: MAP kinase scaffold activity
namespace: molecular_function
def: "The binding activity of a molecule that functions as a physical support for the assembly of a multiprotein mitogen-activated protein kinase (MAPK) complex. Binds multiple kinases of the MAPKKK cascade, and also upstream signaling proteins, permitting those molecules to function in a coordinated way. Bringing together multiple enzymes and their substrates enables the signal to be transduced quickly and efficiently." [PMID:12511654, PMID:15213240, PMID:9405336]
synonym: "MAP-kinase scaffold protein activity" EXACT []
is_a: GO:0035591 ! signaling adaptor activity
+is_a: GO:0140378 ! protein complex scaffold activity
relationship: has_part GO:0051019 ! mitogen-activated protein kinase binding
relationship: part_of GO:0000165 ! MAPK cascade
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14286" xsd:anyURI
@@ -55785,7 +57034,7 @@
id: GO:0005081
name: obsolete receptor signaling protein serine/threonine phosphatase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "receptor signaling protein serine/threonine phosphatase signaling protein activity" EXACT []
synonym: "receptor signalling protein serine/threonine phosphatase signalling protein activity" EXACT []
@@ -55796,7 +57045,7 @@
id: GO:0005082
name: obsolete receptor signaling protein tyrosine phosphatase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "receptor signaling protein tyrosine phosphatase signaling protein activity" EXACT []
synonym: "receptor signalling protein tyrosine phosphatase signalling protein activity" EXACT []
@@ -55881,6 +57130,7 @@
xref: Reactome:R-HSA-379044 "Liganded Gs-activating GPCR acts as a GEF for Gs"
xref: Reactome:R-HSA-379048 "Liganded Gq/11-activating GPCRs act as GEFs for Gq/11"
xref: Reactome:R-HSA-380073 "Liganded Gi-activating GPCR acts as a GEF for Gi"
+xref: Reactome:R-HSA-381727 "RAP1A exchanges GDP for GTP"
xref: Reactome:R-HSA-389348 "Activation of Rac1 by pVav1"
xref: Reactome:R-HSA-389350 "Activation of Cdc42 by pVav1"
xref: Reactome:R-HSA-392054 "NCAM1:pFAK:Grb2:Sos-mediated nucleotide exchange of Ras"
@@ -55896,6 +57146,7 @@
xref: Reactome:R-HSA-3965444 "WNT:FZD complex promotes G-protein nucleotide exchange"
xref: Reactome:R-HSA-399938 "Activation of Rac1 by FARP2"
xref: Reactome:R-HSA-399995 "Muscarinic Acetylcholine Receptor M3 activates Gq"
+xref: Reactome:R-HSA-400037 "Gi,Go Heterotrimeric G-protein complex dissociates"
xref: Reactome:R-HSA-400092 "Alpha-2A,alpha-2C Adrenergic Receptors activate Gi.Go heterotrimeric G proteins"
xref: Reactome:R-HSA-4093336 "p-TIAM1 exchanges GTP for GDP on RAC1, activating it"
xref: Reactome:R-HSA-416530 "FFAR1:FFAR1 ligands activate Gq"
@@ -56606,7 +57857,7 @@
id: GO:0005149
name: interleukin-1 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-1 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-1 receptor." [GOC:curators]
synonym: "IL-1" NARROW []
synonym: "interleukin-1 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -56645,7 +57896,7 @@
id: GO:0005153
name: interleukin-8 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-8 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-8 receptor." [GOC:curators]
subset: goslim_chembl
synonym: "IL-8" NARROW []
synonym: "interleukin-8 receptor ligand" NARROW []
@@ -56991,7 +58242,7 @@
id: GO:0005187
name: obsolete storage protein
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes a cellular location rather than a function.
synonym: "storage protein" EXACT []
is_obsolete: true
@@ -57129,7 +58380,7 @@
id: GO:0005202
name: obsolete collagen
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not represent a molecular function.
synonym: "collagen" EXACT []
is_obsolete: true
@@ -57139,7 +58390,7 @@
id: GO:0005203
name: obsolete proteoglycan
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) of a gene product, not a molecular function.
synonym: "proteoglycan" EXACT []
is_obsolete: true
@@ -57148,7 +58399,7 @@
id: GO:0005204
name: obsolete chondroitin sulfate proteoglycan
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) of a gene product, not a molecular function.
synonym: "chondroitin sulfate proteoglycan" EXACT []
synonym: "chondroitin sulphate proteoglycan" EXACT []
@@ -57158,7 +58409,7 @@
id: GO:0005205
name: obsolete chondroitin sulfate/dermatan sulfate proteoglycan
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) of a gene product, not a molecular function.
synonym: "chondroitin sulfate/dermatan sulfate proteoglycan" EXACT []
synonym: "chondroitin sulphate/dermatan sulphate proteoglycan" EXACT []
@@ -57440,7 +58691,7 @@
id: GO:0005241
name: obsolete inward rectifier channel
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "inward rectifier channel" EXACT []
is_obsolete: true
@@ -57513,6 +58764,7 @@
xref: Reactome:R-HSA-5577213 "LTCC multimer transports Ca2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-9701055 "TRPA1 tetramer transports Ca2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-9701141 "TRPV1 transports Ca2+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-9905934 "CaV3.2 (CACNA1H:CACNA2D1:CACNB1,2,3:CACNG7) transports calcium from the extracellular region to the cytosol"
is_a: GO:0005262 ! calcium channel activity
is_a: GO:0022843 ! voltage-gated monoatomic cation channel activity
@@ -57654,12 +58906,9 @@
synonym: "cation channel activity" BROAD []
synonym: "cation diffusion facilitator activity" EXACT []
synonym: "non-selective cation channel activity" NARROW []
-xref: Reactome:R-HSA-1168376 "STIM1 oligomerizes"
xref: Reactome:R-HSA-1296043 "Activation of HCN channels"
-xref: Reactome:R-HSA-169683 "IP3R:I(1,4,5)P3 tetramer transports Ca2+ from ER lumen to cytosol"
xref: Reactome:R-HSA-2089943 "TRPC1 translocates calcium from the extracellular region to the cytosol"
xref: Reactome:R-HSA-426223 "Cation influx mediated by TRPC3/6/7"
-xref: Reactome:R-HSA-4420052 "Decreasing cGMP concentration promotes intracellular Ca2+ release in response to WNT"
xref: Reactome:R-HSA-9706720 "SARS-CoV-1 E transports Ca2+"
xref: Reactome:R-HSA-9712190 "cAMP:olfactory CNG channel translocates Na+ and Ca2+ from the extracellular region to the cytosol"
xref: Reactome:R-HSA-9754616 "SARS-CoV-2 E pentamer transports Ca2+"
@@ -58070,6 +59319,7 @@
alt_id: GO:1901677
def: "Enables the transfer of phosphate ions from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Secondary active transporters include symporters and antiporters." [GOC:mtg_transport]
synonym: "inorganic phosphate transmembrane transporter activity" EXACT []
+xref: Reactome:R-HSA-5226964 "ANKH transports PPi from cytosol to extracellular region"
is_a: GO:0015291 ! secondary active transmembrane transporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27121" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -58088,7 +59338,7 @@
id: GO:0005318
name: obsolete phosphate:hydrogen symporter
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
synonym: "phosphate:hydrogen symporter" EXACT []
synonym: "phosphate:proton symporter activity" EXACT []
is_obsolete: true
@@ -58096,14 +59346,16 @@
[Term]
id: GO:0005319
-name: lipid transporter activity
+name: lipid carrier activity
namespace: molecular_function
-def: "Enables the directed movement of lipids into, out of or within a cell, or between cells." [GOC:ai]
-synonym: "apolipoprotein" RELATED []
+def: "Directly binding to a specific lipid and delivering it either to an acceptor molecule or to a specific location." [GOC:curators]
+synonym: "apolipoprotein" NARROW []
+synonym: "lipid transporter activity" BROAD []
synonym: "lipophorin" NARROW []
xref: Reactome:R-HSA-1369028 "ABCAs mediate lipid efflux"
xref: Reactome:R-HSA-1369052 "ABCAs mediate lipid influx"
xref: Reactome:R-HSA-174786 "ApoB-48 + 40 triacylglycerol + 60 phospholipid => ApoB-48:TG:PL complex"
+xref: Reactome:R-HSA-5334794 "FABPs bind LCFAs"
xref: Reactome:R-HSA-5682285 "ABCA12 transports lipids from cytosol to extracellular region"
xref: Reactome:R-HSA-5682311 "Defective ABCA12 does not transport lipids from cytosol to extracellular region"
xref: Reactome:R-HSA-5683672 "Defective ABCA3 does not transport PC, PG from ER membrane to lamellar body"
@@ -58112,8 +59364,9 @@
xref: Reactome:R-HSA-6801250 "TRIAP1:PRELID1, PRELID3A transports PA from the outer to the inner mitochondrial membrane"
xref: Reactome:R-HSA-8848053 "ABCA5 transports CHOL from lysosomal lumen to cytosol"
xref: Reactome:R-HSA-8866329 "MTTP lipidates APOB-100, forming a pre-VLDL"
-is_a: GO:0005215 ! transporter activity
-relationship: part_of GO:0006869 ! lipid transport
+xref: Reactome:R-HSA-8873834 "STARD10 transports PC from ER membrane to lamellar body membrane"
+is_a: GO:0140104 ! molecular carrier activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
[Term]
id: GO:0005320
@@ -58168,15 +59421,28 @@
def: "Enables the transfer of a long-chain fatty acid from one side of a membrane to the other. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons." [ISBN:0198506732]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
synonym: "long-chain fatty acid transporter activity" RELATED []
+xref: Reactome:R-HSA-2026996 "FABP1 transports fatty acids into the nucleus"
xref: Reactome:R-HSA-2046087 "Translocation of tetracosahexaenoyl-CoA to peroxisomes"
xref: Reactome:R-HSA-2046093 "Translocation of tetracosapentaenoyl-CoA to peroxisomes"
xref: Reactome:R-HSA-382575 "ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix"
-xref: Reactome:R-HSA-434381 "CD36 (FAT) translocates palmitate from the extracellular region to the cytosol"
+xref: Reactome:R-HSA-434381 "CD36 (FAT) translocates a long chain fatty acid from the extracellular region to the cytosol"
xref: Reactome:R-HSA-5684043 "Defective ABCD1 does not transfer LCFAs from cytosol to peroxisomal matrix"
+xref: RHEA:33655
xref: RHEA:39283
+xref: RHEA:39807
+xref: RHEA:45252
+xref: RHEA:45256
+xref: RHEA:45264
+xref: RHEA:71395
is_a: GO:0015245 ! fatty acid transmembrane transporter activity
relationship: part_of GO:0015909 ! long-chain fatty acid transport
property_value: skos:exactMatch RHEA:39283
+property_value: skos:narrowMatch RHEA:33655
+property_value: skos:narrowMatch RHEA:39807
+property_value: skos:narrowMatch RHEA:45252
+property_value: skos:narrowMatch RHEA:45256
+property_value: skos:narrowMatch RHEA:45264
+property_value: skos:narrowMatch RHEA:71395
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14793" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26996" xsd:anyURI
@@ -58257,7 +59523,7 @@
synonym: "norepinephrine transmembrane transporter activity" EXACT []
synonym: "norepinephrine:sodium:chloride symporter activity" EXACT []
synonym: "sodium/norepinephrine symporter activity" EXACT []
-xref: Reactome:R-HSA-443997 "SLC6A2 cotransports NAd, Na+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-443997 "SLC6A2 cotransports NAd, Na+,Cl- from extracellular region to cytosol"
xref: Reactome:R-HSA-5659764 "Defective SLC6A2 does not cotransport NAd, Na+ from extracellular region to cytosol"
xref: Wikipedia:Norepinephrine_transporter
is_a: GO:0008504 ! monoamine transmembrane transporter activity
@@ -58371,7 +59637,7 @@
name: purine nucleobase transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, from one side of a membrane to the other." [ISBN:0198506732]
-synonym: "purine base transmembrane transporter activity" EXACT [GOC:go_curators]
+synonym: "purine base transmembrane transporter activity" EXACT [GOC:curators]
synonym: "purine transmembrane transporter activity" RELATED []
is_a: GO:0015205 ! nucleobase transmembrane transporter activity
relationship: part_of GO:1904823 ! purine nucleobase transmembrane transport
@@ -58400,7 +59666,7 @@
name: pyrimidine nucleobase transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of pyrimidine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, from one side of a membrane to the other." [GOC:ai]
-synonym: "pyrimidine base transmembrane transporter activity" EXACT [GOC:go_curators]
+synonym: "pyrimidine base transmembrane transporter activity" EXACT [GOC:curators]
synonym: "pyrimidine transmembrane transporter activity" RELATED []
is_a: GO:0015205 ! nucleobase transmembrane transporter activity
relationship: part_of GO:0015855 ! pyrimidine nucleobase transport
@@ -58474,8 +59740,6 @@
synonym: "glucose permease activity" EXACT []
synonym: "glucose transmembrane transporter activity" EXACT []
synonym: "lactose/glucose efflux transporter activity" NARROW []
-xref: Reactome:R-HSA-499981 "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2"
-xref: Reactome:R-HSA-5653873 "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27326" xsd:anyURI
is_obsolete: true
replaced_by: GO:0055056
@@ -58578,6 +59842,11 @@
namespace: molecular_function
def: "Enables the transfer of myo-inositol from one side of a membrane to the other. Myo-inositol is 1,2,3,4,5/4,6-cyclohexanehexol, a growth factor for animals and microorganisms." [GOC:ai]
synonym: "vitamin Bh transporter activity" EXACT []
+xref: Reactome:R-HSA-1855155 "I(1,3,4,5,6)P5 transports from the ER lumen to the cytosol"
+xref: Reactome:R-HSA-1855164 "IP6 transports from the cytosol to the ER lumen"
+xref: Reactome:R-HSA-1855186 "I(1,3,4,5)P4 transports from the cytosol to the ER lumen"
+xref: Reactome:R-HSA-1855195 "I(1,3,4,5,6)P5 transports from the cytosol to the ER lumen"
+xref: Reactome:R-HSA-1855217 "I(1,4,5)P3 transports from the ER lumen to the cytosol"
is_a: GO:0015166 ! polyol transmembrane transporter activity
relationship: part_of GO:0015798 ! myo-inositol transport
@@ -58665,7 +59934,7 @@
synonym: "copper uptake transmembrane transporter activity" RELATED []
synonym: "intracellular copper ion transporter" NARROW []
synonym: "plasma membrane copper transporter" NARROW []
-xref: Reactome:R-HSA-437300 "SLC31A1 transports Cu2+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-437300 "SLC31A1 transports Cu1+ from extracellular region to cytosol"
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
relationship: part_of GO:0035434 ! copper ion transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -58754,6 +60023,7 @@
xref: Reactome:R-HSA-442422 "SLC39A1-4 transports Zn2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5654125 "Defective SLC39A4 does not transport Zn2+ from extracellular region to cytosol"
xref: Reactome:R-HSA-9820566 "ZnT5 transports zinc into the golgi apparatus"
+xref: Reactome:R-HSA-9928035 "ZnuABC transports Zn2+ to cytosol"
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
relationship: part_of GO:0071577 ! zinc ion transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
@@ -59033,7 +60303,7 @@
namespace: molecular_function
def: "Enables the transfer of a GDP-fucose from one side of a membrane to the other. GDP-fucose is a substance composed of fucose in glycosidic linkage with guanosine diphosphate." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
xref: Reactome:R-HSA-5653596 "Defective SLC35C1 does not transport UDP-Fuc from cytosol to Golgi lumen"
-xref: Reactome:R-HSA-742345 "SLC35C1 transport UDP-Fuc from cytosol to Golgi lumen"
+xref: Reactome:R-HSA-742345 "SLC35C1 transport GDP-Fuc from cytosol to Golgi lumen"
is_a: GO:0036080 ! purine nucleotide-sugar transmembrane transporter activity
relationship: part_of GO:0015783 ! GDP-fucose transmembrane transport
@@ -59111,7 +60381,7 @@
namespace: molecular_function
alt_id: GO:0005453
alt_id: GO:0005454
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not provide a useful functional classification.
synonym: "small-molecule carrier or transporter" EXACT []
is_obsolete: true
@@ -59157,7 +60427,7 @@
synonym: "carnitine/acyl carnitine carrier activity" EXACT []
synonym: "carnitine:acyl carnitine carrier activity" EXACT []
synonym: "fatty acyl carnitine carrier" EXACT []
-xref: Reactome:R-HSA-200424 "Exchange of palmitoylcarnitine and carnitine across the inner mitochondrial membrane"
+xref: Reactome:R-HSA-200424 "Exchange of acylcarnitine and carnitine across the inner mitochondrial membrane"
is_a: GO:0015226 ! carnitine transmembrane transporter activity
is_a: GO:0015227 ! O-acyl-L-carnitine transmembrane transporter activity
is_a: GO:0015297 ! antiporter activity
@@ -59175,7 +60445,7 @@
id: GO:0005479
name: obsolete vacuolar assembly
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a biological process and not a molecular function.
synonym: "vacuolar assembly" EXACT []
is_obsolete: true
@@ -59185,7 +60455,7 @@
id: GO:0005480
name: obsolete vesicle transport
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a biological process and not a molecular function.
synonym: "vesicle transport" EXACT []
is_obsolete: true
@@ -59195,7 +60465,7 @@
id: GO:0005481
name: obsolete vesicle fusion
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a biological process and not a molecular function.
synonym: "vesicle fusion" EXACT []
is_obsolete: true
@@ -59208,7 +60478,7 @@
id: GO:0005482
name: obsolete vesicle targeting
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a biological process and not a molecular function.
synonym: "vesicle targeting" EXACT []
is_obsolete: true
@@ -59240,6 +60510,8 @@
synonym: "v-SNARE activity" NARROW []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
relationship: part_of GO:0061025 ! membrane fusion
+relationship: part_of GO:0140522 ! fusogenic activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31564" xsd:anyURI
[Term]
id: GO:0005488
@@ -59442,7 +60714,7 @@
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
-def: "Binding to a protein." [GOC:go_curators]
+def: "Binding to a protein." [GOC:curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
@@ -59486,7 +60758,7 @@
id: GO:0005519
name: cytoskeletal regulatory protein binding
namespace: molecular_function
-def: "Binding to a protein involved in modulating the reorganization of the cytoskeleton." [GOC:go_curators, PMID:15163540]
+def: "Binding to a protein involved in modulating the reorganization of the cytoskeleton." [GOC:curators, PMID:15163540]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -59641,7 +60913,7 @@
namespace: molecular_function
def: "Binding to hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine." [GOC:jl]
synonym: "hyaluronan binding" EXACT []
-is_a: GO:0005539 ! glycosaminoglycan binding
+is_a: GO:0031406 ! carboxylic acid binding
[Term]
id: GO:0005541
@@ -59686,7 +60958,7 @@
name: 1-phosphatidylinositol binding
namespace: molecular_function
def: "Binding to a phosphatidylinositol, a glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol." [ISBN:0198506732]
-is_a: GO:0035091 ! phosphatidylinositol binding
+is_a: GO:0005543 ! phospholipid binding
[Term]
id: GO:0005546
@@ -59711,10 +60983,11 @@
[Term]
id: GO:0005548
-name: phospholipid transporter activity
+name: obsolete phospholipid transporter activity
namespace: molecular_function
alt_id: GO:0008497
-def: "Enables the directed movement of phospholipids into, out of or within a cell, or between cells. Phospholipids are a class of lipids containing phosphoric acid as a mono- or diester." [GOC:ai, ISBN:0198506732]
+def: "OBSOLETE. Enables the directed movement of phospholipids into, out of or within a cell, or between cells. Phospholipids are a class of lipids containing phosphoric acid as a mono- or diester." [GOC:ai, ISBN:0198506732]
+comment: This term was obsoleted because it refers to the substrate rather than to the transport mechanism as a primary classification.
xref: Reactome:R-HSA-216757 "4xPALM-C-p-2S-ABCA1 tetramer transports PL from transport vesicle membrane to plasma membrane"
xref: Reactome:R-HSA-382553 "ABCA7:Apo1A-mediated phospholipid efflux"
xref: Reactome:R-HSA-5678706 "ABCB4 transports PC from plasma membrane to extracellular region"
@@ -59722,8 +60995,11 @@
xref: Reactome:R-HSA-8857662 "ESYT1:ESYT2:ESYT3 transport GPL from plasma membrane to ER membrane"
xref: Reactome:R-HSA-8865637 "MFSD2A transports LPC from extracellular region to plasma membrane"
xref: Reactome:R-HSA-8867876 "OSBPL5,8,10 exchange PS with PI4P from ER membrane to plasma membrane"
-is_a: GO:0005319 ! lipid transporter activity
-relationship: part_of GO:0015914 ! phospholipid transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31460" xsd:anyURI
+is_obsolete: true
+consider: GO:0120014
+consider: GO:0170055
[Term]
id: GO:0005549
@@ -59744,7 +61020,7 @@
id: GO:0005551
name: obsolete ubiquitin
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a gene product.
is_obsolete: true
consider: GO:0016567
@@ -59754,7 +61030,7 @@
id: GO:0005552
name: obsolete polyubiquitin
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a gene product and not a molecular function.
synonym: "polyubiquitin" EXACT []
is_obsolete: true
@@ -59961,11 +61237,12 @@
id: GO:0005576
name: extracellular region
namespace: cellular_component
-def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:go_curators]
+def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GOC:curators]
comment: Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_flybase_ribbon
subset: goslim_generic
@@ -59990,8 +61267,7 @@
synonym: "fibrinogen alpha chain" NARROW []
synonym: "fibrinogen beta chain" NARROW []
synonym: "fibrinogen gamma chain" NARROW []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0005579
@@ -60038,6 +61314,7 @@
namespace: cellular_component
def: "Any triple helical collagen trimer that forms fibrils." [PMID:21421911]
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
intersection_of: GO:0005581 ! collagen trimer
intersection_of: part_of GO:0098643 ! fibrillar collagen complex
disjoint_from: GO:0030936 ! transmembrane collagen trimer
@@ -60089,6 +61366,7 @@
namespace: cellular_component
def: "A collagen heterotrimer containing type VI alpha chains in alpha1(VI)alpha2(VI)alpha3(VI) trimers; type VI collagen triple helices associate to form beaded fibrils." [PMID:19693541, PMID:21421911]
is_a: GO:0140158 ! von-Willerbrand-factor-A-domain-rich collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0098647 ! collagen beaded filament
[Term]
@@ -60097,6 +61375,7 @@
namespace: cellular_component
def: "A collagen homotrimer of alpha1(VII) chains; type VII collagen triple helices form antiparallel dimer, which in turn associate laterally to form anchoring fibrils that connect type IV collagen in the basal lamina to plaques in the underlying connective tissue. It binds laminin." [PMID:19693541]
is_a: GO:0140158 ! von-Willerbrand-factor-A-domain-rich collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0098648 ! collagen anchoring fibril
[Term]
@@ -60105,7 +61384,7 @@
namespace: cellular_component
def: "A collagen heterotrimer containing type VIII alpha chains; [alpha1(VIII)2]alpha2(VIII) and alpha1(VIII)[alpha2(VIII)]2 trimers have been observed; type VIII collagen triple helices associate to form regular hexagonal nets." [PMID:21421911]
is_a: GO:0098642 ! network-forming collagen trimer
-relationship: part_of GO:0140155 ! hexagonal collagen network of basement membrane
+relationship: part_of GO:0098646 ! hexagonal collagen network
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30148" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31070" xsd:anyURI
@@ -60125,6 +61404,7 @@
comment: The acronym FACIT stands for fibril-associated collagen with interrupted triple helix.
xref: Wikipedia:FACIT_collagen
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140153 ! FACIT collagen complex
[Term]
@@ -60173,7 +61453,7 @@
def: "A collagen homotrimer of alpha1(X) chains; type X collagen triple helices form hexagonal networks (sheets)." [PMID:21421911]
comment: Collagen X trimers have been observed to form hexagonal lattices in vitro, but in vivo they have been found in a fibril associated form (PMID:19693541).
is_a: GO:0098642 ! network-forming collagen trimer
-relationship: part_of GO:0098646 ! interstitial hexagonal collagen network
+relationship: part_of GO:0098646 ! hexagonal collagen network
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29415" xsd:anyURI
[Term]
@@ -60188,8 +61468,8 @@
name: classical-complement-pathway C3/C5 convertase complex
namespace: cellular_component
def: "A heterodimeric protein complex that catalyzes the cleavage of complement components C3 and C5, and acts in the classical pathway of complement activation; consists of one monomer of C2a and one monomer of C4b; C2a is the catalytic subunit, but cannot catalyze cleavage alone." [GOC:mah]
+is_a: GO:0140392 ! extracellular protein-containing complex
is_a: GO:1902494 ! catalytic complex
-relationship: part_of GO:0005615 ! extracellular space
[Term]
id: GO:0005602
@@ -60197,9 +61477,8 @@
namespace: cellular_component
def: "A protein complex composed of six subunits of C1q, each formed of the three homologous polypeptide chains C1QA, C1QB, and C1QB, and tetramer of two C1QR and two C1QS polypeptide chains." [GOC:add, ISBN:0781735149]
synonym: "complement component C1q complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: has_part GO:0062167 ! complement component C1q complex
-relationship: part_of GO:0005576 ! extracellular region
[Term]
id: GO:0005603
@@ -60319,25 +61598,22 @@
[Term]
id: GO:0005615
-name: extracellular space
+name: obsolete extracellular space
namespace: cellular_component
-def: "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684]
-comment: Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
-subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_generic
+def: "OBSOLETE. That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." [ISBN:0198547684]
+comment: This term was obsoleted because it represents the same concept as extracellular region; GO:0005576.
synonym: "intercellular space" RELATED []
xref: NIF_Subcellular:sao1425028079
-is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31545" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0005576
[Term]
id: GO:0005616
name: larval serum protein complex
namespace: cellular_component
def: "A multisubunit protein complex which, in Drosophila, is a heterohexamer of three subunits, alpha, beta and gamma. The complex is thought to store amino acids for synthesis of adult proteins." [GOC:jl, PMID:6781759]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0005617
@@ -60375,7 +61651,7 @@
id: GO:0005619
name: ascospore wall
namespace: cellular_component
-def: "The specialized cell wall of the ascospore (spore), which is the product of meiotic division. Examples of this component are found in Fungi." [GOC:vw, ISBN:0879693568]
+def: "The specialized cell wall of the ascospore (spore), which is the product of meiotic division. Examples of this component are found in Fungi." [GOC:vw, PMID:36266346]
synonym: "fungal-type spore wall" BROAD [GOC:mah]
is_a: GO:0009277 ! fungal-type cell wall
is_a: GO:0031160 ! spore wall
@@ -60410,7 +61686,7 @@
id: GO:0005623
name: obsolete cell
namespace: cellular_component
-def: "OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
+def: "OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:curators]
comment: This term was obsoleted because it was redundant with the root class of the cell ontology, CL:0000000.
xref: NIF_Subcellular:sao1813327414
xref: Wikipedia:Cell_(biology)
@@ -60506,7 +61782,7 @@
id: GO:0005634
name: nucleus
namespace: cellular_component
-def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators]
+def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:curators]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
@@ -60568,7 +61844,7 @@
id: GO:0005639
name: obsolete integral component of nuclear inner membrane
namespace: cellular_component
-def: "OBSOLETE. The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+def: "OBSOLETE. The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:curators]
comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to nuclear inner membrane" NARROW []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23424" xsd:anyURI
@@ -61691,7 +62967,7 @@
id: GO:0005755
name: obsolete hydrogen-transporting ATP synthase, coupling factor CF(0)
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "hydrogen-transporting ATP synthase, coupling factor CF(0)" EXACT []
is_obsolete: true
@@ -62208,7 +63484,7 @@
id: GO:0005799
name: obsolete coatomer
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because its position and synonym implied that it confused a coated vesicle with the coat itself.
synonym: "coatomer" EXACT []
synonym: "COPI vesicle" RELATED []
@@ -62220,7 +63496,7 @@
id: GO:0005800
name: obsolete COPII vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
synonym: "COPII vesicle" EXACT []
is_obsolete: true
@@ -62275,7 +63551,7 @@
id: GO:0005804
name: obsolete secretory vesicle membrane
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because its parent was made obsolete.
synonym: "secretory vesicle membrane" EXACT []
is_obsolete: true
@@ -62286,7 +63562,7 @@
id: GO:0005805
name: obsolete ER-Golgi transport vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
synonym: "ER-Golgi transport vesicle" EXACT []
is_obsolete: true
@@ -62296,7 +63572,7 @@
id: GO:0005806
name: obsolete Golgi-ER transport vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
synonym: "Golgi-ER transport vesicle" EXACT []
is_obsolete: true
@@ -62306,7 +63582,7 @@
id: GO:0005808
name: obsolete Golgi-plasma membrane transport vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; a personal communication from John Armstrong indicated that a replacement term was not required, as TGN-Golgi transport is likely to be mediated by tubules rather than vesicles.
synonym: "Golgi-plasma membrane transport vesicle" EXACT []
is_obsolete: true
@@ -62316,7 +63592,7 @@
id: GO:0005809
name: obsolete Golgi-vacuole transport vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
synonym: "Golgi-vacuole transport vesicle" EXACT []
is_obsolete: true
@@ -62326,7 +63602,7 @@
id: GO:0005810
name: obsolete endocytotic transport vesicle
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology suggested that a new term was required.
synonym: "endocytotic transport vesicle" EXACT []
is_obsolete: true
@@ -63037,7 +64313,7 @@
id: GO:0005888
name: obsolete proteoglycan integral to plasma membrane
namespace: cellular_component
-def: "OBSOLETE. Penetrating at least one phospholipid bilayer of a plasma membrane and consisting of proteoglycan. Also refers to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC:go_curators]
+def: "OBSOLETE. Penetrating at least one phospholipid bilayer of a plasma membrane and consisting of proteoglycan. Also refers to the state of being buried in the bilayer with no exposure outside the bilayer." [GOC:curators]
comment: This term was made obsolete because it describes the composition (i.e. proteoglycan) and not the location of a gene product.
synonym: "proteoglycan integral to plasma membrane" EXACT []
is_obsolete: true
@@ -63202,7 +64478,7 @@
id: GO:0005906
name: obsolete clathrin adaptor
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was positioned incorrectly, so the replacement term has a definition different from what this term appeared to mean.
synonym: "adaptin" RELATED []
synonym: "clathrin adaptor" EXACT []
@@ -63213,7 +64489,7 @@
id: GO:0005907
name: obsolete HA1 clathrin adaptor
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology was erroneous.
synonym: "AP1" RELATED []
synonym: "HA1 clathrin adaptor" EXACT []
@@ -63224,7 +64500,7 @@
id: GO:0005908
name: obsolete HA2 clathrin adaptor
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete as part of a general reorganization of vesicle and vesicle coat terms; its position in the ontology was erroneous.
synonym: "AP2" RELATED []
synonym: "HA2 clathrin adaptor" EXACT []
@@ -63880,7 +65156,6 @@
subset: goslim_prokaryote
subset: goslim_yeast
synonym: "carbohydrate metabolism" EXACT []
-xref: Reactome:R-HSA-71387 "Metabolism of carbohydrates"
xref: Wikipedia:Carbohydrate_metabolism
is_a: GO:0044238 ! primary metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22880" xsd:anyURI
@@ -63933,7 +65208,7 @@
id: GO:0005979
name: regulation of glycogen biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:curators]
synonym: "regulation of glycogen anabolism" EXACT []
synonym: "regulation of glycogen biosynthesis" EXACT []
synonym: "regulation of glycogen formation" EXACT []
@@ -63965,7 +65240,7 @@
id: GO:0005981
name: regulation of glycogen catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:curators]
synonym: "regulation of glycogen breakdown" EXACT []
synonym: "regulation of glycogen catabolism" EXACT []
synonym: "regulation of glycogen degradation" EXACT []
@@ -63992,9 +65267,19 @@
synonym: "starch breakdown" EXACT []
synonym: "starch catabolism" EXACT []
synonym: "starch degradation" EXACT []
+xref: MetaCyc:PWY-6724
+xref: MetaCyc:PWY-6731
+xref: MetaCyc:PWY-6735
+xref: MetaCyc:PWY-6737
xref: MetaCyc:PWY-842
is_a: GO:0005982 ! starch metabolic process
is_a: GO:0009251 ! glucan catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6724
+property_value: skos:narrowMatch MetaCyc:PWY-6731
+property_value: skos:narrowMatch MetaCyc:PWY-6735
+property_value: skos:narrowMatch MetaCyc:PWY-6737
+property_value: skos:narrowMatch MetaCyc:PWY-842
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0005984
@@ -64008,7 +65293,7 @@
id: GO:0005985
name: sucrose metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:go_curators]
+def: "The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:curators]
synonym: "sucrose metabolism" EXACT []
is_a: GO:0005984 ! disaccharide metabolic process
@@ -64016,20 +65301,26 @@
id: GO:0005986
name: sucrose biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:curators]
synonym: "sucrose anabolism" EXACT []
synonym: "sucrose biosynthesis" EXACT []
synonym: "sucrose formation" EXACT []
synonym: "sucrose synthesis" EXACT []
+xref: MetaCyc:PWY-7238
+xref: MetaCyc:PWY-7347
xref: MetaCyc:SUCSYN-PWY
is_a: GO:0005985 ! sucrose metabolic process
is_a: GO:0046351 ! disaccharide biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-7238
+property_value: skos:narrowMatch MetaCyc:PWY-7347
+property_value: skos:narrowMatch MetaCyc:SUCSYN-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0005987
name: sucrose catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of sucrose, the disaccharide fructofuranosyl-glucopyranoside." [GOC:curators]
synonym: "sucrose breakdown" EXACT []
synonym: "sucrose catabolism" EXACT []
synonym: "sucrose degradation" EXACT []
@@ -64040,7 +65331,7 @@
id: GO:0005988
name: lactose metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose." [GOC:go_curators]
+def: "The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose." [GOC:curators]
synonym: "lactose metabolism" EXACT []
is_a: GO:0005984 ! disaccharide metabolic process
@@ -64048,7 +65339,7 @@
id: GO:0005989
name: lactose biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of lactose, the disaccharide galactopyranosyl-glucose." [GOC:curators]
synonym: "lactose anabolism" EXACT []
synonym: "lactose biosynthesis" EXACT []
synonym: "lactose formation" EXACT []
@@ -64061,12 +65352,15 @@
id: GO:0005990
name: lactose catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of lactose, the disaccharide galactopyranosyl-glucose." [GOC:curators]
synonym: "lactose breakdown" EXACT []
synonym: "lactose catabolism" EXACT []
synonym: "lactose degradation" EXACT []
+xref: MetaCyc:BGALACT-PWY
is_a: GO:0005988 ! lactose metabolic process
is_a: GO:0046352 ! disaccharide catabolic process
+property_value: skos:narrowMatch MetaCyc:BGALACT-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0005991
@@ -64094,19 +65388,26 @@
synonym: "trehalose biosynthesis" EXACT []
synonym: "trehalose formation" EXACT []
synonym: "trehalose synthesis" EXACT []
+xref: MetaCyc:PWY-2622
xref: MetaCyc:PWY-2661
+xref: MetaCyc:PWY-5983
+xref: MetaCyc:PWY-5985
xref: MetaCyc:PWY-881
xref: MetaCyc:TREHALOSESYN-PWY
xref: MetaCyc:TRESYN-PWY
is_a: GO:0005991 ! trehalose metabolic process
is_a: GO:0046351 ! disaccharide biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-2622
property_value: skos:narrowMatch MetaCyc:PWY-2661
+property_value: skos:narrowMatch MetaCyc:PWY-5983
+property_value: skos:narrowMatch MetaCyc:PWY-5985
property_value: skos:narrowMatch MetaCyc:PWY-881
property_value: skos:narrowMatch MetaCyc:TREHALOSESYN-PWY
property_value: skos:narrowMatch MetaCyc:TRESYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27083" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27111" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0005993
@@ -64183,7 +65484,6 @@
synonym: "xylulose breakdown" EXACT []
synonym: "xylulose catabolism" EXACT []
synonym: "xylulose degradation" EXACT []
-xref: MetaCyc:XYLCAT-PWY
is_a: GO:0005997 ! xylulose metabolic process
is_a: GO:0019323 ! pentose catabolic process
@@ -64336,9 +65636,11 @@
synonym: "5-phosphoribosyl-1-pyrophosphate biosynthesis" EXACT []
synonym: "5-phosphoribosyl-1-pyrophosphate biosynthetic process" EXACT []
synonym: "PRPP biosynthetic process" EXACT []
-xref: Reactome:R-HSA-73843 "5-Phosphoribose 1-diphosphate biosynthesis"
+xref: MetaCyc:PWY0-662
is_a: GO:0046390 ! ribose phosphate biosynthetic process
is_a: GO:0046391 ! 5-phosphoribose 1-diphosphate metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY0-662
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0006016
@@ -64481,7 +65783,6 @@
synonym: "glycosaminoglycan breakdown" EXACT []
synonym: "glycosaminoglycan catabolism" EXACT []
synonym: "glycosaminoglycan degradation" EXACT []
-xref: Reactome:R-HSA-2024101 "CS/DS degradation"
is_a: GO:0006026 ! aminoglycan catabolic process
is_a: GO:0030203 ! glycosaminoglycan metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29745" xsd:anyURI
@@ -64505,6 +65806,7 @@
def: "The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [PMID:35536939]
synonym: "proteoglycan metabolism" EXACT []
synonym: "proteoglycan sulfate transfer" NARROW []
+xref: Reactome:R-HSA-1793185 "Chondroitin sulfate/dermatan sulfate metabolism"
is_a: GO:0009100 ! glycoprotein metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29745" xsd:anyURI
@@ -64546,12 +65848,14 @@
synonym: "chitin breakdown" EXACT []
synonym: "chitin catabolism" EXACT []
synonym: "chitin degradation" EXACT []
+xref: MetaCyc:PWY-6855
xref: MetaCyc:PWY-6902
xref: MetaCyc:PWY-7118
xref: MetaCyc:PWY-7822
is_a: GO:0006026 ! aminoglycan catabolic process
is_a: GO:0006030 ! chitin metabolic process
is_a: GO:1901072 ! glucosamine-containing compound catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6855
property_value: skos:narrowMatch MetaCyc:PWY-6902
property_value: skos:narrowMatch MetaCyc:PWY-7118
property_value: skos:narrowMatch MetaCyc:PWY-7822
@@ -64698,6 +66002,7 @@
def: "The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein." [ISBN:0198506732]
synonym: "N-acetylglucosamine metabolism" EXACT []
is_a: GO:0006040 ! amino sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0006045
@@ -64710,6 +66015,7 @@
synonym: "N-acetylglucosamine synthesis" EXACT []
is_a: GO:0006044 ! N-acetylglucosamine metabolic process
is_a: GO:1901073 ! glucosamine-containing compound biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0006046
@@ -64725,6 +66031,7 @@
is_a: GO:1901072 ! glucosamine-containing compound catabolic process
property_value: skos:narrowMatch MetaCyc:GLUAMCAT-PWY
property_value: skos:narrowMatch MetaCyc:PWY-6517
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
@@ -64891,36 +66198,43 @@
[Term]
id: GO:0006060
-name: sorbitol metabolic process
+name: D-sorbitol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group." [ISBN:0198506732]
synonym: "sorbitol metabolism" EXACT []
-xref: MetaCyc:P461-PWY
is_a: GO:0006059 ! hexitol metabolic process
[Term]
id: GO:0006061
-name: sorbitol biosynthetic process
+name: D-sorbitol biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group." [ISBN:0198506732]
synonym: "sorbitol anabolism" EXACT []
synonym: "sorbitol biosynthesis" EXACT []
synonym: "sorbitol formation" EXACT []
synonym: "sorbitol synthesis" EXACT []
-is_a: GO:0006060 ! sorbitol metabolic process
+xref: MetaCyc:PWY-5054
+xref: MetaCyc:PWY-5530
+is_a: GO:0006060 ! D-sorbitol metabolic process
is_a: GO:0019406 ! hexitol biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-5054
+property_value: skos:narrowMatch MetaCyc:PWY-5530
[Term]
id: GO:0006062
-name: sorbitol catabolic process
+name: D-sorbitol catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of sorbitol (D-glucitol), one of the ten stereoisomeric hexitols. It can be derived from glucose by reduction of the aldehyde group." [ISBN:0198506732]
synonym: "sorbitol breakdown" EXACT []
synonym: "sorbitol catabolism" EXACT []
synonym: "sorbitol degradation" EXACT []
+xref: MetaCyc:PWY-4101
xref: MetaCyc:SORBDEG-PWY
-is_a: GO:0006060 ! sorbitol metabolic process
+is_a: GO:0006060 ! D-sorbitol metabolic process
is_a: GO:0019407 ! hexitol catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-4101
+property_value: skos:narrowMatch MetaCyc:SORBDEG-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006063
@@ -64936,7 +66250,7 @@
id: GO:0006064
name: glucuronate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid." [GOC:curators]
synonym: "glucuronate breakdown" EXACT []
synonym: "glucuronate catabolism" EXACT []
synonym: "glucuronate degradation" EXACT []
@@ -64967,10 +66281,12 @@
name: alcohol metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [ISBN:0198506732]
+subset: gocheck_do_not_annotate
subset: goslim_drosophila
subset: goslim_pir
synonym: "alcohol metabolism" EXACT []
is_a: GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
[Term]
id: GO:0006067
@@ -65005,7 +66321,7 @@
id: GO:0006070
name: octanol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving octanol, the 8-carbon alcohol with the formula C8H17OH." [GOC:go_curators]
+def: "The chemical reactions and pathways involving octanol, the 8-carbon alcohol with the formula C8H17OH." [GOC:curators]
synonym: "octanol metabolism" EXACT []
is_a: GO:0034308 ! primary alcohol metabolic process
is_a: GO:1903173 ! fatty alcohol metabolic process
@@ -65016,15 +66332,15 @@
namespace: biological_process
def: "The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids." [GOC:ai, ISBN:0198506732]
synonym: "glycerol metabolism" EXACT []
-xref: MetaCyc:GLYCEROLMETAB-PWY
is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0019751 ! polyol metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006072
name: glycerol-3-phosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol." [GOC:curators, ISBN:0198506732]
synonym: "glycerol-3-phosphate metabolism" EXACT []
is_a: GO:0052646 ! alditol phosphate metabolic process
@@ -65142,7 +66458,7 @@
id: GO:0006081
name: aldehyde metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." [GOC:curators, ISBN:0198506732]
subset: goslim_pir
synonym: "aldehyde metabolism" EXACT []
synonym: "alkanal metabolic process" EXACT []
@@ -65163,7 +66479,7 @@
id: GO:0006083
name: acetate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving acetate, the anion of acetic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving acetate, the anion of acetic acid." [GOC:curators]
synonym: "acetate metabolism" EXACT []
is_a: GO:0032787 ! monocarboxylic acid metabolic process
@@ -65181,14 +66497,28 @@
id: GO:0006085
name: acetyl-CoA biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated." [GOC:curators]
synonym: "acetyl-CoA anabolism" EXACT []
synonym: "acetyl-CoA biosynthesis" EXACT []
synonym: "acetyl-CoA formation" EXACT []
synonym: "acetyl-CoA synthesis" EXACT []
+xref: MetaCyc:ACETATEUTIL-PWY
xref: MetaCyc:Acetyl-CoA-Biosynthesis
+xref: MetaCyc:ETOH-ACETYLCOA-ANA-PWY
+xref: MetaCyc:PWY-5172
+xref: MetaCyc:PWY66-161
+xref: MetaCyc:PWY66-162
+xref: MetaCyc:PWY66-21
is_a: GO:0006084 ! acetyl-CoA metabolic process
is_a: GO:0071616 ! acyl-CoA biosynthetic process
+property_value: skos:narrowMatch MetaCyc:ACETATEUTIL-PWY
+property_value: skos:narrowMatch MetaCyc:ETOH-ACETYLCOA-ANA-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5172
+property_value: skos:narrowMatch MetaCyc:PWY66-161
+property_value: skos:narrowMatch MetaCyc:PWY66-162
+property_value: skos:narrowMatch MetaCyc:PWY66-21
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31666" xsd:anyURI
[Term]
id: GO:0006086
@@ -65202,6 +66532,8 @@
synonym: "oxidative decarboxylation of pyruvate" EXACT []
synonym: "pyruvate decarboxylation" NARROW []
synonym: "pyruvate dehydrogenase pathway" EXACT []
+xref: MetaCyc:PWY-6970
+xref: MetaCyc:PWY-8275
xref: MetaCyc:PYRUVDEHYD-PWY
xref: Reactome:R-HSA-9861559 "PDH complex synthesizes acetyl-CoA from PYR"
is_a: GO:0006085 ! acetyl-CoA biosynthetic process
@@ -65210,9 +66542,13 @@
relationship: has_part GO:0004739 ! pyruvate dehydrogenase (acetyl-transferring) activity
relationship: has_part GO:0004742 ! dihydrolipoyllysine-residue acetyltransferase activity
relationship: part_of GO:0009060 ! aerobic respiration
+property_value: skos:narrowMatch MetaCyc:PWY-6970
+property_value: skos:narrowMatch MetaCyc:PWY-8275
+property_value: skos:narrowMatch MetaCyc:PYRUVDEHYD-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24348" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30067" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30126" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006088
@@ -65241,16 +66577,15 @@
name: pyruvate metabolic process
namespace: biological_process
alt_id: GO:0006087
-def: "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_drosophila
synonym: "pyruvate dehydrogenase bypass" RELATED []
synonym: "pyruvate metabolism" EXACT []
-xref: MetaCyc:P41-PWY
-xref: Reactome:R-HSA-70268 "Pyruvate metabolism"
xref: Wikipedia:Pyruvic_acid
is_a: GO:0032787 ! monocarboxylic acid metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29541" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006091
@@ -65488,7 +66823,7 @@
id: GO:0006109
name: regulation of carbohydrate metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." [GOC:curators]
synonym: "regulation of carbohydrate metabolism" EXACT []
is_a: GO:0080090 ! regulation of primary metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -65500,7 +66835,7 @@
name: regulation of glycolytic process
namespace: biological_process
alt_id: GO:0090525
-def: "Any process that modulates the frequency, rate or extent of glycolysis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of glycolysis." [GOC:curators]
synonym: "regulation of glycolysis involved in cellular glucose homeostasis" EXACT []
xref: Reactome:R-HSA-170822 "Regulation of Glucokinase by Glucokinase Regulatory Protein"
is_a: GO:0033121 ! regulation of purine nucleotide catabolic process
@@ -65516,7 +66851,7 @@
name: regulation of gluconeogenesis
namespace: biological_process
alt_id: GO:0090526
-def: "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." [GOC:curators]
synonym: "regulation of gluconeogenesis involved in cellular glucose homeostasis" RELATED []
synonym: "regulation of glucose biosynthesis" BROAD []
synonym: "regulation of glucose biosynthetic process" BROAD []
@@ -65596,7 +66931,7 @@
id: GO:0006117
name: acetaldehyde metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol." [GOC:go_curators]
+def: "The chemical reactions and pathways involving acetaldehyde, a colorless, flammable liquid intermediate in the metabolism of alcohol." [GOC:curators]
synonym: "acetaldehyde metabolism" EXACT []
synonym: "ethanal metabolic process" EXACT []
synonym: "ethanal metabolism" EXACT []
@@ -65696,7 +67031,7 @@
id: GO:0006126
name: obsolete other pathways of electron transport
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was an unnecessary grouping term.
synonym: "other pathways of electron transport" EXACT []
is_obsolete: true
@@ -65817,6 +67152,7 @@
namespace: biological_process
alt_id: GO:0055134
def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai]
+subset: gocheck_do_not_annotate
subset: goslim_pir
subset: goslim_plant
synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
@@ -65825,12 +67161,13 @@
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
is_a: GO:0044238 ! primary metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
[Term]
id: GO:0006140
name: regulation of nucleotide metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:curators]
synonym: "regulation of nucleotide metabolism" EXACT []
is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process
is_a: GO:0051174 ! regulation of phosphorus metabolic process
@@ -65843,8 +67180,8 @@
id: GO:0006141
name: regulation of purine nucleobase metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines." [GOC:go_curators]
-synonym: "regulation of purine base metabolic process" EXACT [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines." [GOC:curators]
+synonym: "regulation of purine base metabolic process" EXACT [GOC:curators]
synonym: "regulation of purine base metabolism" EXACT []
is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
@@ -65856,9 +67193,9 @@
id: GO:0006142
name: obsolete regulation of pyrimidine nucleobase metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
-synonym: "regulation of pyrimidine base metabolic process" EXACT [GOC:go_curators]
+synonym: "regulation of pyrimidine base metabolic process" EXACT [GOC:curators]
synonym: "regulation of pyrimidine base metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30570" xsd:anyURI
is_obsolete: true
@@ -65867,7 +67204,7 @@
id: GO:0006143
name: obsolete purine metabolic process
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more appropriate terms were created.
synonym: "purine metabolic process" EXACT []
is_obsolete: true
@@ -65879,8 +67216,8 @@
id: GO:0006144
name: purine nucleobase metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [GOC:go_curators]
-synonym: "purine base metabolic process" EXACT [GOC:go_curators]
+def: "The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [GOC:curators]
+synonym: "purine base metabolic process" EXACT [GOC:curators]
synonym: "purine base metabolism" EXACT []
synonym: "purine metabolic process" NARROW []
synonym: "purine metabolism" NARROW []
@@ -65891,9 +67228,9 @@
id: GO:0006145
name: purine nucleobase catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [GOC:curators]
synonym: "purine base breakdown" EXACT []
-synonym: "purine base catabolic process" EXACT [GOC:go_curators]
+synonym: "purine base catabolic process" EXACT [GOC:curators]
synonym: "purine base catabolism" EXACT []
synonym: "purine base degradation" EXACT []
is_a: GO:0006144 ! purine nucleobase metabolic process
@@ -65915,7 +67252,7 @@
id: GO:0006147
name: guanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:curators]
synonym: "guanine breakdown" EXACT []
synonym: "guanine catabolism" EXACT []
synonym: "guanine degradation" EXACT []
@@ -65926,7 +67263,7 @@
id: GO:0006148
name: inosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:curators]
synonym: "inosine breakdown" EXACT []
synonym: "inosine catabolism" EXACT []
synonym: "inosine degradation" EXACT []
@@ -65937,18 +67274,19 @@
id: GO:0006149
name: deoxyinosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of deoxyinosine, hypoxanthine deoxyriboside." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of deoxyinosine, hypoxanthine deoxyriboside." [GOC:curators]
synonym: "deoxyinosine breakdown" EXACT []
synonym: "deoxyinosine catabolism" EXACT []
synonym: "deoxyinosine degradation" EXACT []
is_a: GO:0046094 ! deoxyinosine metabolic process
+is_a: GO:0046121 ! 2'-deoxyribonucleoside catabolic process
is_a: GO:0046124 ! purine deoxyribonucleoside catabolic process
[Term]
id: GO:0006152
name: purine nucleoside catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:curators]
synonym: "purine nucleoside breakdown" EXACT []
synonym: "purine nucleoside catabolism" EXACT []
synonym: "purine nucleoside degradation" EXACT []
@@ -65971,7 +67309,7 @@
name: adenosine catabolic process
namespace: biological_process
alt_id: GO:0006156
-def: "The chemical reactions and pathways resulting in the breakdown of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:curators]
synonym: "adenosine breakdown" EXACT []
synonym: "adenosine catabolism" EXACT []
synonym: "adenosine degradation" EXACT []
@@ -65997,12 +67335,13 @@
name: deoxyadenosine catabolic process
namespace: biological_process
alt_id: GO:0006159
-def: "The chemical reactions and pathways resulting in the breakdown of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyadenosine breakdown" EXACT []
synonym: "deoxyadenosine catabolism" EXACT []
synonym: "deoxyadenosine degradation" EXACT []
synonym: "deoxyadenosine phosphorolysis" RELATED []
is_a: GO:0046090 ! deoxyadenosine metabolic process
+is_a: GO:0046121 ! 2'-deoxyribonucleoside catabolic process
is_a: GO:0046124 ! purine deoxyribonucleoside catabolic process
[Term]
@@ -66023,6 +67362,7 @@
synonym: "deoxyguanosine breakdown" EXACT []
synonym: "deoxyguanosine catabolism" EXACT []
synonym: "deoxyguanosine degradation" EXACT []
+is_a: GO:0046121 ! 2'-deoxyribonucleoside catabolic process
is_a: GO:0046124 ! purine deoxyribonucleoside catabolic process
[Term]
@@ -66039,7 +67379,7 @@
id: GO:0006163
name: purine nucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine metabolic process" NARROW []
synonym: "purine metabolism" NARROW []
synonym: "purine nucleotide metabolism" EXACT []
@@ -66050,15 +67390,15 @@
id: GO:0006164
name: purine nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleotide anabolism" EXACT []
synonym: "purine nucleotide biosynthesis" EXACT []
synonym: "purine nucleotide formation" EXACT []
synonym: "purine nucleotide synthesis" EXACT []
-xref: MetaCyc:DENOVOPURINE2-PWY
is_a: GO:0006163 ! purine nucleotide metabolic process
is_a: GO:0009165 ! nucleotide biosynthetic process
is_a: GO:0072522 ! purine-containing compound biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006165
@@ -66073,7 +67413,6 @@
name: purine ribonucleoside salvage
namespace: biological_process
def: "Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis." [GOC:jl]
-xref: MetaCyc:P121-PWY
is_a: GO:0043101 ! purine-containing compound salvage
is_a: GO:0043174 ! nucleoside salvage
is_a: GO:0046129 ! purine ribonucleoside biosynthetic process
@@ -66082,7 +67421,7 @@
id: GO:0006167
name: AMP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate." [GOC:curators, ISBN:0198506732]
synonym: "AMP anabolism" EXACT []
synonym: "AMP biosynthesis" EXACT []
synonym: "AMP formation" EXACT []
@@ -66098,8 +67437,16 @@
def: "Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis." [GOC:jl]
synonym: "adenine salvage pathway" EXACT []
synonym: "adenine, hypoxanthine and their nucleoside salvage" BROAD []
+xref: MetaCyc:PWY-6610
is_a: GO:0043096 ! purine nucleobase salvage
is_a: GO:0046084 ! adenine biosynthetic process
+property_value: skos:broadMatch MetaCyc:P121-PWY
+property_value: skos:broadMatch MetaCyc:PWY-6605
+property_value: skos:broadMatch MetaCyc:PWY-6609
+property_value: skos:broadMatch MetaCyc:PWY-6611
+property_value: skos:broadMatch MetaCyc:PWY-6619
+property_value: skos:exactMatch MetaCyc:PWY-6610
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006169
@@ -66109,6 +67456,12 @@
synonym: "adenine, hypoxanthine and their nucleoside salvage" BROAD []
is_a: GO:0006166 ! purine ribonucleoside salvage
is_a: GO:0046086 ! adenosine biosynthetic process
+property_value: skos:broadMatch MetaCyc:P121-PWY
+property_value: skos:broadMatch MetaCyc:PWY-6605
+property_value: skos:broadMatch MetaCyc:PWY-6609
+property_value: skos:broadMatch MetaCyc:PWY-6611
+property_value: skos:broadMatch MetaCyc:PWY-6619
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006170
@@ -66402,7 +67755,7 @@
id: GO:0006195
name: purine nucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleotide breakdown" EXACT []
synonym: "purine nucleotide catabolism" EXACT []
synonym: "purine nucleotide degradation" EXACT []
@@ -66525,7 +67878,7 @@
id: GO:0006205
name: obsolete pyrimidine metabolic process
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more appropriate terms were created.
synonym: "pyrimidine metabolic process" EXACT []
is_obsolete: true
@@ -66537,8 +67890,8 @@
id: GO:0006206
name: pyrimidine nucleobase metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:go_curators]
-synonym: "pyrimidine base metabolic process" EXACT [GOC:go_curators]
+def: "The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:curators]
+synonym: "pyrimidine base metabolic process" EXACT [GOC:curators]
synonym: "pyrimidine base metabolism" EXACT []
synonym: "pyrimidine metabolic process" RELATED []
synonym: "pyrimidine metabolism" RELATED []
@@ -66552,7 +67905,7 @@
def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors." [GOC:mah, ISBN:0716720094]
synonym: "'de novo' pyrimidine base anabolism" EXACT []
synonym: "'de novo' pyrimidine base biosynthesis" EXACT []
-synonym: "'de novo' pyrimidine base biosynthetic process" EXACT [GOC:go_curators]
+synonym: "'de novo' pyrimidine base biosynthetic process" EXACT [GOC:curators]
synonym: "'de novo' pyrimidine base formation" EXACT []
synonym: "'de novo' pyrimidine base synthesis" EXACT []
is_a: GO:0019856 ! pyrimidine nucleobase biosynthetic process
@@ -66561,9 +67914,9 @@
id: GO:0006208
name: pyrimidine nucleobase catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:curators]
synonym: "pyrimidine base breakdown" EXACT []
-synonym: "pyrimidine base catabolic process" EXACT [GOC:go_curators]
+synonym: "pyrimidine base catabolic process" EXACT [GOC:curators]
synonym: "pyrimidine base catabolism" EXACT []
synonym: "pyrimidine base degradation" EXACT []
is_a: GO:0006206 ! pyrimidine nucleobase metabolic process
@@ -66574,7 +67927,7 @@
id: GO:0006209
name: cytosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives." [GOC:curators]
synonym: "cytosine breakdown" EXACT []
synonym: "cytosine catabolism" EXACT []
synonym: "cytosine degradation" EXACT []
@@ -66585,7 +67938,7 @@
id: GO:0006210
name: thymine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:curators]
synonym: "thymine breakdown" EXACT []
synonym: "thymine catabolism" EXACT []
synonym: "thymine degradation" EXACT []
@@ -66596,7 +67949,7 @@
id: GO:0006211
name: obsolete 5-methylcytosine catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 5-methylcytosine, a methylated base of DNA." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 5-methylcytosine, a methylated base of DNA." [GOC:curators]
comment: This term was obsoleted because it it redundant with chromosomal 5-methylcytosine DNA demethylation pathway ; GO:0141166 or its children.
synonym: "5-methylcytosine breakdown" EXACT []
synonym: "5-methylcytosine catabolism" EXACT []
@@ -66609,7 +67962,7 @@
id: GO:0006212
name: uracil catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:curators]
synonym: "uracil breakdown" EXACT []
synonym: "uracil catabolism" EXACT []
synonym: "uracil degradation" EXACT []
@@ -66632,7 +67985,7 @@
name: thymidine catabolic process
namespace: biological_process
alt_id: GO:0006215
-def: "The chemical reactions and pathways resulting in the breakdown of thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:curators]
synonym: "deoxyribosylthymine catabolic process" EXACT []
synonym: "deoxyribosylthymine catabolism" EXACT []
synonym: "thymidine breakdown" EXACT []
@@ -66656,7 +68009,7 @@
id: GO:0006217
name: deoxycytidine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxycytidine breakdown" EXACT []
synonym: "deoxycytidine catabolism" EXACT []
synonym: "deoxycytidine degradation" EXACT []
@@ -66667,7 +68020,7 @@
id: GO:0006218
name: uridine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:curators]
synonym: "uridine breakdown" EXACT []
synonym: "uridine catabolism" EXACT []
synonym: "uridine degradation" EXACT []
@@ -66678,7 +68031,7 @@
id: GO:0006219
name: deoxyuridine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyuridine breakdown" EXACT []
synonym: "deoxyuridine catabolism" EXACT []
synonym: "deoxyuridine degradation" EXACT []
@@ -66689,7 +68042,7 @@
id: GO:0006220
name: pyrimidine nucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine metabolic process" BROAD []
synonym: "pyrimidine metabolism" BROAD []
synonym: "pyrimidine nucleotide metabolism" EXACT []
@@ -66700,7 +68053,7 @@
id: GO:0006221
name: pyrimidine nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleotide anabolism" EXACT []
synonym: "pyrimidine nucleotide biosynthesis" EXACT []
synonym: "pyrimidine nucleotide formation" EXACT []
@@ -66961,7 +68314,7 @@
id: GO:0006244
name: pyrimidine nucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleotide breakdown" EXACT []
synonym: "pyrimidine nucleotide catabolism" EXACT []
synonym: "pyrimidine nucleotide degradation" EXACT []
@@ -67194,6 +68547,7 @@
synonym: "mtDNA replication" EXACT []
synonym: "mtDNA synthesis" RELATED []
synonym: "replication of mitochondrial DNA" EXACT []
+xref: Reactome:R-HSA-9913635 "Strand-asynchronous mitochondrial DNA replication"
is_a: GO:0006261 ! DNA-templated DNA replication
is_a: GO:0032042 ! mitochondrial DNA metabolic process
intersection_of: GO:0006260 ! DNA replication
@@ -67317,7 +68671,7 @@
id: GO:0006275
name: regulation of DNA replication
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of DNA replication." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of DNA replication." [GOC:curators]
is_a: GO:0051052 ! regulation of DNA metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006260 ! DNA replication
@@ -67399,7 +68753,7 @@
id: GO:0006282
name: regulation of DNA repair
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of DNA repair." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of DNA repair." [GOC:curators]
subset: goslim_metagenomics
is_a: GO:0051052 ! regulation of DNA metabolic process
is_a: GO:0080135 ! regulation of cellular response to stress
@@ -67657,7 +69011,7 @@
id: GO:0006308
name: DNA catabolic process
namespace: biological_process
-def: "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:go_curators, ISBN:0198506732]
+def: "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:curators, ISBN:0198506732]
synonym: "DNA breakdown" EXACT []
synonym: "DNA catabolism" EXACT []
synonym: "DNA degradation" EXACT []
@@ -67796,7 +69150,7 @@
id: GO:0006326
name: obsolete bent DNA binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "bent DNA binding" EXACT []
is_obsolete: true
@@ -67806,7 +69160,7 @@
id: GO:0006327
name: obsolete random coil binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "random coil binding" EXACT []
is_obsolete: true
@@ -67815,7 +69169,7 @@
id: GO:0006328
name: obsolete AT binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "AT binding" EXACT []
is_obsolete: true
@@ -67825,7 +69179,7 @@
id: GO:0006329
name: obsolete satellite DNA binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "satellite DNA binding" EXACT []
is_obsolete: true
@@ -67837,7 +69191,7 @@
namespace: biological_process
alt_id: GO:0006331
alt_id: GO:0006332
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "single-stranded DNA binding" EXACT []
is_obsolete: true
@@ -67895,7 +69249,7 @@
id: GO:0006339
name: obsolete positive regulation of transcription of homeotic gene (trithorax group)
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "positive regulation of transcription of homeotic gene (trithorax group)" EXACT []
is_obsolete: true
@@ -67907,7 +69261,7 @@
id: GO:0006340
name: obsolete negative regulation of transcription of homeotic gene (Polycomb group)
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "negative regulation of transcription of homeotic gene (Polycomb group)" EXACT []
is_obsolete: true
@@ -68052,7 +69406,7 @@
alt_id: GO:0032583
alt_id: GO:0045449
alt_id: GO:0061019
-def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
subset: goslim_drosophila
subset: goslim_generic
subset: goslim_prokaryote
@@ -68063,6 +69417,7 @@
synonym: "regulation of transcription, DNA-templated" EXACT []
synonym: "transcriptional control" BROAD []
xref: Reactome:R-HSA-9013695 "NOTCH4 Intracellular Domain Regulates Transcription"
+xref: Reactome:R-HSA-9708530 "Regulation of BACH1 activity"
xref: Reactome:R-HSA-9762293 "Regulation of CDH11 gene transcription"
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:2001141 ! regulation of RNA biosynthetic process
@@ -68075,7 +69430,7 @@
id: GO:0006356
name: regulation of transcription by RNA polymerase I
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:curators]
synonym: "regulation of transcription from Pol I promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase I promoter" EXACT []
is_a: GO:0006355 ! regulation of DNA-templated transcription
@@ -68089,7 +69444,7 @@
namespace: biological_process
alt_id: GO:0006358
alt_id: GO:0010551
-def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:go_curators, GOC:txnOH]
+def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II." [GOC:curators, GOC:txnOH]
synonym: "global transcription regulation from Pol II promoter" RELATED []
synonym: "regulation of gene-specific transcription from RNA polymerase II promoter" RELATED []
synonym: "regulation of global transcription from Pol II promoter" RELATED []
@@ -68106,7 +69461,7 @@
id: GO:0006359
name: regulation of transcription by RNA polymerase III
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III." [GOC:curators]
synonym: "regulation of transcription from Pol III promoter" EXACT []
synonym: "regulation of transcription from RNA polymerase III promoter" EXACT []
is_a: GO:0006355 ! regulation of DNA-templated transcription
@@ -68363,7 +69718,7 @@
id: GO:0006380
name: obsolete poly-A binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "poly-A binding" EXACT []
is_obsolete: true
@@ -68602,6 +69957,7 @@
synonym: "RNA breakdown" EXACT []
synonym: "RNA catabolism" EXACT []
synonym: "RNA degradation" EXACT []
+xref: Reactome:R-HSA-9930044 "Nuclear RNA decay"
is_a: GO:0016070 ! RNA metabolic process
is_a: GO:0141188 ! nucleic acid catabolic process
@@ -68719,7 +70075,7 @@
alt_id: GO:0006416
alt_id: GO:0006453
alt_id: GO:0043037
-def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators]
+def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:curators]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -68979,7 +70335,7 @@
id: GO:0006446
name: regulation of translational initiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of translational initiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of translational initiation." [GOC:curators]
is_a: GO:0006417 ! regulation of translation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006413 ! translational initiation
@@ -68996,7 +70352,7 @@
id: GO:0006448
name: regulation of translational elongation
namespace: biological_process
-def: "Any process that modulates the frequency, rate, extent or accuracy of translational elongation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate, extent or accuracy of translational elongation." [GOC:curators]
is_a: GO:0006417 ! regulation of translation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006414 ! translational elongation
@@ -69006,7 +70362,7 @@
id: GO:0006449
name: regulation of translational termination
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of translational termination." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of translational termination." [GOC:curators]
is_a: GO:0006417 ! regulation of translation
is_a: GO:0043244 ! regulation of protein-containing complex disassembly
intersection_of: GO:0065007 ! biological regulation
@@ -69046,7 +70402,7 @@
alt_id: GO:0007022
alt_id: GO:0007024
alt_id: GO:0007025
-def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:go_curators, GOC:rb]
+def: "The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure." [GOC:curators, GOC:rb]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
@@ -69069,6 +70425,7 @@
synonym: "non-chaperonin molecular chaperone ATPase activity" RELATED []
synonym: "protein complex assembly, multichaperone pathway" RELATED []
xref: Reactome:R-HSA-389960 "Formation of tubulin folding intermediates by CCT/TriC"
+xref: Reactome:R-HSA-390450 "Folding of actin by CCT/TriC"
xref: Reactome:R-HSA-390466 "Chaperonin-mediated protein folding"
xref: Reactome:R-HSA-532668 "N-glycan trimming in the ER and Calnexin/Calreticulin cycle"
xref: Wikipedia:Protein_folding
@@ -69099,7 +70456,7 @@
id: GO:0006460
name: obsolete peptidyl-prolyl isomerase B reaction
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "peptidyl-prolyl isomerase B reaction" EXACT []
is_obsolete: true
@@ -69130,7 +70487,6 @@
def: "OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell." [GOC:mah, PMID:31214988]
comment: This term was obsoleted because it reprenset a molecular function, signal peptidase activity ; GO:0009003.
synonym: "leader peptide processing" EXACT []
-xref: Reactome:R-HSA-159782 "Removal of aminoterminal propeptides from gamma-carboxylated proteins"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30479" xsd:anyURI
is_obsolete: true
replaced_by: GO:0051604
@@ -69152,7 +70508,6 @@
namespace: biological_process
def: "The process of introducing a phosphate group on to a protein." [GOC:hb]
subset: gocheck_obsoletion_candidate
-subset: goslim_yeast
synonym: "protein amino acid phosphorylation" EXACT [GOC:bf]
is_a: GO:0016310 ! phosphorylation
is_a: GO:0036211 ! protein modification process
@@ -69161,7 +70516,7 @@
id: GO:0006469
name: negative regulation of protein kinase activity
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "down regulation of protein kinase activity" EXACT []
synonym: "down-regulation of protein kinase activity" EXACT []
@@ -69180,7 +70535,6 @@
namespace: biological_process
def: "The process of removing one or more phosphoric residues from a protein." [GOC:hb]
subset: gocheck_obsoletion_candidate
-subset: goslim_yeast
synonym: "protein amino acid dephosphorylation" EXACT [GOC:bf]
is_a: GO:0016311 ! dephosphorylation
is_a: GO:0036211 ! protein modification process
@@ -69343,6 +70697,8 @@
synonym: "N-glycan biosynthesis" RELATED []
synonym: "N-glycan metabolism" RELATED []
synonym: "protein amino acid N-linked glycosylation" EXACT [GOC:bf]
+xref: Reactome:R-HSA-446203 "Asparagine N-linked glycosylation"
+xref: Reactome:R-HSA-480985 "Synthesis of dolichyl-phosphate-glucose"
is_a: GO:0009101 ! glycoprotein biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29770" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30595" xsd:anyURI
@@ -69359,6 +70715,7 @@
synonym: "N-linked glycan precursor biosynthesis" EXACT [PMID:8666161]
synonym: "N-linked glycan precursor biosynthetic process" EXACT [PMID:8666161]
synonym: "oligosaccharide-PP-dolichol assembly" EXACT []
+xref: Reactome:R-HSA-162699 "Synthesis of dolichyl-phosphate mannose"
xref: Reactome:R-HSA-446193 "Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein"
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
relationship: part_of GO:0006487 ! protein N-linked glycosylation
@@ -69374,7 +70731,6 @@
synonym: "dolichyl diphosphate biosynthesis" EXACT []
synonym: "dolichyl diphosphate formation" EXACT []
synonym: "dolichyl diphosphate synthesis" EXACT []
-xref: Reactome:R-HSA-446199 "Synthesis of Dolichyl-phosphate"
is_a: GO:0008654 ! phospholipid biosynthetic process
relationship: part_of GO:0006488 ! dolichol-linked oligosaccharide biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30376" xsd:anyURI
@@ -69431,7 +70787,7 @@
id: GO:0006495
name: obsolete terminal O-glycosylation
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators, GOC:jsg]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators, GOC:jsg]
comment: This term was made obsolete because there is no evidence for the existence of this process.
synonym: "terminal O-glycosylation" EXACT []
is_obsolete: true
@@ -69455,7 +70811,6 @@
comment: For non-covalent interactions with a lipid, consider instead the term 'lipid binding ; GO:0008289' and its children.
subset: gocheck_obsoletion_candidate
subset: goslim_drosophila
-subset: goslim_yeast
synonym: "lipid:protein modification" EXACT []
synonym: "protein amino acid lipidation" EXACT [GOC:bf]
xref: RESID:AA0059
@@ -69563,15 +70918,15 @@
synonym: "GPI anchor metabolism" EXACT []
synonym: "GPI/GSI anchor metabolic process" BROAD []
synonym: "GPI/GSI anchor metabolism" BROAD []
+is_a: GO:0006650 ! glycerophospholipid metabolic process
is_a: GO:0006664 ! glycolipid metabolic process
-is_a: GO:0046488 ! phosphatidylinositol metabolic process
[Term]
id: GO:0006506
name: GPI anchor biosynthetic process
namespace: biological_process
alt_id: GO:0015998
-def: "The chemical reactions and pathways resulting in the formation of a glycosylphosphatidylinositol (GPI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The phosphatidylinositol group is linked via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via an ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GPI anchors have variants on this canonical linkage." [GOC:go_curators, ISBN:0198547684]
+def: "The chemical reactions and pathways resulting in the formation of a glycosylphosphatidylinositol (GPI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The phosphatidylinositol group is linked via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via an ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GPI anchors have variants on this canonical linkage." [GOC:curators, ISBN:0198547684]
synonym: "glycosylphosphatidylinositol biosynthesis" EXACT []
synonym: "glycosylphosphatidylinositol biosynthetic process" EXACT []
synonym: "GPI anchor anabolism" EXACT []
@@ -69580,12 +70935,17 @@
synonym: "GPI anchor synthesis" EXACT []
synonym: "GPI/GSI anchor biosynthesis" BROAD []
synonym: "GPI/GSI anchor biosynthetic process" BROAD []
+xref: MetaCyc:PWY-8600
+xref: MetaCyc:PWY-8601
xref: Reactome:R-HSA-162710 "Synthesis of glycosylphosphatidylinositol (GPI)"
is_a: GO:0006505 ! GPI anchor metabolic process
-is_a: GO:0006661 ! phosphatidylinositol biosynthetic process
is_a: GO:0009247 ! glycolipid biosynthetic process
+is_a: GO:0046474 ! glycerophospholipid biosynthetic process
relationship: part_of GO:0180046 ! GPI anchored protein biosynthesis
+property_value: skos:narrowMatch MetaCyc:PWY-8600
+property_value: skos:narrowMatch MetaCyc:PWY-8601
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28227" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30568" xsd:anyURI
[Term]
id: GO:0006507
@@ -69641,7 +71001,7 @@
namespace: biological_process
alt_id: GO:0042787
alt_id: GO:0043432
-def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein." [GOC:curators]
synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein breakdown" NARROW []
synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolic process" NARROW []
synonym: "myofibrillar protein ubiquitination during ubiquitin-dependent protein catabolism" NARROW []
@@ -69699,7 +71059,7 @@
id: GO:0006516
name: glycoprotein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:curators, ISBN:0198506732]
synonym: "glycoprotein breakdown" EXACT []
synonym: "glycoprotein catabolism" EXACT []
synonym: "glycoprotein degradation" EXACT []
@@ -69721,7 +71081,7 @@
id: GO:0006518
name: peptide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:go_curators]
+def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [GOC:curators]
subset: goslim_pir
synonym: "peptide metabolism" EXACT []
xref: Reactome:R-HSA-2980736 "Peptide hormone metabolism"
@@ -69752,9 +71112,8 @@
id: GO:0006521
name: regulation of amino acid metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." [GOC:curators]
synonym: "regulation of amino acid metabolism" EXACT []
-xref: Reactome:R-HSA-350562 "Regulation of ornithine decarboxylase (ODC)"
is_a: GO:0080090 ! regulation of primary metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006520 ! amino acid metabolic process
@@ -69763,29 +71122,32 @@
[Term]
id: GO:0006522
-name: alanine metabolic process
+name: obsolete alanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving alanine, 2-aminopropanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "alanine metabolism" EXACT []
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0042852
+consider: GO:0042853
[Term]
id: GO:0006523
name: alanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of alanine, 2-aminopropanoic acid." [GOC:curators]
synonym: "alanine anabolism" EXACT []
synonym: "alanine biosynthesis" EXACT []
synonym: "alanine formation" EXACT []
synonym: "alanine synthesis" EXACT []
-is_a: GO:0006522 ! alanine metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
id: GO:0006524
name: obsolete alanine catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of alanine, 2-aminopropanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of alanine, 2-aminopropanoic acid." [GOC:curators]
comment: The reason for obsoletion is that a more specific term has been created.
synonym: "alanine breakdown" EXACT []
synonym: "alanine catabolism" EXACT []
@@ -69798,7 +71160,7 @@
id: GO:0006525
name: arginine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:curators]
synonym: "arginine metabolism" EXACT []
xref: Wikipedia:Arginine
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -69814,20 +71176,23 @@
synonym: "arginine synthesis" EXACT []
xref: MetaCyc:ARGSYN-PWY
xref: MetaCyc:ARGSYNBSUB-PWY
+xref: MetaCyc:PWY-5154
xref: MetaCyc:PWY-7400
is_a: GO:0006525 ! arginine metabolic process
is_a: GO:0009084 ! L-glutamine family amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:ARGSYN-PWY
property_value: skos:narrowMatch MetaCyc:ARGSYNBSUB-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5154
property_value: skos:narrowMatch MetaCyc:PWY-7400
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28686" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0006527
name: L-arginine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-arginine." [GOC:curators]
synonym: "arginine breakdown" EXACT []
synonym: "arginine catabolism" EXACT []
synonym: "arginine degradation" EXACT []
@@ -69863,21 +71228,21 @@
property_value: skos:narrowMatch MetaCyc:PWY-8187
property_value: skos:narrowMatch MetaCyc:PWY0-823
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006528
name: asparagine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving asparagine, 2-amino-3-carbamoylpropanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving asparagine, 2-amino-3-carbamoylpropanoic acid." [GOC:curators]
synonym: "asparagine metabolism" EXACT []
-xref: MetaCyc:ASPARAGINESYN-PWY
is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0006529
name: obsolete asparagine biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine, 2-amino-3-carbamoylpropanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine, 2-amino-3-carbamoylpropanoic acid." [GOC:curators]
comment: The reason for obsoletion is that more specific terms were created.
synonym: "asparagine anabolism" EXACT []
synonym: "asparagine biosynthesis" EXACT []
@@ -69891,24 +71256,25 @@
id: GO:0006530
name: L-asparagine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-asparagine, 2-amino-3-carbamoylpropanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-asparagine." [GOC:curators]
synonym: "asparagine breakdown" EXACT []
synonym: "asparagine catabolism" EXACT []
synonym: "asparagine degradation" EXACT []
xref: MetaCyc:ASPARAGINE-DEG1-PWY
xref: MetaCyc:PWY-4002
-is_a: GO:0070982 ! L-asparagine metabolic process
+is_a: GO:0006528 ! asparagine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:ASPARAGINE-DEG1-PWY
property_value: skos:narrowMatch MetaCyc:PWY-4002
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006531
name: aspartate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid." [GOC:curators, ISBN:0198506732]
synonym: "aspartate metabolism" EXACT []
is_a: GO:0043648 ! dicarboxylic acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -69917,7 +71283,7 @@
id: GO:0006532
name: L-aspartate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid." [GOC:go_curators, ISBN:0198506732, MetaCyc:ASPARTATESYN-PWY]
+def: "The chemical reactions and pathways resulting in the formation of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid." [GOC:curators, ISBN:0198506732, MetaCyc:ASPARTATESYN-PWY]
synonym: "aspartate anabolism" EXACT []
synonym: "aspartate biosynthesis" EXACT []
synonym: "aspartate formation" EXACT []
@@ -69932,7 +71298,7 @@
id: GO:0006533
name: L-aspartate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of L-aspartate." [GOC:curators]
synonym: "aspartate breakdown" EXACT []
synonym: "aspartate catabolism" EXACT []
synonym: "aspartate degradation" EXACT []
@@ -69947,36 +71313,40 @@
property_value: skos:narrowMatch MetaCyc:PWY-8291
property_value: skos:narrowMatch MetaCyc:PWY-8294
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006534
-name: cysteine metabolic process
+name: obsolete cysteine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "cysteine metabolism" EXACT []
xref: Wikipedia:Cysteine_metabolism
-is_a: GO:0000096 ! sulfur amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+consider: GO:0019344
+consider: GO:0019448
[Term]
id: GO:0006535
-name: L-cysteine biosynthetic process from L-serine
+name: obsolete L-cysteine biosynthetic process from L-serine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cysteine from L- serine." [MetaCyc:CYSTSYN-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of cysteine from L- serine." [GOC:curators]
+comment: This term was obsoleted because it is too specific and is outside the scope of GO.
synonym: "cysteine anabolism from serine" EXACT []
synonym: "cysteine formation from serine" EXACT []
synonym: "cysteine synthesis from serine" EXACT []
-xref: MetaCyc:CYSTSYN-PWY
-is_a: GO:0006563 ! L-serine metabolic process
-is_a: GO:0019344 ! L-cysteine biosynthetic process
-property_value: skos:exactMatch MetaCyc:CYSTSYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30758" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019344
[Term]
id: GO:0006536
name: glutamate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid." [GOC:curators]
synonym: "glutamate metabolism" EXACT []
synonym: "glutamic acid metabolic process" EXACT []
synonym: "glutamic acid metabolism" EXACT []
@@ -69988,7 +71358,7 @@
id: GO:0006537
name: obsolete glutamate biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." [GOC:curators]
comment: This is a duplicate term.
synonym: "glutamate anabolism" EXACT []
synonym: "glutamate biosynthesis" EXACT []
@@ -70009,7 +71379,7 @@
name: L-glutamate catabolic process
namespace: biological_process
alt_id: GO:0019459
-def: "The chemical reactions and pathways resulting in the breakdown of L-glutamate, the anion of 2-aminopentanedioic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-glutamate." [GOC:curators]
synonym: "glutamate breakdown" EXACT []
synonym: "glutamate catabolism" EXACT []
synonym: "glutamate deamidation" RELATED []
@@ -70029,13 +71399,14 @@
property_value: skos:narrowMatch MetaCyc:PWY-5766
property_value: skos:narrowMatch MetaCyc:PWY0-1305
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006539
name: obsolete glutamate catabolic process via 2-oxoglutarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate 2-oxoglutarate." [GOC:go_curators]
-comment: The reason for obsoletion is that this term is equivalent to GO:0019552 glutamate catabolic process via 2-hydroxyglutarate, XREF the same MetaCyc pathway.
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate 2-oxoglutarate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate breakdown via 2-oxoglutarate" EXACT []
synonym: "glutamate catabolic process via 2-ketoglutarate" EXACT []
synonym: "glutamate catabolic process via alpha-ketoglutarate" EXACT []
@@ -70046,40 +71417,37 @@
synonym: "glutamate degradation via 2-oxoglutarate" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28390" xsd:anyURI
is_obsolete: true
-replaced_by: GO:0019552
[Term]
id: GO:0006540
-name: gamma-aminobutyrate shunt
+name: GABA shunt
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of succinate from L-glutamate. Also known as GABA (gamma-aminobutyrate) shunt since it channels glutamate into the TCA cycle bypassing two steps of that cycle. There are three enzymes involved in the GABA shunt: glutamate decarboxylase (GAD), GABA aminotransferase (GABA-TA), and succinate semialdehyde dehydrogenase (SSADH). These three enzymes acting in concert to convert glutamate into succinate. The GABA shunt is predominantly associated with neurotransmission in the mammalian brain. It is also present in nonneuronal cells, in plants, in unicellular eukaryotes, and in prokaryotes." [PMID:12740438]
-comment: Note that the third step in this pathway (conversion of succinate semialdehyde to succinate) can be catalyzed by NAD-dependent or NADP-dependent succinate semialdehyde dehydrogenase (EC:1.2.1.24 and EC:1.2.1.79, respectively).
+def: "The chemical reactions and pathways resulting in the formation of succinate from L-glutamate via gamma-aminobutyrate (GABA), bypassing two steps of the TCA cycle. It operates through the sequential conversion of glutamate to GABA by glutamate decarboxylase, transamination of GABA to succinic semialdehyde by GABA transaminase, and oxidation of succinic semialdehyde to succinate by succinate semialdehyde dehydrogenase." [PMID:39703920]
synonym: "4-aminobutyrate shunt" EXACT []
-synonym: "degradation of glutamate to succinate through GABA" EXACT [MetaCyc:GLUDEG-I-PWY]
-synonym: "GABA shunt" EXACT []
synonym: "gamma aminobutyrate shunt" EXACT []
+synonym: "gamma-aminobutyrate shunt" EXACT []
synonym: "glutamate decarboxylation to succinate" EXACT []
-synonym: "glutamate degradation via 4-aminobutyrate" EXACT [MetaCyc:GLUDEG-I-PWY]
-synonym: "glutamate degradation via GABA" EXACT [MetaCyc:GLUDEG-I-PWY]
xref: MetaCyc:GLUDEG-I-PWY
xref: MetaCyc:PWY-8346
is_a: GO:0006105 ! succinate metabolic process
-is_a: GO:0006538 ! L-glutamate catabolic process
-relationship: has_part GO:0004351 ! glutamate decarboxylase activity
-relationship: has_part GO:0034386 ! 4-aminobutyrate:2-oxoglutarate transaminase activity
+is_a: GO:0006536 ! glutamate metabolic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
property_value: skos:narrowMatch MetaCyc:GLUDEG-I-PWY
property_value: skos:narrowMatch MetaCyc:PWY-8346
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28355" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28802" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
[Term]
id: GO:0006541
-name: glutamine metabolic process
+name: L-glutamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC:ai]
synonym: "glutamine metabolism" EXACT []
-is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
[Term]
id: GO:0006542
@@ -70091,9 +71459,7 @@
synonym: "glutamine biosynthesis" EXACT []
synonym: "glutamine formation" EXACT []
synonym: "glutamine synthesis" EXACT []
-xref: MetaCyc:GLNSYN-PWY
xref: MetaCyc:PWY-6549
-property_value: skos:narrowMatch MetaCyc:GLNSYN-PWY
property_value: skos:narrowMatch MetaCyc:PWY-6549
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31068" xsd:anyURI
is_obsolete: true
@@ -70103,25 +71469,26 @@
id: GO:0006543
name: L-glutamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-glutamine, 2-amino-4-carbamoylbutanoic acid." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of L-glutamine." [GOC:curators]
synonym: "glutamine breakdown" EXACT []
synonym: "glutamine catabolism" EXACT []
synonym: "glutamine degradation" EXACT []
xref: MetaCyc:GLUTAMINDEG-PWY
xref: MetaCyc:GLUTAMINEFUM-PWY
-is_a: GO:0006541 ! glutamine metabolic process
+is_a: GO:0006541 ! L-glutamine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:GLUTAMINDEG-PWY
property_value: skos:narrowMatch MetaCyc:GLUTAMINEFUM-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28154" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006544
name: glycine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycine, aminoethanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving glycine, aminoethanoic acid." [GOC:curators]
synonym: "glycine metabolism" EXACT []
is_a: GO:0170039 ! proteinogenic amino acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -70130,22 +71497,31 @@
id: GO:0006545
name: glycine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid." [GOC:go_curators, MetaCyc:GLYCINE-SYN2-PWY]
+def: "The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid." [GOC:curators, MetaCyc:GLYCINE-SYN2-PWY]
synonym: "glycine anabolism" EXACT []
synonym: "glycine biosynthesis" EXACT []
synonym: "glycine formation" EXACT []
synonym: "glycine synthesis" EXACT []
xref: MetaCyc:GLYCINE-SYN2-PWY
+xref: MetaCyc:GLYSYN-ALA-PWY
+xref: MetaCyc:GLYSYN-PWY
+xref: MetaCyc:GLYSYN-THR-PWY
+xref: MetaCyc:PWY-8551
is_a: GO:0006544 ! glycine metabolic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:GLYCINE-SYN2-PWY
+property_value: skos:narrowMatch MetaCyc:GLYSYN-ALA-PWY
+property_value: skos:narrowMatch MetaCyc:GLYSYN-PWY
+property_value: skos:narrowMatch MetaCyc:GLYSYN-THR-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-8551
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0006546
name: glycine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of glycine." [GOC:curators]
synonym: "glycine breakdown" EXACT []
synonym: "glycine catabolism" EXACT []
synonym: "glycine degradation" EXACT []
@@ -70156,25 +71532,27 @@
is_a: GO:1901606 ! alpha-amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:PWY0-1608
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006547
-name: L-histidine metabolic process
+name: obsolete L-histidine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "histidine metabolic process" BROAD []
synonym: "histidine metabolism" EXACT []
xref: Wikipedia:Histidine
-is_a: GO:0009072 ! aromatic amino acid metabolic process
-is_a: GO:0052803 ! imidazole-containing compound metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0000105
+consider: GO:0006548
[Term]
id: GO:0006548
name: L-histidine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-histidine." [GOC:curators]
synonym: "histidine breakdown" EXACT []
synonym: "histidine catabolic process" BROAD []
synonym: "histidine catabolism" EXACT []
@@ -70186,7 +71564,6 @@
xref: MetaCyc:PWY-5030
xref: MetaCyc:PWY-5031
xref: Reactome:R-HSA-70921 "Histidine catabolism"
-is_a: GO:0006547 ! L-histidine metabolic process
is_a: GO:0009074 ! aromatic amino acid family catabolic process
is_a: GO:0052805 ! imidazole-containing compound catabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
@@ -70198,6 +71575,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-5030
property_value: skos:narrowMatch MetaCyc:PWY-5031
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006549
@@ -70212,7 +71590,7 @@
id: GO:0006550
name: L-isoleucine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of L-isoleucine." [GOC:curators]
synonym: "isoleucine breakdown" EXACT []
synonym: "isoleucine catabolism" EXACT []
synonym: "isoleucine degradation" EXACT []
@@ -70226,6 +71604,7 @@
property_value: skos:narrowMatch MetaCyc:ILEUDEG-PWY
property_value: skos:narrowMatch MetaCyc:PWY-5078
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006551
@@ -70242,7 +71621,7 @@
id: GO:0006552
name: L-leucine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-leucine, 2-amino-4-methylpentanoic acid." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of L-leucine." [GOC:curators]
synonym: "L-leucine breakdown" EXACT []
synonym: "L-leucine catabolism" EXACT []
synonym: "L-leucine degradation" EXACT []
@@ -70262,21 +71641,26 @@
property_value: skos:narrowMatch MetaCyc:PWY-7767
property_value: skos:narrowMatch MetaCyc:PWY-8185
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006553
-name: lysine metabolic process
+name: obsolete lysine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "lysine metabolism" EXACT []
xref: Wikipedia:Lysine
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0009085
+consider: GO:0019477
[Term]
id: GO:0006554
name: obsolete lysine catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of lysine, 2,6-diaminohexanoic acid." [GOC:curators]
comment: The reason for obsoletion is that more specific terms were created.
synonym: "lysine breakdown" EXACT []
synonym: "lysine catabolism" EXACT []
@@ -70288,21 +71672,23 @@
[Term]
id: GO:0006555
-name: methionine metabolic process
+name: L-methionine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways involving L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
synonym: "methionine and threonine metabolic process" BROAD []
synonym: "methionine and threonine metabolism" BROAD []
synonym: "methionine metabolism" EXACT []
xref: UM-BBD_pathwayID:met
is_a: GO:0000096 ! sulfur amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31318" xsd:anyURI
[Term]
id: GO:0006556
name: S-adenosylmethionine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism." [GOC:curators, ISBN:0198506732]
synonym: "S-adenosyl methionine biosynthesis" EXACT []
synonym: "S-adenosyl methionine biosynthetic process" EXACT []
synonym: "S-adenosylmethionine anabolism" EXACT []
@@ -70346,7 +71732,7 @@
id: GO:0006559
name: L-phenylalanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-phenylalanine, 2-amino-3-phenylpropanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-phenylalanine." [GOC:curators]
synonym: "L-phenylalanine breakdown" EXACT []
synonym: "L-phenylalanine catabolism" EXACT []
synonym: "L-phenylalanine degradation" EXACT []
@@ -70367,6 +71753,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-7158
property_value: skos:narrowMatch MetaCyc:PWY-8014
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006560
@@ -70396,7 +71783,7 @@
id: GO:0006562
name: L-proline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of L-proline." [GOC:curators]
synonym: "proline breakdown" EXACT []
synonym: "proline catabolism" EXACT []
synonym: "proline degradation" EXACT []
@@ -70409,6 +71796,7 @@
property_value: skos:narrowMatch MetaCyc:PROUT-PWY
property_value: skos:narrowMatch MetaCyc:PWY-8186
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006563
@@ -70416,6 +71804,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [GOC:ai, GOC:jsg]
synonym: "L-serine metabolism" EXACT []
+xref: Reactome:R-HSA-977347 "Serine metabolism"
is_a: GO:0170033 ! L-amino acid metabolic process
is_a: GO:0170039 ! proteinogenic amino acid metabolic process
@@ -70428,19 +71817,21 @@
synonym: "L-serine biosynthesis" EXACT []
synonym: "L-serine formation" EXACT []
synonym: "L-serine synthesis" EXACT []
+xref: MetaCyc:PWY-8011
xref: MetaCyc:SERSYN-PWY
-xref: Reactome:R-HSA-977347 "Serine biosynthesis"
is_a: GO:0006563 ! L-serine metabolic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
-property_value: skos:exactMatch MetaCyc:SERSYN-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-8011
+property_value: skos:narrowMatch MetaCyc:SERSYN-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0006565
name: L-serine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-serine to pyruvate and free ammonium." [MetaCyc:SERDEG-PWY]
+def: "The chemical reactions and pathways resulting in the breakdown of L-serine." [GOC:curators]
synonym: "L-serine breakdown" EXACT []
synonym: "L-serine catabolism" EXACT []
synonym: "L-serine degradation" EXACT []
@@ -70450,6 +71841,7 @@
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:exactMatch MetaCyc:SERDEG-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30758" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006566
@@ -70466,7 +71858,7 @@
id: GO:0006567
name: L-threonine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of L-threonine." [GOC:curators]
synonym: "threonine breakdown" EXACT []
synonym: "threonine catabolism" EXACT []
synonym: "threonine degradation" EXACT []
@@ -70485,6 +71877,7 @@
property_value: skos:narrowMatch MetaCyc:THRDLCTCAT-PWY
property_value: skos:narrowMatch MetaCyc:THREONINE-DEG2-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006568
@@ -70503,7 +71896,7 @@
id: GO:0006569
name: L-tryptophan catabolic process
namespace: biological_process
-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]
+def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan." [GOC:curators]
synonym: "tryptophan breakdown" EXACT []
synonym: "tryptophan catabolic process" RELATED []
synonym: "tryptophan catabolic process, using tryptophanase" NARROW []
@@ -70543,12 +71936,13 @@
property_value: skos:narrowMatch MetaCyc:TRYPDEG-PWY
property_value: skos:narrowMatch MetaCyc:TRYPTOPHAN-DEGRADATION-1
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006570
name: tyrosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:curators]
synonym: "tyrosine metabolism" EXACT []
xref: UM-BBD_pathwayID:tyr
xref: Wikipedia:Tyrosine
@@ -70560,21 +71954,31 @@
id: GO:0006571
name: L-tyrosine biosynthetic process
namespace: biological_process
+alt_id: GO:0019291
def: "The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:sm]
synonym: "tyrosine anabolism" EXACT []
synonym: "tyrosine biosynthesis" EXACT []
synonym: "tyrosine formation" EXACT []
synonym: "tyrosine synthesis" EXACT []
+xref: MetaCyc:PWY-3461
+xref: MetaCyc:PWY-6120
+xref: MetaCyc:PWY-6134
+xref: MetaCyc:TYRSYN
is_a: GO:0006570 ! tyrosine metabolic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:1902223 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-3461
+property_value: skos:narrowMatch MetaCyc:PWY-6120
+property_value: skos:narrowMatch MetaCyc:PWY-6134
+property_value: skos:narrowMatch MetaCyc:TYRSYN
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20583" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0006572
name: L-tyrosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-tyrosine." [GOC:curators]
synonym: "tyrosine breakdown" EXACT []
synonym: "tyrosine catabolism" EXACT []
synonym: "tyrosine degradation" EXACT []
@@ -70594,6 +71998,7 @@
property_value: skos:narrowMatch MetaCyc:PWY3O-4108
property_value: skos:narrowMatch MetaCyc:TYRFUMCAT-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006573
@@ -70609,7 +72014,7 @@
name: L-valine catabolic process
namespace: biological_process
alt_id: GO:1990292
-def: "The chemical reactions and pathways resulting in the breakdown of L-valine, 2-amino-3-methylbutanoic acid." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of L-valine." [GOC:curators]
synonym: "valine breakdown" EXACT []
synonym: "valine catabolism" EXACT []
synonym: "valine degradation" EXACT []
@@ -70625,6 +72030,7 @@
property_value: skos:narrowMatch MetaCyc:VALDEG-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31221" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006575
@@ -70711,7 +72117,7 @@
id: GO:0006582
name: melanin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom." [GOC:go_curators]
+def: "The chemical reactions and pathways involving melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom." [GOC:curators]
synonym: "melanin metabolism" EXACT []
is_a: GO:0018958 ! phenol-containing compound metabolic process
is_a: GO:0019748 ! secondary metabolic process
@@ -70721,7 +72127,7 @@
id: GO:0006583
name: melanin biosynthetic process from tyrosine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of melanin from other compounds, including tyrosine." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of melanin from other compounds, including tyrosine." [GOC:curators]
synonym: "melanin anabolism from tyrosine" EXACT []
synonym: "melanin formation from tyrosine" EXACT []
synonym: "melanin synthesis from tyrosine" EXACT []
@@ -70770,9 +72176,9 @@
synonym: "serotonin synthesis from tryptophan" EXACT []
is_a: GO:0006568 ! L-tryptophan metabolic process
is_a: GO:0042427 ! serotonin biosynthetic process
-property_value: skos:relatedMatch MetaCyc:PWY-6030
-property_value: skos:relatedMatch MetaCyc:PWY-8475
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31021" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31658" xsd:anyURI
[Term]
id: GO:0006588
@@ -70826,17 +72232,22 @@
synonym: "ornithine formation" EXACT []
synonym: "ornithine synthesis" EXACT []
xref: MetaCyc:ARGININE-SYN4-PWY
+xref: MetaCyc:GLUTORN-PWY
+xref: MetaCyc:PWY-6922
is_a: GO:0006591 ! ornithine metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:ARGININE-SYN4-PWY
+property_value: skos:narrowMatch MetaCyc:GLUTORN-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6922
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
[Term]
id: GO:0006593
name: L-ornithine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis." [GOC:jl, ISBN:0192801023]
+def: "The chemical reactions and pathways resulting in the breakdown of L-ornithine." [GOC:curators]
synonym: "ornithine breakdown" EXACT []
synonym: "ornithine catabolism" EXACT []
synonym: "ornithine degradation" EXACT []
@@ -70844,6 +72255,7 @@
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0006595
@@ -70892,11 +72304,14 @@
name: polyamine catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of polyamines, any organic compound containing two or more amino groups." [ISBN:0198506732]
+synonym: "polyamine back-conversion" RELATED []
synonym: "polyamine breakdown" EXACT []
synonym: "polyamine catabolism" EXACT []
synonym: "polyamine degradation" EXACT []
+synonym: "polyamine interconversion" RELATED []
is_a: GO:0006595 ! polyamine metabolic process
is_a: GO:0042402 ! biogenic amine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0006599
@@ -71282,7 +72697,7 @@
id: GO:0006630
name: obsolete lipid binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "lipid binding" EXACT []
is_obsolete: true
@@ -71494,7 +72909,7 @@
id: GO:0006649
name: phospholipid transfer to membrane
namespace: biological_process
-def: "The transfer of a phospholipid from its site of synthesis to the plasma membrane." [GOC:go_curators]
+def: "The transfer of a phospholipid from its site of synthesis to the plasma membrane." [GOC:curators]
is_a: GO:0015914 ! phospholipid transport
relationship: part_of GO:0061024 ! membrane organization
@@ -71639,8 +73054,9 @@
xref: Reactome:R-HSA-1660514 "Synthesis of PIPs at the Golgi membrane"
xref: Reactome:R-HSA-1660516 "Synthesis of PIPs at the early endosome membrane"
xref: Reactome:R-HSA-1660517 "Synthesis of PIPs at the late endosome membrane"
-is_a: GO:0046474 ! glycerophospholipid biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0046488 ! phosphatidylinositol metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0006662
@@ -71993,7 +73409,7 @@
id: GO:0006694
name: steroid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification." [GOC:curators]
synonym: "steroid anabolism" EXACT []
synonym: "steroid biosynthesis" EXACT []
synonym: "steroid formation" EXACT []
@@ -72060,7 +73476,7 @@
id: GO:0006699
name: bile acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:curators]
synonym: "bile acid anabolism" EXACT []
synonym: "bile acid biosynthesis" EXACT []
synonym: "bile acid formation" EXACT []
@@ -72158,7 +73574,7 @@
id: GO:0006706
name: steroid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." [GOC:curators]
synonym: "steroid breakdown" EXACT []
synonym: "steroid catabolism" EXACT []
synonym: "steroid degradation" EXACT []
@@ -72278,7 +73694,7 @@
id: GO:0006716
name: juvenile hormone metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684]
+def: "The chemical reactions and pathways involving juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:curators, ISBN:0198547684]
synonym: "juvenile hormone metabolism" EXACT []
is_a: GO:0006714 ! sesquiterpenoid metabolic process
is_a: GO:0042445 ! hormone metabolic process
@@ -72287,7 +73703,7 @@
id: GO:0006717
name: obsolete juvenile hormone binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "juvenile hormone binding" EXACT []
is_obsolete: true
@@ -72297,7 +73713,7 @@
id: GO:0006718
name: juvenile hormone biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684]
+def: "The chemical reactions and pathways resulting in the formation of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:curators, ISBN:0198547684]
synonym: "juvenile hormone anabolism" EXACT []
synonym: "juvenile hormone biosynthesis" EXACT []
synonym: "juvenile hormone formation" EXACT []
@@ -72310,7 +73726,7 @@
id: GO:0006719
name: juvenile hormone catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684]
+def: "The chemical reactions and pathways resulting in the breakdown of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:curators, ISBN:0198547684]
synonym: "juvenile hormone breakdown" EXACT []
synonym: "juvenile hormone catabolism" EXACT []
synonym: "juvenile hormone degradation" EXACT []
@@ -72684,7 +74100,7 @@
id: GO:0006748
name: obsolete lipoamide metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "lipoamide metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -72697,6 +74113,7 @@
def: "The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle." [ISBN:0198506732]
synonym: "glutathione metabolism" EXACT []
synonym: "oxidized glutathione reduction" NARROW []
+xref: Reactome:R-HSA-174403 "Glutathione synthesis and recycling"
is_a: GO:0006575 ! modified amino acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
@@ -72710,7 +74127,6 @@
synonym: "glutathione formation" EXACT []
synonym: "glutathione synthesis" EXACT []
xref: MetaCyc:GLUTATHIONESYN-PWY
-xref: Reactome:R-HSA-174403 "Glutathione synthesis and recycling"
is_a: GO:0006749 ! glutathione metabolic process
is_a: GO:0019184 ! nonribosomal peptide biosynthetic process
is_a: GO:0042398 ! modified amino acid biosynthetic process
@@ -72744,7 +74160,7 @@
namespace: biological_process
alt_id: GO:0006758
alt_id: GO:0006759
-def: "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [GOC:curators, ISBN:0198506732]
synonym: "ATP anabolism" EXACT []
synonym: "ATP biosynthesis" EXACT []
synonym: "ATP formation" EXACT []
@@ -72849,7 +74265,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water." [GOC:jl]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "water-soluble vitamin metabolism" EXACT []
-xref: Reactome:R-HSA-196849 "Metabolism of water-soluble vitamins and cofactors"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
is_obsolete: true
@@ -72927,7 +74342,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water." [GOC:jl, ISBN:0198506732]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "fat-soluble vitamin metabolism" EXACT []
-xref: Reactome:R-HSA-6806667 "Metabolism of fat-soluble vitamins"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
is_obsolete: true
@@ -73012,7 +74426,7 @@
id: GO:0006782
name: protoporphyrinogen IX biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX." [GOC:curators]
synonym: "protoporphyrinogen IX anabolism" EXACT []
synonym: "protoporphyrinogen IX biosynthesis" EXACT []
synonym: "protoporphyrinogen IX formation" EXACT []
@@ -73032,7 +74446,6 @@
synonym: "heme biosynthesis" EXACT []
synonym: "heme formation" EXACT []
synonym: "heme synthesis" EXACT []
-xref: MetaCyc:HEMESYN2-PWY
xref: Reactome:R-HSA-189451 "Heme biosynthesis"
is_a: GO:0006779 ! porphyrin-containing compound biosynthetic process
is_a: GO:0042168 ! heme metabolic process
@@ -73064,7 +74477,18 @@
synonym: "heme B synthesis" EXACT []
synonym: "protoheme biosynthesis" EXACT []
synonym: "protoheme biosynthetic process" EXACT []
+xref: MetaCyc:HEME-BIOSYNTHESIS-II
+xref: MetaCyc:HEME-BIOSYNTHESIS-II-1
+xref: MetaCyc:HEMESYN2-PWY
+xref: MetaCyc:PWY-7552
+xref: MetaCyc:PWY-7766
is_a: GO:0006783 ! heme biosynthetic process
+property_value: skos:narrowMatch MetaCyc:HEME-BIOSYNTHESIS-II
+property_value: skos:narrowMatch MetaCyc:HEME-BIOSYNTHESIS-II-1
+property_value: skos:narrowMatch MetaCyc:HEMESYN2-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-7552
+property_value: skos:narrowMatch MetaCyc:PWY-7766
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0006786
@@ -73138,7 +74562,7 @@
id: GO:0006792
name: regulation of sulfur utilization
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of sulfur utilization." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of sulfur utilization." [GOC:curators]
synonym: "regulation of sulphur utilization" EXACT []
is_a: GO:0032107 ! regulation of response to nutrient levels
intersection_of: GO:0065007 ! biological regulation
@@ -73165,7 +74589,7 @@
id: GO:0006795
name: regulation of phosphorus utilization
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of phosphorus utilization." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of phosphorus utilization." [GOC:curators]
is_a: GO:0051174 ! regulation of phosphorus metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006794 ! phosphorus utilization
@@ -73184,7 +74608,7 @@
id: GO:0006797
name: polyphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a polyphosphate, the anion or salt of polyphosphoric acid." [GOC:curators, ISBN:0198506732]
synonym: "polyphosphate metabolism" EXACT []
is_a: GO:0006793 ! phosphorus metabolic process
is_a: GO:0043436 ! oxoacid metabolic process
@@ -73193,7 +74617,7 @@
id: GO:0006798
name: polyphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid." [GOC:curators, ISBN:0198506732]
synonym: "polyphosphate breakdown" EXACT []
synonym: "polyphosphate catabolism" EXACT []
synonym: "polyphosphate degradation" EXACT []
@@ -73299,7 +74723,7 @@
id: GO:0006806
name: obsolete insecticide resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "insecticide resistance" EXACT []
is_obsolete: true
@@ -73319,7 +74743,7 @@
id: GO:0006808
name: regulation of nitrogen utilization
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of nitrogen utilization." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of nitrogen utilization." [GOC:curators]
subset: goslim_metagenomics
is_a: GO:0032107 ! regulation of response to nutrient levels
intersection_of: GO:0065007 ! biological regulation
@@ -73372,7 +74796,6 @@
subset: goslim_pir
subset: goslim_yeast
synonym: "ion transport" BROAD []
-xref: Reactome:R-HSA-425393 "Transport of inorganic cations/anions and amino acids/oligopeptides"
is_a: GO:0006810 ! transport
[Term]
@@ -73426,7 +74849,7 @@
id: GO:0006815
name: obsolete sodium/potassium transport
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it is a composite term that represents two individual processes.
synonym: "sodium/potassium transport" EXACT []
is_obsolete: true
@@ -73538,7 +74961,7 @@
id: GO:0006832
name: obsolete small molecule transport
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was an unnecessary grouping term.
synonym: "small molecule transport" EXACT []
is_obsolete: true
@@ -73573,6 +74996,7 @@
xref: Reactome:R-HSA-210500 "Glutamate Neurotransmitter Release Cycle"
xref: Reactome:R-HSA-212676 "Dopamine Neurotransmitter Release Cycle"
xref: Reactome:R-HSA-264642 "Acetylcholine Neurotransmitter Release Cycle"
+xref: Reactome:R-HSA-442660 "SLC-mediated transport of neurotransmitters"
is_a: GO:0006810 ! transport
[Term]
@@ -73587,7 +75011,7 @@
id: GO:0006838
name: obsolete allantoin/allantoate transport
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it is a composite term that represents two individual processes.
synonym: "allantoin/allantoate transport" EXACT []
is_obsolete: true
@@ -73782,7 +75206,7 @@
id: GO:0006858
name: extracellular transport
namespace: biological_process
-def: "The transport of substances that occurs outside cells." [GOC:go_curators]
+def: "The transport of substances that occurs outside cells." [GOC:curators]
is_a: GO:0006810 ! transport
intersection_of: GO:0006810 ! transport
intersection_of: occurs_in GO:0005576 ! extracellular region
@@ -73822,7 +75246,7 @@
alt_id: GO:0015852
def: "The directed movement of purine bases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [ISBN:0198506732]
synonym: "purine base transmembrane transport" EXACT [GOC:mah]
-synonym: "purine base transport" EXACT [GOC:go_curators]
+synonym: "purine base transport" EXACT [GOC:curators]
synonym: "purine transmembrane transport" RELATED [GOC:mah]
synonym: "purine transport" RELATED []
is_a: GO:0015851 ! nucleobase transport
@@ -73842,7 +75266,7 @@
def: "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
-xref: Reactome:R-HSA-352230 "Amino acid transport across the plasma membrane"
+xref: Reactome:R-HSA-9958863 "SLC-mediated transport of amino acids"
is_a: GO:0006810 ! transport
[Term]
@@ -73857,14 +75281,15 @@
[Term]
id: GO:0006868
-name: glutamine transport
+name: L-glutamine transport
namespace: biological_process
alt_id: GO:0015815
def: "The directed movement of glutamine, 2-amino-4-carbamoylbutanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-synonym: "L-glutamine transport" NARROW []
+synonym: "glutamine transport" BROAD []
+is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
-is_a: GO:0071705 ! nitrogen compound transport
+is_a: GO:0015807 ! L-amino acid transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0006869
@@ -74012,7 +75437,7 @@
id: GO:0006884
name: cell volume homeostasis
namespace: biological_process
-def: "Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell." [GOC:curators, GOC:dph, GOC:tb]
synonym: "regulation of cell volume" EXACT [GOC:dph, GOC:tb]
is_a: GO:0008361 ! regulation of cell size
is_a: GO:0019725 ! cellular homeostasis
@@ -74021,7 +75446,7 @@
id: GO:0006885
name: regulation of pH
namespace: biological_process
-def: "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell." [GOC:curators, GOC:dph, GOC:tb]
synonym: "hydrogen ion homeostasis" EXACT [GOC:dph, GOC:tb]
is_a: GO:0055080 ! monoatomic cation homeostasis
is_a: GO:0065007 ! biological regulation
@@ -74074,6 +75499,7 @@
synonym: "rough ER to cis-Golgi vesicle-mediated transport" EXACT []
xref: Reactome:R-HSA-159763 "Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus"
xref: Reactome:R-HSA-199977 "ER to Golgi Anterograde Transport"
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
is_a: GO:0048193 ! Golgi vesicle transport
relationship: occurs_in GO:0005737 ! cytoplasm
@@ -74082,7 +75508,7 @@
id: GO:0006889
name: obsolete regulation of calcium in ER
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the concentration of calcium in the endoplasmic reticulum." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the concentration of calcium in the endoplasmic reticulum." [GOC:curators]
comment: This term was made obsolete because the term name is ambiguous and as a result, the term was incorrectly placed in the ontology (it was a descendant of 'protein transport').
synonym: "regulation of calcium in ER" EXACT []
is_obsolete: true
@@ -74155,6 +75581,7 @@
synonym: "TGN to endosome transport" EXACT []
synonym: "trans-Golgi to endosome transport" EXACT []
is_a: GO:0006892 ! post-Golgi vesicle-mediated transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016482 ! cytosolic transport
[Term]
@@ -74165,6 +75592,7 @@
synonym: "Golgi to vacuole vesicle-mediated transport" EXACT []
is_a: GO:0006892 ! post-Golgi vesicle-mediated transport
is_a: GO:0007034 ! vacuolar transport
+is_a: GO:0010496 ! intercellular transport
[Term]
id: GO:0006897
@@ -74250,7 +75678,7 @@
id: GO:0006905
name: obsolete vesicle transport
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous.
synonym: "vesicle transport" EXACT []
is_obsolete: true
@@ -74331,7 +75759,7 @@
name: nucleocytoplasmic transport
namespace: biological_process
alt_id: GO:0000063
-def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:go_curators]
+def: "The directed movement of molecules between the nucleus and the cytoplasm." [GOC:curators]
comment: Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
subset: goslim_chembl
subset: goslim_drosophila
@@ -74365,7 +75793,7 @@
namespace: biological_process
alt_id: GO:0006917
alt_id: GO:0008632
-def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263]
+def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:curators, GOC:dhl, GOC:ecd, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263]
synonym: "activation of apoptosis" NARROW []
synonym: "apoptosis" NARROW []
synonym: "apoptosis activator activity" RELATED []
@@ -74392,7 +75820,7 @@
id: GO:0006918
name: obsolete induction of apoptosis by p53
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more accurate terms were created.
synonym: "induction of apoptosis by p53" EXACT []
is_obsolete: true
@@ -74407,7 +75835,6 @@
synonym: "activation of caspase activity" NARROW []
synonym: "activation of metacaspase activity" NARROW []
synonym: "caspase activation" EXACT [GOC:dph, GOC:tb]
-xref: Reactome:R-HSA-69416 "Dimerization of procaspase-8"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
@@ -74415,7 +75842,7 @@
id: GO:0006920
name: obsolete commitment to apoptosis
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more accurate terms were created.
synonym: "commitment to apoptosis" EXACT []
is_obsolete: true
@@ -74605,7 +76032,7 @@
id: GO:0006937
name: regulation of muscle contraction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of muscle contraction." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of muscle contraction." [GOC:curators]
is_a: GO:0090257 ! regulation of muscle system process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006936 ! muscle contraction
@@ -74623,7 +76050,7 @@
id: GO:0006940
name: regulation of smooth muscle contraction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of smooth muscle contraction." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of smooth muscle contraction." [GOC:curators]
is_a: GO:0006937 ! regulation of muscle contraction
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006939 ! smooth muscle contraction
@@ -74641,7 +76068,7 @@
id: GO:0006942
name: regulation of striated muscle contraction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of striated muscle contraction." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of striated muscle contraction." [GOC:curators]
is_a: GO:0006937 ! regulation of muscle contraction
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006941 ! striated muscle contraction
@@ -74679,19 +76106,19 @@
synonym: "viral-induced cell-cell fusion" EXACT []
synonym: "viral-induced host cell-cell fusion" EXACT []
synonym: "viral-induced membrane fusion" NARROW []
-xref: Reactome:R-HSA-9733458 "Induction of Cell-Cell Fusion"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28984" xsd:anyURI
is_obsolete: true
replaced_by: GO:0060141
[Term]
id: GO:0006949
-name: syncytium formation
+name: obsolete syncytium formation
namespace: biological_process
-def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732]
-subset: goslim_pir
-is_a: GO:0009987 ! cellular process
-is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
+def: "OBSOLETE. The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
+is_obsolete: true
+consider: GO:0000768
[Term]
id: GO:0006950
@@ -74715,7 +76142,7 @@
namespace: biological_process
alt_id: GO:0002217
alt_id: GO:0042829
-def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:go_curators]
+def: "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." [GOC:curators]
synonym: "antimicrobial peptide activity" RELATED []
synonym: "defence response" EXACT []
synonym: "defense/immunity protein activity" RELATED []
@@ -74794,7 +76221,7 @@
id: GO:0006962
name: male-specific antibacterial humoral response
namespace: biological_process
-def: "An immune response against bacteria, specific to males and mediated through a body fluid." [GOC:go_curators]
+def: "An immune response against bacteria, specific to males and mediated through a body fluid." [GOC:curators]
is_a: GO:0019731 ! antibacterial humoral response
is_a: GO:0050831 ! male-specific defense response to bacterium
@@ -74938,7 +76365,7 @@
name: DNA damage response
namespace: biological_process
alt_id: GO:0034984
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [GOC:curators]
subset: goslim_yeast
synonym: "cellular DNA damage response" EXACT []
synonym: "cellular response to DNA damage stimulus" EXACT []
@@ -74951,11 +76378,9 @@
id: GO:0006977
name: obsolete DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
namespace: biological_process
-def: "OBSOLETE. A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle." [GOC:curators]
comment: The reason for obsoletion is that this term is about down stream effects, not the signaling pathway itself.
synonym: "positive regulation of cell cycle arrest by p53-mediated DNA damage response" EXACT [GOC:dph, GOC:mah]
-xref: Reactome:R-HSA-6791312 "TP53 Regulates Transcription of Cell Cycle Genes"
-xref: Reactome:R-HSA-69563 "p53-Dependent G1 DNA Damage Response"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26003" xsd:anyURI
is_obsolete: true
replaced_by: GO:0030330
@@ -75176,7 +76601,7 @@
id: GO:0007002
name: obsolete centromere binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "centromere binding" EXACT []
is_obsolete: true
@@ -75186,7 +76611,7 @@
id: GO:0007003
name: obsolete telomere binding
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function and not a biological process.
synonym: "telomere binding" EXACT []
is_obsolete: true
@@ -75291,7 +76716,7 @@
id: GO:0007011
name: obsolete regulation of cytoskeleton
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:curators]
comment: This term was made obsolete because cytoskeleton is neither a process nor a trait, so the term made no sense.
synonym: "regulation of cytoskeleton" EXACT []
is_obsolete: true
@@ -75364,7 +76789,7 @@
id: GO:0007020
name: microtubule nucleation
namespace: biological_process
-def: "The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation)." [GOC:go_curators, ISBN:0815316194, PMID:12517712]
+def: "The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation)." [GOC:curators, ISBN:0815316194, PMID:12517712]
xref: Wikipedia:Microtubule_nucleation
is_a: GO:0000226 ! microtubule cytoskeleton organization
relationship: part_of GO:0046785 ! microtubule polymerization
@@ -75511,7 +76936,7 @@
id: GO:0007035
name: vacuolar acidification
namespace: biological_process
-def: "Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion." [GOC:jid]
+def: "Any process that reduces the pH of the vacuole, corresponding to an increase in hydrogen ion concentration." [GOC:jid]
is_a: GO:0051452 ! intracellular pH reduction
[Term]
@@ -75569,10 +76994,9 @@
id: GO:0007042
name: lysosomal lumen acidification
namespace: biological_process
-def: "Any process that reduces the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion." [GOC:jid]
+def: "Any process that reduces the pH of the lysosomal lumen, corresponding to an increase in hydrogen ion concentration." [GOC:jid]
synonym: "lysosome pH reduction" EXACT [GOC:bf, GOC:rph]
is_a: GO:0007035 ! vacuolar acidification
-is_a: GO:0035751 ! regulation of lysosomal lumen pH
[Term]
id: GO:0007043
@@ -75598,7 +77022,7 @@
id: GO:0007048
name: obsolete oncogenesis
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a pathological process.
synonym: "oncogenesis" EXACT []
is_obsolete: true
@@ -75607,7 +77031,7 @@
id: GO:0007049
name: cell cycle
namespace: biological_process
-def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle]
+def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:curators, GOC:mtg_cell_cycle]
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_candida
@@ -75626,7 +77050,7 @@
name: spindle organization
namespace: biological_process
alt_id: GO:0043146
-def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart." [GOC:go_curators, GOC:mah]
+def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart." [GOC:curators, GOC:mah]
synonym: "spindle organisation" EXACT []
synonym: "spindle organization and biogenesis" RELATED [GOC:mah]
synonym: "spindle stabilization" RELATED []
@@ -75640,7 +77064,7 @@
alt_id: GO:0000071
alt_id: GO:0030472
alt_id: GO:0043148
-def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle." [GOC:go_curators, GOC:mah]
+def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle." [GOC:curators, GOC:mah]
comment: In fission yeast most mitotic spindle organization occurs in the nucleus.
synonym: "mitotic spindle organisation" EXACT []
synonym: "mitotic spindle organisation in nucleus" NARROW []
@@ -75762,7 +77186,7 @@
id: GO:0007063
name: regulation of sister chromatid cohesion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of sister chromatid cohesion." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of sister chromatid cohesion." [GOC:curators]
is_a: GO:0010564 ! regulation of cell cycle process
is_a: GO:0033044 ! regulation of chromosome organization
intersection_of: GO:0065007 ! biological regulation
@@ -75794,7 +77218,7 @@
id: GO:0007068
name: obsolete negative regulation of transcription during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "down regulation of transcription during mitosis" EXACT [GOC:mah]
synonym: "down-regulation of transcription during mitosis" EXACT [GOC:mah]
@@ -75811,7 +77235,7 @@
id: GO:0007069
name: obsolete negative regulation of transcription from RNA polymerase I promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "down regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah]
synonym: "down-regulation of transcription from RNA polymerase I promoter during mitosis" EXACT [GOC:mah]
@@ -75829,7 +77253,7 @@
id: GO:0007070
name: obsolete negative regulation of transcription from RNA polymerase II promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "down regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah]
synonym: "down-regulation of transcription from RNA polymerase II promoter during mitosis" EXACT [GOC:mah]
@@ -75847,7 +77271,7 @@
id: GO:0007071
name: obsolete negative regulation of transcription from RNA polymerase III promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "down regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah]
synonym: "down-regulation of transcription from RNA polymerase III promoter during mitosis" EXACT [GOC:mah]
@@ -76049,7 +77473,7 @@
id: GO:0007088
name: regulation of mitotic nuclear division
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mitosis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of mitosis." [GOC:curators]
synonym: "regulation of mitosis" EXACT []
is_a: GO:0007346 ! regulation of mitotic cell cycle
is_a: GO:0010564 ! regulation of cell cycle process
@@ -76070,7 +77494,7 @@
id: GO:0007090
name: obsolete regulation of S phase of mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of the progression through the S phase of the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of the progression through the S phase of the mitotic cell cycle." [GOC:curators]
comment: This term was made obsolete as part of the cell cycle overhaul. This is because it was decided that cell cycle phases are intervals and so cannot be regulated, rather it is the transitions between the phases that are regulated.
synonym: "regulation of S phase of mitotic cell cycle" EXACT []
synonym: "regulation of S-phase of mitotic cell cycle" EXACT []
@@ -76280,7 +77704,7 @@
id: GO:0007106
name: obsolete cytokinesis, protein recruitment
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was not defined.
synonym: "cytokinesis, protein recruitment" EXACT []
is_obsolete: true
@@ -76370,7 +77794,7 @@
id: GO:0007115
name: obsolete bud site selection/establishment of cell polarity (sensu Saccharomyces)
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents two processes.
synonym: "bud site selection/establishment of cell polarity (sensu Saccharomyces)" EXACT []
is_obsolete: true
@@ -76393,7 +77817,7 @@
id: GO:0007117
name: budding cell bud growth
namespace: biological_process
-def: "The process in which the bud portion of a cell that reproduces by budding irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:go_curators]
+def: "The process in which the bud portion of a cell that reproduces by budding irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:curators]
synonym: "bud growth" BROAD []
is_a: GO:0040007 ! growth
relationship: part_of GO:0007114 ! cell budding
@@ -76402,7 +77826,7 @@
id: GO:0007118
name: budding cell apical bud growth
namespace: biological_process
-def: "Growth at the tip of a bud, in a cell that reproduces by budding." [GOC:go_curators]
+def: "Growth at the tip of a bud, in a cell that reproduces by budding." [GOC:curators]
synonym: "apical bud growth" BROAD []
is_a: GO:0007117 ! budding cell bud growth
@@ -76410,7 +77834,7 @@
id: GO:0007119
name: budding cell isotropic bud growth
namespace: biological_process
-def: "Unlocalized bud growth such that the entire surface of the bud expands evenly, in a cell that reproduces by budding." [GOC:go_curators]
+def: "Unlocalized bud growth such that the entire surface of the bud expands evenly, in a cell that reproduces by budding." [GOC:curators]
synonym: "isotropic bud growth" BROAD []
is_a: GO:0007117 ! budding cell bud growth
@@ -76775,7 +78199,7 @@
id: GO:0007158
name: neuron cell-cell adhesion
namespace: biological_process
-def: "The attachment of a neuron to another cell via adhesion molecules." [GOC:go_curators]
+def: "The attachment of a neuron to another cell via adhesion molecules." [GOC:curators]
synonym: "neuron adhesion" EXACT []
synonym: "neuronal cell adhesion" EXACT []
is_a: GO:0098609 ! cell-cell adhesion
@@ -76784,7 +78208,7 @@
id: GO:0007159
name: leukocyte cell-cell adhesion
namespace: biological_process
-def: "The attachment of a leukocyte to another cell via adhesion molecules." [GOC:go_curators]
+def: "The attachment of a leukocyte to another cell via adhesion molecules." [GOC:curators]
synonym: "leukocyte adhesion" EXACT []
synonym: "leukocyte cell adhesion" EXACT []
is_a: GO:0098609 ! cell-cell adhesion
@@ -76808,7 +78232,7 @@
id: GO:0007162
name: negative regulation of cell adhesion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion." [GOC:curators]
synonym: "cell adhesion receptor inhibitor activity" RELATED []
synonym: "down regulation of cell adhesion" EXACT []
synonym: "down-regulation of cell adhesion" EXACT []
@@ -76852,7 +78276,7 @@
alt_id: GO:0023016
alt_id: GO:0023033
alt_id: GO:0023045
-def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11]
+def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:curators, GOC:mtg_signaling_feb11]
comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
subset: goslim_candida
subset: goslim_chembl
@@ -76981,7 +78405,7 @@
name: negative regulation of epidermal growth factor-activated receptor activity
namespace: biological_process
alt_id: GO:0007177
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "down regulation of epidermal growth factor receptor activity" EXACT []
synonym: "down-regulation of epidermal growth factor receptor activity" EXACT []
@@ -77003,7 +78427,7 @@
id: GO:0007176
name: obsolete regulation of epidermal growth factor-activated receptor activity
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of EGF-activated receptor activity." [GOC:dph, GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of EGF-activated receptor activity." [GOC:curators, GOC:dph]
comment: This term was obsoleted because it represents a molecular function. Consider molecular function regulator activity ; GO:0098772 or a child.
synonym: "regulation of EGF receptor activity" EXACT []
synonym: "regulation of EGFR activity" EXACT []
@@ -77247,7 +78671,7 @@
id: GO:0007194
name: negative regulation of adenylate cyclase activity
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of adenylate cyclase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "adenylate cyclase inhibitor" RELATED []
synonym: "down regulation of adenylate cyclase activity" EXACT []
@@ -77555,7 +78979,7 @@
name: Notch signaling pathway
namespace: biological_process
alt_id: GO:0030179
-def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Notch on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, GOC:signaling]
+def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Notch on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:curators, GOC:signaling]
synonym: "N signaling pathway" EXACT []
synonym: "N signalling pathway" EXACT []
synonym: "Notch receptor signaling pathway" EXACT []
@@ -77847,7 +79271,7 @@
id: GO:0007251
name: obsolete activation of the inhibitor of kappa kinase
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because its meaning was unclear.
synonym: "activation of the inhibitor of kappa kinase" EXACT []
is_obsolete: true
@@ -77981,14 +79405,13 @@
[Term]
id: GO:0007263
-name: nitric oxide mediated signal transduction
+name: obsolete nitric oxide mediated signal transduction
namespace: biological_process
-def: "An intracellular signaling cassette that starts with production of nitric oxide, detection by receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and ends with the activation of downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms." [GOC:jl, PMID:21549190]
-synonym: "nitric oxide signaling" EXACT [GOC:bf]
-synonym: "nitric oxide-mediated signal transduction" EXACT []
-synonym: "NO mediated signal transduction" EXACT []
-synonym: "NO-mediated signal transduction" EXACT []
-is_a: GO:0141124 ! intracellular signaling cassette
+def: "OBSOLETE. An intracellular signaling cassette that starts with production of nitric oxide, detection by receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and ends with the activation of downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms." [GOC:jl, PMID:21549190]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0038060
[Term]
id: GO:0007264
@@ -78147,7 +79570,7 @@
id: GO:0007278
name: pole cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a pole cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a pole cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
is_a: GO:0001709 ! cell fate determination
is_a: GO:0003006 ! developmental process involved in reproduction
relationship: part_of GO:0007277 ! pole cell development
@@ -78176,7 +79599,7 @@
id: GO:0007281
name: germ cell development
namespace: biological_process
-def: "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." [GOC:curators]
synonym: "gametogenesis" NARROW []
synonym: "germ-cell development" EXACT []
synonym: "primordial germ cell development" NARROW []
@@ -78228,7 +79651,7 @@
id: GO:0007286
name: spermatid development
namespace: biological_process
-def: "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." [GOC:dph, GOC:go_curators]
+def: "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." [GOC:curators, GOC:dph]
synonym: "spermatid cell development" EXACT []
synonym: "spermiogenesis" EXACT []
xref: Wikipedia:Spermiogenesis
@@ -78365,7 +79788,7 @@
namespace: biological_process
def: "Transfer of constituents synthesized in the ovarian nurse cells to the oocyte, through the ring canals, as the egg chamber is growing. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, ISBN:0879694238]
synonym: "nurse cell to oocyte transport" BROAD []
-is_a: GO:0006810 ! transport
+is_a: GO:0010496 ! intercellular transport
relationship: part_of GO:0048477 ! oogenesis
[Term]
@@ -78629,7 +80052,7 @@
id: GO:0007329
name: obsolete positive regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:curators]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "activation of transcription from RNA polymerase II promoter by pheromones" NARROW []
synonym: "positive regulation of transcription from Pol II promoter by pheromones" EXACT []
@@ -78705,7 +80128,6 @@
def: "The binding and fusion of a sperm, with the plasma membrane of the oocyte as part of the process of single fertilization. In sperm with flagella, binding occurs at the posterior (post-acrosomal) region of the sperm head." [GOC:dph, GOC:jl, PMID:17644969]
synonym: "sperm-oocyte fusion" NARROW []
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0045026 ! plasma membrane fusion
relationship: part_of GO:0007338 ! single fertilization
[Term]
@@ -78740,7 +80162,7 @@
id: GO:0007346
name: regulation of mitotic cell cycle
namespace: biological_process
-def: "Any process that modulates the rate or extent of progress through the mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the rate or extent of progress through the mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "mitotic cell cycle modulation" EXACT []
synonym: "mitotic cell cycle regulation" EXACT []
synonym: "mitotic cell cycle regulator" RELATED []
@@ -78758,7 +80180,7 @@
id: GO:0007347
name: regulation of preblastoderm mitotic cell cycle
namespace: biological_process
-def: "A cell cycle process that modulates the rate or extent of the progression through the preblastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "A cell cycle process that modulates the rate or extent of the progression through the preblastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "modulation of preblastoderm mitotic cell cycle progression" EXACT []
synonym: "preblastoderm mitotic cell cycle modulation" EXACT []
synonym: "preblastoderm mitotic cell cycle regulation" EXACT []
@@ -78774,7 +80196,7 @@
id: GO:0007348
name: regulation of syncytial blastoderm mitotic cell cycle
namespace: biological_process
-def: "A cell cycle process that modulates the rate or extent of the progression through the syncytial blastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "A cell cycle process that modulates the rate or extent of the progression through the syncytial blastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "modulation of syncytial blastoderm cell cycle progression" EXACT []
synonym: "regulation of progression through syncytial blastoderm mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
synonym: "regulation of syncytial blastoderm cell cycle" EXACT []
@@ -78793,7 +80215,7 @@
name: cellularization
namespace: biological_process
alt_id: GO:0009796
-def: "The separation of a multi-nucleate cell or syncytium into individual cells. An example of this is found in Drosophila melanogaster embryo development." [GOC:go_curators, GOC:mtg_sensu, ISBN:0716731363]
+def: "The separation of a multi-nucleate cell or syncytium into individual cells. An example of this is found in Drosophila melanogaster embryo development." [GOC:curators, GOC:mtg_sensu, ISBN:0716731363]
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0007275 ! multicellular organism development
@@ -79135,7 +80557,7 @@
id: GO:0007389
name: pattern specification process
namespace: biological_process
-def: "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." [GOC:go_curators, GOC:isa_complete, ISBN:0521436125]
+def: "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." [GOC:curators, GOC:isa_complete, ISBN:0521436125]
subset: goslim_drosophila
synonym: "pattern biosynthesis" RELATED []
synonym: "pattern formation" RELATED []
@@ -79171,7 +80593,7 @@
id: GO:0007393
name: dorsal closure, leading edge cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell within the dorsal ectoderm becomes capable of differentiating autonomously into a leading edge cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:bf, GOC:go_curators, PMID:12147138]
+def: "The cell fate determination process in which a cell within the dorsal ectoderm becomes capable of differentiating autonomously into a leading edge cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:bf, GOC:curators, PMID:12147138]
is_a: GO:0035028 ! leading edge cell fate determination
intersection_of: GO:0035028 ! leading edge cell fate determination
intersection_of: part_of GO:0007391 ! dorsal closure
@@ -79238,7 +80660,7 @@
alt_id: GO:0007408
alt_id: GO:0043347
alt_id: GO:0043348
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus." [GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus." [GOC:curators]
synonym: "neuroblast cell fate determination" EXACT []
synonym: "neuroblast identity determination" EXACT []
is_a: GO:0001709 ! cell fate determination
@@ -79259,7 +80681,7 @@
id: GO:0007402
name: ganglion mother cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a ganglion mother cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a ganglion mother cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
is_a: GO:0001709 ! cell fate determination
[Term]
@@ -79267,7 +80689,7 @@
name: glial cell fate determination
namespace: biological_process
alt_id: GO:0043361
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, GOC:mtg_sensu]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a glial cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0001709 ! cell fate determination
relationship: part_of GO:0021781 ! glial cell fate commitment
@@ -79304,7 +80726,7 @@
namespace: biological_process
alt_id: GO:0043351
alt_id: GO:0043352
-def: "A change in the morphology or behavior of a neuroblast resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:go_curators, GOC:mtg_sensu]
+def: "A change in the morphology or behavior of a neuroblast resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0001775 ! cell activation
relationship: part_of GO:0048699 ! generation of neurons
@@ -79397,7 +80819,7 @@
id: GO:0007418
name: ventral midline development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the ventral midline over time, from its formation to the mature structure. In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, PMID:12075342]
+def: "The process whose specific outcome is the progression of the ventral midline over time, from its formation to the mature structure. In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:curators, PMID:12075342]
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0007417 ! central nervous system development
@@ -79405,7 +80827,7 @@
id: GO:0007419
name: ventral cord development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms." [GOC:bf, GOC:go_curators, PMID:30826502]
+def: "The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms." [GOC:bf, GOC:curators, PMID:30826502]
is_a: GO:0048513 ! animal organ development
relationship: part_of GO:0007417 ! central nervous system development
@@ -79430,7 +80852,7 @@
id: GO:0007422
name: peripheral nervous system development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GOC:go_curators, UBERON:0000010]
+def: "The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GOC:curators, UBERON:0000010]
is_a: GO:0048731 ! system development
relationship: part_of GO:0007399 ! nervous system development
@@ -79438,7 +80860,7 @@
id: GO:0007423
name: sensory organ development
namespace: biological_process
-def: "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:curators]
subset: goslim_drosophila
synonym: "sense organ development" EXACT [GOC:dph]
is_a: GO:0048513 ! animal organ development
@@ -79561,7 +80983,7 @@
id: GO:0007437
name: adult salivary gland morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the adult salivary gland are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the adult salivary gland are generated and organized." [GOC:curators]
is_a: GO:0007435 ! salivary gland morphogenesis
[Term]
@@ -79593,7 +81015,7 @@
id: GO:0007441
name: anterior midgut (ectodermal) morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the anterior midgut (ectodermal) are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the anterior midgut (ectodermal) are generated and organized." [GOC:curators]
is_a: GO:0002009 ! morphogenesis of an epithelium
relationship: part_of GO:0048567 ! ectodermal digestive tract morphogenesis
@@ -79768,7 +81190,7 @@
id: GO:0007468
name: obsolete regulation of rhodopsin gene expression
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of rhodopsin gene expression. This includes transcriptional, translational, or posttranslational regulation." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of rhodopsin gene expression. This includes transcriptional, translational, or posttranslational regulation." [GOC:curators, GOC:dph, GOC:tb]
comment: This term was obsoleted because it refers to a specific gene product. The gene product should be captured as an annotation extension using 'has input'.
synonym: "regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb]
is_obsolete: true
@@ -79984,7 +81406,7 @@
id: GO:0007493
name: endodermal cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into an endoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, ISBN:0878932437]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into an endoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators, ISBN:0878932437]
comment: Note that this term was 'endoderm determination'. Changed string to make it more consistent with parent term 'cell fate determination'.
synonym: "endoderm cell fate determination" EXACT []
is_a: GO:0001709 ! cell fate determination
@@ -80018,7 +81440,7 @@
id: GO:0007497
name: posterior midgut development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the posterior midgut over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the posterior midgut over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0007494 ! midgut development
@@ -80043,7 +81465,7 @@
id: GO:0007500
name: mesodermal cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, ISBN:0878932437]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators, ISBN:0878932437]
comment: Note that this term was 'mesoderm determination'. Changed string to make more consistent with parent term 'cell fate determination'.
synonym: "mesoderm cell fate determination" EXACT []
is_a: GO:0001709 ! cell fate determination
@@ -80053,7 +81475,7 @@
id: GO:0007501
name: mesodermal cell fate specification
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:curators]
comment: Note that this term was 'fate specification in mesoderm'. String of term was changed to correspond to format of sibling terms 'endoderm cell fate specification' and 'ectoderm cell fate specification'.
synonym: "mesoderm cell fate specification" EXACT []
is_a: GO:0001708 ! cell fate specification
@@ -80135,7 +81557,7 @@
id: GO:0007510
name: cardioblast cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a cardioblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a cardioblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
is_a: GO:0060913 ! cardiac cell fate determination
relationship: part_of GO:0042684 ! cardioblast cell fate commitment
@@ -80179,7 +81601,7 @@
id: GO:0007518
name: myoblast fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a myoblast regardless of its environment; upon determination, the cell fate cannot be reversed. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a myoblast regardless of its environment; upon determination, the cell fate cannot be reversed. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:curators]
is_a: GO:0001709 ! cell fate determination
relationship: part_of GO:0048625 ! myoblast fate commitment
@@ -80198,14 +81620,14 @@
name: myoblast fusion
namespace: biological_process
def: "A process in which non-proliferating myoblasts fuse to existing fibers or to myotubes to form new fibers. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:mtg_muscle]
-is_a: GO:0000768 ! syncytium formation by plasma membrane fusion
+is_a: GO:0000768 ! syncytium formation by cell-cell fusion
relationship: part_of GO:0014902 ! myotube differentiation
[Term]
id: GO:0007521
name: muscle cell fate determination
namespace: biological_process
-def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a muscle cell regardless of its environment; upon determination, the cell fate cannot be reversed." [CL:0000187, GOC:go_curators]
+def: "The cell fate determination process in which a cell becomes capable of differentiating autonomously into a muscle cell regardless of its environment; upon determination, the cell fate cannot be reversed." [CL:0000187, GOC:curators]
is_a: GO:0001709 ! cell fate determination
relationship: part_of GO:0042693 ! muscle cell fate commitment
@@ -80213,7 +81635,7 @@
id: GO:0007522
name: visceral muscle development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the visceral muscle over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the visceral muscle over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0007517 ! muscle organ development
[Term]
@@ -80291,7 +81713,7 @@
id: GO:0007532
name: regulation of mating-type specific transcription, DNA-templated
namespace: biological_process
-def: "Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
synonym: "mating-type specific transcriptional control" EXACT []
synonym: "regulation of mating-type specific transcription, DNA-dependent" EXACT [GOC:txnOH]
is_a: GO:0006355 ! regulation of DNA-templated transcription
@@ -80503,7 +81925,7 @@
id: GO:0007554
name: regulation of ecdysteroid biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:curators]
synonym: "regulation of ecdysteroid anabolism" EXACT []
synonym: "regulation of ecdysteroid biosynthesis" EXACT []
synonym: "regulation of ecdysteroid formation" EXACT []
@@ -80519,7 +81941,7 @@
id: GO:0007555
name: regulation of ecdysteroid secretion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell." [GOC:curators]
is_a: GO:2000831 ! regulation of steroid hormone secretion
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0045457 ! ecdysteroid secretion
@@ -80529,7 +81951,7 @@
id: GO:0007556
name: obsolete regulation of juvenile hormone metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "regulation of juvenile hormone metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30570" xsd:anyURI
@@ -80539,7 +81961,7 @@
id: GO:0007557
name: regulation of juvenile hormone biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:curators]
synonym: "regulation of juvenile hormone anabolism" EXACT []
synonym: "regulation of juvenile hormone biosynthesis" EXACT []
synonym: "regulation of juvenile hormone formation" EXACT []
@@ -80555,7 +81977,7 @@
id: GO:0007558
name: regulation of juvenile hormone secretion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of juvenile hormone secretion." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of juvenile hormone secretion." [GOC:curators]
is_a: GO:0032368 ! regulation of lipid transport
is_a: GO:0044060 ! regulation of endocrine process
is_a: GO:0046883 ! regulation of hormone secretion
@@ -80607,7 +82029,7 @@
id: GO:0007563
name: regulation of eclosion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the emergence of an insect from a pupa-case or of a larva from an egg." [GOC:go_curators, ISBN:0198600461]
+def: "Any process that modulates the frequency, rate or extent of the emergence of an insect from a pupa-case or of a larva from an egg." [GOC:curators, ISBN:0198600461]
is_a: GO:2000026 ! regulation of multicellular organismal development
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0007562 ! eclosion
@@ -80617,7 +82039,7 @@
id: GO:0007564
name: regulation of chitin-based cuticle tanning
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of chitin-based cuticular tanning." [GOC:go_curators, GOC:jid, GOC:mtg_sensu]
+def: "Any process that modulates the frequency, rate or extent of chitin-based cuticular tanning." [GOC:curators, GOC:jid, GOC:mtg_sensu]
synonym: "regulation of cuticle hardening" NARROW []
synonym: "regulation of cuticle tanning" EXACT []
is_a: GO:2000026 ! regulation of multicellular organismal development
@@ -80683,7 +82105,7 @@
id: GO:0007570
name: obsolete age dependent accumulation of genetic damage
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent accumulation of genetic damage" EXACT []
is_obsolete: true
@@ -80705,7 +82127,7 @@
id: GO:0007572
name: obsolete age dependent decreased translational activity
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent decreased translational activity" EXACT []
is_obsolete: true
@@ -80714,7 +82136,7 @@
id: GO:0007573
name: obsolete age dependent increased protein content
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not describe a biological process.
synonym: "age dependent increased protein content" EXACT []
is_obsolete: true
@@ -80802,7 +82224,7 @@
id: GO:0007583
name: obsolete killer activity
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it is ambiguous; 'killer activity' could refer to several different processes.
synonym: "killer activity" EXACT []
is_obsolete: true
@@ -80812,7 +82234,7 @@
id: GO:0007584
name: response to nutrient
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus." [GOC:curators]
synonym: "nutritional response pathway" NARROW []
synonym: "response to nutrients" EXACT []
is_a: GO:0031667 ! response to nutrient levels
@@ -80862,7 +82284,7 @@
id: GO:0007590
name: obsolete fat body metabolic process (sensu Insecta)
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving the fat body. A fat body is a fat-containing cellular structure which serves as an energy reserve. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving the fat body. A fat body is a fat-containing cellular structure which serves as an energy reserve. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." [GOC:curators, ISBN:0198506732]
comment: This term was made obsolete because it represents metabolism within the fat body not of the fat body.
synonym: "fat body metabolic process (sensu Insecta)" EXACT []
is_obsolete: true
@@ -80992,7 +82414,7 @@
id: GO:0007602
name: phototransduction
namespace: biological_process
-def: "The sequence of reactions within a cell required to convert absorbed photons into a molecular signal." [GOC:go_curators]
+def: "The sequence of reactions within a cell required to convert absorbed photons into a molecular signal." [GOC:curators]
synonym: "opsin" RELATED []
synonym: "phototransduction, visible light, light adaptation" NARROW []
synonym: "phototrophin mediated phototransduction" NARROW []
@@ -81004,7 +82426,7 @@
id: GO:0007603
name: phototransduction, visible light
namespace: biological_process
-def: "The sequence of reactions within a cell required to convert absorbed photons from visible light into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." [GOC:go_curators, ISBN:0198506732]
+def: "The sequence of reactions within a cell required to convert absorbed photons from visible light into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." [GOC:curators, ISBN:0198506732]
synonym: "visual cascade" EXACT [PMID:1962207, PMID:9822721]
synonym: "visual transduction" EXACT [PMID:10611962]
xref: Reactome:R-HSA-2187338 "Visual phototransduction"
@@ -81015,7 +82437,7 @@
id: GO:0007604
name: phototransduction, UV
namespace: biological_process
-def: "The sequence of reactions within a cell required to convert absorbed photons from UV light into a molecular signal; ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 400 nanometers." [GOC:go_curators, ISBN:0198506732]
+def: "The sequence of reactions within a cell required to convert absorbed photons from UV light into a molecular signal; ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 400 nanometers." [GOC:curators, ISBN:0198506732]
synonym: "phototransduction, ultraviolet light" EXACT []
synonym: "phototransduction, ultraviolet radiation" EXACT []
synonym: "phototransduction, UV light" EXACT []
@@ -81194,14 +82616,14 @@
name: circadian rhythm
namespace: biological_process
alt_id: GO:0050895
-def: "Any biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:go_curators]
+def: "Any biological process in an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:curators]
subset: goslim_drosophila
subset: goslim_plant
subset: goslim_plant_ribbon
synonym: "circadian process" EXACT []
synonym: "circadian response" RELATED []
synonym: "response to circadian rhythm" RELATED []
-xref: Reactome:R-HSA-400253 "Circadian Clock"
+xref: Reactome:R-HSA-9909396 "Circadian clock"
xref: Wikipedia:Circadian_rhythm
is_a: GO:0048511 ! rhythmic process
@@ -81329,7 +82751,7 @@
id: GO:0007635
name: chemosensory behavior
namespace: biological_process
-def: "Behavior that is dependent upon the sensation of chemicals." [GOC:go_curators]
+def: "Behavior that is dependent upon the sensation of chemicals." [GOC:curators]
synonym: "behavioral response to chemical stimulus" EXACT []
synonym: "behavioural response to chemical stimulus" EXACT []
synonym: "chemosensory behaviour" EXACT []
@@ -81361,7 +82783,7 @@
id: GO:0007638
name: mechanosensory behavior
namespace: biological_process
-def: "Behavior that is dependent upon the sensation of a mechanical stimulus." [GOC:go_curators]
+def: "Behavior that is dependent upon the sensation of a mechanical stimulus." [GOC:curators]
synonym: "behavioral response to mechanical stimulus" EXACT []
synonym: "behavioural response to mechanical stimulus" EXACT []
synonym: "mechanosensory behaviour" EXACT []
@@ -81482,7 +82904,7 @@
id: GO:0008016
name: regulation of heart contraction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body." [GOC:curators, GOC:dph, GOC:tb]
synonym: "regulation of cardiac contraction" EXACT []
is_a: GO:1903522 ! regulation of blood circulation
intersection_of: GO:0065007 ! biological regulation
@@ -81513,7 +82935,7 @@
id: GO:0008019
name: obsolete macrophage receptor activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because its name is ambiguous, and it was never defined.
synonym: "macrophage receptor activity" EXACT []
is_obsolete: true
@@ -81612,7 +83034,7 @@
def: "Enables the transfer of monocarboxylic acids from one side of a membrane to the other. A monocarboxylic acid is an organic acid with one COOH group." [GOC:ai]
synonym: "monocarboxylate carrier" NARROW []
synonym: "prostaglandin/thromboxane transporter activity" NARROW []
-xref: Reactome:R-HSA-429749 "SLC5A8 transports monocarboxylates from extracellular region to cytosol"
+xref: Reactome:R-HSA-429749 "SLC5A8 (SMCT) co-transports monocarboxylates and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-433698 "SLC16A3,7,8 cotransport monocarboxylates, H+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5624211 "Defective SLC16A1 does not cotransport monocarboxylates, H+ from extracellular region to cytosol"
xref: Reactome:R-HSA-9645220 "SLC16A1:BSG cotransports monocarboxylates, H+ from extracellular region to cytosol"
@@ -81686,7 +83108,7 @@
id: GO:0008037
name: cell recognition
namespace: biological_process
-def: "The process in which a cell in an organism interprets its surroundings." [GOC:go_curators]
+def: "The process in which a cell in an organism interprets its surroundings." [GOC:curators]
subset: goslim_pir
synonym: "recognition of surroundings by cell" EXACT []
is_a: GO:0009987 ! cellular process
@@ -81695,7 +83117,7 @@
id: GO:0008038
name: neuron recognition
namespace: biological_process
-def: "The process in which a neuronal cell in a multicellular organism interprets its surroundings." [GOC:go_curators]
+def: "The process in which a neuronal cell in a multicellular organism interprets its surroundings." [GOC:curators]
synonym: "neuronal cell recognition" EXACT []
is_a: GO:0008037 ! cell recognition
relationship: part_of GO:0048666 ! neuron development
@@ -81713,7 +83135,7 @@
id: GO:0008041
name: obsolete storage protein of fat body (sensu Insecta)
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it describes a cellular location rather than a function.
synonym: "storage protein of fat body (sensu Insecta)" EXACT []
is_obsolete: true
@@ -81780,6 +83202,7 @@
def: "A molecular function regulator that increases a catalytic activity." [GOC:pdt]
comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
synonym: "metalloenzyme activator activity" NARROW []
+xref: Reactome:R-HSA-9948070 "POMGNT1 catalyzes FKRP:FKTN:RXYLT1 formation"
is_a: GO:0030234 ! enzyme regulator activity
is_a: GO:0140677 ! molecular function activator activity
relationship: positively_regulates GO:0003824 ! catalytic activity
@@ -81904,7 +83327,7 @@
id: GO:0008063
name: Toll signaling pathway
namespace: biological_process
-def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Toll on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:11135568, PMID:19126860]
+def: "The series of molecular signals initiated by an extracellular ligand binding to the receptor Toll on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:curators, PMID:11135568, PMID:19126860]
synonym: "Tl signaling pathway" EXACT []
synonym: "Tl signalling pathway" EXACT []
synonym: "Toll signalling pathway" EXACT []
@@ -82002,6 +83425,7 @@
name: ornithine decarboxylase inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of ornithine decarboxylase." [GOC:jl]
+xref: Reactome:R-HSA-350567 "Antizyme OAZ binds to Ornithine decarboxylase"
is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0042979 ! ornithine decarboxylase regulator activity
relationship: negatively_regulates GO:0004586 ! ornithine decarboxylase activity
@@ -82075,6 +83499,7 @@
xref: Reactome:R-HSA-2473152 "Acetylation of SMC3 subunit of centromeric chromatin associated cohesin by ESCO1 or ESCO2"
xref: Reactome:R-HSA-6790987 "NAT10 acetylates cytidine-1337 and cytidine-1842 of 18S rRNA yielding 4-acetylcytidine-1377 and 4-acetylcytidine-1842"
xref: Reactome:R-HSA-9636560 "Eis acetylates DUSP16"
+xref: Reactome:R-HSA-9913373 "AAC(6)-Ib acetylates ciprofloxacin"
is_a: GO:0016407 ! acetyltransferase activity
is_a: GO:0016410 ! N-acyltransferase activity
@@ -82304,6 +83729,27 @@
synonym: "NADP-aldehyde reductase activity" EXACT []
xref: EC:1.1.1.2
xref: MetaCyc:ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN
+xref: Reactome:R-HSA-192033 "4-cholesten-7alpha-ol-3-one is reduced to 5beta-cholestan-7alpha-ol-3-one"
+xref: Reactome:R-HSA-192036 "5Beta-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha, 12alpha-triol"
+xref: Reactome:R-HSA-192067 "4-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholesten-7alpha, 12alpha-diol-3-one"
+xref: Reactome:R-HSA-192160 "5beta-cholestan-7alpha-ol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha-diol"
+xref: Reactome:R-HSA-193746 "4-cholesten-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-7alpha,24(S)-diol-3-one"
+xref: Reactome:R-HSA-193755 "4-cholesten-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,24(S)-triol-3-one"
+xref: Reactome:R-HSA-193758 "5beta-cholestan-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,24(S)-triol"
+xref: Reactome:R-HSA-193781 "5Beta-cholestan-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol"
+xref: Reactome:R-HSA-193800 "5Beta-cholestan-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,27-tetrol"
+xref: Reactome:R-HSA-193821 "4-cholesten-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,27-triol-3-one"
+xref: Reactome:R-HSA-193824 "4-cholesten-7alpha,27-diol-3-one is reduced to 5beta-cholestan-7alpha,27-diol-3-one"
+xref: Reactome:R-HSA-193841 "5beta-cholestan-7alpha,27-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,27-triol"
+xref: Reactome:R-HSA-198845 "CYB5A:heme reduces Asc.- to AscH-"
+xref: Reactome:R-HSA-2855252 "AKRs reduce RBP2:atRAL to RBP2:atROL"
+xref: Reactome:R-HSA-5423637 "AKR dimers reduce AFBDHO to AFBDOH"
+xref: Reactome:R-HSA-5692232 "AKR1A1 oxidises BaPtDHD to BaP-7,8-dione"
+xref: Reactome:R-HSA-9027531 "Dehydrogenase dehydrogenates 13-HDHA to 13-oxo-DHA"
+xref: Reactome:R-HSA-9027562 "Dehydrogenase dehydrogenates 17-HDHA to 17-oxo-DHA"
+xref: Reactome:R-HSA-9027598 "Dehydrogenase dehydrogenates 13(R)-HDPAn-3 to 13-oxo-DPAn-3"
+xref: Reactome:R-HSA-9027600 "Dehydrogenase dehydrogenates 17-HDPAn-3 to 17-oxo-DPAn-3"
+xref: Reactome:R-HSA-9937340 "DHRSX reduces dolichal to dolichol"
xref: RHEA:15937
is_a: GO:0018455 ! alcohol dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.1.1.2
@@ -82346,10 +83792,12 @@
xref: Reactome:R-HSA-9036987 "FUT2 transfers Fuc to Type 1 chains to form H antigen-sec"
xref: Reactome:R-HSA-9603982 "FUT2 transfers Fuc to LeA to form LeB"
xref: Reactome:R-HSA-9603983 "FUT2 transfers Fuc to LeX to form LeY"
+xref: RHEA:48792
xref: RHEA:50664
is_a: GO:0031127 ! alpha-(1,2)-fucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.69
property_value: skos:exactMatch RHEA:50664
+property_value: skos:narrowMatch RHEA:48792
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -82393,29 +83841,33 @@
xref: EC:2.4.1.150
xref: MetaCyc:2.4.1.150-RXN
xref: RHEA:17413
+xref: RHEA:54820
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.150
property_value: skos:exactMatch RHEA:17413
property_value: skos:narrowMatch MetaCyc:2.4.1.150-RXN
+property_value: skos:narrowMatch RHEA:54820
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30174" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0008110
-name: L-histidine:2-oxoglutarate aminotransferase activity
+name: L-histidine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-histidine = 3-(imidazol-5-yl)pyruvate + L-glutamate." [EC:2.6.1.38, RHEA:16565]
+def: "Catalysis of the reaction: L-histidine + 2-oxoglutarate = 3-(imidazol-5-yl)pyruvate + L-glutamate." [RHEA:16565]
synonym: "histidine aminotransferase activity" BROAD []
synonym: "histidine transaminase activity" BROAD [EC:2.6.1.38]
synonym: "histidine-2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.38]
+synonym: "L-histidine:2-oxoglutarate aminotransferase activity" EXACT []
xref: EC:2.6.1.38
xref: KEGG_REACTION:R01161
xref: MetaCyc:HISTTRANSAM-RXN
xref: RHEA:16565
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.38
property_value: skos:exactMatch RHEA:16565
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0008111
@@ -82431,9 +83883,15 @@
xref: Reactome:R-HSA-193763 "Isomerization of 25(R) TetraHCA-CoA to (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA"
xref: Reactome:R-HSA-389897 "Isomerization of (2R)-pristanoyl-CoA to (2S)-pristanoyl-CoA"
xref: RHEA:12657
+xref: RHEA:46724
+xref: RHEA:63172
+xref: RHEA:63176
is_a: GO:0016854 ! racemase and epimerase activity
property_value: skos:exactMatch EC:5.1.99.4
property_value: skos:exactMatch RHEA:12657
+property_value: skos:narrowMatch RHEA:46724
+property_value: skos:narrowMatch RHEA:63172
+property_value: skos:narrowMatch RHEA:63176
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -82566,9 +84024,15 @@
xref: EC:2.4.3.6
xref: MetaCyc:2.4.99.6-RXN
xref: RHEA:52316
+xref: RHEA:56264
+xref: RHEA:65432
+xref: RHEA:80755
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.6
property_value: skos:exactMatch RHEA:52316
+property_value: skos:narrowMatch RHEA:56264
+property_value: skos:narrowMatch RHEA:65432
+property_value: skos:narrowMatch RHEA:80755
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28444" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -82648,12 +84112,13 @@
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
+is_a: GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
property_value: skos:exactMatch EC:7.1.1.8
property_value: skos:exactMatch RHEA:11484
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20616" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -82728,10 +84193,12 @@
xref: EC:3.1.1.6
xref: MetaCyc:ACETYLESTERASE-RXN
xref: RHEA:12957
+xref: RHEA:58148
xref: UM-BBD_reactionID:r0170
is_a: GO:0034338 ! short-chain carboxylesterase activity
property_value: skos:exactMatch EC:3.1.1.6
property_value: skos:exactMatch RHEA:12957
+property_value: skos:narrowMatch RHEA:58148
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -82807,6 +84274,25 @@
xref: Reactome:R-HSA-5696146 "AOC2 deaminates TYR"
xref: Reactome:R-HSA-5696183 "AOC3 deaminates BZAM"
xref: RHEA:16153
+xref: RHEA:25265
+xref: RHEA:27946
+xref: RHEA:30591
+xref: RHEA:35107
+xref: RHEA:59416
+xref: RHEA:59420
+xref: RHEA:59424
+xref: RHEA:59596
+xref: RHEA:59600
+xref: RHEA:59604
+xref: RHEA:69072
+xref: RHEA:69076
+xref: RHEA:69132
+xref: RHEA:69136
+xref: RHEA:69144
+xref: RHEA:69148
+xref: RHEA:70283
+xref: RHEA:71015
+xref: RHEA:78367
is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.4.3.21
property_value: skos:exactMatch KEGG_REACTION:R01853
@@ -82816,6 +84302,25 @@
property_value: skos:narrowMatch KEGG_REACTION:R02613
property_value: skos:narrowMatch MetaCyc:RXN-10817
property_value: skos:narrowMatch MetaCyc:RXN-1401
+property_value: skos:narrowMatch RHEA:25265
+property_value: skos:narrowMatch RHEA:27946
+property_value: skos:narrowMatch RHEA:30591
+property_value: skos:narrowMatch RHEA:35107
+property_value: skos:narrowMatch RHEA:59416
+property_value: skos:narrowMatch RHEA:59420
+property_value: skos:narrowMatch RHEA:59424
+property_value: skos:narrowMatch RHEA:59596
+property_value: skos:narrowMatch RHEA:59600
+property_value: skos:narrowMatch RHEA:59604
+property_value: skos:narrowMatch RHEA:69072
+property_value: skos:narrowMatch RHEA:69076
+property_value: skos:narrowMatch RHEA:69132
+property_value: skos:narrowMatch RHEA:69136
+property_value: skos:narrowMatch RHEA:69144
+property_value: skos:narrowMatch RHEA:69148
+property_value: skos:narrowMatch RHEA:70283
+property_value: skos:narrowMatch RHEA:71015
+property_value: skos:narrowMatch RHEA:78367
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -82903,17 +84408,18 @@
xref: MetaCyc:NADH-DEHYDROG-A-RXN
xref: Reactome:R-HSA-163217 "Complex I oxidises NADH to NAD+, reduces CoQ to CoQH2"
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
+is_a: GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0003954 ! NADH dehydrogenase activity
-relationship: has_part GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:7.1.1.2
property_value: skos:exactMatch RHEA:29091
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20616" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25784" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27641" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -83073,7 +84579,7 @@
namespace: biological_process
alt_id: GO:0044236
alt_id: GO:0044710
-def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684]
+def: "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation." [GOC:curators, ISBN:0198547684]
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
subset: gocheck_do_not_annotate
subset: goslim_chembl
@@ -83144,7 +84650,7 @@
id: GO:0008156
name: negative regulation of DNA replication
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication." [GOC:curators]
synonym: "DNA replication inhibitor" RELATED []
synonym: "down regulation of DNA replication" EXACT []
synonym: "down-regulation of DNA replication" EXACT []
@@ -83167,7 +84673,7 @@
id: GO:0008158
name: hedgehog receptor activity
namespace: molecular_function
-def: "Combining with a member of the hedgehog protein family and transmitting the signal across the membrane to initiate a change in cell activity." [GOC:bf, GOC:go_curators, PMID:9278137]
+def: "Combining with a member of the hedgehog protein family and transmitting the signal across the membrane to initiate a change in cell activity." [GOC:bf, GOC:curators, PMID:9278137]
synonym: "patched activity" EXACT []
is_a: GO:0004888 ! transmembrane signaling receptor activity
relationship: has_part GO:0097108 ! hedgehog family protein binding
@@ -83194,7 +84700,7 @@
id: GO:0008161
name: obsolete carbamate resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "carbamate resistance" EXACT []
is_obsolete: true
@@ -83204,7 +84710,7 @@
id: GO:0008162
name: obsolete cyclodiene resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "cyclodiene resistance" EXACT []
is_obsolete: true
@@ -83214,7 +84720,7 @@
id: GO:0008163
name: obsolete DDT resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "DDT resistance" EXACT []
is_obsolete: true
@@ -83224,7 +84730,7 @@
id: GO:0008164
name: obsolete organophosphorus resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "organophosphorus resistance" EXACT []
is_obsolete: true
@@ -83234,7 +84740,7 @@
id: GO:0008165
name: obsolete pyrethroid resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "pyrethroid resistance" EXACT []
is_obsolete: true
@@ -83244,7 +84750,7 @@
id: GO:0008166
name: obsolete viral replication
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it covers multiple processes and is now covered by more specific terms.
synonym: "viral replication" EXACT []
is_obsolete: true
@@ -83254,7 +84760,7 @@
id: GO:0008167
name: obsolete sigma virus replication
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
synonym: "sigma virus replication" EXACT []
is_obsolete: true
replaced_by: GO:0019079
@@ -83273,6 +84779,7 @@
xref: Reactome:R-HSA-212269 "DNMT1,3A,3B:PRC2 methylates cytosine and histone H3"
xref: Reactome:R-HSA-379387 "COMT transfers Met to DA to form 3MT"
xref: Reactome:R-HSA-379464 "COMT transfers Met to DOPAC to form HVA"
+xref: Reactome:R-HSA-5333608 "GSSebGalNac is reduced and methylated to MeSebGalNac"
xref: Reactome:R-HSA-6800149 "N6AMT1:TRMT112 transfers CH3 group from AdoMet to MMAIII"
xref: Reactome:R-HSA-71286 "guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine"
xref: Reactome:R-HSA-9710490 "The GSDME gene promoter is hypermethylated"
@@ -83339,7 +84846,7 @@
id: GO:0008175
name: tRNA methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule." [GOC:mah]
+def: "Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside." [GOC:mah]
xref: Reactome:R-HSA-6782879 "TYW3 methylates yW-86 yielding yW-72 at nucleotide 37 of tRNA(Phe)"
xref: Reactome:R-HSA-6782881 "LCMT2 methylates yW-72 yielding yW-58 at nucleotide 37 of tRNA(Phe)"
xref: Reactome:R-HSA-6782890 "LCMT2 methoxycarbonylates yW-58 yielding yW (wybutosine) at nucleotide 37 of tRNA(Phe)"
@@ -83389,11 +84896,17 @@
xref: MetaCyc:RXN-14971
xref: Reactome:R-HSA-163213 "Transfer of electrons through the succinate dehydrogenase complex"
xref: Reactome:R-HSA-70994 "SDH complex dehydrogenates succinate"
+xref: RHEA:13713
+xref: RHEA:27834
xref: RHEA:40523
+xref: RHEA:75711
is_a: GO:0000104 ! succinate dehydrogenase activity
is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
property_value: skos:exactMatch EC:1.3.5.1
property_value: skos:exactMatch RHEA:40523
+property_value: skos:narrowMatch RHEA:13713
+property_value: skos:narrowMatch RHEA:27834
+property_value: skos:narrowMatch RHEA:75711
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26087" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27915" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -83422,7 +84935,7 @@
id: GO:0008181
name: obsolete tumor suppressor
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not represent a true biological function, rather a pathology that occurs when a particular gene product is inactivated in some way.
synonym: "tumor suppressor" EXACT []
is_obsolete: true
@@ -83555,9 +85068,27 @@
xref: Reactome:R-HSA-6797630 "LRPP4(LRPP1-3,5) hydrolyse LPA"
xref: Reactome:R-HSA-75899 "1,2-diacyl-glycerol 3-phosphate + H2O => 1,2-diacyl-glycerol + orthophosphate"
xref: RHEA:27429
+xref: RHEA:41255
+xref: RHEA:42860
+xref: RHEA:43236
+xref: RHEA:43252
+xref: RHEA:43256
+xref: RHEA:43260
+xref: RHEA:43280
+xref: RHEA:43284
+xref: RHEA:43296
is_a: GO:0042577 ! lipid phosphatase activity
property_value: skos:exactMatch EC:3.1.3.4
property_value: skos:exactMatch RHEA:27429
+property_value: skos:narrowMatch RHEA:41255
+property_value: skos:narrowMatch RHEA:42860
+property_value: skos:narrowMatch RHEA:43236
+property_value: skos:narrowMatch RHEA:43252
+property_value: skos:narrowMatch RHEA:43256
+property_value: skos:narrowMatch RHEA:43260
+property_value: skos:narrowMatch RHEA:43280
+property_value: skos:narrowMatch RHEA:43284
+property_value: skos:narrowMatch RHEA:43296
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24252" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25209" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -83585,6 +85116,7 @@
name: ferrous iron binding
namespace: molecular_function
def: "Binding to a ferrous iron ion, Fe(II)." [GOC:ai]
+xref: Reactome:R-HSA-1362416 "Frataxin binds iron"
is_a: GO:0005506 ! iron ion binding
[Term]
@@ -83656,7 +85188,7 @@
id: GO:0008206
name: bile acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:go_curators]
+def: "The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:curators]
synonym: "bile acid metabolism" EXACT []
xref: Reactome:R-HSA-194068 "Bile acid and bile salt metabolism"
is_a: GO:0008202 ! steroid metabolic process
@@ -83728,7 +85260,6 @@
namespace: biological_process
def: "The addition of an alkyl group to a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom." [GOC:ma]
subset: gocheck_obsoletion_candidate
-subset: goslim_yeast
synonym: "protein amino acid alkylation" EXACT [GOC:bf]
is_a: GO:0036211 ! protein modification process
@@ -83817,7 +85348,7 @@
id: GO:0008224
name: obsolete Gram-positive antibacterial peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, Gram-positive bacterial cells." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, Gram-positive bacterial cells." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "Gram-positive antibacterial peptide activity" EXACT []
is_obsolete: true
@@ -83827,7 +85358,7 @@
id: GO:0008225
name: obsolete Gram-negative antibacterial peptide activity
namespace: molecular_function
-def: "OBSOLETE. Inhibits the growth of, or directly kills, Gram-negative bacterial cells." [GOC:go_curators]
+def: "OBSOLETE. Inhibits the growth of, or directly kills, Gram-negative bacterial cells." [GOC:curators]
comment: This term was made obsolete because it describes involvement in a process and not a function.
synonym: "Gram-negative antibacterial peptide activity" EXACT []
is_obsolete: true
@@ -83926,6 +85457,7 @@
xref: Reactome:R-HSA-5684864 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPB"
xref: Reactome:R-HSA-5685902 "NAPSA, CTSH, PGA3-5 cleave pro-SFTPC"
xref: Reactome:R-HSA-6803060 "DCD(63-110) is processed to DCD(63-109)"
+xref: Reactome:R-HSA-9935547 "Lysosomal degradation of ubiqutinated CDH1"
is_a: GO:0016787 ! hydrolase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:3.4.-.-
@@ -83939,7 +85471,7 @@
def: "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE]
synonym: "cysteine protease activity" NARROW []
synonym: "thiol protease activity" NARROW []
-xref: Reactome:R-HSA-2022381 "Cathepsin Z (Cathepsin X) hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
+xref: Reactome:R-HSA-2022381 "Cathepsin Z (Cathepsin X) hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-32) (Angiotensin-(1-8))"
xref: Reactome:R-HSA-2467775 "Autocleavage of ESPL1 (Separase)"
xref: Reactome:R-HSA-2467809 "ESPL1 (Separase) cleaves centromeric cohesin"
xref: Reactome:R-HSA-5660752 "USP9X deubiquitinates Ub-SNCA"
@@ -83961,7 +85493,7 @@
def: "Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine)." [https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE]
synonym: "serine protease activity" NARROW []
xref: Reactome:R-HSA-1461993 "pro-HD5 is cleaved by trypsin"
-xref: Reactome:R-HSA-2022383 "Chymase hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
+xref: Reactome:R-HSA-2022383 "Chymase hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-32) (Angiotensin-(1-8))"
xref: Reactome:R-HSA-3132753 "Pancreatic proteases degrade TCN1:RCbl"
xref: Reactome:R-HSA-6801766 "Trypsin cleaves REG3A or REG3G to generate REG3A,G(38-175)"
xref: Reactome:R-HSA-9839072 "HTRA2 degrades APP (Amyloid-beta precursor protein)"
@@ -83979,10 +85511,10 @@
xref: Reactome:R-HSA-157629 "NOTCH2-ligand complex is cleaved to produce NEXT2"
xref: Reactome:R-HSA-157632 "Complex of NOTCH1 with its ligand is cleaved to produce NEXT1"
xref: Reactome:R-HSA-193679 "alpha-secretase cleaves the p75NTR extracellular domain"
-xref: Reactome:R-HSA-2022368 "MME:Zn2+ (Neprilysin) hydrolyses AGT(34-42)"
-xref: Reactome:R-HSA-2022393 "ANPEP:Zn2+ hydrolyzes Angiotensin-(2-8) to Angiotensin-(3-8)"
-xref: Reactome:R-HSA-2022396 "MME:Zn2+ (Neprilysin) hydrolyses AGT(34-43)"
-xref: Reactome:R-HSA-2022399 "ENPEP:Zn2+ hydrolyzes Angiotensin-(1-8) to Angiotensin-(2-8)"
+xref: Reactome:R-HSA-2022368 "MME:Zn2+ (Neprilysin) hydrolyses AGT(25-33) (Angiotensin-(1-9)) to AGT(25-31) (Angiotensin-(1-7)"
+xref: Reactome:R-HSA-2022393 "ANPEP:Zn2+ hydrolyzes AGT(26-32) (Angiotensin-(2-8)) to AGT(27-32) (Angiotensin-(3-8))"
+xref: Reactome:R-HSA-2022396 "MME:Zn2+ (Neprilysin) hydrolyses AGT(25-34) (Angiotensin-(1-10)) to AGT(25-31) (Angiotensin-(1-7))"
+xref: Reactome:R-HSA-2022399 "ENPEP:Zn2+ hydrolyzes AGT(25-32) (Angiotensin-(1-8)) to AGT(26-32) (Angiotensin-(2-8))"
xref: Reactome:R-HSA-2220944 "ADAM10/17 cleaves ligand-bound NOTCH1 PEST domain mutants to produce NEXT1 PEST domain mutants"
xref: Reactome:R-HSA-2220976 "NOTCH1 HD+PEST domain mutants are cleaved by ADAM10/17 irrespective of ligand binding"
xref: Reactome:R-HSA-2666278 "NOTCH1 t(7;9)(NOTCH1:M1580_K2555) is cleaved to produce NEXT1"
@@ -84079,6 +85611,7 @@
xref: EC:3.4.19.2
xref: MetaCyc:ACYLAMINOACYL-PEPTIDASE-RXN
xref: MetaCyc:PEPTIDYL-GLYCINAMIDASE-RXN
+xref: Reactome:R-HSA-5696365 "ASRGL1 hydrolyses aspartame to L-Asp, L-Phe, MeOH"
is_a: GO:0008233 ! peptidase activity
property_value: skos:exactMatch EC:3.4.19.-
property_value: skos:narrowMatch EC:3.4.19.1
@@ -84123,7 +85656,7 @@
id: GO:0008245
name: obsolete lysosomal membrane hydrogen-transporting ATPase
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "lysosomal membrane hydrogen-transporting ATPase" EXACT []
synonym: "V-ATPase" RELATED []
@@ -84181,7 +85714,7 @@
id: GO:0008251
name: tRNA-specific adenosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine + H2O = inosine + NH3, in a tRNA molecule." [GOC:mah]
+def: "Catalysis of the reaction: adenosine + H2O = inosine + NH4+, in a tRNA molecule." [GOC:mah]
synonym: "tRNA-adenosine deaminase activity" EXACT []
xref: Reactome:R-HSA-6782311 "ADAT2:ADAT3 (hetADAT) deaminates adenosine-34 in tRNAs"
xref: Reactome:R-HSA-6782336 "ADAT1 deaminates adenosine-37 in tRNA(Ala)"
@@ -84244,9 +85777,19 @@
xref: Reactome:R-HSA-8940074 "NT5E:Zn2+ hydrolyses NMN"
xref: Reactome:R-HSA-9755078 "NT5C2 tetramer dephosphorylates RBV-MP"
xref: RHEA:12484
+xref: RHEA:27714
+xref: RHEA:27718
+xref: RHEA:29359
+xref: RHEA:29375
+xref: RHEA:30815
is_a: GO:0008252 ! nucleotidase activity
property_value: skos:exactMatch EC:3.1.3.5
property_value: skos:exactMatch RHEA:12484
+property_value: skos:narrowMatch RHEA:27714
+property_value: skos:narrowMatch RHEA:27718
+property_value: skos:narrowMatch RHEA:29359
+property_value: skos:narrowMatch RHEA:29375
+property_value: skos:narrowMatch RHEA:30815
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -84262,9 +85805,17 @@
xref: EC:3.1.3.6
xref: MetaCyc:3-NUCLEOTID-RXN
xref: RHEA:10144
+xref: RHEA:27862
+xref: RHEA:27890
+xref: RHEA:27894
+xref: RHEA:27898
is_a: GO:0008252 ! nucleotidase activity
property_value: skos:exactMatch EC:3.1.3.6
property_value: skos:exactMatch RHEA:10144
+property_value: skos:narrowMatch RHEA:27862
+property_value: skos:narrowMatch RHEA:27890
+property_value: skos:narrowMatch RHEA:27894
+property_value: skos:narrowMatch RHEA:27898
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -84410,7 +85961,7 @@
id: GO:0008268
name: obsolete receptor signaling protein tyrosine kinase signaling protein activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the meaning of the term is ambiguous and it incorporates process information.
synonym: "receptor signaling protein tyrosine kinase signaling protein activity" EXACT []
synonym: "receptor signalling protein tyrosine kinase signalling protein activity" EXACT []
@@ -84506,7 +86057,7 @@
id: GO:0008277
name: regulation of G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway." [GOC:curators]
synonym: "regulation of G protein coupled receptor protein signaling pathway" EXACT []
synonym: "regulation of G protein coupled receptor protein signalling pathway" EXACT []
synonym: "regulation of G-protein coupled receptor protein signaling pathway" EXACT []
@@ -84588,7 +86139,7 @@
id: GO:0008284
name: positive regulation of cell population proliferation
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of cell proliferation." [GOC:go_curators]
+def: "Any process that activates or increases the rate or extent of cell proliferation." [GOC:curators]
synonym: "activation of cell proliferation" NARROW []
synonym: "positive regulation of cell proliferation" RELATED []
synonym: "stimulation of cell proliferation" NARROW []
@@ -84605,7 +86156,7 @@
id: GO:0008285
name: negative regulation of cell population proliferation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC:go_curators]
+def: "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC:curators]
synonym: "down regulation of cell proliferation" EXACT []
synonym: "down-regulation of cell proliferation" EXACT []
synonym: "downregulation of cell proliferation" EXACT []
@@ -84671,7 +86222,7 @@
id: GO:0008290
name: F-actin capping protein complex
namespace: cellular_component
-def: "A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments." [GOC:go_curators, ISBN:0198599560]
+def: "A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments." [GOC:curators, ISBN:0198599560]
subset: goslim_pir
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0015629 ! actin cytoskeleton
@@ -84700,7 +86251,7 @@
id: GO:0008293
name: torso signaling pathway
namespace: biological_process
-def: "The series of molecular signals initiated by an extracellular ligand binding to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:go_curators, PMID:8343949]
+def: "The series of molecular signals initiated by an extracellular ligand binding to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:curators, PMID:8343949]
synonym: "torso signalling pathway" EXACT []
is_a: GO:0007169 ! cell surface receptor protein tyrosine kinase signaling pathway
@@ -84720,7 +86271,7 @@
id: GO:0008295
name: spermidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:curators, ISBN:0198506732]
synonym: "spermidine anabolism" EXACT []
synonym: "spermidine biosynthesis" EXACT []
synonym: "spermidine formation" EXACT []
@@ -84842,7 +86393,7 @@
id: GO:0008304
name: obsolete eukaryotic translation initiation factor 4 complex
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "eIF-4" EXACT []
synonym: "eukaryotic translation initiation factor 4 complex" EXACT []
@@ -85015,12 +86566,13 @@
[Term]
id: GO:0008320
-name: protein transmembrane transporter activity
+name: transmembrane protein transporter activity
namespace: molecular_function
alt_id: GO:0015266
alt_id: GO:0015463
def: "Enables the transfer of a protein from one side of a membrane to the other." [GOC:jl]
synonym: "protein channel activity" RELATED []
+synonym: "protein transmembrane transporter activity" EXACT []
xref: Reactome:R-HSA-1268022 "TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space"
xref: Reactome:R-HSA-1299475 "TIMM23 PAM translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix"
xref: Reactome:R-HSA-184269 "Monoubiquitinated N-myristoyl GAG polyprotein is targeted to the late endosomal vesicle membrane by the ESCRT-I complex"
@@ -85041,6 +86593,7 @@
xref: Reactome:R-HSA-9636375 "SecA2 transports SapM from cytoplasm to cytosol"
xref: Reactome:R-HSA-9698930 "HCMV C Nucleocapsid Translocation"
xref: Reactome:R-HSA-9698933 "HCMV B Nucleocapsid Translocation"
+xref: Reactome:R-HSA-9760705 "GspD2:GspC2:GspS2 transports LT from periplasmic to extracellular space"
is_a: GO:0022884 ! macromolecule transmembrane transporter activity
is_a: GO:0140318 ! protein transporter activity
relationship: part_of GO:0071806 ! protein transmembrane transport
@@ -85118,6 +86671,7 @@
namespace: biological_process
def: "The directed movement of substances from endosomes to lysosomes." [GOC:ai, ISBN:0716731363]
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016192 ! vesicle-mediated transport
[Term]
@@ -85187,7 +86741,7 @@
id: GO:0008341
name: obsolete response to cocaine (sensu Insecta)
namespace: biological_process
-def: "OBSOLETE. A change in state or activity of a mature individual as the result of a cocaine stimulus. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." [GOC:go_curators, GOC:jid]
+def: "OBSOLETE. A change in state or activity of a mature individual as the result of a cocaine stimulus. As in, but not restricted to, the true insects (Insecta, ncbi_taxonomy_id:50557)." [GOC:curators, GOC:jid]
comment: This term was made obsolete because there is no clear difference between the sensu Insecta term and the generic term.
synonym: "response to cocaine (sensu Insecta)" EXACT []
is_obsolete: true
@@ -85237,7 +86791,7 @@
id: GO:0008346
name: larval walking behavior
namespace: biological_process
-def: "The behavior of a larval organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg." [GOC:go_curators, GOC:pr]
+def: "The behavior of a larval organism relating to the progression of that organism along the ground by the process of lifting and setting down each leg." [GOC:curators, GOC:pr]
synonym: "larval walking behaviour" EXACT []
is_a: GO:0008345 ! larval locomotory behavior
is_a: GO:0090659 ! walking behavior
@@ -85258,7 +86812,7 @@
namespace: biological_process
alt_id: GO:0042154
alt_id: GO:0042155
-def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response." [GOC:curators]
synonym: "attenuation of antimicrobial humoral response" EXACT []
synonym: "down regulation of antimicrobial humoral response" EXACT []
synonym: "down-regulation of antimicrobial humoral response" EXACT []
@@ -85393,7 +86947,7 @@
namespace: biological_process
alt_id: GO:0045788
alt_id: GO:0045789
-def: "Any process that modulates the surface configuration of a cell." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the surface configuration of a cell." [GOC:curators, GOC:dph, GOC:tb]
is_a: GO:0022604 ! regulation of cell morphogenesis
is_a: GO:0065008 ! regulation of biological quality
@@ -85401,7 +86955,7 @@
id: GO:0008361
name: regulation of cell size
namespace: biological_process
-def: "Any process that modulates the size of a cell." [GOC:go_curators]
+def: "Any process that modulates the size of a cell." [GOC:curators]
synonym: "cell size control" EXACT []
is_a: GO:0032535 ! regulation of cellular component size
@@ -85469,7 +87023,7 @@
id: GO:0008369
name: obsolete molecular function
namespace: molecular_function
-def: "OBSOLETE. These are terms that have been removed from the active function ontology." [GOC:go_curators]
+def: "OBSOLETE. These are terms that have been removed from the active function ontology." [GOC:curators]
comment: This term was made obsolete because it is unnecessary in the OBO flat file format.
is_obsolete: true
@@ -85477,7 +87031,7 @@
id: GO:0008370
name: obsolete cellular component
namespace: cellular_component
-def: "OBSOLETE. These are terms that have been removed from the active component ontology." [GOC:go_curators]
+def: "OBSOLETE. These are terms that have been removed from the active component ontology." [GOC:curators]
comment: This term was made obsolete because it is unnecessary in the OBO flat file format.
is_obsolete: true
@@ -85485,7 +87039,7 @@
id: GO:0008371
name: obsolete biological process
namespace: biological_process
-def: "OBSOLETE. These are terms that have been removed from the active process ontology." [GOC:go_curators]
+def: "OBSOLETE. These are terms that have been removed from the active process ontology." [GOC:curators]
comment: This term was made obsolete because it is unnecessary in the OBO flat file format.
is_obsolete: true
@@ -85528,8 +87082,8 @@
namespace: molecular_function
def: "Catalysis of the transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar." [ISBN:0198506732]
synonym: "GlcNAc transferase activity" EXACT []
+xref: Reactome:R-HSA-5617037 "POMGNT1 transfers GlcNAc from UDP-GlcNAc to Man-O-Ser-DAG1"
xref: Reactome:R-HSA-5694487 "A4GNT transfers GlcNAc to core 2 mucins"
-xref: Reactome:R-HSA-8879117 "POMGNT2 transfers GlcNAc to Man-DAG1"
xref: Reactome:R-HSA-9683648 "Spike trimer glycoside chains are extended"
xref: Reactome:R-HSA-9694656 "Spike trimer glycoside chains are extended"
is_a: GO:0008194 ! UDP-glycosyltransferase activity
@@ -85573,7 +87127,7 @@
name: thioredoxin peroxidase activity
namespace: molecular_function
alt_id: GO:0009031
-def: "Catalysis of the reaction: [thioredoxin]-dithiol + hydrogen peroxide = [thioredoxin]-disulfide + H2O." [RHEA:63528]
+def: "Catalysis of the reaction: [thioredoxin]-dithiol + H2O2 = [thioredoxin]-disulfide + H2O." [RHEA:63528]
synonym: "thiol peroxidase activity" EXACT []
synonym: "TPx activity" EXACT []
synonym: "TrxPx activity" EXACT []
@@ -85706,10 +87260,16 @@
namespace: molecular_function
def: "Catalysis of the reaction: reduced [NADPH-hemoprotein reductase] + O2 + a steroid = oxidized [NADPH-hemoprotein reductase] + H2O + H+ + 15alpha-hydroxy steroid." [PMID:2703500, RHEA:83179]
synonym: "cytochrome P450 CYP2A4" NARROW []
+xref: RHEA:83131
+xref: RHEA:83163
+xref: RHEA:83167
xref: RHEA:83179
is_a: GO:0008395 ! steroid hydroxylase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: skos:exactMatch RHEA:83179
+property_value: skos:narrowMatch RHEA:83131
+property_value: skos:narrowMatch RHEA:83163
+property_value: skos:narrowMatch RHEA:83167
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29066" xsd:anyURI
[Term]
@@ -85826,6 +87386,9 @@
xref: KEGG_REACTION:R07204
xref: MetaCyc:1.14.13.95-RXN
xref: MetaCyc:1.14.13.96-RXN
+xref: Reactome:R-HSA-192157 "CYP8B1 12-hydroxylates 4CHOL7aOLONE"
+xref: Reactome:R-HSA-193709 "CYP8B1 12-hydroxylates 4CHOL7a,24(S)DIOL"
+xref: Reactome:R-HSA-193845 "CYP8B1 12-hydroxylates 4CHOL7a,27DONE"
xref: RHEA:15261
xref: RHEA:46752
xref: RHEA:65700
@@ -85857,15 +87420,20 @@
synonym: "sterol 14alpha-demethylase activity" RELATED []
xref: EC:1.14.14.154
xref: MetaCyc:1.14.13.70-RXN
+xref: Reactome:R-HSA-9947148 "CYP51A1 14-demethylates 24,25-dhLAN to 4,4-diMeCholesta-8,14-dien-3-ol"
xref: RHEA:14917
xref: RHEA:25286
+xref: RHEA:45960
xref: RHEA:54028
+xref: RHEA:75439
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
is_a: GO:0032451 ! demethylase activity
property_value: skos:exactMatch EC:1.14.14.154
property_value: skos:exactMatch RHEA:54028
property_value: skos:narrowMatch RHEA:14917
property_value: skos:narrowMatch RHEA:25286
+property_value: skos:narrowMatch RHEA:45960
+property_value: skos:narrowMatch RHEA:75439
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22523" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -85917,9 +87485,13 @@
synonym: "arachidonic acid 14,15-epoxygenase activity" EXACT []
synonym: "cytochrome P450 CYP2C29" NARROW []
synonym: "cytochrome P450 CYP2C39" NARROW []
+xref: RHEA:49856
+xref: RHEA:49860
xref: RHEA:51472
is_a: GO:0008392 ! arachidonate epoxygenase activity
property_value: skos:exactMatch RHEA:51472
+property_value: skos:narrowMatch RHEA:49856
+property_value: skos:narrowMatch RHEA:49860
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -85929,9 +87501,13 @@
def: "Catalysis of an NADPH- and oxygen-dependent reaction that converts arachidonic acid to cis-11,12-epoxyeicosatrienoic acid." [http://lipidlibrary.aocs.org/Lipids/eic_hete/index.htm, PMID:10681399, RHEA:51480]
synonym: "arachidonic acid 11,12-epoxygenase activity" EXACT []
synonym: "cytochrome P450 CYP2C38" NARROW []
+xref: RHEA:49876
+xref: RHEA:49880
xref: RHEA:51480
is_a: GO:0008392 ! arachidonate epoxygenase activity
property_value: skos:exactMatch RHEA:51480
+property_value: skos:narrowMatch RHEA:49876
+property_value: skos:narrowMatch RHEA:49880
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -85949,7 +87525,7 @@
id: GO:0008407
name: chaeta morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the chaeta are generated and organized. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell." [FBbt:00005177, GOC:bf, GOC:cjm, GOC:dos, GOC:go_curators]
+def: "The process in which the anatomical structures of the chaeta are generated and organized. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell." [FBbt:00005177, GOC:bf, GOC:cjm, GOC:curators, GOC:dos]
synonym: "bristle morphogenesis" NARROW [GOC:bf, GOC:dos]
is_a: GO:0009887 ! animal organ morphogenesis
relationship: part_of GO:0022416 ! chaeta development
@@ -86007,11 +87583,22 @@
synonym: "PHB polyprenyl diphosphate transferase activity" EXACT []
xref: EC:2.5.1.39
xref: MetaCyc:RXN-11368
+xref: Reactome:R-HSA-2162192 "COQ2 ligates all-E-10PrP2 to PHB"
+xref: RHEA:17709
+xref: RHEA:27782
xref: RHEA:44504
+xref: RHEA:44556
+xref: RHEA:44560
+xref: RHEA:44564
is_a: GO:0004659 ! prenyltransferase activity
property_value: skos:exactMatch EC:2.5.1.39
property_value: skos:exactMatch MetaCyc:RXN-11368
property_value: skos:exactMatch RHEA:44504
+property_value: skos:narrowMatch RHEA:17709
+property_value: skos:narrowMatch RHEA:27782
+property_value: skos:narrowMatch RHEA:44556
+property_value: skos:narrowMatch RHEA:44560
+property_value: skos:narrowMatch RHEA:44564
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26830" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29264" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29428" xsd:anyURI
@@ -86048,6 +87635,8 @@
def: "Catalysis of the transfer of a fucosyl group to an acceptor molecule, typically another carbohydrate or a lipid." [GOC:ai]
xref: Reactome:R-HSA-9033949 "FUT1 transfers Fuc to Type 2 chains to form H antigen-RBC"
xref: Reactome:R-HSA-9846332 "FUT1,2 transfer fucose to gangliosides"
+xref: Reactome:R-HSA-9935449 "FUT10 O-fucosylates EMI domain-containing proteins"
+xref: Reactome:R-HSA-9935469 "FUT11 O-fucosylates EMI domain-containing proteins"
is_a: GO:0016758 ! hexosyltransferase activity
[Term]
@@ -86193,11 +87782,21 @@
synonym: "ubiquinone biosynthetic process methyltransferase activity" BROAD []
xref: EC:2.1.1.201
xref: Reactome:R-HSA-2162188 "COQ5 methylates MDMQ10H2"
+xref: RHEA:27774
xref: RHEA:28286
+xref: RHEA:44752
+xref: RHEA:44756
+xref: RHEA:44760
+xref: RHEA:44764
is_a: GO:0008169 ! C-methyltransferase activity
relationship: part_of GO:0006744 ! ubiquinone biosynthetic process
property_value: skos:exactMatch EC:2.1.1.201
property_value: skos:exactMatch RHEA:28286
+property_value: skos:narrowMatch RHEA:27774
+property_value: skos:narrowMatch RHEA:44752
+property_value: skos:narrowMatch RHEA:44756
+property_value: skos:narrowMatch RHEA:44760
+property_value: skos:narrowMatch RHEA:44764
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25591" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25682" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29420" xsd:anyURI
@@ -86239,6 +87838,7 @@
name: phosphatidylethanolamine binding
namespace: molecular_function
def: "Binding to a phosphatidylethanolamine, a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine." [ISBN:0198506732]
+xref: Reactome:R-HSA-9842115 "PSAP(195-273) dimer binds PE"
is_a: GO:0005543 ! phospholipid binding
[Term]
@@ -86374,9 +87974,13 @@
xref: Reactome:R-HSA-508473 "methylmalonyl semialdehyde + NADH + H+ <=> beta-hydroxyisobutyrate + NAD+"
xref: Reactome:R-HSA-70885 "beta-hydroxyisobutyrate + NAD+ <=> methylmalonyl semialdehyde + NADH + H+"
xref: RHEA:17681
+xref: RHEA:31275
+xref: RHEA:56972
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.31
property_value: skos:exactMatch RHEA:17681
+property_value: skos:narrowMatch RHEA:31275
+property_value: skos:narrowMatch RHEA:56972
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -86519,7 +88123,7 @@
synonym: "O,N-disulfate O-sulfohydrolase activity" RELATED [EC:3.1.6.14]
xref: EC:3.1.6.14
xref: MetaCyc:3.1.6.14-RXN
-xref: Reactome:R-HSA-1638032 "N-acetylglucosamine 6-sulfatase (GNS) hydrolyses 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of keratan sulfate"
+xref: Reactome:R-HSA-1638032 "GNS:Ca2+ cleaves sulfate from GlcNAc-6-sulfate units of keratan sulfate"
xref: Reactome:R-HSA-2263495 "Defective GNS does not hydrolyse 6-sulfate from GlcNAc6S"
is_a: GO:0008484 ! sulfuric ester hydrolase activity
property_value: skos:exactMatch EC:3.1.6.14
@@ -86566,12 +88170,13 @@
[Term]
id: GO:0008453
-name: alanine-glyoxylate transaminase activity
+name: L-alanine:glyoxylate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine." [EC:2.6.1.44]
+def: "Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine." [RHEA:24248]
synonym: "AGT activity" RELATED [EC:2.6.1.44]
synonym: "alanine--glyoxylate aminotransferase activity" RELATED [EC:2.6.1.44]
synonym: "alanine-glyoxylate aminotransferase activity" EXACT []
+synonym: "alanine-glyoxylate transaminase activity" EXACT []
synonym: "alanine-glyoxylic aminotransferase activity" RELATED [EC:2.6.1.44]
synonym: "L-alanine-glycine transaminase activity" RELATED [EC:2.6.1.44]
synonym: "L-alanine:glyoxylate aminotransferase activity" RELATED [EC:2.6.1.44]
@@ -86580,10 +88185,11 @@
xref: Reactome:R-HSA-389684 "glyoxylate + alanine => glycine + pyruvate [peroxisome]"
xref: Reactome:R-HSA-904864 "Mitochondrial AGXT2 tetramer transaminates glyoxylate and alanine to glycine and pyruvate"
xref: RHEA:24248
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.44
property_value: skos:exactMatch RHEA:24248
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0008454
@@ -86844,7 +88450,7 @@
xref: MetaCyc:2.8.2.29-RXN
xref: MetaCyc:2.8.2.30-RXN
xref: Reactome:R-HSA-2076383 "HS3ST1 sulfates GlcN at C3 in heparan sulfate"
-xref: Reactome:R-HSA-2076611 "HS3STs sulfate GlcN at C3 in heparan sulfate"
+xref: Reactome:R-HSA-2076611 "HS3ST2-6 sulfate GlcN at C3 in heparan sulfate"
xref: RHEA:15461
is_a: GO:0034483 ! heparan sulfate sulfotransferase activity
property_value: skos:exactMatch RHEA:15461
@@ -87033,9 +88639,11 @@
xref: EC:3.2.2.1
xref: MetaCyc:PURINE-NUCLEOSIDASE-RXN
xref: RHEA:23344
+xref: RHEA:30771
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
property_value: skos:exactMatch EC:3.2.2.1
property_value: skos:exactMatch RHEA:23344
+property_value: skos:narrowMatch RHEA:30771
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -87080,12 +88688,16 @@
synonym: "tRNA-guanosine(34) queuine transglycosylase" EXACT [EC:2.4.2.64]
xref: EC:2.4.2.64
xref: MetaCyc:QUEUOSINE-TRNA-RIBOSYLTRANSFERASE-RXN
-xref: Reactome:R-HSA-6782443 "QTRT1:QTRTD1 exchange guanine for queuosine at guanosine-34 of tRNA(Tyr)"
+xref: Reactome:R-HSA-6782443 "QTRT1:QTRTD1 exchanges guanine for queuine at guanosine-34 of tRNA(Asn),tRNA(Asp),tRNA(His),tRNA(Tyr) yielding queuosine-34 tRNA(Asn),tRNA(Asp),tRNA(His),tRNA(Tyr)"
xref: RHEA:16633
+xref: RHEA:78299
+xref: RHEA:78303
is_a: GO:0016763 ! pentosyltransferase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: skos:exactMatch EC:2.4.2.64
property_value: skos:exactMatch RHEA:16633
+property_value: skos:narrowMatch RHEA:78299
+property_value: skos:narrowMatch RHEA:78303
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25797" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -87122,11 +88734,25 @@
synonym: "sphingosine kinase (phosphorylating)" RELATED [EC:2.7.1.91]
xref: EC:2.7.1.91
xref: MetaCyc:SPHINGANINE-KINASE-RXN
+xref: Reactome:R-HSA-5218845 "p-SPHK1 phosphorylates sphingosine to sphingosine 1-phosphate"
+xref: Reactome:R-HSA-9625814 "SPHK1 phosphorylates sphingosine in response to E2 stimulation"
+xref: RHEA:15465
+xref: RHEA:33563
+xref: RHEA:34715
+xref: RHEA:34747
+xref: RHEA:35847
xref: RHEA:51496
+xref: RHEA:63956
is_a: GO:0001727 ! lipid kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.91
property_value: skos:exactMatch RHEA:51496
+property_value: skos:narrowMatch RHEA:15465
+property_value: skos:narrowMatch RHEA:33563
+property_value: skos:narrowMatch RHEA:34715
+property_value: skos:narrowMatch RHEA:34747
+property_value: skos:narrowMatch RHEA:35847
+property_value: skos:narrowMatch RHEA:63956
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -87134,7 +88760,6 @@
name: sulfite oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + O2 + sulfite = H2O2 + H+ + sulfate." [RHEA:24600]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "sulfite:oxygen oxidoreductase activity" RELATED [EC:1.8.3.1]
synonym: "sulphite oxidase activity" EXACT []
xref: EC:1.8.3.1
@@ -87147,8 +88772,8 @@
property_value: skos:exactMatch KEGG_REACTION:R00533
property_value: skos:exactMatch MetaCyc:SULFITE-OXIDASE-RXN
property_value: skos:exactMatch RHEA:24600
-property_value: skos:relatedMatch MetaCyc:PWY-5326
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0008483
@@ -87341,7 +88966,6 @@
synonym: "UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity" EXACT []
xref: EC:2.4.1.86
xref: MetaCyc:2.4.1.86-RXN
-xref: Reactome:R-HSA-914010 "Addition of GlcNAc to the Tn antigen forms a Core 3 glycoprotein"
xref: Reactome:R-HSA-9603989 "B3GALTs transfer Gal to GlcNAc-1,3-Gal-R to form Type 1 chain"
xref: Reactome:R-HSA-9845516 "B3GALT4 transfers Gal to gangliosides"
xref: RHEA:16045
@@ -87387,13 +89011,11 @@
alt_id: GO:0015201
def: "Enables the transfer of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), from one side of a membrane to the other." [GOC:mah]
xref: Reactome:R-HSA-372542 "Loading of dopamine into synaptic veiscles"
-xref: Reactome:R-HSA-379393 "SLC6A3 cotransports DA, Na+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-379393 "SLC6A3 cotransports DA, Na+, Cl- from extracellular region to cytosol"
xref: Reactome:R-HSA-380586 "loading of Serotonin in synaptic vesicles"
xref: Reactome:R-HSA-380620 "Reuptake of serotonin from the synapse"
-xref: Reactome:R-HSA-444160 "VMAT1/2 can mediate the transport of biogenic amines"
xref: Reactome:R-HSA-5660706 "Defective SLC6A3 does not cotransport DA, Na+ from extracellular region to cytosol"
is_a: GO:0022804 ! active transmembrane transporter activity
-relationship: part_of GO:0015844 ! monoamine transport
[Term]
id: GO:0008506
@@ -87504,7 +89126,6 @@
comment: The reason for obsoletion is that this term was an unnecessary and confusing grouping term.
synonym: "organic cation porter activity" RELATED []
synonym: "polyspecific organic cation transmembrane transporter activity" NARROW []
-xref: Reactome:R-HSA-549241 "SLC22A4 cotransports ERGT, Na+ from extracellular region to cytosol"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0015291
@@ -87515,9 +89136,6 @@
namespace: molecular_function
def: "OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai]
comment: he reason for obsoletion is that this term was an unnecessary and confusing grouping term.
-xref: Reactome:R-HSA-2142859 "Growing HA is extruded from the cell by ABCC5"
-xref: Reactome:R-HSA-561041 "OAT1-3 transport organic anions with antiport of dicarboxylic acids"
-xref: Reactome:R-HSA-9794830 "SLC22A8 transports Cipro into renal cell"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0022857
@@ -87551,11 +89169,9 @@
synonym: "folic acid transporter activity" RELATED []
synonym: "vitamin B9 transporter activity" EXACT []
synonym: "vitamin M transporter activity" EXACT []
-xref: Reactome:R-HSA-200646 "Cytosolic folate export across the plasma membrane"
xref: Reactome:R-HSA-200652 "SLC19A1 transports 5-methyl-THF from extracellular region to cytosol"
xref: Reactome:R-HSA-200680 "SLC25A32 transports THF from cytosol to mitochondrial matrix"
xref: Reactome:R-HSA-200720 "SLC25A32 transports THF from mitochondrial matrix to cytosol"
-xref: Reactome:R-HSA-200729 "SLC46A1 transports FOLA from extracellular region to cytosol"
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
@@ -87646,11 +89262,15 @@
[Term]
id: GO:0008525
-name: phosphatidylcholine transporter activity
+name: phosphatidylcholine intramembrane carrier activity
namespace: molecular_function
-def: "Enables the directed movement of phosphatidylcholine into, out of or within a cell, or between cells. Phosphatidylcholine refers to a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline." [GOC:ai, ISBN:0198506732]
+def: "Enables the transport of phosphatidylcholine from a region of a membrane to a different region on the same membrane." [GOC:ai, ISBN:0198506732]
+synonym: "phosphatidylcholine intramembrane transporter activity" BROAD []
synonym: "phosphatidylcholine transmembrane transporter activity" NARROW [GOC:bf, GOC:vw]
-is_a: GO:0005548 ! phospholipid transporter activity
+synonym: "phosphatidylcholine transporter activity" BROAD []
+is_a: GO:0140303 ! intramembrane lipid carrier activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/10882" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
[Term]
id: GO:0008526
@@ -87665,7 +89285,7 @@
xref: Reactome:R-HSA-1483229 "PI:PITPNB is transported from the ER membrane to the Golgi membrane"
xref: Reactome:R-HSA-8869241 "PITPNM1,2,3 exchange PI for PA"
xref: Reactome:R-HSA-8874470 "TNFAIP8 proteins transfer PI(4,5)P2, PI(3,4,5)P3 from cytosolic vesicles to plasma membrane"
-is_a: GO:0120014 ! phospholipid transfer activity
+is_a: GO:0120013 ! lipid transfer activity
relationship: has_part GO:0035091 ! phosphatidylinositol binding
created_by: krc
creation_date: 2017-03-17T04:22:47Z
@@ -87753,12 +89373,17 @@
xref: MetaCyc:2.4.1.149-RXN
xref: MetaCyc:2.4.1.163-RXN
xref: Reactome:R-HSA-2025724 "B3GNT1,2,3,4,7 add GlcNAc to form Keratan-PG"
+xref: Reactome:R-HSA-9931297 "B3GNT3 mediated CD274 glycosylation in Golgi"
xref: RHEA:14389
+xref: RHEA:82955
+xref: RHEA:82971
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.149
property_value: skos:exactMatch MetaCyc:2.4.1.149-RXN
property_value: skos:exactMatch RHEA:14389
property_value: skos:narrowMatch MetaCyc:2.4.1.163-RXN
+property_value: skos:narrowMatch RHEA:82955
+property_value: skos:narrowMatch RHEA:82971
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -87889,7 +89514,7 @@
id: GO:0008544
name: epidermis development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:go_curators, UBERON:0001003]
+def: "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:curators, UBERON:0001003]
synonym: "hypodermis development" RELATED [GOC:kmv, GOC:rk]
is_a: GO:0009888 ! tissue development
@@ -88129,6 +89754,7 @@
xref: EC:7.6.2.2
xref: MetaCyc:3.6.3.44-RXN
xref: Reactome:R-HSA-9757139 "ABCB1,ABCC2 transport ATVs from cytosol to extracellular region"
+xref: Reactome:R-HSA-9911514 "MacA:MacB:TolC transports azithromycin from the cytosol to the periplasm"
xref: RHEA:33147
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -88155,6 +89781,8 @@
synonym: "ATPase-coupled protein transporter activity" EXACT []
xref: EC:7.4.2.8
xref: MetaCyc:3.6.3.50-RXN
+xref: Reactome:R-HSA-9760310 "SecA:SecYEG transports proteins from cytosol to periplasmic space"
+xref: Reactome:R-HSA-9926041 "HlyB:HlyD:TolC transports HlyA from cytosol to periplasm"
is_a: GO:0015450 ! protein-transporting ATPase activity
property_value: skos:exactMatch EC:7.4.2.8
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30815" xsd:anyURI
@@ -88356,7 +89984,7 @@
id: GO:0008582
name: regulation of synaptic assembly at neuromuscular junction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of synaptic assembly at neuromuscular junctions." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of synaptic assembly at neuromuscular junctions." [GOC:curators]
synonym: "regulation of synaptic growth at neuromuscular junction" RELATED []
is_a: GO:0048638 ! regulation of developmental growth
is_a: GO:0051963 ! regulation of synapse assembly
@@ -88420,7 +90048,7 @@
namespace: biological_process
alt_id: GO:0007226
alt_id: GO:0043109
-def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of smoothened signaling." [GOC:curators]
synonym: "regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd]
synonym: "regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd]
synonym: "regulation of smoothened activity" RELATED []
@@ -88436,7 +90064,7 @@
id: GO:0008591
name: regulation of Wnt signaling pathway, calcium modulating pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:curators, GOC:dph, GOC:tb]
synonym: "regulation of frizzled-2 signaling pathway" EXACT []
synonym: "regulation of frizzled-2 signalling pathway" EXACT []
synonym: "regulation of Wnt receptor signaling pathway, calcium modulating pathway" EXACT []
@@ -88450,7 +90078,7 @@
id: GO:0008592
name: regulation of Toll signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the Tl signaling pathway." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the Tl signaling pathway." [GOC:curators]
synonym: "regulation of Tl signaling pathway" EXACT []
synonym: "regulation of Tl signalling pathway" EXACT []
synonym: "regulation of Toll signalling pathway" EXACT []
@@ -88463,7 +90091,7 @@
id: GO:0008593
name: regulation of Notch signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the Notch signaling pathway." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the Notch signaling pathway." [GOC:curators]
synonym: "regulation of N signaling pathway" EXACT []
synonym: "regulation of N signalling pathway" EXACT []
synonym: "regulation of Notch signalling pathway" EXACT []
@@ -88578,16 +90206,18 @@
xref: MetaCyc:ALKYLGLYCERONE-PHOSPHATE-SYNTHASE-RXN
xref: Reactome:R-HSA-390427 "1-palmitoylglycerone phosphate + hexadecanol => O-hexadecylglycerone phosphate + palmitate"
xref: RHEA:36171
+xref: RHEA:40659
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
property_value: skos:exactMatch EC:2.5.1.26
property_value: skos:exactMatch RHEA:36171
+property_value: skos:narrowMatch RHEA:40659
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0008610
name: lipid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:curators]
synonym: "lipid anabolism" EXACT []
synonym: "lipid biosynthesis" EXACT []
synonym: "lipid formation" EXACT []
@@ -88629,11 +90259,13 @@
synonym: "hypusine synthesis from peptidyl-lysine" EXACT []
synonym: "hypusinylation" EXACT []
synonym: "protein hypusination" EXACT []
+xref: MetaCyc:PWY-5905
xref: Reactome:R-HSA-204626 "Hypusine synthesis from eIF5A-lysine"
is_a: GO:0018205 ! peptidyl-lysine modification
is_a: GO:0051604 ! protein maturation
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
[Term]
id: GO:0008613
@@ -88772,7 +90404,7 @@
id: GO:0008630
name: intrinsic apoptotic signaling pathway in response to DNA damage
namespace: biological_process
-def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:curators, GOC:mtg_apoptosis]
synonym: "DNA damage response, signal transduction resulting in induction of apoptosis" RELATED []
is_a: GO:0006974 ! DNA damage response
is_a: GO:0097193 ! intrinsic apoptotic signaling pathway
@@ -88800,7 +90432,7 @@
id: GO:0008634
name: obsolete negative regulation of survival gene product expression
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:dph, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:curators, GOC:dph, GOC:mtg_apoptosis, GOC:tb]
comment: This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
synonym: "down regulation of survival gene product activity" BROAD []
synonym: "down-regulation of survival gene product activity" BROAD []
@@ -88819,7 +90451,6 @@
comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "activation of caspase activity by cytochrome c" NARROW []
synonym: "caspase activation via cytochrome c" EXACT [GOC:dph, GOC:tb]
-xref: Reactome:R-HSA-111459 "Activation of caspases through apoptosome-mediated cleavage"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
@@ -88915,7 +90546,8 @@
id: GO:0008649
name: rRNA methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule." [GOC:mah]
+def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside." [GOC:mah]
+xref: Reactome:R-HSA-9911509 "RMTases methylate 16S ribosomal RNA"
is_a: GO:0008173 ! RNA methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
is_a: GO:0140102 ! catalytic activity, acting on a rRNA
@@ -88923,14 +90555,23 @@
[Term]
id: GO:0008650
-name: rRNA (uridine-2'-O-)-methyltransferase activity
+name: rRNA (uridine-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a uridine in rRNA + S-adenosyl-L-methionine = a 2'-O-methyluridine in rRNA + S-adenosyl-L-homocysteine + H+." [RHEA:54152]
+synonym: "rRNA (uridine-2'-O-)-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-6793127 "MRM2 (FTSJ2) methylates uridine-1369 of 16S rRNA yielding 2'-O-methyluridine"
+xref: RHEA:42720
+xref: RHEA:43092
+xref: RHEA:47760
+xref: RHEA:47764
xref: RHEA:54152
is_a: GO:0016436 ! rRNA (uridine) methyltransferase activity
is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
property_value: skos:exactMatch RHEA:54152
+property_value: skos:narrowMatch RHEA:42720
+property_value: skos:narrowMatch RHEA:43092
+property_value: skos:narrowMatch RHEA:47760
+property_value: skos:narrowMatch RHEA:47764
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29545" xsd:anyURI
@@ -89124,9 +90765,17 @@
xref: EC:3.1.4.16
xref: MetaCyc:CYCPHOSDIESTER-RXN
xref: RHEA:19621
+xref: RHEA:27858
+xref: RHEA:27878
+xref: RHEA:27882
+xref: RHEA:27886
is_a: GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
property_value: skos:exactMatch EC:3.1.4.16
property_value: skos:exactMatch RHEA:19621
+property_value: skos:narrowMatch RHEA:27858
+property_value: skos:narrowMatch RHEA:27878
+property_value: skos:narrowMatch RHEA:27882
+property_value: skos:narrowMatch RHEA:27886
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -89663,10 +91312,20 @@
synonym: "UbiX" RELATED []
xref: EC:4.1.1.98
xref: MetaCyc:RXN-15309
+xref: RHEA:27778
xref: RHEA:41680
+xref: RHEA:44568
+xref: RHEA:44572
+xref: RHEA:44576
+xref: RHEA:44580
is_a: GO:0016831 ! carboxy-lyase activity
property_value: skos:exactMatch EC:4.1.1.98
property_value: skos:exactMatch RHEA:41680
+property_value: skos:narrowMatch RHEA:27778
+property_value: skos:narrowMatch RHEA:44568
+property_value: skos:narrowMatch RHEA:44572
+property_value: skos:narrowMatch RHEA:44576
+property_value: skos:narrowMatch RHEA:44580
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30159" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -89751,10 +91410,12 @@
xref: MetaCyc:4OH2OXOGLUTARALDOL-RXN
xref: Reactome:R-HSA-6784423 "HOGA1 tetramer aldol-cleaves 4-OH-2-oxoglutarate (HOG) to glyoxylate and pyruvate"
xref: RHEA:18169
+xref: RHEA:30687
is_a: GO:0016833 ! oxo-acid-lyase activity
property_value: skos:exactMatch EC:4.1.3.16
property_value: skos:exactMatch RHEA:18169
property_value: skos:narrowMatch MetaCyc:4OH2OXOGLUTARALDOL-RXN
+property_value: skos:narrowMatch RHEA:30687
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28306" xsd:anyURI
[Term]
@@ -89972,11 +91633,13 @@
synonym: "ADP-heptose:LPS heptosyltransferase activity" EXACT [MetaCyc:LIPA-CORESYN-PWY]
xref: EC:2.4.99.24
xref: MetaCyc:RXN-22477
+xref: RHEA:28538
xref: RHEA:74071
is_a: GO:0008920 ! lipopolysaccharide heptosyltransferase activity
property_value: skos:exactMatch EC:2.4.99.24
property_value: skos:exactMatch MetaCyc:RXN-22477
property_value: skos:exactMatch RHEA:74071
+property_value: skos:narrowMatch RHEA:28538
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
[Term]
@@ -90050,16 +91713,26 @@
id: GO:0008718
name: D-amino-acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a D-amino acid + H2O + acceptor = a 2-oxo acid + NH3 + reduced acceptor." [RHEA:18125]
+def: "Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+." [RHEA:18125]
synonym: "D-amino-acid:(acceptor) oxidoreductase (deaminating)" EXACT []
synonym: "D-amino-acid:acceptor oxidoreductase (deaminating)" EXACT []
xref: EC:1.4.5.1
xref: MetaCyc:RXN-11193
xref: RHEA:18125
+xref: RHEA:37219
+xref: RHEA:37255
+xref: RHEA:43572
+xref: RHEA:45996
+xref: RHEA:55948
is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
property_value: skos:exactMatch RHEA:18125
property_value: skos:narrowMatch EC:1.4.5.1
property_value: skos:narrowMatch MetaCyc:RXN-11193
+property_value: skos:narrowMatch RHEA:37219
+property_value: skos:narrowMatch RHEA:37255
+property_value: skos:narrowMatch RHEA:43572
+property_value: skos:narrowMatch RHEA:45996
+property_value: skos:narrowMatch RHEA:55948
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
[Term]
@@ -90100,7 +91773,7 @@
id: GO:0008721
name: D-serine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-serine = pyruvate + NH3." [EC:4.3.1.18]
+def: "Catalysis of the reaction: D-serine = pyruvate + NH4+." [RHEA:13977]
synonym: "D-hydroxy amino acid dehydratase activity" BROAD [EC:4.3.1.18]
synonym: "D-hydroxyaminoacid dehydratase activity" RELATED [EC:4.3.1.18]
synonym: "D-serine ammonia-lyase (pyruvate-forming)" RELATED [EC:4.3.1.18]
@@ -90165,9 +91838,15 @@
xref: EC:1.14.14.5
xref: MetaCyc:RXN0-280
xref: RHEA:23064
+xref: RHEA:29307
+xref: RHEA:29715
+xref: RHEA:29727
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: skos:exactMatch EC:1.14.14.5
property_value: skos:exactMatch RHEA:23064
+property_value: skos:narrowMatch RHEA:29307
+property_value: skos:narrowMatch RHEA:29715
+property_value: skos:narrowMatch RHEA:29727
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -90413,7 +92092,6 @@
xref: EC:1.1.1.103
xref: KEGG_REACTION:R01465
xref: MetaCyc:THREODEHYD-RXN
-xref: Reactome:R-HSA-6798667 "TDH tetramer oxidises L-Thr to 2A-3OB"
xref: RHEA:13161
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.103
@@ -90569,6 +92247,9 @@
xref: MetaCyc:RXN0-271
xref: MetaCyc:RXN0-7385
xref: RHEA:46164
+xref: RHEA:61980
+xref: RHEA:63492
+xref: RHEA:83239
is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity
is_a: GO:0003959 ! NADPH dehydrogenase activity
property_value: skos:exactMatch EC:1.6.5.10
@@ -90576,6 +92257,9 @@
property_value: skos:exactMatch MetaCyc:RXN0-7385
property_value: skos:exactMatch RHEA:46164
property_value: skos:narrowMatch MetaCyc:RXN0-271
+property_value: skos:narrowMatch RHEA:61980
+property_value: skos:narrowMatch RHEA:63492
+property_value: skos:narrowMatch RHEA:83239
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
[Term]
@@ -90613,7 +92297,6 @@
xref: MetaCyc:O-SUCCINYLBENZOATE-COA-LIG-RXN
xref: RHEA:17009
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.26
property_value: skos:exactMatch RHEA:17009
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -91040,10 +92723,12 @@
synonym: "uridine diphosphoacetylglucosamine acyltransferase activity" RELATED [EC:2.3.1.129]
xref: EC:2.3.1.129
xref: MetaCyc:RXN-22480
+xref: RHEA:13925
xref: RHEA:67812
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.129
property_value: skos:exactMatch RHEA:67812
+property_value: skos:narrowMatch RHEA:13925
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30177" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -91080,9 +92765,11 @@
xref: MetaCyc:RXN-9990
xref: Reactome:R-HSA-4084982 "CMAS transfers CMP from CTP to Neu5Ac, forming CMP-Neu5Ac"
xref: RHEA:11344
+xref: RHEA:80843
is_a: GO:0070567 ! cytidylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.43
property_value: skos:exactMatch RHEA:11344
+property_value: skos:narrowMatch RHEA:80843
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -91231,12 +92918,13 @@
[Term]
id: GO:0008791
-name: arginine N-succinyltransferase activity
+name: L-arginine N-succinyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: succinyl-CoA + L-arginine = CoA + N2-succinyl-L-arginine." [EC:2.3.1.109]
+def: "Catalysis of the reaction: succinyl-CoA + L-arginine = N2-succinyl-L-arginine + CoA + H+." [RHEA:15185]
synonym: "AOST activity" RELATED [EC:2.3.1.109]
synonym: "arginine and ornithine N(2)-succinyltransferase activity" RELATED [EC:2.3.1.109]
synonym: "arginine and ornithine N2-succinyltransferase activity" RELATED [EC:2.3.1.109]
+synonym: "arginine N-succinyltransferase activity" BROAD []
synonym: "arginine succinyltransferase activity" RELATED [EC:2.3.1.109]
synonym: "AST activity" RELATED [EC:2.3.1.109]
synonym: "AstA" RELATED [EC:2.3.1.109]
@@ -91246,9 +92934,11 @@
xref: MetaCyc:ARGININE-N-SUCCINYLTRANSFERASE-RXN
xref: RHEA:15185
is_a: GO:0016749 ! N-succinyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.109
property_value: skos:exactMatch RHEA:15185
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0008792
@@ -91270,19 +92960,22 @@
[Term]
id: GO:0008793
-name: aromatic-amino-acid transaminase activity
+name: aromatic-amino-acid:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: an L-alpha aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate." [RHEA:17533]
synonym: "ArAT" RELATED [EC:2.6.1.57]
synonym: "aromatic amino acid aminotransferase activity" EXACT [EC:2.6.1.57]
synonym: "aromatic amino acid transferase activity" EXACT []
synonym: "aromatic aminotransferase activity" EXACT []
+synonym: "aromatic-amino-acid transaminase activity" BROAD []
synonym: "aromatic-amino-acid:2-oxoglutarate aminotransferase activity" EXACT []
+xref: EC:2.6.1.57
xref: MetaCyc:2.6.1.57-RXN
xref: RHEA:17533
-is_a: GO:0008483 ! transaminase activity
-property_value: skos:broadMatch EC:2.6.1.57
+is_a: GO:0140385 ! amino acid transaminase activity
+property_value: skos:exactMatch EC:2.6.1.57
property_value: skos:exactMatch RHEA:17533
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0008794
@@ -91305,7 +92998,7 @@
namespace: molecular_function
alt_id: GO:0008749
alt_id: GO:0016965
-def: "Catalysis of the reaction: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+." [EC:6.3.1.5]
+def: "Catalysis of the reaction: deamido-NAD+ + NH4+ + ATP = AMP + diphosphate + NAD+ + H+." [RHEA:21188]
synonym: "deamido-NAD+:ammonia ligase (AMP-forming)" RELATED [EC:6.3.1.5]
synonym: "diphosphopyridine nucleotide synthetase activity" RELATED [EC:6.3.1.5]
synonym: "NAD synthase (AMP-forming)" EXACT []
@@ -91334,7 +93027,7 @@
id: GO:0008797
name: aspartate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-aspartate = fumarate + NH3." [EC:4.3.1.1]
+def: "Catalysis of the reaction: L-aspartate = fumarate + NH4+." [RHEA:16601]
synonym: "aspartase activity" RELATED [EC:4.3.1.1]
synonym: "fumaric aminase activity" RELATED [EC:4.3.1.1]
synonym: "L-aspartase activity" RELATED [EC:4.3.1.1]
@@ -91358,7 +93051,6 @@
xref: EC:3.4.19.5
xref: MetaCyc:3.4.19.5-RXN
xref: Reactome:R-HSA-5692495 "BACE1 cleaves APP(18-770) to APP(18-671) and APP(672-770)"
-xref: Reactome:R-HSA-5696365 "ASRGL1 hydrolyses aspartame to L-Asp, L-Phe"
is_a: GO:0008242 ! omega peptidase activity
is_a: GO:0070003 ! threonine-type peptidase activity
property_value: skos:exactMatch EC:3.4.19.5
@@ -91382,6 +93074,11 @@
synonym: "penicillinase I, II" RELATED [EC:3.5.2.6]
xref: EC:3.5.2.6
xref: MetaCyc:BETA-LACTAMASE-RXN
+xref: Reactome:R-HSA-9911513 "BlaSHV-12 hydrolyzes ceftriaxone"
+xref: Reactome:R-HSA-9911515 "KPC-2 hydrolyzes cephalothin"
+xref: Reactome:R-HSA-9911518 "OXA-9 hydrolyzes penicillin G"
+xref: Reactome:R-HSA-9911519 "BlaSHV-12 hydrolyzes cephalothin"
+xref: Reactome:R-HSA-9911520 "TEM-1 hydrolyzes penicillin G"
xref: RHEA:20401
is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
property_value: skos:exactMatch EC:3.5.2.6
@@ -91456,7 +93153,7 @@
id: GO:0008804
name: carbamate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + NH3 + CO2 = ADP + carbamoyl phosphate." [EC:2.7.2.2]
+def: "Catalysis of the reaction: hydrogencarbonate + NH4+ + ATP = carbamoyl phosphate + ADP + H2O + H+." [RHEA:10152]
synonym: "ATP:carbamate phosphotransferase activity" RELATED [EC:2.7.2.2]
synonym: "carbamoyl phosphokinase activity" RELATED [EC:2.7.2.2]
synonym: "carbamyl phosphokinase activity" RELATED [EC:2.7.2.2]
@@ -91618,9 +93315,11 @@
xref: MetaCyc:CHD-RXN
xref: Reactome:R-HSA-6797961 "CHDH oxidises Cho to BETALD"
xref: RHEA:17433
+xref: RHEA:33051
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: skos:exactMatch EC:1.1.99.1
property_value: skos:exactMatch RHEA:17433
+property_value: skos:narrowMatch RHEA:33051
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -91913,7 +93612,7 @@
id: GO:0008829
name: dCTP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dCTP + H2O = dUTP + NH3." [EC:3.5.4.13]
+def: "Catalysis of the reaction: dCTP + H2O + H+ = dUTP + NH4+." [RHEA:22680]
synonym: "5-methyl-dCTP deaminase activity" RELATED [EC:3.5.4.13]
synonym: "dCTP aminohydrolase activity" RELATED [EC:3.5.4.13]
synonym: "deoxycytidine triphosphate deaminase activity" RELATED [EC:3.5.4.13]
@@ -92097,7 +93796,7 @@
id: GO:0008838
name: diaminopropionate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,3-diaminopropionate + H2O = pyruvate + 2 NH3." [EC:4.3.1.15]
+def: "Catalysis of the reaction: 2,3-diaminopropanoate + H2O + H+ = pyruvate + 2 NH4+." [EC:4.3.1.15]
synonym: "2,3-diaminopropionate ammonia-lyase (adding H2O; pyruvate-forming)" RELATED [EC:4.3.1.15]
synonym: "2,3-diaminopropionate ammonia-lyase activity" RELATED [EC:4.3.1.15]
synonym: "alpha,beta-diaminopropionate ammonia-lyase activity" RELATED [EC:4.3.1.15]
@@ -92275,6 +93974,7 @@
def: "Catalysis of the reaction: enterobactin + 3 H2O = 3 N-23-dihydroxybenzoyl-L-serine + 3 H+." [MetaCyc:RXN0-1661, PMID:4565531]
synonym: "enterobactin esterase activity" EXACT []
xref: MetaCyc:RXN0-1661
+xref: Reactome:R-HSA-9911599 "Fes hydrolyses ferrienterobactin to DHBS"
xref: RHEA:28018
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
property_value: skos:exactMatch RHEA:28018
@@ -92284,7 +93984,7 @@
id: GO:0008851
name: ethanolamine ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethanolamine = acetaldehyde + NH3." [EC:4.3.1.7]
+def: "Catalysis of the reaction: ethanolamine = acetaldehyde + NH4+." [RHEA:15313]
synonym: "ethanolamine ammonia-lyase (acetaldehyde-forming) activity" RELATED [EC:4.3.1.7]
synonym: "ethanolamine deaminase activity" RELATED [EC:4.3.1.7]
xref: EC:4.3.1.7
@@ -92904,9 +94604,15 @@
xref: Reactome:R-HSA-1483107 "GPETA is hydrolyzed to ETA and G3P by GPCPD1"
xref: Reactome:R-HSA-1483116 "GPCho is hydrolyzed to Cho and G3P by GPCPD1"
xref: RHEA:12969
+xref: RHEA:29319
+xref: RHEA:29875
+xref: RHEA:29907
is_a: GO:0008081 ! phosphoric diester hydrolase activity
property_value: skos:exactMatch EC:3.1.4.46
property_value: skos:exactMatch RHEA:12969
+property_value: skos:narrowMatch RHEA:29319
+property_value: skos:narrowMatch RHEA:29875
+property_value: skos:narrowMatch RHEA:29907
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -92920,15 +94626,17 @@
xref: MetaCyc:AKBLIG-RXN
xref: RHEA:20736
is_a: GO:0016453 ! C-acetyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.29
property_value: skos:exactMatch RHEA:20736
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0008892
name: guanine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanine + H2O = xanthine + NH3." [EC:3.5.4.3]
+def: "Catalysis of the reaction: guanine + H2O + H+ = xanthine + NH4+." [RHEA:14665]
synonym: "GAH activity" RELATED [EC:3.5.4.3]
synonym: "guanase activity" RELATED [EC:3.5.4.3]
synonym: "guanine aminase activity" RELATED [EC:3.5.4.3]
@@ -93020,9 +94728,11 @@
xref: MetaCyc:HOLO-ACP-SYNTH-RXN
xref: Reactome:R-HSA-199202 "Phosphopantetheine conjugation of the ACP domain of FAS"
xref: RHEA:12068
+xref: RHEA:53968
is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
property_value: skos:exactMatch EC:2.7.8.7
property_value: skos:exactMatch RHEA:12068
+property_value: skos:narrowMatch RHEA:53968
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18113" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -93368,11 +95078,13 @@
xref: EC:2.4.1.182
xref: KEGG_REACTION:R04606
xref: MetaCyc:RXN-22484
+xref: RHEA:22668
xref: RHEA:67828
is_a: GO:0008194 ! UDP-glycosyltransferase activity
is_a: GO:0016758 ! hexosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.182
property_value: skos:exactMatch RHEA:67828
+property_value: skos:narrowMatch RHEA:22668
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30154" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -93475,10 +95187,16 @@
xref: EC:6.2.1.20
xref: KEGG_REACTION:R07325
xref: MetaCyc:ACYLACPSYNTH-RXN
+xref: RHEA:10696
xref: RHEA:45588
+xref: RHEA:63628
+xref: RHEA:64888
is_a: GO:0015645 ! fatty acid ligase activity
property_value: skos:exactMatch EC:6.2.1.20
property_value: skos:exactMatch RHEA:45588
+property_value: skos:narrowMatch RHEA:10696
+property_value: skos:narrowMatch RHEA:63628
+property_value: skos:narrowMatch RHEA:64888
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -93510,6 +95228,7 @@
xref: EC:1.1.5.4
xref: MetaCyc:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
xref: MetaCyc:RXNI-3
+xref: RHEA:29083
xref: RHEA:30095
xref: RHEA:46012
is_a: GO:0016615 ! malate dehydrogenase activity
@@ -93518,6 +95237,7 @@
property_value: skos:exactMatch MetaCyc:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
property_value: skos:exactMatch RHEA:46012
property_value: skos:narrowMatch MetaCyc:RXNI-3
+property_value: skos:narrowMatch RHEA:29083
property_value: skos:narrowMatch RHEA:30095
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -93542,16 +95262,15 @@
name: mannitol-1-phosphate 5-dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-mannitol 1-phosphate + NAD+ = D-fructose 6-phosphate + NADH + H+." [EC:1.1.1.17]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
xref: EC:1.1.1.17
xref: MetaCyc:MANNPDEHYDROG-RXN
xref: RHEA:19661
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.17
property_value: skos:exactMatch RHEA:19661
-property_value: skos:relatedMatch MetaCyc:MANNIDEG-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0008927
@@ -94006,6 +95725,7 @@
synonym: "undecaprenyldiphospho-N-acetyl-D-glucosaminyl-(1->4)-(N-acetyl-D-muramoylpentapeptide):undecaprenyldiphospho-(N-acetyl-D-glucosaminyl-(1->4)-N-acetyl-D-muramoylpentapeptide) disaccharidetransferase activity" RELATED [EC:2.4.99.28]
xref: EC:2.4.99.28
xref: MetaCyc:RXN-14712
+xref: Reactome:R-HSA-9911463 "MrcB elongates peptidoglycan"
xref: RHEA:23708
is_a: GO:0016758 ! hexosyltransferase activity
property_value: skos:exactMatch EC:2.4.99.28
@@ -94238,10 +95958,25 @@
xref: Reactome:R-HSA-1482920 "PG is hydrolyzed to 2-acyl LPG by PLA2[14]"
xref: Reactome:R-HSA-1482932 "PI is hydrolyzed to 2-acyl LPI by PLA2[13]"
xref: Reactome:R-HSA-5694485 "ABHD3 hydrolyses LPC(14:0) to 1AGPC"
+xref: Reactome:R-HSA-8869425 "PLA1A hydrolyses PS to 2-acyl LPS"
+xref: RHEA:18689
+xref: RHEA:35263
+xref: RHEA:42212
+xref: RHEA:44408
+xref: RHEA:44648
+xref: RHEA:62032
xref: RHEA:67424
+xref: RHEA:67428
is_a: GO:0140322 ! A1-type glycerophospholipase activity
property_value: skos:exactMatch EC:3.1.1.32
property_value: skos:exactMatch RHEA:67424
+property_value: skos:narrowMatch RHEA:18689
+property_value: skos:narrowMatch RHEA:35263
+property_value: skos:narrowMatch RHEA:42212
+property_value: skos:narrowMatch RHEA:44408
+property_value: skos:narrowMatch RHEA:44648
+property_value: skos:narrowMatch RHEA:62032
+property_value: skos:narrowMatch RHEA:67428
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
[Term]
@@ -94407,11 +96142,11 @@
[Term]
id: GO:0008982
-name: protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+name: protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
namespace: molecular_function
alt_id: GO:0015455
alt_id: GO:0015456
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, PMID:16339738, PMID:31214989]
synonym: "enzyme II of the phosphotransferase system" RELATED []
synonym: "PEP--sugar phosphotransferase enzyme II activity" EXACT []
synonym: "PEP-dependent phosphotransferase enzyme II" RELATED []
@@ -94419,6 +96154,7 @@
synonym: "phosphohistidinoprotein-hexose phosphotransferase activity" RELATED []
synonym: "phosphoprotein factor-hexose phosophotransferase activity" RELATED []
synonym: "phosphotransfer-driven group translocator" BROAD []
+synonym: "protein-N(PI)-phosphohistidine-sugar phosphotransferase activity" RELATED []
synonym: "protein-Np-phosphohistidine-sugar phosphotransferase activity" EXACT []
synonym: "PTS permease activity" RELATED []
synonym: "PTS transporter" RELATED []
@@ -94426,6 +96162,7 @@
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0022804 ! active transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0008983
@@ -94541,10 +96278,14 @@
synonym: "ribosomal ribonucleate adenine 6-methyltransferase activity" RELATED []
synonym: "S-adenosyl-L-methionine:rRNA (adenine-6-N-)-methyltransferase activity" RELATED []
synonym: "S-adenosyl-L-methionine:rRNA (adenine-N6-)-methyltransferase activity" RELATED []
+xref: RHEA:58724
xref: RHEA:58728
+xref: RHEA:62612
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity
property_value: skos:exactMatch RHEA:58728
+property_value: skos:narrowMatch RHEA:58724
+property_value: skos:narrowMatch RHEA:62612
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
[Term]
@@ -94698,12 +96439,16 @@
xref: EC:2.3.1.266
xref: EC:2.3.1.267
xref: MetaCyc:RXN-17860
+xref: RHEA:43752
+xref: RHEA:43756
xref: RHEA:50500
is_a: GO:0004596 ! protein-N-terminal amino-acid acetyltransferase activity
property_value: skos:exactMatch MetaCyc:RXN-17860
property_value: skos:exactMatch RHEA:50500
property_value: skos:narrowMatch EC:2.3.1.266
property_value: skos:narrowMatch EC:2.3.1.267
+property_value: skos:narrowMatch RHEA:43752
+property_value: skos:narrowMatch RHEA:43756
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23472" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27532" xsd:anyURI
@@ -94726,13 +96471,14 @@
[Term]
id: GO:0009001
-name: serine O-acetyltransferase activity
+name: L-serine O-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-serine + acetyl-CoA = O-acetyl-L-serine + CoA." [RHEA:24560]
synonym: "acetyl-CoA:L-serine O-acetyltransferase activity" RELATED [EC:2.3.1.30]
synonym: "L-serine acetyltransferase activity" RELATED [EC:2.3.1.30]
synonym: "SATase activity" RELATED [EC:2.3.1.30]
synonym: "serine acetyltransferase activity" RELATED [EC:2.3.1.30]
+synonym: "serine O-acetyltransferase activity" BROAD []
synonym: "serine transacetylase activity" RELATED [EC:2.3.1.30]
xref: EC:2.3.1.30
xref: KEGG_REACTION:R00586
@@ -94740,9 +96486,11 @@
xref: RHEA:24560
is_a: GO:0016412 ! serine O-acyltransferase activity
is_a: GO:0016413 ! O-acetyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.30
property_value: skos:exactMatch RHEA:24560
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0009002
@@ -95008,12 +96756,13 @@
[Term]
id: GO:0009016
-name: succinyldiaminopimelate transaminase activity
+name: succinyldiaminopimelate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + N-succinyl-LL-2,6-diaminopimelate = L-2-succinylamino-6-oxopimelate + L-glutamate." [EC:2.6.1.17, RHEA:11960]
+def: "Catalysis of the reaction: N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate." [RHEA:11960]
synonym: "N-succinyl-L-2,6-diaminoheptanedioate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.17]
synonym: "N-succinyl-L-diaminopimelic glutamic transaminase activity" RELATED [EC:2.6.1.17]
synonym: "succinyldiaminopimelate aminotransferase activity" EXACT []
+synonym: "succinyldiaminopimelate transaminase activity" EXACT []
synonym: "succinyldiaminopimelate transferase activity" RELATED [EC:2.6.1.17]
xref: EC:2.6.1.17
xref: KEGG_REACTION:R04475
@@ -95023,6 +96772,7 @@
property_value: skos:exactMatch EC:2.6.1.17
property_value: skos:exactMatch RHEA:11960
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0009017
@@ -95108,7 +96858,7 @@
id: GO:0009023
name: obsolete tRNA sulfurtransferase
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: L-cysteine + activated-tRNA = L-serine + tRNA containing a thionucleotide." [EC:2.8.1.4, GOC:go_curators]
+def: "OBSOLETE. Catalysis of the reaction: L-cysteine + activated-tRNA = L-serine + tRNA containing a thionucleotide." [EC:2.8.1.4, GOC:curators]
synonym: "tRNA sulfurtransferase" EXACT []
synonym: "tRNA sulphurtransferase activity" EXACT []
is_obsolete: true
@@ -95221,11 +96971,13 @@
xref: EC:2.7.1.130
xref: KEGG_REACTION:R04657
xref: MetaCyc:RXN-22485
+xref: RHEA:20700
xref: RHEA:67840
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.130
property_value: skos:exactMatch RHEA:67840
+property_value: skos:narrowMatch RHEA:20700
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30158" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -95287,7 +97039,6 @@
name: tryptophanase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-tryptophan + H2O = indole + NH4 + pyruvate." [RHEA:19553]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-tryptophan indole-lyase (deaminating) activity" RELATED [EC:4.1.99.1]
synonym: "L-tryptophan indole-lyase (deaminating; pyruvate forming) activity" RELATED [EC:4.1.99.1]
synonym: "L-tryptophan indole-lyase activity" RELATED [EC:4.1.99.1]
@@ -95305,8 +97056,8 @@
property_value: skos:exactMatch KEGG_REACTION:R00673
property_value: skos:exactMatch MetaCyc:TRYPTOPHAN-RXN
property_value: skos:exactMatch RHEA:19553
-property_value: skos:relatedMatch MetaCyc:TRYPDEG-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0009035
@@ -95371,7 +97122,7 @@
id: GO:0009039
name: urease activity
namespace: molecular_function
-def: "Catalysis of the reaction: urea + H2O = CO2 + 2 NH3." [EC:3.5.1.5, RHEA:20557]
+def: "Catalysis of the reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+." [RHEA:20557]
synonym: "urea amidohydrolase activity" RELATED [EC:3.5.1.5]
xref: EC:3.5.1.5
xref: MetaCyc:UREASE-RXN
@@ -95398,7 +97149,7 @@
id: GO:0009041
name: obsolete UMP/dUMP kinase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP." [GOC:go_curators]
+def: "OBSOLETE. Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP." [GOC:curators]
comment: The reason for obsoletion is that this term was an unnecessary grouping term.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24402" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25991" xsd:anyURI
@@ -95409,23 +97160,25 @@
[Term]
id: GO:0009042
-name: valine-pyruvate transaminase activity
+name: L-valine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-valine + pyruvate = 3-methyl-2-oxobutanoate + L-alanine." [EC:2.6.1.66, RHEA:22912]
+def: "Catalysis of the reaction: L-valine + pyruvate = 3-methyl-2-oxobutanoate + L-alanine." [RHEA:22912]
synonym: "alanine--valine transaminase activity" RELATED [EC:2.6.1.66]
synonym: "alanine-oxoisovalerate aminotransferase activity" RELATED [EC:2.6.1.66]
synonym: "L-valine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.66]
synonym: "transaminase C activity" NARROW [EC:2.6.1.66]
synonym: "valine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.66]
synonym: "valine-pyruvate aminotransferase activity" EXACT []
+synonym: "valine-pyruvate transaminase activity" EXACT []
xref: EC:2.6.1.66
xref: KEGG_REACTION:R01215
xref: MetaCyc:VALINE-PYRUVATE-AMINOTRANSFER-RXN
xref: RHEA:22912
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.66
property_value: skos:exactMatch RHEA:22912
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0009044
@@ -95515,7 +97268,7 @@
id: GO:0009050
name: glycopeptide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycopeptides, a compound in which carbohydrate is covalently attached to an oligopeptide composed of residues of L and/or D-amino acids. The term usually denotes a product of proteolytic degradation of a glycoprotein but includes glycated peptide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of glycopeptides, a compound in which carbohydrate is covalently attached to an oligopeptide composed of residues of L and/or D-amino acids. The term usually denotes a product of proteolytic degradation of a glycoprotein but includes glycated peptide." [GOC:curators, ISBN:0198506732]
synonym: "glycopeptide breakdown" EXACT []
synonym: "glycopeptide catabolism" EXACT []
synonym: "glycopeptide degradation" EXACT []
@@ -95582,7 +97335,6 @@
synonym: "electron donor activity" NARROW []
synonym: "electron transporter activity" RELATED []
xref: Reactome:R-HSA-169260 "Reducing equivalents from beta-oxidation of fatty acids transfer to ETF"
-xref: Reactome:R-HSA-2564826 "4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold"
is_a: GO:0003674 ! molecular_function
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21334" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26572" xsd:anyURI
@@ -95684,7 +97436,6 @@
name: aerobic respiration
namespace: biological_process
def: "The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor." [GOC:das, GOC:jl, ISBN:0140513590]
-xref: MetaCyc:PWY-3781
xref: Wikipedia:Cellular_respiration#Aerobic_respiration
is_a: GO:0045333 ! cellular respiration
@@ -95702,7 +97453,7 @@
id: GO:0009062
name: fatty acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes." [GOC:curators]
synonym: "fatty acid breakdown" EXACT []
synonym: "fatty acid catabolism" EXACT []
synonym: "fatty acid degradation" EXACT []
@@ -95733,7 +97484,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai]
comment: The reason for obsoletion is that this is an unnecessary grouping term.
synonym: "glutamine family amino acid metabolism" EXACT []
-xref: Reactome:R-HSA-8964539 "Glutamate and glutamine metabolism"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
is_obsolete: true
@@ -95756,7 +97506,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine." [GOC:ai]
comment: The reason for obsoletion is that this is an unnecessary grouping term.
synonym: "aspartate family amino acid metabolism" EXACT []
-xref: Reactome:R-HSA-8963693 "Aspartate and asparagine metabolism"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
is_obsolete: true
@@ -95764,16 +97513,15 @@
id: GO:0009067
name: aspartate family amino acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine." [GOC:ai, MetaCyc:PWY0-781]
+def: "The chemical reactions and pathways resulting in the formation of amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine." [GOC:ai]
synonym: "aspartate family amino acid anabolism" EXACT []
synonym: "aspartate family amino acid biosynthesis" EXACT []
synonym: "aspartate family amino acid formation" EXACT []
synonym: "aspartate family amino acid synthesis" EXACT []
-xref: MetaCyc:PWY0-781
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
-property_value: skos:exactMatch MetaCyc:PWY0-781
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009068
@@ -95806,14 +97554,9 @@
synonym: "serine family amino acid biosynthesis" EXACT []
synonym: "serine family amino acid formation" EXACT []
synonym: "serine family amino acid synthesis" EXACT []
-xref: MetaCyc:PWY-6292
-xref: MetaCyc:SER-GLYSYN-PWY
-xref: MetaCyc:SULFATE-CYS-PWY
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
-property_value: skos:narrowMatch MetaCyc:PWY-6292
-property_value: skos:narrowMatch MetaCyc:SER-GLYSYN-PWY
-property_value: skos:narrowMatch MetaCyc:SULFATE-CYS-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009071
@@ -95831,7 +97574,7 @@
id: GO:0009072
name: aromatic amino acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:curators]
synonym: "aromatic amino acid family metabolic process" EXACT []
synonym: "aromatic amino acid family metabolism" EXACT []
xref: Reactome:R-HSA-8963691 "Phenylalanine and tyrosine metabolism"
@@ -95843,7 +97586,7 @@
name: aromatic amino acid family biosynthetic process
namespace: biological_process
alt_id: GO:0016089
-def: "The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:curators]
synonym: "aromatic amino acid family anabolism" EXACT []
synonym: "aromatic amino acid family biosynthesis" EXACT []
synonym: "aromatic amino acid family biosynthetic process, shikimate pathway" RELATED []
@@ -95857,7 +97600,7 @@
id: GO:0009074
name: aromatic amino acid family catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:curators]
synonym: "aromatic amino acid family breakdown" EXACT []
synonym: "aromatic amino acid family catabolism" EXACT []
synonym: "aromatic amino acid family degradation" EXACT []
@@ -95873,7 +97616,6 @@
synonym: "histidine family amino acid metabolic process" EXACT []
synonym: "histidine family amino acid metabolism" EXACT []
is_obsolete: true
-replaced_by: GO:0006547
[Term]
id: GO:0009076
@@ -95909,7 +97651,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving any amino acid that requires pyruvate for its synthesis, e.g. alanine." [GOC:jl]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "pyruvate family amino acid metabolism" EXACT []
-xref: Reactome:R-HSA-8964540 "Alanine metabolism"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
is_obsolete: true
@@ -95977,32 +97718,41 @@
id: GO:0009084
name: L-glutamine family amino acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai, MetaCyc:GLUTAMINE-SYN]
+def: "The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:ai]
synonym: "glutamine family amino acid anabolism" EXACT []
synonym: "glutamine family amino acid biosynthesis" EXACT []
synonym: "glutamine family amino acid formation" EXACT []
synonym: "glutamine family amino acid synthesis" EXACT []
-xref: MetaCyc:GLUTAMINE-SYN
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
-property_value: skos:exactMatch MetaCyc:GLUTAMINE-SYN
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009085
name: L-lysine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-lysine, 2,6-diaminohexanoic acid." [GOC:go_curators, MetaCyc:LYSINE-SYN]
+def: "The chemical reactions and pathways resulting in the formation of L-lysine, 2,6-diaminohexanoic acid." [GOC:curators]
synonym: "lysine anabolism" EXACT []
synonym: "lysine biosynthesis" EXACT []
synonym: "lysine formation" EXACT []
synonym: "lysine synthesis" EXACT []
-xref: MetaCyc:LYSINE-SYN
-is_a: GO:0006553 ! lysine metabolic process
+xref: MetaCyc:DAPLYSINESYN-PWY
+xref: MetaCyc:LYSINE-AMINOAD-PWY
+xref: MetaCyc:PWY-2941
+xref: MetaCyc:PWY-2942
+xref: MetaCyc:PWY-3081
+xref: MetaCyc:PWY-5097
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
-property_value: skos:exactMatch MetaCyc:LYSINE-SYN
+property_value: skos:narrowMatch MetaCyc:DAPLYSINESYN-PWY
+property_value: skos:narrowMatch MetaCyc:LYSINE-AMINOAD-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-2941
+property_value: skos:narrowMatch MetaCyc:PWY-2942
+property_value: skos:narrowMatch MetaCyc:PWY-3081
+property_value: skos:narrowMatch MetaCyc:PWY-5097
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009086
@@ -96022,7 +97772,7 @@
id: GO:0009087
name: L-methionine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of L-methionine." [GOC:curators]
synonym: "methionine breakdown" EXACT []
synonym: "methionine catabolism" EXACT []
synonym: "methionine degradation" EXACT []
@@ -96031,36 +97781,37 @@
xref: MetaCyc:PWY-701
xref: UM-BBD_pathwayID:met
is_a: GO:0000098 ! sulfur amino acid catabolic process
-is_a: GO:0006555 ! methionine metabolic process
+is_a: GO:0006555 ! L-methionine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:METHIONINE-DEG1-PWY
property_value: skos:narrowMatch MetaCyc:PWY-5082
property_value: skos:narrowMatch MetaCyc:PWY-701
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0009088
name: L-threonine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732, MetaCyc:THRESYN-PWY]
+def: "The chemical reactions and pathways resulting in the formation of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins." [GOC:jl, ISBN:0198506732]
synonym: "threonine anabolism" EXACT []
synonym: "threonine biosynthesis" EXACT []
synonym: "threonine formation" EXACT []
synonym: "threonine synthesis" EXACT []
xref: MetaCyc:HOMOSER-THRESYN-PWY
-xref: MetaCyc:THRESYN-PWY
is_a: GO:0006566 ! L-threonine metabolic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:HOMOSER-THRESYN-PWY
-property_value: skos:narrowMatch MetaCyc:THRESYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009089
-name: L-lysine biosynthetic process via diaminopimelate
+name: obsolete L-lysine biosynthetic process via diaminopimelate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "diaminopimelate pathway" EXACT []
synonym: "diaminopimelic acid pathway" EXACT []
synonym: "lysine anabolism via diaminopimelate" EXACT []
@@ -96068,14 +97819,16 @@
synonym: "lysine biosynthetic process via diaminopimelic acid" EXACT []
synonym: "lysine formation via diaminopimelate" EXACT []
synonym: "lysine synthesis via diaminopimelate" EXACT []
-is_a: GO:0009085 ! L-lysine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0009090
name: L-homoserine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid." [GOC:go_curators, ISBN:0198506732, MetaCyc:HOMOSERSYN-PWY]
+def: "The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid." [GOC:curators, ISBN:0198506732, MetaCyc:HOMOSERSYN-PWY]
synonym: "homoserine anabolism" EXACT []
synonym: "homoserine biosynthesis" EXACT []
synonym: "homoserine formation" EXACT []
@@ -96089,17 +97842,17 @@
[Term]
id: GO:0009091
-name: L-homoserine catabolic process
+name: obsolete L-homoserine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of homoserine, alpha-amino-gamma-hydroxybutyric acid." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of homoserine, alpha-amino-gamma-hydroxybutyric acid." [ISBN:0198506732]
+comment: This term was obsoleted because there is no evidence that a specific pathway for L-homoserine degradation exists.
synonym: "homoserine breakdown" EXACT []
synonym: "homoserine catabolism" EXACT []
synonym: "homoserine degradation" EXACT []
-is_a: GO:0009092 ! L-homoserine metabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0009092
@@ -96115,7 +97868,7 @@
id: GO:0009093
name: obsolete cysteine catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:curators]
comment: The reason for obsoletion is that a more specific term has been created.
synonym: "cysteine breakdown" EXACT []
synonym: "cysteine catabolism" EXACT []
@@ -96140,9 +97893,16 @@
synonym: "phenylalanine biosynthetic process" BROAD []
synonym: "phenylalanine biosynthetic process, prephenate pathway" RELATED []
synonym: "phenylalanine biosynthetic process, shikimate pathway" RELATED []
+xref: MetaCyc:PHESYN
+xref: MetaCyc:PWY-3462
+xref: MetaCyc:PWY-7432
is_a: GO:0006558 ! L-phenylalanine metabolic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:1902223 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PHESYN
+property_value: skos:narrowMatch MetaCyc:PWY-3462
+property_value: skos:narrowMatch MetaCyc:PWY-7432
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0009095
@@ -96160,17 +97920,17 @@
[Term]
id: GO:0009097
-name: isoleucine biosynthetic process
+name: obsolete isoleucine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid." [GOC:ai]
+comment: The reason for obsoletion is that more specific terms were created.
synonym: "isoleucine anabolism" EXACT []
synonym: "isoleucine biosynthesis" EXACT []
synonym: "isoleucine formation" EXACT []
synonym: "isoleucine synthesis" EXACT []
-xref: MetaCyc:ILEUSYN-PWY
-is_a: GO:0006549 ! isoleucine metabolic process
-is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
-is_a: GO:1901607 ! alpha-amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30848" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:1901705
[Term]
id: GO:0009098
@@ -96204,14 +97964,14 @@
relationship: has_part GO:0003984 ! acetolactate synthase activity
relationship: has_part GO:0004160 ! dihydroxy-acid dehydratase activity
relationship: has_part GO:0004455 ! ketol-acid reductoisomerase activity
-relationship: has_part GO:0052655 ! L-valine-2-oxoglutarate transaminase activity
+relationship: has_part GO:0052655 ! L-valine:2-oxoglutarate transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28686" xsd:anyURI
[Term]
id: GO:0009100
name: glycoprotein metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:curators, ISBN:0198506732]
subset: goslim_drosophila
synonym: "glycoprotein metabolism" EXACT []
is_a: GO:0019538 ! protein metabolic process
@@ -96345,7 +98105,7 @@
id: GO:0009110
name: vitamin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:curators, ISBN:0198506732]
synonym: "vitamin anabolism" EXACT []
synonym: "vitamin biosynthesis" EXACT []
synonym: "vitamin formation" EXACT []
@@ -96380,13 +98140,13 @@
def: "The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine." [ISBN:0198506732]
synonym: "purine base anabolism" EXACT []
synonym: "purine base biosynthesis" EXACT []
-synonym: "purine base biosynthetic process" EXACT [GOC:go_curators]
+synonym: "purine base biosynthetic process" EXACT [GOC:curators]
synonym: "purine base formation" EXACT []
synonym: "purine base synthesis" EXACT []
-xref: MetaCyc:PWY-841
is_a: GO:0006144 ! purine nucleobase metabolic process
is_a: GO:0046112 ! nucleobase biosynthetic process
is_a: GO:0072522 ! purine-containing compound biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009114
@@ -96406,7 +98166,7 @@
name: xanthine catabolic process
namespace: biological_process
alt_id: GO:0006151
-def: "The chemical reactions and pathways resulting in the breakdown of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:curators]
synonym: "xanthine breakdown" EXACT []
synonym: "xanthine catabolism" EXACT []
synonym: "xanthine degradation" EXACT []
@@ -96437,7 +98197,7 @@
id: GO:0009118
name: regulation of nucleoside metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:curators]
synonym: "regulation of nucleoside metabolism" EXACT []
is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
@@ -96455,17 +98215,19 @@
[Term]
id: GO:0009120
-name: deoxyribonucleoside metabolic process
+name: 2'-deoxyribonucleoside metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside)." [GOC:jl, ISBN:0140512713]
+synonym: "deoxyribonucleoside metabolic process" EXACT []
synonym: "deoxyribonucleoside metabolism" EXACT []
is_a: GO:0009116 ! nucleoside metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0009123
name: nucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside monophosphate metabolism" EXACT []
is_a: GO:0006753 ! nucleoside phosphate metabolic process
@@ -96473,7 +98235,7 @@
id: GO:0009124
name: nucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside monophosphate anabolism" EXACT []
synonym: "nucleoside monophosphate biosynthesis" EXACT []
synonym: "nucleoside monophosphate formation" EXACT []
@@ -96485,7 +98247,7 @@
id: GO:0009125
name: nucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside monophosphate breakdown" EXACT []
synonym: "nucleoside monophosphate catabolism" EXACT []
synonym: "nucleoside monophosphate degradation" EXACT []
@@ -96496,7 +98258,7 @@
id: GO:0009126
name: purine nucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside monophosphate metabolism" EXACT []
is_a: GO:0009123 ! nucleoside monophosphate metabolic process
@@ -96504,7 +98266,7 @@
id: GO:0009127
name: purine nucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside monophosphate anabolism" EXACT []
synonym: "purine nucleoside monophosphate biosynthesis" EXACT []
synonym: "purine nucleoside monophosphate formation" EXACT []
@@ -96516,7 +98278,7 @@
id: GO:0009128
name: purine nucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside monophosphate breakdown" EXACT []
synonym: "purine nucleoside monophosphate catabolism" EXACT []
synonym: "purine nucleoside monophosphate degradation" EXACT []
@@ -96527,7 +98289,7 @@
id: GO:0009129
name: pyrimidine nucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside monophosphate metabolism" EXACT []
is_a: GO:0009123 ! nucleoside monophosphate metabolic process
@@ -96535,7 +98297,7 @@
id: GO:0009130
name: pyrimidine nucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside monophosphate anabolism" EXACT []
synonym: "pyrimidine nucleoside monophosphate biosynthesis" EXACT []
synonym: "pyrimidine nucleoside monophosphate formation" EXACT []
@@ -96547,7 +98309,7 @@
id: GO:0009131
name: pyrimidine nucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside monophosphate breakdown" EXACT []
synonym: "pyrimidine nucleoside monophosphate catabolism" EXACT []
synonym: "pyrimidine nucleoside monophosphate degradation" EXACT []
@@ -96558,7 +98320,7 @@
id: GO:0009132
name: nucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside diphosphate metabolism" EXACT []
is_a: GO:0006753 ! nucleoside phosphate metabolic process
@@ -96566,7 +98328,7 @@
id: GO:0009133
name: nucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside diphosphate anabolism" EXACT []
synonym: "nucleoside diphosphate biosynthesis" EXACT []
synonym: "nucleoside diphosphate formation" EXACT []
@@ -96578,7 +98340,7 @@
id: GO:0009134
name: nucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside diphosphate breakdown" EXACT []
synonym: "nucleoside diphosphate catabolism" EXACT []
synonym: "nucleoside diphosphate degradation" EXACT []
@@ -96589,7 +98351,7 @@
id: GO:0009135
name: purine nucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside diphosphate metabolism" EXACT []
is_a: GO:0009132 ! nucleoside diphosphate metabolic process
@@ -96597,7 +98359,7 @@
id: GO:0009136
name: purine nucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside diphosphate anabolism" EXACT []
synonym: "purine nucleoside diphosphate biosynthesis" EXACT []
synonym: "purine nucleoside diphosphate formation" EXACT []
@@ -96609,7 +98371,7 @@
id: GO:0009137
name: purine nucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside diphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside diphosphate breakdown" EXACT []
synonym: "purine nucleoside diphosphate catabolism" EXACT []
synonym: "purine nucleoside diphosphate degradation" EXACT []
@@ -96620,7 +98382,7 @@
id: GO:0009138
name: pyrimidine nucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside diphosphate metabolism" EXACT []
is_a: GO:0009132 ! nucleoside diphosphate metabolic process
@@ -96628,7 +98390,7 @@
id: GO:0009139
name: pyrimidine nucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside diphosphate anabolism" EXACT []
synonym: "pyrimidine nucleoside diphosphate biosynthesis" EXACT []
synonym: "pyrimidine nucleoside diphosphate formation" EXACT []
@@ -96640,7 +98402,7 @@
id: GO:0009140
name: pyrimidine nucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside diphosphate breakdown" EXACT []
synonym: "pyrimidine nucleoside diphosphate catabolism" EXACT []
synonym: "pyrimidine nucleoside diphosphate degradation" EXACT []
@@ -96651,7 +98413,7 @@
id: GO:0009141
name: nucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside triphosphate metabolism" EXACT []
is_a: GO:0006753 ! nucleoside phosphate metabolic process
@@ -96659,7 +98421,7 @@
id: GO:0009142
name: nucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside triphosphate anabolism" EXACT []
synonym: "nucleoside triphosphate biosynthesis" EXACT []
synonym: "nucleoside triphosphate formation" EXACT []
@@ -96671,7 +98433,7 @@
id: GO:0009143
name: nucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "nucleoside triphosphate breakdown" EXACT []
synonym: "nucleoside triphosphate catabolism" EXACT []
synonym: "nucleoside triphosphate degradation" EXACT []
@@ -96682,7 +98444,7 @@
id: GO:0009144
name: purine nucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside triphosphate metabolism" EXACT []
is_a: GO:0009141 ! nucleoside triphosphate metabolic process
@@ -96690,7 +98452,7 @@
id: GO:0009145
name: purine nucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside triphosphate anabolism" EXACT []
synonym: "purine nucleoside triphosphate biosynthesis" EXACT []
synonym: "purine nucleoside triphosphate formation" EXACT []
@@ -96702,7 +98464,7 @@
id: GO:0009146
name: purine nucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine nucleoside triphosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine nucleoside triphosphate breakdown" EXACT []
synonym: "purine nucleoside triphosphate catabolism" EXACT []
synonym: "purine nucleoside triphosphate degradation" EXACT []
@@ -96713,7 +98475,7 @@
id: GO:0009147
name: pyrimidine nucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside triphosphate metabolism" EXACT []
is_a: GO:0009141 ! nucleoside triphosphate metabolic process
@@ -96721,7 +98483,7 @@
id: GO:0009148
name: pyrimidine nucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside triphosphate anabolism" EXACT []
synonym: "pyrimidine nucleoside triphosphate biosynthesis" EXACT []
synonym: "pyrimidine nucleoside triphosphate formation" EXACT []
@@ -96733,7 +98495,7 @@
id: GO:0009149
name: pyrimidine nucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose or deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine nucleoside triphosphate breakdown" EXACT []
synonym: "pyrimidine nucleoside triphosphate catabolism" EXACT []
synonym: "pyrimidine nucleoside triphosphate degradation" EXACT []
@@ -96744,7 +98506,7 @@
id: GO:0009150
name: purine ribonucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleotide metabolism" EXACT []
is_a: GO:0006163 ! purine nucleotide metabolic process
is_a: GO:0009259 ! ribonucleotide metabolic process
@@ -96753,7 +98515,7 @@
id: GO:0009151
name: purine deoxyribonucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleotide metabolism" EXACT []
is_a: GO:0006163 ! purine nucleotide metabolic process
is_a: GO:0009394 ! 2'-deoxyribonucleotide metabolic process
@@ -96762,7 +98524,7 @@
id: GO:0009152
name: purine ribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleotide anabolism" EXACT []
synonym: "purine ribonucleotide biosynthesis" EXACT []
synonym: "purine ribonucleotide formation" EXACT []
@@ -96775,7 +98537,7 @@
id: GO:0009153
name: purine deoxyribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleotide anabolism" EXACT []
synonym: "purine deoxyribonucleotide biosynthesis" EXACT []
synonym: "purine deoxyribonucleotide formation" EXACT []
@@ -96788,7 +98550,7 @@
id: GO:0009154
name: purine ribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleotide breakdown" EXACT []
synonym: "purine ribonucleotide catabolism" EXACT []
synonym: "purine ribonucleotide degradation" EXACT []
@@ -96800,20 +98562,19 @@
id: GO:0009155
name: purine deoxyribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a purine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleotide breakdown" EXACT []
synonym: "purine deoxyribonucleotide catabolism" EXACT []
synonym: "purine deoxyribonucleotide degradation" EXACT []
is_a: GO:0006195 ! purine nucleotide catabolic process
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
-is_a: GO:0009264 ! deoxyribonucleotide catabolic process
is_a: GO:0046386 ! deoxyribose phosphate catabolic process
[Term]
id: GO:0009156
name: ribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside monophosphate anabolism" EXACT []
synonym: "ribonucleoside monophosphate biosynthesis" EXACT []
synonym: "ribonucleoside monophosphate formation" EXACT []
@@ -96824,7 +98585,7 @@
id: GO:0009157
name: deoxyribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside monophosphate anabolism" EXACT []
synonym: "deoxyribonucleoside monophosphate biosynthesis" EXACT []
synonym: "deoxyribonucleoside monophosphate formation" EXACT []
@@ -96835,7 +98596,7 @@
id: GO:0009158
name: ribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside monophosphate breakdown" EXACT []
synonym: "ribonucleoside monophosphate catabolism" EXACT []
synonym: "ribonucleoside monophosphate degradation" EXACT []
@@ -96845,7 +98606,7 @@
id: GO:0009159
name: deoxyribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside monophosphate breakdown" EXACT []
synonym: "deoxyribonucleoside monophosphate catabolism" EXACT []
synonym: "deoxyribonucleoside monophosphate degradation" EXACT []
@@ -96855,7 +98616,7 @@
id: GO:0009161
name: obsolete ribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "ribonucleoside monophosphate metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -96865,7 +98626,7 @@
id: GO:0009162
name: obsolete deoxyribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "deoxyribonucleoside monophosphate metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -96900,7 +98661,7 @@
id: GO:0009165
name: nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:curators]
synonym: "nucleotide anabolism" EXACT []
synonym: "nucleotide biosynthesis" EXACT []
synonym: "nucleotide formation" EXACT []
@@ -96912,7 +98673,7 @@
id: GO:0009166
name: nucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates)." [GOC:curators]
synonym: "nucleotide breakdown" EXACT []
synonym: "nucleotide catabolism" EXACT []
synonym: "nucleotide degradation" EXACT []
@@ -96923,7 +98684,7 @@
id: GO:0009167
name: purine ribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside monophosphate metabolism" EXACT []
is_a: GO:0009126 ! purine nucleoside monophosphate metabolic process
@@ -96931,7 +98692,7 @@
id: GO:0009168
name: purine ribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside monophosphate anabolism" EXACT []
synonym: "purine ribonucleoside monophosphate biosynthesis" EXACT []
synonym: "purine ribonucleoside monophosphate formation" EXACT []
@@ -96945,7 +98706,7 @@
id: GO:0009169
name: purine ribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside monophosphate breakdown" EXACT []
synonym: "purine ribonucleoside monophosphate catabolism" EXACT []
synonym: "purine ribonucleoside monophosphate degradation" EXACT []
@@ -96957,7 +98718,7 @@
id: GO:0009170
name: purine deoxyribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside monophosphate metabolism" EXACT []
is_a: GO:0009126 ! purine nucleoside monophosphate metabolic process
@@ -96965,7 +98726,7 @@
id: GO:0009171
name: purine deoxyribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside monophosphate anabolism" EXACT []
synonym: "purine deoxyribonucleoside monophosphate biosynthesis" EXACT []
synonym: "purine deoxyribonucleoside monophosphate formation" EXACT []
@@ -96978,7 +98739,7 @@
id: GO:0009172
name: purine deoxyribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside monophosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside monophosphate breakdown" EXACT []
synonym: "purine deoxyribonucleoside monophosphate catabolism" EXACT []
synonym: "purine deoxyribonucleoside monophosphate degradation" EXACT []
@@ -96990,7 +98751,7 @@
id: GO:0009173
name: pyrimidine ribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside monophosphate metabolism" EXACT []
is_a: GO:0009129 ! pyrimidine nucleoside monophosphate metabolic process
@@ -96998,7 +98759,7 @@
id: GO:0009174
name: pyrimidine ribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside monophosphate anabolism" EXACT []
synonym: "pyrimidine ribonucleoside monophosphate biosynthesis" EXACT []
synonym: "pyrimidine ribonucleoside monophosphate formation" EXACT []
@@ -97011,7 +98772,7 @@
id: GO:0009175
name: pyrimidine ribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside monophosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside monophosphate breakdown" EXACT []
synonym: "pyrimidine ribonucleoside monophosphate catabolism" EXACT []
synonym: "pyrimidine ribonucleoside monophosphate degradation" EXACT []
@@ -97023,7 +98784,7 @@
id: GO:0009176
name: pyrimidine deoxyribonucleoside monophosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside monophosphate metabolism" EXACT []
is_a: GO:0009129 ! pyrimidine nucleoside monophosphate metabolic process
@@ -97031,7 +98792,7 @@
id: GO:0009177
name: pyrimidine deoxyribonucleoside monophosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside monophosphate anabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside monophosphate biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleoside monophosphate formation" EXACT []
@@ -97044,7 +98805,7 @@
id: GO:0009178
name: pyrimidine deoxyribonucleoside monophosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxynucleoside monophosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with phosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside monophosphate breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleoside monophosphate catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside monophosphate degradation" EXACT []
@@ -97056,7 +98817,7 @@
id: GO:0009179
name: purine ribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside diphosphate metabolism" EXACT []
is_a: GO:0009135 ! purine nucleoside diphosphate metabolic process
is_a: GO:0009185 ! ribonucleoside diphosphate metabolic process
@@ -97065,7 +98826,7 @@
id: GO:0009180
name: purine ribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside diphosphate anabolism" EXACT []
synonym: "purine ribonucleoside diphosphate biosynthesis" EXACT []
synonym: "purine ribonucleoside diphosphate formation" EXACT []
@@ -97078,7 +98839,7 @@
id: GO:0009181
name: purine ribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside diphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside diphosphate breakdown" EXACT []
synonym: "purine ribonucleoside diphosphate catabolism" EXACT []
synonym: "purine ribonucleoside diphosphate degradation" EXACT []
@@ -97090,7 +98851,7 @@
id: GO:0009182
name: purine deoxyribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside diphosphate metabolism" EXACT []
is_a: GO:0009135 ! purine nucleoside diphosphate metabolic process
@@ -97098,7 +98859,7 @@
id: GO:0009183
name: purine deoxyribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside diphosphate anabolism" EXACT []
synonym: "purine deoxyribonucleoside diphosphate biosynthesis" EXACT []
synonym: "purine deoxyribonucleoside diphosphate formation" EXACT []
@@ -97111,7 +98872,7 @@
id: GO:0009184
name: purine deoxyribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside diphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside diphosphate breakdown" EXACT []
synonym: "purine deoxyribonucleoside diphosphate catabolism" EXACT []
synonym: "purine deoxyribonucleoside diphosphate degradation" EXACT []
@@ -97123,7 +98884,7 @@
id: GO:0009185
name: ribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside diphosphate metabolism" EXACT []
is_a: GO:0009132 ! nucleoside diphosphate metabolic process
@@ -97131,7 +98892,7 @@
id: GO:0009186
name: obsolete deoxyribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "deoxyribonucleoside diphosphate metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -97141,7 +98902,7 @@
id: GO:0009187
name: cyclic nucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:curators, ISBN:0198506732]
synonym: "cyclic nucleotide metabolism" EXACT []
is_a: GO:0009117 ! nucleotide metabolic process
@@ -97149,7 +98910,7 @@
id: GO:0009188
name: ribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside diphosphate anabolism" EXACT []
synonym: "ribonucleoside diphosphate biosynthesis" EXACT []
synonym: "ribonucleoside diphosphate formation" EXACT []
@@ -97161,7 +98922,7 @@
id: GO:0009189
name: deoxyribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside diphosphate anabolism" EXACT []
synonym: "deoxyribonucleoside diphosphate biosynthesis" EXACT []
synonym: "deoxyribonucleoside diphosphate formation" EXACT []
@@ -97172,7 +98933,7 @@
id: GO:0009190
name: cyclic nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:curators, ISBN:0198506732]
synonym: "cyclic nucleotide anabolism" EXACT []
synonym: "cyclic nucleotide biosynthesis" EXACT []
synonym: "cyclic nucleotide formation" EXACT []
@@ -97184,7 +98945,7 @@
id: GO:0009191
name: ribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside diphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside diphosphate breakdown" EXACT []
synonym: "ribonucleoside diphosphate catabolism" EXACT []
synonym: "ribonucleoside diphosphate degradation" EXACT []
@@ -97195,7 +98956,7 @@
id: GO:0009192
name: deoxyribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside diphosphate breakdown" EXACT []
synonym: "deoxyribonucleoside diphosphate catabolism" EXACT []
synonym: "deoxyribonucleoside diphosphate degradation" EXACT []
@@ -97205,7 +98966,7 @@
id: GO:0009193
name: pyrimidine ribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside diphosphate metabolism" EXACT []
is_a: GO:0009138 ! pyrimidine nucleoside diphosphate metabolic process
is_a: GO:0009185 ! ribonucleoside diphosphate metabolic process
@@ -97214,7 +98975,7 @@
id: GO:0009194
name: pyrimidine ribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside diphosphate anabolism" EXACT []
synonym: "pyrimidine ribonucleoside diphosphate biosynthesis" EXACT []
synonym: "pyrimidine ribonucleoside diphosphate formation" EXACT []
@@ -97227,7 +98988,7 @@
id: GO:0009195
name: pyrimidine ribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside diphosphate breakdown" EXACT []
synonym: "pyrimidine ribonucleoside diphosphate catabolism" EXACT []
synonym: "pyrimidine ribonucleoside diphosphate degradation" EXACT []
@@ -97239,7 +99000,7 @@
id: GO:0009196
name: pyrimidine deoxyribonucleoside diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine deoxynucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine deoxynucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside diphosphate metabolism" EXACT []
is_a: GO:0009138 ! pyrimidine nucleoside diphosphate metabolic process
@@ -97247,7 +99008,7 @@
id: GO:0009197
name: pyrimidine deoxyribonucleoside diphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxyribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxyribonucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside diphosphate anabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate formation" EXACT []
@@ -97260,7 +99021,7 @@
id: GO:0009198
name: pyrimidine deoxyribonucleoside diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxynucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxynucleoside diphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with diphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside diphosphate breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate degradation" EXACT []
@@ -97272,7 +99033,7 @@
id: GO:0009199
name: obsolete ribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "ribonucleoside triphosphate metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -97282,7 +99043,7 @@
id: GO:0009200
name: deoxyribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009141 ! nucleoside triphosphate metabolic process
@@ -97290,7 +99051,7 @@
id: GO:0009201
name: ribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside triphosphate anabolism" EXACT []
synonym: "ribonucleoside triphosphate biosynthesis" EXACT []
synonym: "ribonucleoside triphosphate formation" EXACT []
@@ -97301,7 +99062,7 @@
id: GO:0009202
name: deoxyribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside triphosphate anabolism" EXACT []
synonym: "deoxyribonucleoside triphosphate biosynthesis" EXACT []
synonym: "deoxyribonucleoside triphosphate formation" EXACT []
@@ -97313,7 +99074,7 @@
id: GO:0009203
name: ribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleoside triphosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleoside triphosphate breakdown" EXACT []
synonym: "ribonucleoside triphosphate catabolism" EXACT []
synonym: "ribonucleoside triphosphate degradation" EXACT []
@@ -97323,7 +99084,7 @@
id: GO:0009204
name: deoxyribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside triphosphate breakdown" EXACT []
synonym: "deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "deoxyribonucleoside triphosphate degradation" EXACT []
@@ -97334,7 +99095,7 @@
id: GO:0009205
name: purine ribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process
@@ -97342,7 +99103,7 @@
id: GO:0009206
name: purine ribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside triphosphate anabolism" EXACT []
synonym: "purine ribonucleoside triphosphate biosynthesis" EXACT []
synonym: "purine ribonucleoside triphosphate formation" EXACT []
@@ -97355,7 +99116,7 @@
id: GO:0009207
name: purine ribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine ribonucleoside triphosphate breakdown" EXACT []
synonym: "purine ribonucleoside triphosphate catabolism" EXACT []
synonym: "purine ribonucleoside triphosphate degradation" EXACT []
@@ -97367,7 +99128,7 @@
id: GO:0009208
name: pyrimidine ribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009147 ! pyrimidine nucleoside triphosphate metabolic process
@@ -97375,7 +99136,7 @@
id: GO:0009209
name: pyrimidine ribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside triphosphate anabolism" EXACT []
synonym: "pyrimidine ribonucleoside triphosphate biosynthesis" EXACT []
synonym: "pyrimidine ribonucleoside triphosphate formation" EXACT []
@@ -97388,7 +99149,7 @@
id: GO:0009210
name: pyrimidine ribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine ribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleoside triphosphate breakdown" EXACT []
synonym: "pyrimidine ribonucleoside triphosphate catabolism" EXACT []
synonym: "pyrimidine ribonucleoside triphosphate degradation" EXACT []
@@ -97400,7 +99161,7 @@
id: GO:0009211
name: pyrimidine deoxyribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009147 ! pyrimidine nucleoside triphosphate metabolic process
@@ -97408,7 +99169,7 @@
id: GO:0009212
name: pyrimidine deoxyribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside triphosphate anabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate formation" EXACT []
@@ -97420,7 +99181,7 @@
id: GO:0009213
name: pyrimidine deoxyribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of pyrimidine deoxyribonucleoside triphosphate, a compound consisting of a pyrimidine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleoside triphosphate breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside triphosphate degradation" EXACT []
@@ -97431,7 +99192,7 @@
id: GO:0009214
name: cyclic nucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:curators, ISBN:0198506732]
synonym: "cyclic nucleotide breakdown" EXACT []
synonym: "cyclic nucleotide catabolism" EXACT []
synonym: "cyclic nucleotide degradation" EXACT []
@@ -97442,7 +99203,7 @@
id: GO:0009215
name: purine deoxyribonucleoside triphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process
is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
@@ -97451,7 +99212,7 @@
id: GO:0009216
name: purine deoxyribonucleoside triphosphate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside triphosphate anabolism" EXACT []
synonym: "purine deoxyribonucleoside triphosphate biosynthesis" EXACT []
synonym: "purine deoxyribonucleoside triphosphate formation" EXACT []
@@ -97464,7 +99225,7 @@
id: GO:0009217
name: purine deoxyribonucleoside triphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside triphosphate breakdown" EXACT []
synonym: "purine deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "purine deoxyribonucleoside triphosphate degradation" EXACT []
@@ -97476,7 +99237,7 @@
id: GO:0009218
name: pyrimidine ribonucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleotide metabolism" EXACT []
is_a: GO:0006220 ! pyrimidine nucleotide metabolic process
is_a: GO:0009259 ! ribonucleotide metabolic process
@@ -97485,7 +99246,7 @@
id: GO:0009219
name: pyrimidine deoxyribonucleotide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a pyrimidine deoxynucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a pyrimidine deoxynucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleotide metabolism" EXACT []
is_a: GO:0006220 ! pyrimidine nucleotide metabolic process
is_a: GO:0009394 ! 2'-deoxyribonucleotide metabolic process
@@ -97494,7 +99255,7 @@
id: GO:0009220
name: pyrimidine ribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleotide anabolism" EXACT []
synonym: "pyrimidine ribonucleotide biosynthesis" EXACT []
synonym: "pyrimidine ribonucleotide formation" EXACT []
@@ -97508,7 +99269,7 @@
id: GO:0009221
name: pyrimidine deoxyribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a pyrimidine deoxyribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a pyrimidine deoxyribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleotide anabolism" EXACT []
synonym: "pyrimidine deoxyribonucleotide biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleotide formation" EXACT []
@@ -97522,7 +99283,7 @@
id: GO:0009222
name: pyrimidine ribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine ribonucleotide breakdown" EXACT []
synonym: "pyrimidine ribonucleotide catabolism" EXACT []
synonym: "pyrimidine ribonucleotide degradation" EXACT []
@@ -97534,13 +99295,12 @@
id: GO:0009223
name: pyrimidine deoxyribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine deoxyribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a pyrimidine deoxyribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "pyrimidine deoxyribonucleotide breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleotide catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleotide degradation" EXACT []
is_a: GO:0006244 ! pyrimidine nucleotide catabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
-is_a: GO:0009264 ! deoxyribonucleotide catabolic process
is_a: GO:0046386 ! deoxyribose phosphate catabolic process
[Term]
@@ -97605,10 +99365,10 @@
synonym: "thiamine synthesis" EXACT []
synonym: "vitamin B1 biosynthesis" EXACT []
synonym: "vitamin B1 biosynthetic process" EXACT []
-xref: MetaCyc:THISYN-PWY
is_a: GO:0006772 ! thiamine metabolic process
is_a: GO:0034309 ! primary alcohol biosynthetic process
is_a: GO:0042724 ! thiamine-containing compound biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009229
@@ -97658,11 +99418,15 @@
synonym: "vitamin B2 biosynthetic process" EXACT []
synonym: "vitamin G biosynthesis" EXACT []
synonym: "vitamin G biosynthetic process" EXACT []
-xref: MetaCyc:RIBOSYN2-PWY
xref: Wikipedia:Riboflavin
is_a: GO:0006771 ! riboflavin metabolic process
is_a: GO:0042364 ! water-soluble vitamin biosynthetic process
is_a: GO:0042727 ! flavin-containing compound biosynthetic process
+property_value: skos:broadMatch MetaCyc:PWY-616
+property_value: skos:broadMatch MetaCyc:PWY-6168
+property_value: skos:broadMatch MetaCyc:PWY66-366
+property_value: skos:broadMatch MetaCyc:RIBOSYN2-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009232
@@ -97717,7 +99481,7 @@
id: GO:0009235
name: cobalamin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:go_curators]
+def: "The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:curators]
synonym: "cobalamin metabolism" EXACT []
synonym: "vitamin B12 metabolic process" EXACT []
synonym: "vitamin B12 metabolism" EXACT []
@@ -97768,7 +99532,7 @@
namespace: biological_process
alt_id: GO:0031191
alt_id: GO:0031192
-def: "The chemical reactions and pathways resulting in the formation of enterobactin, a catechol-derived siderochrome of Enterobacteria; enterobactin (N',N',N''-(2,6,10-trioxo-1,5,9-triacyclodecane-3,7,11-triyl)tris(2,3-dihydroxy)benzamide) is a self-triester of 2,3-dihydroxy-N-benzoyl-L-serine and a product of the shikimate pathway." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of enterobactin, a catechol-derived siderochrome of Enterobacteria; enterobactin (N',N',N''-(2,6,10-trioxo-1,5,9-triacyclodecane-3,7,11-triyl)tris(2,3-dihydroxy)benzamide) is a self-triester of 2,3-dihydroxy-N-benzoyl-L-serine and a product of the shikimate pathway." [GOC:curators]
synonym: "enterobactin anabolism" EXACT []
synonym: "enterobactin biosynthesis" EXACT []
synonym: "enterobactin biosynthetic process, peptide formation" NARROW []
@@ -97873,12 +99637,11 @@
id: GO:0009247
name: glycolipid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide)." [GOC:curators]
synonym: "glycolipid anabolism" EXACT []
synonym: "glycolipid biosynthesis" EXACT []
synonym: "glycolipid formation" EXACT []
synonym: "glycolipid synthesis" EXACT []
-xref: MetaCyc:PWY-401
is_a: GO:0006664 ! glycolipid metabolic process
is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -97914,7 +99677,7 @@
id: GO:0009250
name: glucan biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues." [GOC:curators]
synonym: "glucan anabolism" EXACT []
synonym: "glucan biosynthesis" EXACT []
synonym: "glucan formation" EXACT []
@@ -97926,7 +99689,7 @@
id: GO:0009251
name: glucan catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues." [GOC:curators]
synonym: "glucan breakdown" EXACT []
synonym: "glucan catabolism" EXACT []
synonym: "glucan degradation" EXACT []
@@ -98037,7 +99800,7 @@
name: ribonucleotide metabolic process
namespace: biological_process
alt_id: GO:0009121
-def: "The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleotide metabolism" EXACT []
is_a: GO:0009117 ! nucleotide metabolic process
is_a: GO:0019693 ! ribose phosphate metabolic process
@@ -98046,7 +99809,7 @@
id: GO:0009260
name: ribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleotide anabolism" EXACT []
synonym: "ribonucleotide biosynthesis" EXACT []
synonym: "ribonucleotide formation" EXACT []
@@ -98059,7 +99822,7 @@
id: GO:0009261
name: ribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a ribonucleotide, a compound consisting of ribonucleoside (a base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators, ISBN:0198506732]
synonym: "ribonucleotide breakdown" EXACT []
synonym: "ribonucleotide catabolism" EXACT []
synonym: "ribonucleotide degradation" EXACT []
@@ -98073,35 +99836,35 @@
namespace: biological_process
alt_id: GO:0009122
alt_id: GO:0009393
-def: "The chemical reactions and pathways involving a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators]
synonym: "deoxyribonucleotide metabolism" EXACT []
-is_a: GO:0009117 ! nucleotide metabolic process
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
+is_a: GO:0008152 ! metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0009263
name: deoxyribonucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators]
synonym: "deoxyribonucleotide anabolism" EXACT []
synonym: "deoxyribonucleotide biosynthesis" EXACT []
synonym: "deoxyribonucleotide formation" EXACT []
synonym: "deoxyribonucleotide synthesis" EXACT []
-is_a: GO:0009165 ! nucleotide biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0009262 ! deoxyribonucleotide metabolic process
-is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0009264
name: deoxyribonucleotide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:curators]
synonym: "deoxyribonucleotide breakdown" EXACT []
synonym: "deoxyribonucleotide catabolism" EXACT []
synonym: "deoxyribonucleotide degradation" EXACT []
-is_a: GO:0009166 ! nucleotide catabolic process
+is_a: GO:0009056 ! catabolic process
is_a: GO:0009262 ! deoxyribonucleotide metabolic process
-is_a: GO:1901136 ! carbohydrate derivative catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0009265
@@ -98112,7 +99875,7 @@
synonym: "2'-deoxyribonucleotide biosynthesis" EXACT []
synonym: "2'-deoxyribonucleotide formation" EXACT []
synonym: "2'-deoxyribonucleotide synthesis" EXACT []
-is_a: GO:0009263 ! deoxyribonucleotide biosynthetic process
+is_a: GO:0009165 ! nucleotide biosynthetic process
is_a: GO:0009394 ! 2'-deoxyribonucleotide metabolic process
is_a: GO:0046385 ! deoxyribose phosphate biosynthetic process
@@ -98167,7 +99930,7 @@
id: GO:0009272
name: fungal-type cell wall biogenesis
namespace: biological_process
-def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a fungal-type cell wall. The fungal-type cell wall contains beta-glucan and may contain chitin." [GOC:go_curators, GOC:mtg_sensu]
+def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a fungal-type cell wall. The fungal-type cell wall contains beta-glucan and may contain chitin." [GOC:curators, GOC:mtg_sensu]
synonym: "chitin- and beta-glucan-containing cell wall biogenesis" NARROW [GOC:mah]
synonym: "fungal-type cell wall anabolism" RELATED [GOC:mah]
synonym: "fungal-type cell wall biosynthetic process" RELATED [GOC:mah]
@@ -98180,7 +99943,7 @@
id: GO:0009273
name: peptidoglycan-based cell wall biogenesis
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli." [GOC:curators]
synonym: "cell envelope biosynthesis" BROAD []
synonym: "cell envelope biosynthetic process" BROAD []
synonym: "cell wall anabolism" BROAD []
@@ -98224,7 +99987,7 @@
id: GO:0009277
name: fungal-type cell wall
namespace: cellular_component
-def: "A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure." [GOC:mcc, GOC:mtg_sensu, ISBN:3540601864, PMID:11283274, PMID:16927300, PMID:3319422]
+def: "A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure." [GOC:mcc, GOC:mtg_sensu, ISBN:3540601864, PMID:11283274, PMID:16927300, PMID:3319422, PMID:36266346]
synonym: "beta-glucan-containing cell wall" RELATED []
synonym: "chitin- and beta-glucan-containing cell wall" NARROW []
synonym: "chitin-containing cell wall" RELATED []
@@ -98250,10 +100013,11 @@
subset: goslim_prokaryote_ribbon
synonym: "outer membrane of cell" EXACT []
is_a: GO:0019867 ! outer membrane
+is_a: GO:0030312 ! external encapsulating structure
intersection_of: GO:0019867 ! outer membrane
intersection_of: part_of GO:0030313 ! cell envelope
-relationship: part_of GO:0030312 ! external encapsulating structure
relationship: part_of GO:0030313 ! cell envelope
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0009280
@@ -98586,7 +100350,7 @@
id: GO:0009315
name: obsolete drug resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "drug resistance" EXACT []
is_obsolete: true
@@ -98815,7 +100579,7 @@
id: GO:0009339
name: glycolate oxidase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and hydrogen peroxide (H2O2). The enzyme is a flavoprotein (FMN)." [PMID:4557653, PMID:8606183]
+def: "An enzyme complex that catalyzes the oxidation of 2-hydroxy acid to form 2-oxo acid and H2O2. The enzyme is a flavoprotein (FMN)." [PMID:4557653, PMID:8606183]
is_a: GO:1990204 ! oxidoreductase complex
relationship: part_of GO:0005737 ! cytoplasm
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21246" xsd:anyURI
@@ -99059,7 +100823,7 @@
id: GO:0009371
name: obsolete positive regulation of transcription by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that activates or increases the rate of transcription." [GOC:curators]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "activation of transcription by pheromones" NARROW []
synonym: "stimulation of transcription by pheromones" NARROW []
@@ -99092,7 +100856,7 @@
id: GO:0009373
name: obsolete regulation of transcription by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent of transcription." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent of transcription." [GOC:curators]
comment: This term has been obsoleted because it represents a GO-CAM model.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12739" xsd:anyURI
is_obsolete: true
@@ -99219,10 +100983,12 @@
xref: Reactome:R-HSA-4085028 "GNE phosphorylates ManNAc to ManNAc-6-P"
xref: Reactome:R-HSA-4088322 "Defective GNE does not phosphorylate ManNAc to ManNAc-6-P"
xref: RHEA:23832
+xref: RHEA:25253
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0019200 ! carbohydrate kinase activity
property_value: skos:exactMatch EC:2.7.1.60
property_value: skos:exactMatch RHEA:23832
+property_value: skos:narrowMatch RHEA:25253
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -99256,10 +101022,18 @@
id: GO:0009389
name: dimethyl sulfoxide reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dimethyl sulfoxide + H+ = dimethyl sulfide + H2O." [PMID:8658134]
+def: "Catalysis of the reaction: dimethyl sulfide + a menaquinone + H2O = dimethyl sulfoxide + a menaquinol." [PMID:8658134, RHEA:28494]
synonym: "dimethyl sulphoxide reductase activity" EXACT []
-is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
+synonym: "respiratory dimethylsulfoxide reductase" EXACT [EC:1.8.5.3]
+xref: EC:1.8.5.3
+xref: MetaCyc:DIMESULFREDUCT-RXN
+xref: RHEA:28494
+is_a: GO:0016672 ! oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor
+property_value: skos:exactMatch EC:1.8.5.3
+property_value: skos:exactMatch MetaCyc:DIMESULFREDUCT-RXN
+property_value: skos:exactMatch RHEA:28494
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28261" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
[Term]
id: GO:0009390
@@ -99284,7 +101058,8 @@
namespace: biological_process
def: "The chemical reactions and pathways involving a 2'-deoxyribonucleotide, a compound consisting of 2'-deoxyribonucleoside (a base linked to a 2'-deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar." [GOC:mah]
synonym: "2'-deoxyribonucleotide metabolism" EXACT []
-is_a: GO:0009262 ! deoxyribonucleotide metabolic process
+is_a: GO:0009117 ! nucleotide metabolic process
+is_a: GO:1901135 ! carbohydrate derivative metabolic process
[Term]
id: GO:0009395
@@ -99364,9 +101139,13 @@
namespace: biological_process
def: "The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into ammonium, which is more biologically available." [PMID:32796519, PMID:36344435]
xref: MetaCyc:N2FIX-PWY
+xref: MetaCyc:PWY-7576
xref: Wikipedia:Nitrogen_fixation
is_a: GO:0071941 ! nitrogen cycle metabolic process
+property_value: skos:narrowMatch MetaCyc:N2FIX-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-7576
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27215" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009400
@@ -99401,7 +101180,7 @@
id: GO:0009403
name: toxin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:curators]
subset: goslim_metagenomics
synonym: "toxin anabolism" EXACT []
synonym: "toxin biosynthesis" EXACT []
@@ -99423,7 +101202,7 @@
id: GO:0009405
name: obsolete pathogenesis
namespace: biological_process
-def: "OBSOLETE. The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism." [GOC:go_curators]
+def: "OBSOLETE. The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism." [GOC:curators]
comment: This term was obsoleted because it does not describe a single, normal biological process; rather it is the effect of an interaction between two organisms, under specific conditions.
synonym: "virulence" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/11057" xsd:anyURI
@@ -99436,7 +101215,7 @@
id: GO:0009406
name: obsolete virulence
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a phenotype rather than a biological process.
synonym: "virulence" EXACT []
is_obsolete: true
@@ -99447,7 +101226,7 @@
id: GO:0009407
name: toxin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism." [GOC:curators]
synonym: "toxin breakdown" EXACT []
synonym: "toxin catabolism" EXACT []
synonym: "toxin degradation" EXACT []
@@ -99546,7 +101325,7 @@
id: GO:0009416
name: response to light stimulus
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:go_curators, ISBN:0582227089]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." [GOC:curators, ISBN:0582227089]
subset: goslim_plant
is_a: GO:0009314 ! response to radiation
@@ -99623,8 +101402,14 @@
synonym: "shikimate pathway" EXACT []
synonym: "shikimate synthesis" RELATED []
xref: MetaCyc:ARO-PWY
+xref: MetaCyc:PWY-6163
+xref: MetaCyc:PWY-6165
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
is_a: GO:0046417 ! chorismate metabolic process
+property_value: skos:narrowMatch MetaCyc:ARO-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6163
+property_value: skos:narrowMatch MetaCyc:PWY-6165
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009424
@@ -99758,10 +101543,13 @@
synonym: "glyoxylate breakdown" EXACT []
synonym: "glyoxylate catabolism" EXACT []
synonym: "glyoxylate degradation" EXACT []
-xref: MetaCyc:GLYOXDEG-PWY
is_a: GO:0046185 ! aldehyde catabolic process
is_a: GO:0046487 ! glyoxylate metabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:broadMatch MetaCyc:GLYCOLATEMET-PWY
+property_value: skos:broadMatch MetaCyc:GLYOXDEG-PWY
+property_value: skos:broadMatch MetaCyc:PWY-8576
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009437
@@ -99811,7 +101599,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving glycolate, the anion of hydroxyethanoic acid (glycolic acid)." [GOC:ai, ISBN:0198506732]
synonym: "glycolate metabolism" EXACT []
-xref: MetaCyc:GLYCOLATEMET-PWY
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
@@ -99833,8 +101620,12 @@
def: "Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis." [GOC:jl]
synonym: "pyridoxal 5' phosphate salvage" EXACT []
xref: MetaCyc:PLPSAL-PWY
-is_a: GO:0042823 ! pyridoxal phosphate biosynthetic process
+xref: MetaCyc:PWY-7204
+is_a: GO:0042823 ! pyridoxal 5'-phosphate biosynthetic process
is_a: GO:0043094 ! metabolic compound salvage
+property_value: skos:narrowMatch MetaCyc:PLPSAL-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-7204
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009444
@@ -99858,7 +101649,7 @@
id: GO:0009446
name: putrescine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane; putrescine can be synthesized from arginine or ornithine and is the metabolic precursor of spermidine and spermine." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane; putrescine can be synthesized from arginine or ornithine and is the metabolic precursor of spermidine and spermine." [GOC:curators, ISBN:0198506732]
synonym: "putrescine anabolism" EXACT []
synonym: "putrescine biosynthesis" EXACT []
synonym: "putrescine formation" EXACT []
@@ -99874,12 +101665,23 @@
synonym: "putrescine breakdown" EXACT []
synonym: "putrescine catabolism" EXACT []
synonym: "putrescine degradation" EXACT []
+xref: MetaCyc:PUTDEG-PWY
+xref: MetaCyc:PWY-0
+xref: MetaCyc:PWY-2
+xref: MetaCyc:PWY-3
+xref: MetaCyc:PWY0-1221
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0009445 ! putrescine metabolic process
+property_value: skos:narrowMatch MetaCyc:PUTDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-0
+property_value: skos:narrowMatch MetaCyc:PWY-2
+property_value: skos:narrowMatch MetaCyc:PWY-3
+property_value: skos:narrowMatch MetaCyc:PWY0-1221
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0009448
-name: gamma-aminobutyric acid metabolic process
+name: GABA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [ISBN:0198506732]
comment: See also the biological process term 'neurotransmitter metabolic process ; GO:0042133'.
@@ -99887,46 +101689,48 @@
synonym: "4-aminobutanoate metabolism" EXACT []
synonym: "4-aminobutyrate metabolic process" EXACT []
synonym: "4-aminobutyrate metabolism" EXACT []
-synonym: "GABA metabolic process" EXACT []
synonym: "GABA metabolism" EXACT []
+synonym: "gamma-aminobutyric acid metabolic process" EXACT []
synonym: "gamma-aminobutyric acid metabolism" EXACT []
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
[Term]
id: GO:0009449
-name: gamma-aminobutyric acid biosynthetic process
+name: GABA biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [GOC:ai]
-comment: See also the biological process term 'neurotransmitter biosynthetic process ; GO:0042136'.
+comment: See also the biological process term 'neurotransmitter biosynthetic process ; GO:0042136' and 'GABA shunt ; GO:0006540'.
synonym: "4-aminobutanoate biosynthesis" EXACT []
synonym: "4-aminobutanoate biosynthetic process" EXACT []
synonym: "4-aminobutyrate biosynthesis" EXACT []
synonym: "4-aminobutyrate biosynthetic process" EXACT []
synonym: "GABA biosynthesis" EXACT []
-synonym: "GABA biosynthetic process" EXACT []
synonym: "gamma-aminobutyric acid anabolism" EXACT []
synonym: "gamma-aminobutyric acid biosynthesis" EXACT []
+synonym: "gamma-aminobutyric acid biosynthetic process" EXACT []
synonym: "gamma-aminobutyric acid formation" EXACT []
synonym: "gamma-aminobutyric acid synthesis" EXACT []
xref: Reactome:R-HSA-888568 "GABA synthesis"
is_a: GO:0008652 ! amino acid biosynthetic process
-is_a: GO:0009448 ! gamma-aminobutyric acid metabolic process
+is_a: GO:0009448 ! GABA metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
[Term]
id: GO:0009450
-name: gamma-aminobutyric acid catabolic process
+name: GABA catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [GOC:ai]
-comment: See also the biological process term 'neurotransmitter catabolic process ; GO:0042135'.
+def: "The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA)." [GOC:curators]
+comment: See also the biological process term 'neurotransmitter catabolic process ; GO:0042135' and 'GABA shunt ; GO:0006540'.
synonym: "4-aminobutanoate catabolic process" EXACT []
synonym: "4-aminobutanoate catabolism" EXACT []
synonym: "4-aminobutyrate catabolic process" EXACT []
synonym: "4-aminobutyrate catabolism" EXACT []
-synonym: "GABA catabolic process" EXACT []
synonym: "GABA catabolism" EXACT []
synonym: "gamma-aminobutyric acid breakdown" EXACT []
+synonym: "gamma-aminobutyric acid catabolic process" EXACT []
synonym: "gamma-aminobutyric acid catabolism" EXACT []
synonym: "gamma-aminobutyric acid degradation" EXACT []
xref: MetaCyc:PWY-5022
@@ -99936,7 +101740,7 @@
xref: MetaCyc:PWY-6537
xref: Reactome:R-HSA-916853 "Degradation of GABA"
is_a: GO:0009063 ! amino acid catabolic process
-is_a: GO:0009448 ! gamma-aminobutyric acid metabolic process
+is_a: GO:0009448 ! GABA metabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:PWY-5022
property_value: skos:narrowMatch MetaCyc:PWY-6473
@@ -99944,13 +101748,15 @@
property_value: skos:narrowMatch MetaCyc:PWY-6536
property_value: skos:narrowMatch MetaCyc:PWY-6537
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
[Term]
id: GO:0009451
name: RNA modification
namespace: biological_process
alt_id: GO:0016547
-def: "The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically." [GOC:go_curators, ISBN:1555811337]
+def: "The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically." [GOC:curators, ISBN:1555811337]
comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing.
subset: goslim_yeast
synonym: "RNA editing" NARROW [GOC:hjd]
@@ -100494,7 +102300,7 @@
id: GO:0009505
name: plant-type cell wall
namespace: cellular_component
-def: "A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances." [ISBN:0471245208]
+def: "A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances." [ISBN:0471245208, PMID:39878232]
synonym: "cellulose and pectin-containing cell wall" EXACT []
synonym: "plant cell wall" NARROW []
is_a: GO:0005618 ! cell wall
@@ -100717,14 +102523,14 @@
id: GO:0009530
name: primary cell wall
namespace: cellular_component
-def: "A plant cell wall that is still able to expand, permitting cell growth. Primary cell walls contain more pectin than secondary walls and no lignin is present." [GOC:jid, PMID:9442872]
+def: "A plant cell wall that is still able to expand, permitting cell growth. Primary cell walls contain more pectin than secondary walls and no lignin is present." [GOC:jid, PMID:39878232, PMID:9442872]
is_a: GO:0009505 ! plant-type cell wall
[Term]
id: GO:0009531
name: secondary cell wall
namespace: cellular_component
-def: "A plant cell wall that is no longer able to expand and so does not permit growth. Secondary cell walls contain less pectin that primary cell walls. The secondary cell is mostly composed of cellulose and is strengthened with lignin." [GOC:jid, ISBN:0943088399]
+def: "A plant cell wall that is no longer able to expand and so does not permit growth. Secondary cell walls contain less pectin that primary cell walls. The secondary cell is mostly composed of cellulose and is strengthened with lignin." [GOC:jid, ISBN:0943088399, PMID:39878232]
xref: Wikipedia:Secondary_cell_wall
is_a: GO:0009505 ! plant-type cell wall
@@ -101024,6 +102830,8 @@
name: fertilization
namespace: biological_process
def: "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:tb, ISBN:0198506732]
+synonym: "cell-cell fusion" RELATED []
+synonym: "https://github.com/geneontology/go-ontology/issues/31270" RELATED []
synonym: "syngamy" EXACT []
xref: Wikipedia:Fertilisation
is_a: GO:0022414 ! reproductive process
@@ -101152,7 +102960,7 @@
id: GO:0009580
name: obsolete thylakoid (sensu Bacteria)
namespace: cellular_component
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific children exist.
synonym: "thylakoid (sensu Bacteria)" EXACT []
is_obsolete: true
@@ -101181,7 +102989,7 @@
id: GO:0009583
name: detection of light stimulus
namespace: biological_process
-def: "The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal." [GOC:go_curators]
+def: "The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal." [GOC:curators]
synonym: "detection of light" EXACT []
synonym: "perception of light" RELATED []
is_a: GO:0009416 ! response to light stimulus
@@ -101192,7 +103000,7 @@
id: GO:0009584
name: detection of visible light
namespace: biological_process
-def: "The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." [GOC:go_curators, ISBN:0198506732]
+def: "The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." [GOC:curators, ISBN:0198506732]
synonym: "perception of visible light" RELATED []
is_a: GO:0009583 ! detection of light stimulus
@@ -101210,7 +103018,7 @@
id: GO:0009587
name: obsolete phototrophin mediated phototransduction
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
synonym: "phototrophin mediated phototransduction" EXACT []
is_obsolete: true
replaced_by: GO:0007602
@@ -101229,7 +103037,7 @@
id: GO:0009589
name: detection of UV
namespace: biological_process
-def: "The series of events in which an ultraviolet radiation (UV light) stimulus is received and converted into a molecular signal. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC:dos, GOC:go_curators, GOC:hb, ISBN:0198506732]
+def: "The series of events in which an ultraviolet radiation (UV light) stimulus is received and converted into a molecular signal. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." [GOC:curators, GOC:dos, GOC:hb, ISBN:0198506732]
synonym: "detection of ultraviolet light stimulus" EXACT []
synonym: "detection of ultraviolet radiation stimulus" EXACT []
synonym: "detection of UV light stimulus" EXACT []
@@ -101419,7 +103227,7 @@
name: response to wounding
namespace: biological_process
alt_id: GO:0002245
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." [GOC:curators]
synonym: "physiological response to wounding" EXACT []
is_a: GO:0006950 ! response to stress
@@ -101437,7 +103245,7 @@
id: GO:0009614
name: obsolete disease resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "disease resistance" EXACT []
is_obsolete: true
@@ -101487,7 +103295,7 @@
id: GO:0009619
name: obsolete resistance to pathogenic bacteria
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "resistance to pathogenic bacteria" EXACT []
is_obsolete: true
@@ -101506,7 +103314,7 @@
id: GO:0009622
name: obsolete resistance to pathogenic fungi
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "resistance to pathogenic fungi" EXACT []
is_obsolete: true
@@ -101593,7 +103401,7 @@
id: GO:0009632
name: obsolete freezing tolerance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'tolerance' implies a phenotype rather than a biological process.
synonym: "freezing tolerance" EXACT []
is_obsolete: true
@@ -101603,7 +103411,7 @@
id: GO:0009633
name: obsolete drought tolerance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'tolerance' implies a phenotype rather than a biological process.
synonym: "drought tolerance" EXACT []
is_obsolete: true
@@ -101614,7 +103422,7 @@
id: GO:0009634
name: obsolete heavy metal sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "heavy metal sensitivity/resistance" EXACT []
is_obsolete: true
@@ -101688,7 +103496,7 @@
id: GO:0009642
name: response to light intensity
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light intensity stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light intensity stimulus." [GOC:curators]
is_a: GO:0009416 ! response to light stimulus
[Term]
@@ -101704,21 +103512,21 @@
id: GO:0009644
name: response to high light intensity
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a high light intensity stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a high light intensity stimulus." [GOC:curators]
is_a: GO:0009642 ! response to light intensity
[Term]
id: GO:0009645
name: response to low light intensity stimulus
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low light intensity stimulus. Low light intensity is defined as a level of electromagnetic radiation at or below 0.1 micromols/m2." [GOC:go_curators, GOC:mtg_far_red]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low light intensity stimulus. Low light intensity is defined as a level of electromagnetic radiation at or below 0.1 micromols/m2." [GOC:curators, GOC:mtg_far_red]
is_a: GO:0009642 ! response to light intensity
[Term]
id: GO:0009646
name: response to absence of light
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an absence of light stimuli." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an absence of light stimuli." [GOC:curators]
synonym: "response to darkness" RELATED []
is_a: GO:0009642 ! response to light intensity
@@ -101785,7 +103593,7 @@
id: GO:0009653
name: anatomical structure morphogenesis
namespace: biological_process
-def: "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125]
+def: "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:curators, ISBN:0521436125]
synonym: "anatomical structure organization" EXACT []
synonym: "embryogenesis and morphogenesis" BROAD []
synonym: "morphogenesis" EXACT []
@@ -102231,8 +104039,14 @@
synonym: "ethylene formation" EXACT []
synonym: "ethylene synthesis" EXACT []
xref: MetaCyc:ETHYL-PWY
+xref: MetaCyc:PWY-6853
+xref: MetaCyc:PWY-6854
is_a: GO:0009692 ! ethylene metabolic process
is_a: GO:0043450 ! alkene biosynthetic process
+property_value: skos:narrowMatch MetaCyc:ETHYL-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6853
+property_value: skos:narrowMatch MetaCyc:PWY-6854
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009694
@@ -102275,10 +104089,16 @@
synonym: "salicylic acid biosynthesis" EXACT []
synonym: "salicylic acid formation" EXACT []
synonym: "salicylic acid synthesis" EXACT []
+xref: MetaCyc:PWY-6406
+xref: MetaCyc:PWY-8321
xref: MetaCyc:PWY-981
is_a: GO:0009696 ! salicylic acid metabolic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-6406
+property_value: skos:narrowMatch MetaCyc:PWY-8321
+property_value: skos:narrowMatch MetaCyc:PWY-981
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009698
@@ -102461,7 +104281,7 @@
id: GO:0009713
name: catechol-containing compound biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." [GOC:curators]
synonym: "catechol anabolism" RELATED []
synonym: "catechol biosynthesis" RELATED []
synonym: "catechol biosynthetic process" RELATED []
@@ -102484,7 +104304,7 @@
id: GO:0009715
name: chalcone biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of chalcone, phenyl steryl ketone or its hydroxylated derivatives." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of chalcone, phenyl steryl ketone or its hydroxylated derivatives." [GOC:curators]
synonym: "chalcone anabolism" EXACT []
synonym: "chalcone biosynthesis" EXACT []
synonym: "chalcone formation" EXACT []
@@ -103174,7 +104994,7 @@
name: embryo development
namespace: biological_process
alt_id: GO:0009795
-def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:curators, GOC:isa_complete, GOC:mtg_sensu]
subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_plant
@@ -103189,7 +105009,7 @@
id: GO:0009791
name: post-embryonic development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." [GOC:curators]
subset: goslim_plant
is_a: GO:0032501 ! multicellular organismal process
relationship: part_of GO:0007275 ! multicellular organism development
@@ -103198,7 +105018,7 @@
id: GO:0009792
name: embryo development ending in birth or egg hatching
namespace: biological_process
-def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:curators, GOC:isa_complete, GOC:mtg_sensu]
synonym: "embryogenesis" BROAD []
is_a: GO:0009790 ! embryo development
@@ -103206,7 +105026,7 @@
id: GO:0009793
name: embryo development ending in seed dormancy
namespace: biological_process
-def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana." [GOC:curators, GOC:mtg_sensu]
synonym: "embryogenesis" BROAD []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0009790 ! embryo development
@@ -103216,7 +105036,7 @@
id: GO:0009794
name: regulation of mitotic cell cycle, embryonic
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of replication and segregation of genetic material in the embryo." [GOC:curators, GOC:dph, GOC:tb]
synonym: "embryonic mitotic cell cycle modulation" EXACT []
synonym: "embryonic mitotic cell cycle regulation" EXACT []
synonym: "embryonic mitotic cell cycle regulator" RELATED []
@@ -103233,7 +105053,7 @@
id: GO:0009798
name: axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of a pattern along a line or around a point." [GOC:dph, GOC:go_curators, GOC:isa_complete]
+def: "The establishment, maintenance and elaboration of a pattern along a line or around a point." [GOC:curators, GOC:dph, GOC:isa_complete]
synonym: "axis determination" RELATED []
is_a: GO:0007389 ! pattern specification process
@@ -103241,7 +105061,7 @@
id: GO:0009799
name: specification of symmetry
namespace: biological_process
-def: "The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created." [GOC:go_curators]
+def: "The establishment of an organism's body plan or part of an organism such that a similar arrangement in form and relationship of parts around a common axis, or around each side of a plane is created." [GOC:curators]
synonym: "determination of symmetry" EXACT [GOC:dph]
is_a: GO:0007389 ! pattern specification process
@@ -103482,8 +105302,11 @@
synonym: "cytokinin breakdown" EXACT []
synonym: "cytokinin catabolism" EXACT []
synonym: "cytokinin degradation" EXACT []
+xref: MetaCyc:PWY-2841
is_a: GO:0009690 ! cytokinin metabolic process
is_a: GO:0042447 ! hormone catabolic process
+property_value: skos:exactMatch MetaCyc:PWY-2841
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0009824
@@ -103589,7 +105412,7 @@
id: GO:0009832
name: plant-type cell wall biogenesis
namespace: biological_process
-def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellulose and pectin-containing cell wall. An example of this is found in Arabidopsis thaliana." [GOC:go_curators, GOC:lr, GOC:mtg_sensu]
+def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellulose and pectin-containing cell wall. An example of this is found in Arabidopsis thaliana." [GOC:curators, GOC:lr, GOC:mtg_sensu]
synonym: "cell wall anabolism" BROAD []
synonym: "cell wall assembly" BROAD []
synonym: "cell wall biosynthetic process" BROAD []
@@ -103767,7 +105590,7 @@
id: GO:0009849
name: tryptophan-independent indoleacetic acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of indoleacetic acid, independent of tryptophan." [GOC:go_curators, GOC:lm, GOC:lr, PMID:10375566]
+def: "The chemical reactions and pathways resulting in the formation of indoleacetic acid, independent of tryptophan." [GOC:curators, GOC:lm, GOC:lr, PMID:10375566]
synonym: "indoleacetic acid biosynthesis, tryptophan-independent" EXACT []
synonym: "indoleacetic acid biosynthetic process, tryptophan-independent" EXACT []
synonym: "tryptophan-independent IAA biosynthetic process" EXACT []
@@ -103816,8 +105639,14 @@
def: "A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria." [ISBN:0198506732]
synonym: "photorespiratory pathway" EXACT [GOC:cjm]
xref: MetaCyc:PWY-181
+xref: MetaCyc:PWY-8362
+xref: MetaCyc:PWY-8363
xref: Wikipedia:Photorespiration
is_a: GO:0043094 ! metabolic compound salvage
+property_value: skos:narrowMatch MetaCyc:PWY-181
+property_value: skos:narrowMatch MetaCyc:PWY-8362
+property_value: skos:narrowMatch MetaCyc:PWY-8363
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0009854
@@ -103831,7 +105660,7 @@
id: GO:0009855
name: determination of bilateral symmetry
namespace: biological_process
-def: "The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:go_curators]
+def: "The establishment of an organism's body plan or part of an organism with respect to a single longitudinal plane. The pattern can either be symmetric, such that the halves are mirror images, or asymmetric where the pattern deviates from this symmetry." [GOC:curators]
synonym: "determination of bilateral asymmetry" EXACT [GOC:dph]
is_a: GO:0009799 ! specification of symmetry
@@ -104067,7 +105896,7 @@
id: GO:0009879
name: determination of radial symmetry
namespace: biological_process
-def: "The establishment of an organism's body plan or a part of an organism such that it is symmetric around a central axis." [GOC:go_curators]
+def: "The establishment of an organism's body plan or a part of an organism such that it is symmetric around a central axis." [GOC:curators]
synonym: "determination of radial asymmetry" EXACT [GOC:dph]
is_a: GO:0009799 ! specification of symmetry
relationship: part_of GO:0009956 ! radial pattern formation
@@ -104076,7 +105905,7 @@
id: GO:0009880
name: embryonic pattern specification
namespace: biological_process
-def: "The process that results in the patterns of cell differentiation that will arise in an embryo." [GOC:go_curators, ISBN:0521436125]
+def: "The process that results in the patterns of cell differentiation that will arise in an embryo." [GOC:curators, ISBN:0521436125]
synonym: "embryonic pattern biosynthesis" BROAD []
synonym: "embryonic pattern formation" BROAD []
synonym: "ventral/lateral system" RELATED []
@@ -104087,7 +105916,7 @@
id: GO:0009881
name: photoreceptor activity
namespace: molecular_function
-def: "The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation." [GOC:ai, GOC:go_curators]
+def: "The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation." [GOC:ai, GOC:curators]
synonym: "blue-sensitive opsin" NARROW []
synonym: "green-sensitive opsin" NARROW []
synonym: "long-wave-sensitive opsin" NARROW []
@@ -104135,7 +105964,7 @@
id: GO:0009886
name: post-embryonic animal morphogenesis
namespace: biological_process
-def: "The process, occurring after animal embryonic development, by which anatomical structures are generated and organized." [GOC:go_curators]
+def: "The process, occurring after animal embryonic development, by which anatomical structures are generated and organized." [GOC:curators]
synonym: "post-embryonic morphogenesis of an anatomical structure" EXACT []
is_a: GO:0009653 ! anatomical structure morphogenesis
relationship: part_of GO:0009791 ! post-embryonic development
@@ -104144,7 +105973,7 @@
id: GO:0009887
name: animal organ morphogenesis
namespace: biological_process
-def: "Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:dgh, GOC:go_curators, ISBN:0471245208, ISBN:0721662544]
+def: "Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:curators, GOC:dgh, ISBN:0471245208, ISBN:0721662544]
synonym: "histogenesis and organogenesis" BROAD []
is_a: GO:0009653 ! anatomical structure morphogenesis
relationship: part_of GO:0048513 ! animal organ development
@@ -104163,7 +105992,7 @@
id: GO:0009889
name: regulation of biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "regulation of anabolism" EXACT []
synonym: "regulation of biosynthesis" EXACT []
@@ -104178,7 +106007,7 @@
id: GO:0009890
name: negative regulation of biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "down regulation of biosynthetic process" EXACT []
synonym: "down-regulation of biosynthetic process" EXACT []
@@ -104199,7 +106028,7 @@
id: GO:0009891
name: positive regulation of biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "activation of biosynthetic process" NARROW []
synonym: "positive regulation of anabolism" EXACT []
@@ -104222,7 +106051,7 @@
name: negative regulation of metabolic process
namespace: biological_process
alt_id: GO:0044252
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "down regulation of metabolic process" EXACT []
synonym: "down-regulation of metabolic process" EXACT []
@@ -104244,7 +106073,7 @@
name: positive regulation of metabolic process
namespace: biological_process
alt_id: GO:0044253
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "activation of metabolic process" NARROW []
synonym: "positive regulation of metabolism" EXACT []
@@ -104256,6 +106085,7 @@
synonym: "up-regulation of metabolic process" EXACT []
synonym: "up-regulation of organismal metabolic process" NARROW []
synonym: "upregulation of metabolic process" EXACT []
+xref: Reactome:R-HSA-163765 "ChREBP activates metabolic gene expression"
is_a: GO:0019222 ! regulation of metabolic process
is_a: GO:0048522 ! positive regulation of cellular process
intersection_of: GO:0065007 ! biological regulation
@@ -104267,7 +106097,7 @@
id: GO:0009894
name: regulation of catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "regulation of breakdown" EXACT []
synonym: "regulation of catabolism" EXACT []
@@ -104281,7 +106111,7 @@
id: GO:0009895
name: negative regulation of catabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:curators]
synonym: "down regulation of catabolic process" EXACT []
synonym: "down-regulation of catabolic process" EXACT []
synonym: "downregulation of catabolic process" EXACT []
@@ -104299,7 +106129,7 @@
id: GO:0009896
name: positive regulation of catabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:curators]
synonym: "activation of catabolic process" NARROW []
synonym: "positive regulation of breakdown" EXACT []
synonym: "positive regulation of catabolism" EXACT []
@@ -104318,24 +106148,26 @@
id: GO:0009897
name: external side of plasma membrane
namespace: cellular_component
-def: "The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:dos, GOC:tb]
+def: "The leaflet of the plasma membrane that faces the extracellular side of the cell, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos, GOC:tb]
synonym: "external leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "juxtamembrane" BROAD []
synonym: "outer surface of cytoplasmic membrane" EXACT []
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0005886 ! plasma membrane
relationship: part_of GO:0009986 ! cell surface
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0009898
name: cytoplasmic side of plasma membrane
namespace: cellular_component
-def: "The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:dos, GOC:tb]
+def: "The leaflet of the plasma membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos, GOC:tb]
synonym: "internal leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "internal side of plasma membrane" EXACT []
synonym: "juxtamembrane" BROAD []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0005886 ! plasma membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0009899
@@ -104419,7 +106251,7 @@
id: GO:0009906
name: response to photoperiod, blue light
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the detection of a blue light photoperiod stimulus. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm." [GOC:go_curators, GOC:mtg_far_red]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the detection of a blue light photoperiod stimulus. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm." [GOC:curators, GOC:mtg_far_red]
is_a: GO:0009637 ! response to blue light
is_a: GO:0009648 ! photoperiodism
@@ -104427,7 +106259,7 @@
id: GO:0009907
name: response to photoperiod, red light
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red light photoperiod stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm." [GOC:go_curators, GOC:mtg_far_red]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a red light photoperiod stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm." [GOC:curators, GOC:mtg_far_red]
is_a: GO:0009648 ! photoperiodism
is_a: GO:0010114 ! response to red light
@@ -104445,7 +106277,7 @@
id: GO:0009909
name: regulation of flower development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of flower development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of flower development." [GOC:curators]
is_a: GO:0048580 ! regulation of post-embryonic development
is_a: GO:0048831 ! regulation of shoot system development
is_a: GO:2000241 ! regulation of reproductive process
@@ -104457,7 +106289,7 @@
id: GO:0009910
name: negative regulation of flower development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of flower development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of flower development." [GOC:curators]
synonym: "down regulation of flower development" EXACT []
synonym: "down-regulation of flower development" EXACT []
synonym: "downregulation of flower development" EXACT []
@@ -104473,7 +106305,7 @@
id: GO:0009911
name: positive regulation of flower development
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of flower development." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of flower development." [GOC:curators]
synonym: "activation of flower development" NARROW []
synonym: "stimulation of flower development" NARROW []
synonym: "up regulation of flower development" EXACT []
@@ -104500,7 +106332,7 @@
name: epidermal cell differentiation
namespace: biological_process
alt_id: GO:0043355
-def: "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." [GOC:dph, GOC:go_curators, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb]
+def: "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." [GOC:curators, GOC:dph, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb]
synonym: "hypodermal cell differentiation" RELATED [GOC:kmv, GOC:rk]
is_a: GO:0030855 ! epithelial cell differentiation
relationship: part_of GO:0008544 ! epidermis development
@@ -104604,9 +106436,63 @@
xref: Reactome:R-HSA-548815 "ELOVL7 elongates ICS-CoA and Mal-CoA to 3ODC-CoA"
xref: Reactome:R-HSA-548830 "ELOVL1,4 elongate TCS-CoA and Mal-CoA to 3OHC-CoA"
xref: RHEA:32727
+xref: RHEA:36515
+xref: RHEA:36519
+xref: RHEA:36531
+xref: RHEA:36807
+xref: RHEA:36819
+xref: RHEA:36843
+xref: RHEA:36851
+xref: RHEA:36859
+xref: RHEA:36871
+xref: RHEA:36875
+xref: RHEA:36907
+xref: RHEA:36911
+xref: RHEA:36915
+xref: RHEA:36919
+xref: RHEA:36923
+xref: RHEA:36927
+xref: RHEA:36943
+xref: RHEA:36947
+xref: RHEA:36963
+xref: RHEA:36967
+xref: RHEA:36979
+xref: RHEA:36983
+xref: RHEA:36995
+xref: RHEA:37095
+xref: RHEA:37243
+xref: RHEA:39291
+xref: RHEA:85827
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.199
property_value: skos:exactMatch RHEA:32727
+property_value: skos:narrowMatch RHEA:36515
+property_value: skos:narrowMatch RHEA:36519
+property_value: skos:narrowMatch RHEA:36531
+property_value: skos:narrowMatch RHEA:36807
+property_value: skos:narrowMatch RHEA:36819
+property_value: skos:narrowMatch RHEA:36843
+property_value: skos:narrowMatch RHEA:36851
+property_value: skos:narrowMatch RHEA:36859
+property_value: skos:narrowMatch RHEA:36871
+property_value: skos:narrowMatch RHEA:36875
+property_value: skos:narrowMatch RHEA:36907
+property_value: skos:narrowMatch RHEA:36911
+property_value: skos:narrowMatch RHEA:36915
+property_value: skos:narrowMatch RHEA:36919
+property_value: skos:narrowMatch RHEA:36923
+property_value: skos:narrowMatch RHEA:36927
+property_value: skos:narrowMatch RHEA:36943
+property_value: skos:narrowMatch RHEA:36947
+property_value: skos:narrowMatch RHEA:36963
+property_value: skos:narrowMatch RHEA:36967
+property_value: skos:narrowMatch RHEA:36979
+property_value: skos:narrowMatch RHEA:36983
+property_value: skos:narrowMatch RHEA:36995
+property_value: skos:narrowMatch RHEA:37095
+property_value: skos:narrowMatch RHEA:37243
+property_value: skos:narrowMatch RHEA:39291
+property_value: skos:narrowMatch RHEA:85827
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24752" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25805" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -104636,7 +106522,7 @@
id: GO:0009925
name: basal plasma membrane
namespace: cellular_component
-def: "The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:go_curators]
+def: "The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:curators]
is_a: GO:0098590 ! plasma membrane region
relationship: part_of GO:0045178 ! basal part of cell
@@ -104726,7 +106612,7 @@
id: GO:0009937
name: regulation of gibberellic acid mediated signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of gibberellic acid mediated signaling." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of gibberellic acid mediated signaling." [GOC:curators]
synonym: "regulation of gibberellic acid mediated signalling" EXACT []
is_a: GO:0009966 ! regulation of signal transduction
intersection_of: GO:0065007 ! biological regulation
@@ -104768,10 +106654,13 @@
[Term]
id: GO:0009940
-name: amino-terminal vacuolar sorting propeptide binding
+name: obsolete amino-terminal vacuolar sorting propeptide binding
namespace: molecular_function
-def: "Binding to an amino terminal propeptide, which functions as a sorting signal to sort away the soluble vacuolar protein from Golgi to lytic vacuole via clathrin-coated vesicles." [GOC:sm, PMID:10871276]
-is_a: GO:0010209 ! vacuolar sorting signal binding
+def: "OBSOLETE. Binding to an amino terminal propeptide, which functions as a sorting signal to sort away the soluble vacuolar protein from Golgi to lytic vacuole via clathrin-coated vesicles." [GOC:sm, PMID:10871276]
+comment: This term was obsolete because it is out of scope for GO; target regions of interactions are not captured.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31410" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0010209
[Term]
id: GO:0009941
@@ -104813,7 +106702,7 @@
id: GO:0009945
name: radial axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of an axis that initiates at a point and radiates outward from the point." [GOC:dph, GOC:go_curators, GOC:isa_complete]
+def: "The establishment, maintenance and elaboration of an axis that initiates at a point and radiates outward from the point." [GOC:curators, GOC:dph, GOC:isa_complete]
is_a: GO:0009798 ! axis specification
relationship: part_of GO:0009956 ! radial pattern formation
@@ -104821,7 +106710,7 @@
id: GO:0009946
name: proximal/distal axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of the proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "The establishment, maintenance and elaboration of the proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC:curators, GOC:dph, GOC:tb]
synonym: "proximal/distal axis determination" RELATED [GOC:dph]
synonym: "proximodistal axis specification" EXACT []
is_a: GO:0009798 ! axis specification
@@ -104841,7 +106730,7 @@
id: GO:0009948
name: anterior/posterior axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:curators, GOC:dph, GOC:tb]
synonym: "anterior/posterior axis determination" RELATED [GOC:dph]
is_a: GO:0009798 ! axis specification
relationship: part_of GO:0009952 ! anterior/posterior pattern specification
@@ -104850,7 +106739,7 @@
id: GO:0009949
name: polarity specification of anterior/posterior axis
namespace: biological_process
-def: "Any process resulting in the establishment of polarity along the anterior/posterior axis." [GOC:go_curators]
+def: "Any process resulting in the establishment of polarity along the anterior/posterior axis." [GOC:curators]
is_a: GO:0065001 ! specification of axis polarity
relationship: part_of GO:0009948 ! anterior/posterior axis specification
@@ -104858,7 +106747,7 @@
id: GO:0009950
name: dorsal/ventral axis specification
namespace: biological_process
-def: "The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:curators, GOC:dph, GOC:tb]
synonym: "dorsal-ventral axis specification" EXACT [GOC:mah]
synonym: "dorsal/ventral axis determination" RELATED [GOC:dph]
synonym: "dorsoventral axis specification" EXACT [GOC:mah]
@@ -104869,7 +106758,7 @@
id: GO:0009951
name: polarity specification of dorsal/ventral axis
namespace: biological_process
-def: "Any process resulting in the establishment of polarity along the dorsal/ventral axis." [GOC:go_curators]
+def: "Any process resulting in the establishment of polarity along the dorsal/ventral axis." [GOC:curators]
synonym: "polarity specification of dorsal-ventral axis" EXACT [GOC:mah]
synonym: "polarity specification of dorsoventral axis" EXACT [GOC:mah]
is_a: GO:0065001 ! specification of axis polarity
@@ -104879,7 +106768,7 @@
id: GO:0009952
name: anterior/posterior pattern specification
namespace: biological_process
-def: "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
+def: "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb]
synonym: "anterior/posterior pattern formation" RELATED []
is_a: GO:0003002 ! regionalization
@@ -104887,7 +106776,7 @@
id: GO:0009953
name: dorsal/ventral pattern formation
namespace: biological_process
-def: "The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:dph, GOC:go_curators, GOC:isa_complete, GOC:tb]
+def: "The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb]
synonym: "dorsal-ventral pattern formation" EXACT [GOC:mah]
synonym: "dorsal/ventral pattern specification" NARROW []
synonym: "dorsoventral pattern formation" EXACT [GOC:mah]
@@ -104897,7 +106786,7 @@
id: GO:0009954
name: proximal/distal pattern formation
namespace: biological_process
-def: "The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC:dph, GOC:go_curators, GOC:isa_complete]
+def: "The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end)." [GOC:curators, GOC:dph, GOC:isa_complete]
synonym: "proximal/distal pattern specification" NARROW []
is_a: GO:0003002 ! regionalization
@@ -104913,7 +106802,7 @@
id: GO:0009956
name: radial pattern formation
namespace: biological_process
-def: "The regionalization process that results in defined areas around a point in which specific types of cell differentiation will occur." [GOC:dph, GOC:go_curators, GOC:isa_complete]
+def: "The regionalization process that results in defined areas around a point in which specific types of cell differentiation will occur." [GOC:curators, GOC:dph, GOC:isa_complete]
synonym: "radial pattern specification" NARROW []
is_a: GO:0003002 ! regionalization
@@ -105019,7 +106908,7 @@
id: GO:0009965
name: leaf morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the leaf are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the leaf are generated and organized." [GOC:curators]
is_a: GO:1905392 ! plant organ morphogenesis
relationship: part_of GO:0010016 ! shoot system morphogenesis
relationship: part_of GO:0048366 ! leaf development
@@ -105202,7 +107091,7 @@
synonym: "delta-pH-dependent protein transporter activity" EXACT []
synonym: "pH-dependent protein transporter activity" EXACT []
synonym: "twin-arginine targeting transmembrane transporter activity" EXACT []
-is_a: GO:0008320 ! protein transmembrane transporter activity
+is_a: GO:0008320 ! transmembrane protein transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
[Term]
@@ -105260,14 +107149,18 @@
alt_id: GO:0016439
def: "Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5." [GOC:mah, RHEA:48348]
comment: Note that this term should not be confused with 'pseudouridylate synthase activity ; GO:0004730', which refers to the formation of free pseudouridine from uracil and ribose-5-phosphate.
-xref: Reactome:R-HSA-6782381 "PUS1 isoform 2 transforms uridine residues to pseudouridine in the anticodon stems of tRNAs"
-xref: Reactome:R-HSA-6786583 "PUS7 transforms uridine to pseudouridine in tRNAs"
-xref: Reactome:R-HSA-6787566 "PUS1 isoform 1 transforms uridine-27, uridine-28 yielding pseudouridine in tRNA(Lys,Ser)"
+xref: Reactome:R-HSA-6782381 "PUS1 isoform 2 isomerizes uridine residues to pseudouridine residues in the anticodon stems of tRNAs"
+xref: Reactome:R-HSA-6786583 "PUS7 isomerizes uridine to pseudouridine in tRNAs"
+xref: Reactome:R-HSA-6787566 "PUS1 isoform 1 isomerizes uridine-27, uridine-28 to pseudouridine residues in tRNA(Lys,Ser)"
xref: Reactome:R-HSA-6790905 "Box H/ACA snoRNP transforms uridine to pseudouridine in pre-rRNA"
-xref: Reactome:R-HSA-8870289 "PUS3 transforms uridine-39 to pseudouridine-39 in tRNA"
+xref: Reactome:R-HSA-8870289 "PUS3 isomerizes uridine-39 to pseudouridine-39 in tRNA"
+xref: Reactome:R-HSA-9936243 "RPUSD4 in the mitochondrial pseudouridylation module transforms uridine-1397 to pseudouridine-1397 in mitochondrial 16S rRNA"
+xref: Reactome:R-HSA-9937369 "RPUSD3,TRUB2 pseudouridylates MT-CO1,MT-CO3 mRNA"
xref: RHEA:48348
+xref: RHEA:56644
is_a: GO:0016866 ! intramolecular transferase activity
property_value: skos:exactMatch RHEA:48348
+property_value: skos:narrowMatch RHEA:56644
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26618" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -105320,7 +107213,7 @@
alt_id: GO:0008151
alt_id: GO:0044763
alt_id: GO:0050875
-def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
+def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:curators, GOC:isa_complete]
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
subset: gocheck_do_not_annotate
subset: goslim_plant
@@ -105358,7 +107251,7 @@
id: GO:0009991
name: obsolete response to extracellular stimulus
namespace: biological_process
-def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:go_curators]
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an extracellular stimulus." [GOC:curators]
comment: The reason for obsoletion is that this term is too vague.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27020" xsd:anyURI
is_obsolete: true
@@ -105378,7 +107271,7 @@
id: GO:0009994
name: oocyte differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete." [GOC:curators, GOC:mtg_sensu]
synonym: "oocyte cell differentiation" EXACT []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0030154 ! cell differentiation
@@ -105388,14 +107281,14 @@
id: GO:0009995
name: soluble molecule recognition
namespace: biological_process
-def: "The recognition of soluble molecules in the environment." [GOC:go_curators]
+def: "The recognition of soluble molecules in the environment." [GOC:curators]
is_a: GO:0009593 ! detection of chemical stimulus
[Term]
id: GO:0009996
name: negative regulation of cell fate specification
namespace: biological_process
-def: "Any process that restricts, stops or prevents a cell from adopting a specific cell fate." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from adopting a specific cell fate." [GOC:curators]
synonym: "down regulation of cell fate specification" EXACT []
synonym: "down-regulation of cell fate specification" EXACT []
synonym: "downregulation of cell fate specification" EXACT []
@@ -105412,7 +107305,7 @@
name: negative regulation of cardioblast cell fate specification
namespace: biological_process
alt_id: GO:0042687
-def: "Any process that restricts, stops or prevents a cell from specifying into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from specifying into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
synonym: "down regulation of cardioblast cell fate specification" EXACT []
synonym: "down-regulation of cardioblast cell fate specification" EXACT []
synonym: "downregulation of cardioblast cell fate specification" EXACT []
@@ -105429,7 +107322,7 @@
id: GO:0009998
name: negative regulation of retinal cone cell fate specification
namespace: biological_process
-def: "Any process that restricts, stops or prevents a cell from specifying into a retinal cone cell." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from specifying into a retinal cone cell." [GOC:curators]
synonym: "down regulation of retinal cone cell fate specification" EXACT []
synonym: "down-regulation of retinal cone cell fate specification" EXACT []
synonym: "downregulation of retinal cone cell fate specification" EXACT []
@@ -105448,7 +107341,7 @@
id: GO:0009999
name: negative regulation of auditory receptor cell fate specification
namespace: biological_process
-def: "Any process that restricts, stops or prevents a cell from specifying into an auditory hair cell." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from specifying into an auditory hair cell." [GOC:curators]
synonym: "down regulation of auditory receptor cell fate specification" EXACT []
synonym: "down-regulation of auditory receptor cell fate specification" EXACT []
synonym: "downregulation of auditory receptor cell fate specification" EXACT []
@@ -105469,7 +107362,7 @@
namespace: biological_process
alt_id: GO:0007404
alt_id: GO:0043360
-def: "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell." [GOC:curators, GOC:mtg_sensu]
synonym: "glia cell differentiation" EXACT []
synonym: "neuroglia differentiation" EXACT []
is_a: GO:0030154 ! cell differentiation
@@ -105479,7 +107372,7 @@
id: GO:0010002
name: cardioblast differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
synonym: "cardiac precursor cell differentiation" EXACT [GOC:mtg_heart]
synonym: "cardioblast cell differentiation" EXACT []
synonym: "cardiomyocyte generation" RELATED []
@@ -105490,7 +107383,7 @@
id: GO:0010004
name: gastrulation involving germ band extension
namespace: biological_process
-def: "A complex and coordinated series of cellular movements, including germ band extension, that occurs at the end of cleavage during embryonic development. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu]
+def: "A complex and coordinated series of cellular movements, including germ band extension, that occurs at the end of cleavage during embryonic development. An example of this process is found in Drosophila melanogaster." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0001703 ! gastrulation with mouth forming first
[Term]
@@ -105531,11 +107424,12 @@
id: GO:0010009
name: cytoplasmic side of endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the endosome membrane that faces the cytoplasm." [GOC:lr]
+def: "The leaflet of the endosome membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:lr]
synonym: "external leaflet of endosome membrane" EXACT [GOC:ab]
synonym: "external side of endosome membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0010008 ! endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0010011
@@ -106660,10 +108554,14 @@
synonym: "phenylacetate breakdown" EXACT []
synonym: "phenylacetate catabolism" EXACT []
synonym: "phenylacetate degradation" EXACT []
+xref: MetaCyc:PWY-1341
xref: MetaCyc:PWY0-321
is_a: GO:0042178 ! xenobiotic catabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-1341
+property_value: skos:narrowMatch MetaCyc:PWY0-321
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0010125
@@ -106715,14 +108613,21 @@
[Term]
id: GO:0010129
-name: anaerobic cyclohexane-1-carboxylate catabolic process
+name: cyclohexane-1-carboxylate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cyclohexane-1-carboxylate, a alicyclic acid, in the absence of oxygen." [GOC:pz]
+def: "The chemical reactions and pathways resulting in the breakdown of cyclohexane-1-carboxylate, an alicyclic acid." [GOC:pz]
synonym: "anaerobic cyclohexane-1-carboxylate breakdown" EXACT []
synonym: "anaerobic cyclohexane-1-carboxylate catabolism" EXACT []
synonym: "anaerobic cyclohexane-1-carboxylate degradation" EXACT []
xref: MetaCyc:PWY-301
+xref: MetaCyc:PWY-8485
+xref: MetaCyc:PWY-8486
is_a: GO:0042178 ! xenobiotic catabolic process
+is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-301
+property_value: skos:narrowMatch MetaCyc:PWY-8485
+property_value: skos:narrowMatch MetaCyc:PWY-8486
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0010130
@@ -107191,12 +109096,16 @@
xref: EC:2.3.3.17
xref: MetaCyc:RXN-18197
xref: MetaCyc:RXN-2202
+xref: RHEA:25601
+xref: RHEA:25605
xref: RHEA:50624
is_a: GO:0046912 ! acyltransferase activity, acyl groups converted into alkyl on transfer
property_value: skos:exactMatch EC:2.3.3.17
property_value: skos:exactMatch MetaCyc:RXN-18197
property_value: skos:exactMatch RHEA:50624
property_value: skos:narrowMatch MetaCyc:RXN-2202
+property_value: skos:narrowMatch RHEA:25601
+property_value: skos:narrowMatch RHEA:25605
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28855" xsd:anyURI
@@ -107488,10 +109397,12 @@
[Term]
id: GO:0010209
-name: vacuolar sorting signal binding
+name: vacuolar sorting signal receptor activity
namespace: molecular_function
def: "Binding to a vacuolar sorting signal, a specific peptide sequence that acts as a signal to localize the protein within the vacuole." [GOC:mah]
-is_a: GO:0005048 ! signal sequence binding
+synonym: "vacuolar sorting signal binding" RELATED []
+is_a: GO:0038024 ! cargo receptor activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31410" xsd:anyURI
[Term]
id: GO:0010210
@@ -107529,7 +109440,7 @@
id: GO:0010214
name: seed coat development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the seed coat over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0048316 ! seed development
@@ -107756,7 +109667,11 @@
synonym: "plastoquinone formation" EXACT []
synonym: "plastoquinone synthesis" EXACT []
xref: MetaCyc:PWY-1581
+xref: MetaCyc:PWY-6978
is_a: GO:1901663 ! quinone biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-1581
+property_value: skos:narrowMatch MetaCyc:PWY-6978
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0010238
@@ -107808,11 +109723,13 @@
synonym: "photosynthetic water oxidation" EXACT []
xref: EC:1.10.3.9
xref: MetaCyc:PSII-RXN
+xref: RHEA:30247
xref: RHEA:36359
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.10.3.9
property_value: skos:exactMatch MetaCyc:PSII-RXN
property_value: skos:exactMatch RHEA:36359
+property_value: skos:narrowMatch RHEA:30247
property_value: skos:relatedMatch MetaCyc:RXN0-5265
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -108218,10 +110135,11 @@
[Term]
id: GO:0010285
-name: L,L-diaminopimelate aminotransferase activity
+name: L,L-diaminopimelate:2-oxoglutarate transaminase activity
namespace: molecular_function
alt_id: GO:0043742
-def: "Catalysis of the reaction: 2-oxoglutarate + LL-2,6-diaminopimelate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H2O + H+." [EC:2.6.1.83, RHEA:23988]
+def: "Catalysis of the reaction: 2-oxoglutarate + LL-2,6-diaminopimelate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H2O + H+." [RHEA:23988]
+synonym: "L,L-diaminopimelate aminotransferase activity" EXACT []
synonym: "LL-2,6-diaminoheptanedioate:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "LL-DAP aminotransferase activity" RELATED [EC:2.6.1.83]
synonym: "LL-DAP-AT activity" RELATED [EC:2.6.1.83]
@@ -108235,6 +110153,7 @@
property_value: skos:exactMatch EC:2.6.1.83
property_value: skos:exactMatch RHEA:23988
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0010286
@@ -108653,7 +110572,6 @@
namespace: biological_process
alt_id: GO:1902534
def: "The infolding of a membrane." [GOC:tb]
-subset: goslim_yeast
synonym: "single-organism membrane invagination" RELATED []
is_a: GO:0061024 ! membrane organization
created_by: jl
@@ -108669,17 +110587,21 @@
[Term]
id: GO:0010326
-name: methionine-oxo-acid transaminase activity
+name: L-methionine:oxo-acid transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: a 2-oxocarboxylate + L-methionine = 4-methylsulfanyl-2-oxobutanoate + an L-alpha-amino acid." [PMID:17056707, RHEA:31763]
+synonym: "methionine-oxo-acid transaminase activity" EXACT []
xref: EC:2.6.1.88
xref: MetaCyc:R15-RXN
xref: RHEA:31763
-is_a: GO:0008483 ! transaminase activity
+xref: RHEA:47800
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.88
property_value: skos:exactMatch RHEA:31763
+property_value: skos:narrowMatch RHEA:47800
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0010327
@@ -108938,12 +110860,10 @@
[Term]
id: GO:0010355
-name: obsolete homogentisate farnesyltransferase activity
+name: homogentisate farnesyltransferase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: homogentisic acid + farnesyl diphosphate = 2-methyl-6-farnesylplastoquinol." [PMID:16989822]
-comment: The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using homogentisate solanesyltransferase activity.
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29344" xsd:anyURI
-is_obsolete: true
+def: "Catalysis of the reaction: homogentisic acid + farnesyl diphosphate = 2-methyl-6-farnesylplastoquinol." [PMID:16989822]
+is_a: GO:0010354 ! homogentisate prenyltransferase activity
[Term]
id: GO:0010356
@@ -109084,10 +111004,7 @@
name: extracellular isoamylase complex
namespace: cellular_component
def: "A protein complex whose composition varies amongst species; in rice it probably exists in a homo-tetramer to homo-hexamer form and in Gram negative bacteria as a dimer. Functions in the hydrolysis of alpha-(1,6)-D-glucosidic branch linkages. Isoamylases in animals are localized in the extracellular space." [GOC:tair_curators]
-is_a: GO:0043033 ! isoamylase complex
-intersection_of: GO:0043033 ! isoamylase complex
-intersection_of: part_of GO:0005576 ! extracellular region
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0010368
@@ -109558,11 +111475,21 @@
xref: EC:2.1.1.114
xref: MetaCyc:RXN-9281
xref: Reactome:R-HSA-2162193 "COQ3 methylates DHDB"
+xref: RHEA:14121
xref: RHEA:44452
+xref: RHEA:44480
+xref: RHEA:44484
+xref: RHEA:44488
+xref: RHEA:44492
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
relationship: part_of GO:0006744 ! ubiquinone biosynthetic process
property_value: skos:exactMatch EC:2.1.1.114
property_value: skos:exactMatch RHEA:44452
+property_value: skos:narrowMatch RHEA:14121
+property_value: skos:narrowMatch RHEA:44480
+property_value: skos:narrowMatch RHEA:44484
+property_value: skos:narrowMatch RHEA:44488
+property_value: skos:narrowMatch RHEA:44492
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26632" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29420" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -109802,7 +111729,7 @@
id: GO:0010446
name: response to alkaline pH
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH > 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:go_curators, GOC:tb, Wikipedia:PH]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH > 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:curators, GOC:tb, Wikipedia:PH]
synonym: "response to alkalinity" BROAD []
synonym: "response to basic pH" EXACT []
is_a: GO:0009268 ! response to pH
@@ -109811,7 +111738,7 @@
id: GO:0010447
name: response to acidic pH
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:go_curators, GOC:tb, Wikipedia:PH]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:curators, GOC:tb, Wikipedia:PH]
comment: This term should be used to annotate instances where a cell or organism is responding to a chemical that is playing the role of an acid (e.g. proton donor) and therefore lowering the pH. If instead you wish to describe a response to a specific acid as a chemical, such as the anion portion of glutamate, please annotate to the appropriate child of GO:0001101 'response to acid chemical'.
synonym: "response to acidity" BROAD []
is_a: GO:0009268 ! response to pH
@@ -110275,6 +112202,7 @@
synonym: "single-organism intercellular transport" RELATED []
is_a: GO:0006810 ! transport
is_a: GO:0009987 ! cellular process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31545" xsd:anyURI
created_by: jl
creation_date: 2013-12-19T13:24:56Z
@@ -110307,6 +112235,7 @@
name: proteasomal ubiquitin-independent protein catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome but do not involve ubiquitin." [GOC:tb]
+xref: Reactome:R-HSA-9912633 "Antigen processing: Ub, ATP-independent proteasomal degradation"
is_a: GO:0010498 ! proteasomal protein catabolic process
[Term]
@@ -110409,7 +112338,8 @@
name: regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
-is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
+is_a: GO:0009889 ! regulation of biosynthetic process
+is_a: GO:0051174 ! regulation of phosphorus metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006661 ! phosphatidylinositol biosynthetic process
relationship: regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -110419,8 +112349,9 @@
name: negative regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
+is_a: GO:0009890 ! negative regulation of biosynthetic process
is_a: GO:0010511 ! regulation of phosphatidylinositol biosynthetic process
-is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
relationship: negatively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -110430,8 +112361,9 @@
name: positive regulation of phosphatidylinositol biosynthetic process
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of phosphatidylinositol." [GOC:dph, GOC:tb, GOC:vw]
+is_a: GO:0009891 ! positive regulation of biosynthetic process
is_a: GO:0010511 ! regulation of phosphatidylinositol biosynthetic process
-is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
relationship: positively_regulates GO:0006661 ! phosphatidylinositol biosynthetic process
@@ -110796,23 +112728,27 @@
name: regulation of macromolecule biosynthetic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb]
+subset: gocheck_do_not_annotate
is_a: GO:0009889 ! regulation of biosynthetic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process
relationship: regulates GO:0009059 ! macromolecule biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31483" xsd:anyURI
[Term]
id: GO:0010557
name: positive regulation of macromolecule biosynthetic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." [GOC:dph, GOC:tb]
+subset: gocheck_do_not_annotate
is_a: GO:0009891 ! positive regulation of biosynthetic process
is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process
relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31483" xsd:anyURI
[Term]
id: GO:0010558
@@ -111064,11 +113000,13 @@
[Term]
id: GO:0010585
-name: glutamine secretion
+name: L-glutamine secretion
namespace: biological_process
def: "The controlled release of glutamine by a cell." [PMID:15208395]
-is_a: GO:0006868 ! glutamine transport
+synonym: "glutamine secretion" EXACT []
+is_a: GO:0006868 ! L-glutamine transport
is_a: GO:0032940 ! secretion by cell
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0010586
@@ -111241,14 +113179,12 @@
[Term]
id: GO:0010602
-name: regulation of 1-aminocyclopropane-1-carboxylate metabolic process
+name: obsolete regulation of 1-aminocyclopropane-1-carboxylate metabolic process
namespace: biological_process
-def: "Regulation of the chemical reactions and pathways involving 1-aminocyclopropane-1-carboxylate, the anion of 1-aminocyclopropane-1-carboxylic acid, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [PMID:18055613]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
-relationship: regulates GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
+def: "OBSOLETE. Regulation of the chemical reactions and pathways involving 1-aminocyclopropane-1-carboxylate, the anion of 1-aminocyclopropane-1-carboxylic acid, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [PMID:18055613]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0010603
@@ -112686,7 +114622,6 @@
synonym: "protein kinase A signal transduction" EXACT [GOC:signaling]
synonym: "protein kinase A signaling cascade" RELATED [GOC:signaling]
synonym: "protein kinase A signalling cascade" RELATED [GOC:mah]
-xref: Reactome:R-HSA-163358 "PKA-mediated phosphorylation of key metabolic factors"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26794" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI
is_obsolete: true
@@ -112804,38 +114739,33 @@
[Term]
id: GO:0010749
-name: regulation of nitric oxide mediated signal transduction
+name: obsolete regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:1902531 ! regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141149
[Term]
id: GO:0010750
-name: positive regulation of nitric oxide mediated signal transduction
+name: obsolete positive regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "positive regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
-is_a: GO:1902533 ! positive regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: positively_regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141150
[Term]
id: GO:0010751
-name: negative regulation of nitric oxide mediated signal transduction
+name: obsolete negative regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "negative regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
-is_a: GO:1902532 ! negative regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: negatively_regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141151
[Term]
id: GO:0010752
@@ -114823,10 +116753,13 @@
[Term]
id: GO:0010944
-name: negative regulation of transcription by competitive promoter binding
+name: obsolete negative regulation of transcription by competitive promoter binding
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site." [GOC:tb]
-is_a: GO:0045892 ! negative regulation of DNA-templated transcription
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site." [GOC:tb]
+comment: This term was obsoleted because it represents a mechanism and is outside the scope of GO.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19894" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0045892
[Term]
id: GO:0010945
@@ -114912,6 +116845,7 @@
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb]
subset: gocheck_obsoletion_candidate
+xref: Reactome:R-HSA-140534 "Caspase activation via Death Receptors in the presence of ligand"
is_a: GO:0010952 ! positive regulation of peptidase activity
is_a: GO:0052548 ! regulation of endopeptidase activity
intersection_of: GO:0065007 ! biological regulation
@@ -114927,6 +116861,7 @@
def: "Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins." [GOC:dph, GOC:tb]
subset: gocheck_obsoletion_candidate
subset: goslim_chembl
+xref: Reactome:R-HSA-5218900 "CASP8 activity is inhibited"
is_a: GO:0010466 ! negative regulation of peptidase activity
is_a: GO:0052548 ! regulation of endopeptidase activity
intersection_of: GO:0065007 ! biological regulation
@@ -118203,7 +120138,6 @@
xref: MetaCyc:2.4.1.135-RXN
xref: Reactome:R-HSA-1889955 "B3GAT dimers transfer GlcA to tetrasaccharide linker"
xref: Reactome:R-HSA-3560802 "Defective B3GAT3 does not transfer GlcA to tetrasaccharide linker"
-xref: Reactome:R-HSA-9638064 "B3GAT3 dimer transfers GlcA to tetrasaccharide linker"
xref: RHEA:24168
is_a: GO:0015020 ! glucuronosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.135
@@ -118304,23 +120238,45 @@
xref: Reactome:R-HSA-2162099 "abacavir + UDP-glucuronate => abacavir 5'-glucuronide + UDP"
xref: Reactome:R-HSA-5604954 "Defective UGT1A4 does not transfer GlcA from UDP-GlcA to BIL"
xref: Reactome:R-HSA-5604975 "Defective UGT1A1 does not transfer GlcA from UDP-GlcA to BIL"
-xref: Reactome:R-HSA-5617143 "B4GAT1:GYLTL1B transfers GlcA from UDP-GlcA to Xyl-GlcA"
+xref: Reactome:R-HSA-5617143 "B4GAT1:LARGE transfers initial GlcA to matriglycan chain"
xref: Reactome:R-HSA-8941701 "UGT1A10 transfers GlcA from UDP-GlcA to GCTN"
xref: Reactome:R-HSA-9036102 "Defective UGT1A1 does not transfer GlcA from UDP-GlcA to BMG"
xref: Reactome:R-HSA-9036104 "Defective UGT1A4 does not transfer GlcA from UDP-GlcA to BMG"
xref: Reactome:R-HSA-9632038 "UGT1A1 tetramer transfers GlcA from UDP-GlcA to BMG to form BDG"
xref: Reactome:R-HSA-9632039 "UGT1A1 transfers GlcA from UDP-GlcA to BIL to form BMG"
-xref: Reactome:R-HSA-9638097 "B4GAT1:LARGE transfers GlcA from UDP-GlcA to Xyl-GlcA"
+xref: Reactome:R-HSA-9638097 "LARGE1,2 elongates matriglycan chain with GlcA"
xref: Reactome:R-HSA-9749977 "UGT1A6 glucuronates ST"
xref: Reactome:R-HSA-9756134 "UGT1A3 lactonizes 2-OH-ATV to 2-OH-ATVL"
xref: Reactome:R-HSA-9756156 "UGT1A3 lactonizes ATV to ATVL"
xref: Reactome:R-HSA-9756183 "UGT1A3 lactonizes 4-OH-ATV to 4-OH-ATVL"
xref: Reactome:R-HSA-9758661 "UGT2B7,2B17,1A3 glucuronidates PRED metabolites"
xref: RHEA:21032
+xref: RHEA:63616
+xref: RHEA:63692
+xref: RHEA:63716
+xref: RHEA:63720
+xref: RHEA:63728
+xref: RHEA:63744
+xref: RHEA:63748
+xref: RHEA:75099
+xref: RHEA:79067
+xref: RHEA:79071
+xref: RHEA:79075
is_a: GO:0008194 ! UDP-glycosyltransferase activity
is_a: GO:0016758 ! hexosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.17
property_value: skos:exactMatch RHEA:21032
+property_value: skos:narrowMatch RHEA:63616
+property_value: skos:narrowMatch RHEA:63692
+property_value: skos:narrowMatch RHEA:63716
+property_value: skos:narrowMatch RHEA:63720
+property_value: skos:narrowMatch RHEA:63728
+property_value: skos:narrowMatch RHEA:63744
+property_value: skos:narrowMatch RHEA:63748
+property_value: skos:narrowMatch RHEA:75099
+property_value: skos:narrowMatch RHEA:79067
+property_value: skos:narrowMatch RHEA:79071
+property_value: skos:narrowMatch RHEA:79075
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28907" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -118380,7 +120336,7 @@
namespace: molecular_function
alt_id: GO:0015027
alt_id: GO:0015028
-def: "Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:go_curators]
+def: "Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity." [GOC:curators]
synonym: "coreceptor, insoluble ligand activity" RELATED [GOC:mah]
synonym: "coreceptor, soluble ligand activity" RELATED [GOC:mah]
is_a: GO:0038023 ! signaling receptor activity
@@ -118453,7 +120409,7 @@
namespace: molecular_function
alt_id: GO:0008895
alt_id: GO:0015037
-def: "Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds." [PMID:7559385]
+def: "Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds." [PMID:18331844]
synonym: "haem lyase disulphide oxidoreductase activity" NARROW []
synonym: "heme lyase disulfide oxidoreductase activity" NARROW []
synonym: "peptide disulfide oxidoreductase activity" EXACT []
@@ -118461,7 +120417,6 @@
synonym: "protein disulfide oxidoreductase activity" EXACT []
synonym: "protein disulfide-oxidoreductase activity" EXACT []
synonym: "protein disulphide oxidoreductase activity" EXACT []
-xref: MetaCyc:DISULFOXRED-RXN
xref: Reactome:R-HSA-1307802 "MIA40:ERV1 (CHCHD4:GFER) oxidizes cysteine residues to cystine disulfide bonds"
xref: Reactome:R-HSA-264997 "P4HB mediates disulfide bond formation in Proinsulin"
xref: Reactome:R-HSA-3299753 "CCS transfers Cu to SOD1 and oxidizes cysteine residues in SOD1"
@@ -118469,6 +120424,7 @@
is_a: GO:0015036 ! disulfide oxidoreductase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20219" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
[Term]
id: GO:0015036
@@ -119094,6 +121050,8 @@
xref: Reactome:R-HSA-1362417 "Mitoferrin translocates iron from the mitochondrial intermembrane space to the mitochondrial matrix"
xref: Reactome:R-HSA-442368 "SLC40A1:HEPH:6Cu2+ transports Fe2+ from cytosol to extracellular region"
xref: Reactome:R-HSA-5655760 "Defective SLC40A1 does not transport Fe3+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-9911596 "FeoAB transports Fe2+ from periplasmic space to the cytosol"
+xref: Reactome:R-HSA-9911598 "EfeUOB transport Fe2+ from periplasmic space to the cytosol"
is_a: GO:0005381 ! iron ion transmembrane transporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -119177,16 +121135,6 @@
namespace: molecular_function
def: "OBSOLETE. Enables the transfer of organic cations from one side of a membrane to the other. Organic cations are atoms or small molecules with a positive charge that contain carbon in covalent linkage." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
comment: The reason for obsoletion is that this term was an unnecessary and confusing grouping term.
-xref: Reactome:R-HSA-2161500 "abacavir [extracellular] => abacavir [cytosol]"
-xref: Reactome:R-HSA-549129 "OCT1 transports organic cations into hepatic cells"
-xref: Reactome:R-HSA-549279 "OCT2 mediates tubular uptake of organic cations in the kidney"
-xref: Reactome:R-HSA-549304 "OCT3 mediates renal clearance of organic cations"
-xref: Reactome:R-HSA-549322 "OCT1 transports organic cations out of hepatic cells"
-xref: Reactome:R-HSA-561054 "OCT2 mediates tubular secretion of organic cations in the kidney"
-xref: Reactome:R-HSA-561072 "OCT3 mediates renal uptake of organic cations"
-xref: Reactome:R-HSA-9794270 "SLCO1A2 transports Cipro(1+) into the cytosol"
-xref: Reactome:R-HSA-9794523 "SLC22A1 transports Cipro into renal cell"
-xref: Reactome:R-HSA-9795207 "SLC22A1 transports Cipro into hepatic cell"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0022857
@@ -119280,7 +121228,7 @@
namespace: molecular_function
def: "Enables the transfer of iodide ions from one side of a membrane to the other." [GOC:ai]
xref: Reactome:R-HSA-209910 "Iodide is taken up by thyroid epithelial cells"
-xref: Reactome:R-HSA-5627802 "SLC26A4 transports I- from cytosol to extracellular region"
+xref: Reactome:R-HSA-5627802 "SLC26A4 exports I- to follicular lumen"
xref: Reactome:R-HSA-5627870 "SLC26A4 does not transport I- from cytosol to extracellular region"
is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
relationship: part_of GO:0015705 ! iodide transport
@@ -119335,8 +121283,9 @@
synonym: "sulfate permease activity" RELATED []
synonym: "sulphate transporter activity" EXACT []
xref: Reactome:R-HSA-3560789 "Defective SLC26A2 does not cotransport extracellular SO4(2-), H+ to cytosol"
-xref: Reactome:R-HSA-427555 "SLC26A1,2 cotransport SO4(2-), H+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-427555 "SLC26A1,2 cotransport SO4(2-), anion from extracellular region to cytosol"
xref: Reactome:R-HSA-8875871 "SLC26A11 transports SO4(2-) from extracellular region to cytosol"
+xref: Reactome:R-HSA-9941470 "SLC26A11 imports SO4(2-) and H+ into cytosol"
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
relationship: part_of GO:1902358 ! sulfate transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -119510,6 +121459,7 @@
name: glucuronate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glucuronate from one side of a membrane to the other. Glucuronate is the uronic acid formally derived from glucose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:ai]
+xref: Reactome:R-HSA-2162229 "SLC17A5 exports GlcA from the lysosome to the cytosol"
is_a: GO:0015133 ! uronic acid transmembrane transporter activity
relationship: part_of GO:0015738 ! glucuronate transmembrane transport
@@ -119739,6 +121689,8 @@
name: polysaccharide transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
+xref: Reactome:R-HSA-9932121 "Unknown transporter exports CA to extracellular space"
+xref: Reactome:R-HSA-9932466 "Bcs complex exports pEtN-cellulose"
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0022884 ! macromolecule transmembrane transporter activity
relationship: part_of GO:0015774 ! polysaccharide transport
@@ -119842,7 +121794,6 @@
synonym: "hydroxy/aromatic amino acid permease activity" RELATED []
xref: Reactome:R-HSA-210439 "glutamate uptake by astrocytes"
xref: Reactome:R-HSA-212642 "L-Glutamine transport into neurons"
-xref: Reactome:R-HSA-351963 "SLC6A18 transports Gly from extracellular region to cytosol"
xref: Reactome:R-HSA-351987 "SLC6A6-mediated uptake of taurine and beta-alanine"
xref: Reactome:R-HSA-352029 "SLC6A12 (BGT-1)-mediated uptake of GABA and betaine"
xref: Reactome:R-HSA-352052 "SLC6A20 cotransports L-Pro, Na+ from the extracellular region to cytosol"
@@ -119856,7 +121807,6 @@
xref: Reactome:R-HSA-352174 "SLC38A3-mediated uptake of glutamine, histidine, asparagine, and alanine"
xref: Reactome:R-HSA-352182 "SLC38A5-mediated uptake of glutamine, histidine, asparagine, and serine"
xref: Reactome:R-HSA-352191 "SLC7A8-mediated uptake of neutral amino acids"
-xref: Reactome:R-HSA-352232 "SLC7A5:SLC3A2 transports neutral amino acids from extracellular region to cytosol"
xref: Reactome:R-HSA-352347 "SLC1A4-mediated exchange of extracellular serine for cytosolic alanine, threonine, or cysteine"
xref: Reactome:R-HSA-352354 "SLC1A4-mediated exchange of extracellular cysteine for cytosolic alanine, serine, or threonine"
xref: Reactome:R-HSA-352364 "SLC1A4-mediated exchange of extracellular alanine for cytosolic serine, threonine, or cysteine"
@@ -119880,7 +121830,6 @@
xref: Reactome:R-HSA-5655702 "Defective SLC3A1 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu"
xref: Reactome:R-HSA-5659674 "Variant SLC6A14 cotransports SLC6A14 ligands, Cl-, 2Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-5659734 "Defective SLC6A19 does not cotransport neutral amino acids, Na+ from extracellular region to cytosol"
-xref: Reactome:R-HSA-5659755 "Defective SLC6A18 does not transport Gly from extracellular region to cytosol"
xref: Reactome:R-HSA-5660694 "Variant SLC6A20 does not cotransport L-Pro, Na+ from extracellulare region to cytosol"
xref: Reactome:R-HSA-5660890 "Defective SLC7A9 (in SLC7A9:SLC3A1) does not exchange L-Arg, CySS-, L-Lys for L-Leu"
xref: Reactome:R-HSA-5660910 "Defective SLC7A7 does not exchange L-Arg for L-Leu, Na+ across the plasma membrane"
@@ -119952,6 +121901,7 @@
def: "Enables the transfer of an L-amino acid from one side of a membrane to the other. L-amino acids are the L-enantiomers of amino acids." [GOC:ai, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0815340729]
synonym: "L-amino acid transporter activity" BROAD []
xref: Reactome:R-HSA-212614 "Glutamine transport from astrocytes"
+xref: Reactome:R-HSA-352232 "SLC7A5:SLC3A2 transports neutral amino acids from extracellular region to cytosol"
is_a: GO:0015171 ! amino acid transmembrane transporter activity
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:1902475 ! L-alpha-amino acid transmembrane transport
@@ -119960,7 +121910,7 @@
id: GO:0015180
name: L-alanine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of L-alanine from one side of a membrane to the other. L-alanine is the L-enantiomer of 2-aminopropanoic acid." [GOC:go_curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of L-alanine from one side of a membrane to the other. L-alanine is the L-enantiomer of 2-aminopropanoic acid." [GOC:curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "L-alanine transporter activity" BROAD []
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0022858 ! alanine transmembrane transporter activity
@@ -119970,7 +121920,7 @@
id: GO:0015182
name: L-asparagine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of L-asparagine from one side of a membrane to the other. L-asparagine is the L-enantiomer of alpha-aminosuccinamic acid." [GOC:go_curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of L-asparagine from one side of a membrane to the other. L-asparagine is the L-enantiomer of alpha-aminosuccinamic acid." [GOC:curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "asparagine/glutamine permease activity" NARROW []
synonym: "L-asparagine transporter activity" BROAD []
is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
@@ -119981,7 +121931,7 @@
id: GO:0015183
name: L-aspartate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of L-aspartate from one side of a membrane to the other. L-aspartate is the anion derived from aspartic acid." [GOC:go_curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of L-aspartate from one side of a membrane to the other. L-aspartate is the anion derived from aspartic acid." [GOC:curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "glutamate/aspartate porter activity" NARROW []
synonym: "glutamate/aspartate:sodium symporter activity" NARROW []
synonym: "L-aspartate transporter activity" BROAD []
@@ -119995,7 +121945,7 @@
id: GO:0015184
name: L-cystine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of L-cystine from one side of a membrane to the other." [GOC:go_curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of L-cystine from one side of a membrane to the other." [GOC:curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "cystine/diaminopimelate porter activity" NARROW []
synonym: "L-cystine transporter activity" BROAD []
xref: Reactome:R-HSA-5340130 "CTNS cotransports CySS-, H+ from lysosomal lumen to cytosol"
@@ -120008,7 +121958,7 @@
id: GO:0015185
name: gamma-aminobutyric acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of gamma-aminobutyric acid from one side of a membrane to the other. Gamma-aminobutyric acid is 4-aminobutyrate (GABA)." [GOC:go_curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of gamma-aminobutyric acid from one side of a membrane to the other. Gamma-aminobutyric acid is 4-aminobutyrate (GABA)." [GOC:curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "4-aminobutanoate transporter activity" EXACT []
synonym: "4-aminobutyrate transporter activity" EXACT []
synonym: "betaine/GABA:sodium symporter activity" NARROW []
@@ -120025,7 +121975,7 @@
synonym: "asparagine/glutamine permease activity" NARROW []
is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
-relationship: part_of GO:0006868 ! glutamine transport
+relationship: part_of GO:0006868 ! L-glutamine transport
[Term]
id: GO:0015187
@@ -120123,7 +122073,6 @@
synonym: "L-serine transporter activity" BROAD []
synonym: "serine transporter activity" BROAD []
synonym: "threonine/serine:sodium symporter activity" RELATED []
-xref: Reactome:R-HSA-8932980 "SERINC3,5,(1,2,4) transport L-Ser from cytosol to plasma membrane"
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
relationship: part_of GO:0015825 ! L-serine transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -120210,7 +122159,7 @@
id: GO:0015207
name: adenine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of adenine, 6-aminopurine, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of adenine, 6-aminopurine, from one side of a membrane to the other." [GOC:curators]
xref: Reactome:R-HSA-163215 "SLC25A5,6 dimers exchange ATP for ADP across the mitochondrial inner membrane"
xref: Reactome:R-HSA-5672027 "ARL2:GTP:ARL2BP:SLC25A4 dimer exchanges ATP for ADP across the mitochondrial inner membrane"
is_a: GO:0005345 ! purine nucleobase transmembrane transporter activity
@@ -120221,7 +122170,7 @@
id: GO:0015208
name: guanine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of guanine, 2-amino-6-hydroxypurine, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of guanine, 2-amino-6-hydroxypurine, from one side of a membrane to the other." [GOC:curators]
is_a: GO:0005345 ! purine nucleobase transmembrane transporter activity
relationship: part_of GO:1903716 ! guanine transmembrane transport
@@ -120229,7 +122178,7 @@
id: GO:0015209
name: cytosine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of cytosine, 4-amino-2-hydroxypyrimidine from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of cytosine, 4-amino-2-hydroxypyrimidine from one side of a membrane to the other." [GOC:curators]
is_a: GO:0005350 ! pyrimidine nucleobase transmembrane transporter activity
relationship: part_of GO:0015856 ! cytosine transport
@@ -120237,7 +122186,7 @@
id: GO:0015210
name: uracil transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of uracil, 2,4-dioxopyrimidine, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of uracil, 2,4-dioxopyrimidine, from one side of a membrane to the other." [GOC:curators]
synonym: "uracil/uridine permease activity" RELATED []
is_a: GO:0005350 ! pyrimidine nucleobase transmembrane transporter activity
relationship: part_of GO:1903791 ! uracil transmembrane transport
@@ -120254,7 +122203,7 @@
id: GO:0015212
name: cytidine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of cytidine, cytosine riboside, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of cytidine, cytosine riboside, from one side of a membrane to the other." [GOC:curators]
is_a: GO:0015214 ! pyrimidine nucleoside transmembrane transporter activity
relationship: part_of GO:0015861 ! cytidine transport
@@ -120262,7 +122211,7 @@
id: GO:0015213
name: uridine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of uridine, uracil riboside, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of uridine, uracil riboside, from one side of a membrane to the other." [GOC:curators]
synonym: "uracil/uridine permease activity" NARROW []
is_a: GO:0015214 ! pyrimidine nucleoside transmembrane transporter activity
relationship: part_of GO:0015862 ! uridine transmembrane transport
@@ -120306,6 +122255,7 @@
name: pyrimidine nucleotide transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a pyrimidine nucleotide, any compound consisting of a pyrimidine nucleoside esterified with (ortho)phosphate, from one side of a membrane to the other." [GOC:ai]
+xref: Reactome:R-HSA-9940804 "SLC35A1,4 import CDP-ribitol"
is_a: GO:0015215 ! nucleotide transmembrane transporter activity
relationship: part_of GO:0006864 ! pyrimidine nucleotide transport
@@ -120468,6 +122418,8 @@
xref: Reactome:R-HSA-917870 "SLC46A1 transports hemes from extracellular region to cytosol"
xref: Reactome:R-HSA-917892 "FLVCR1-1 transports heme from cytosol to extracellular region"
xref: Reactome:R-HSA-9661408 "FLVCR1-2 transports heme from mitochondrial matrix to cytosol"
+xref: Reactome:R-HSA-9927224 "ChuA imports heme to periplasm"
+xref: Reactome:R-HSA-9927930 "DppBCDF transports heme to cytosol"
is_a: GO:0022857 ! transmembrane transporter activity
relationship: part_of GO:0015886 ! heme transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19472" xsd:anyURI
@@ -120558,7 +122510,6 @@
def: "Enables the transfer of aminophospholipids from the exoplasmic to the cytosolic leaflet of a membrane, using energy from the hydrolysis of ATP. Aminophospholipids contain phosphoric acid as a mono- or diester and an amino (NH2) group." [GOC:pg]
synonym: "aminophospholipid transmembrane transporter activity" RELATED []
synonym: "aminophospholipid transporter activity" RELATED []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0140327 ! flippase activity
relationship: part_of GO:0140331 ! aminophospholipid translocation
property_value: skos:broadMatch RHEA:66132
@@ -120755,6 +122706,9 @@
synonym: "substrate-specific channel activity" RELATED []
xref: Reactome:R-HSA-3779381 "H2O2 diffuses from the mitochondrial matrix to the cytosol"
xref: Reactome:R-HSA-8953430 "PXMP2 trimer transports glycolate from cytosol to peroxisomal matrix"
+xref: Reactome:R-HSA-9857649 "p-S373-GJA1:p-S-ITGA5:ITGB1 (p-S373-Connexin-43:p-S-Integrin alpha5:Integrin beta1) transports ATP from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-9857682 "p-S373-GJA1:p-S-ITGA5:ITGB1 (p-S373-Connexin-43:p-S-Integrin alpha5:Integrin beta1) transports prostaglandin E2 (PGE2) from the cytosol to the extracellular region"
+xref: Reactome:R-HSA-9905999 "Pannexin1 (PANX1) channel in a complex with P2RX7 transports ATP from the cytosol to the extracellular region"
xref: TC:1
is_a: GO:0022803 ! passive transmembrane transporter activity
@@ -120897,6 +122851,11 @@
def: "Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria." [GOC:mtg_transport, ISBN:0815340729, PMID:10839820, TC:1.B.1.-.-]
synonym: "outer membrane exporter porin" NARROW []
synonym: "porin" EXACT []
+xref: Reactome:R-HSA-9760573 "TolC complex exports STa"
+xref: Reactome:R-HSA-9911510 "MacA:MacB:TolC transports azithromycin from the periplasm to the extracellular region"
+xref: Reactome:R-HSA-9911516 "AcrA:AcrB:TolC transports antibiotics from the periplasm to the extracellular region"
+xref: Reactome:R-HSA-9914083 "MdtE:MdtF:TolC exports beta-lactams to extracellular space"
+xref: Reactome:R-HSA-9926021 "HlyB:HlyD:TolC transports HlyA from periplasm to extracellular space"
xref: Wikipedia:Porin_(protein)
is_a: GO:0022829 ! wide pore channel activity
@@ -120934,6 +122893,18 @@
synonym: "porter activity" EXACT []
synonym: "porters" EXACT []
synonym: "secondary carrier-type facilitators" EXACT []
+xref: Reactome:R-HSA-549241 "SLC22A4 cotransports ERGT, Na+ from extracellular region to cytosol"
+xref: Reactome:R-HSA-561059 "OAT2 and OAT4 mediate transport of sulphate conjugates"
+xref: Reactome:R-HSA-879562 "SLCO2B1 has a narrow substrate specificity"
+xref: Reactome:R-HSA-879584 "SLCO3A1 isoform 1 has a broad substrate specificity"
+xref: Reactome:R-HSA-879594 "SLCO4C1 mediates the transport of digoxin"
+xref: Reactome:R-HSA-9661397 "SLCO1B1 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
+xref: Reactome:R-HSA-9661446 "BMG, BDG translocates from ER lumen to cytosol"
+xref: Reactome:R-HSA-9661723 "SLCO2B1-3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
+xref: Reactome:R-HSA-9661799 "SLCO1B3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
+xref: Reactome:R-HSA-9749583 "SLC22A7 transports ASA-,ST from extracellular region to cytosol of hepatocytes"
+xref: Reactome:R-HSA-9749607 "SLCO2B1-1 transports ASA- from extracellular region to cytosol of GI cells"
+xref: Reactome:R-HSA-9757010 "SLCO1B1,1B3,2B1-3 transport ATV from extracelluar region to cytosol"
xref: TC:2.A
is_a: GO:0022804 ! active transmembrane transporter activity
@@ -121444,6 +123415,11 @@
synonym: "siderophore transporter activity" RELATED []
synonym: "siderophore-iron transporter activity" RELATED []
xref: Reactome:R-HSA-1222597 "Loaded mycobactin gets imported"
+xref: Reactome:R-HSA-9911605 "FyuA transports Ybt:Fe/Cu from extracellular space to the periplasm"
+xref: Reactome:R-HSA-9928256 "YbtPQ transports Ybt:Fe/Cu to the cytosol"
+xref: Reactome:R-HSA-9930902 "IutA imports FeAer to the periplasm"
+xref: Reactome:R-HSA-9930911 "FhuBCD imports FeAer to the cytosol"
+xref: Reactome:R-HSA-9931043 "FecA:TonB:ExbB:ExbD imports Fe3+-citrates to periplasm"
xref: TC:2.A.1.16.1
xref: TC:2.A.1.16.2
xref: TC:2.A.1.16.3
@@ -121502,19 +123478,8 @@
id: GO:0015347
name: obsolete sodium-independent organic anion transmembrane transporter activity
namespace: molecular_function
-def: "OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other, in a sodium independent manner." [GOC:go_curators]
+def: "OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other, in a sodium independent manner." [GOC:curators]
comment: The reason for obsoletion is that this term was an unnecessary and confusing grouping term.
-xref: Reactome:R-HSA-561059 "OAT2 and OAT4 mediate transport of sulphate conjugates"
-xref: Reactome:R-HSA-879562 "SLCO2B1 has a narrow substrate specificity"
-xref: Reactome:R-HSA-879584 "SLCO3A1 isoform 1 has abroad substrate specificity"
-xref: Reactome:R-HSA-879594 "SLCO4C1 mediates the transport of digoxin"
-xref: Reactome:R-HSA-9661397 "SLCO1B1 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
-xref: Reactome:R-HSA-9661446 "BMG, BDG translocates from ER lumen to cytosol"
-xref: Reactome:R-HSA-9661723 "SLCO2B1-3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
-xref: Reactome:R-HSA-9661799 "SLCO1B3 transports BIL from extracellular region (blood) to cytosol (hepatocyte)"
-xref: Reactome:R-HSA-9749583 "SLC22A7 transports ASA-,ST from extracellular region to cytosol of hepatocytes"
-xref: Reactome:R-HSA-9749607 "SLCO2B1-1 transports ASA- from extracellular region to cytosol of GI cells"
-xref: Reactome:R-HSA-9757010 "SLCO1B1,1B3,2B1-3 transport ATV from extracelluar region to cytosol"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0015291
@@ -122278,10 +124243,12 @@
xref: EC:7.6.2.9
xref: MetaCyc:RXN-8638
xref: RHEA:11036
+xref: RHEA:76247
is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
property_value: skos:exactMatch EC:7.6.2.9
property_value: skos:exactMatch RHEA:11036
+property_value: skos:narrowMatch RHEA:76247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -122354,10 +124321,12 @@
xref: MetaCyc:3.6.3.23-RXN
xref: Reactome:R-HSA-5223317 "ABCB9 transports peptides from cytosol to lysosomal lumen"
xref: RHEA:14429
+xref: RHEA:29763
is_a: GO:0035673 ! oligopeptide transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
property_value: skos:exactMatch EC:7.4.2.6
property_value: skos:exactMatch RHEA:14429
+property_value: skos:narrowMatch RHEA:29763
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -122454,9 +124423,19 @@
xref: EC:7.4.2.1
xref: MetaCyc:3.6.3.21-RXN
xref: RHEA:14673
+xref: RHEA:29039
+xref: RHEA:29879
+xref: RHEA:29883
+xref: RHEA:29887
+xref: RHEA:29891
is_a: GO:0015424 ! ABC-type amino acid transporter activity
property_value: skos:exactMatch EC:7.4.2.1
property_value: skos:exactMatch RHEA:14673
+property_value: skos:narrowMatch RHEA:29039
+property_value: skos:narrowMatch RHEA:29879
+property_value: skos:narrowMatch RHEA:29883
+property_value: skos:narrowMatch RHEA:29887
+property_value: skos:narrowMatch RHEA:29891
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -122530,10 +124509,16 @@
xref: EC:7.6.2.3
xref: MetaCyc:TRANS-RXN-358
xref: RHEA:19121
+xref: RHEA:38963
+xref: RHEA:81611
+xref: RHEA:81663
is_a: GO:0140359 ! ABC-type transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
property_value: skos:exactMatch EC:7.6.2.3
property_value: skos:exactMatch RHEA:19121
+property_value: skos:narrowMatch RHEA:38963
+property_value: skos:narrowMatch RHEA:81611
+property_value: skos:narrowMatch RHEA:81663
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30815" xsd:anyURI
@@ -122852,7 +124837,7 @@
synonym: "P-P-bond-hydrolysis-driven protein transmembrane transporter activity" RELATED []
synonym: "protein translocase activity" EXACT []
xref: Reactome:R-HSA-1222523 "SodB gets secreted"
-is_a: GO:0008320 ! protein transmembrane transporter activity
+is_a: GO:0008320 ! transmembrane protein transporter activity
is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21271" xsd:anyURI
@@ -123941,6 +125926,7 @@
synonym: "N-acetylchitosamine transmembrane transporter activity" EXACT []
synonym: "N-acetylglucosamine permease activity" RELATED []
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30986" xsd:anyURI
[Term]
@@ -124154,6 +126140,7 @@
name: iron chelate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of an iron chelate from one side of a membrane to the other. An iron chelate is a heterocyclic compound having a metal ion attached by coordinate bonds to at least two nonmetal ions." [PMID:17660286]
+xref: Reactome:R-HSA-9931048 "FecBCDE imports Fe3+-citrates to cytosol"
is_a: GO:0022857 ! transmembrane transporter activity
relationship: part_of GO:0033214 ! siderophore-iron import into cell
@@ -124317,6 +126304,8 @@
name: ferric-enterobactin transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of ferric-enterobactin from one side of a membrane to the other." [GOC:ai]
+xref: Reactome:R-HSA-9911602 "FepA:TonB:ExbB:ExbD transports ferrienterobactin from the extracellular region to the periplasmic space"
+xref: Reactome:R-HSA-9911603 "FepC:FepD:FepG transports ferrienterobactin from the periplasmic space to the cytosol"
is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
relationship: part_of GO:0015685 ! ferric-enterobactin import into cell
@@ -124377,7 +126366,7 @@
id: GO:0015626
name: L-diaminopimelate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of L-diaminopimelate from one side of a membrane to the other. L-diaminopimelate is the L-enantiomer anion of 2,6-diaminoheptanedioic acid." [GOC:go_curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
+def: "Enables the transfer of L-diaminopimelate from one side of a membrane to the other. L-diaminopimelate is the L-enantiomer anion of 2,6-diaminoheptanedioic acid." [GOC:curators, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "cystine/diaminopimelate porter activity" NARROW []
synonym: "L-diaminopimelate transporter activity" BROAD []
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
@@ -124724,6 +126713,12 @@
name: alcohol transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of an alcohol from one side of a membrane to the other. An alcohol is any carbon compound that contains a hydroxyl group." [ISBN:0198506732]
+xref: Reactome:R-HSA-192010 "5beta-cholestan-3alpha, 7alpha, 12alpha-triol is translocated from the cytosol to the mitochondrial matrix"
+xref: Reactome:R-HSA-193537 "5beta-cholestan-3alpha, 7alpha-diol is translocated from the cytosol to the mitochondrial matrix"
+xref: Reactome:R-HSA-193715 "5beta-cholestan-3alpha,7alpha,24(S)-triol is translocated from the cytosol to the mitochondrial matrix"
+xref: Reactome:R-HSA-193774 "5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol is translocated from the cytosol to the mitochondrial matrix"
+xref: Reactome:R-HSA-193808 "5beta-cholestan-3alpha,7alpha,27-triol is translocated from the cytosol to the mitochondrial matrix"
+xref: Reactome:R-HSA-193832 "5beta-cholestan-3alpha,7alpha,12alpha,27-tetrol is translocated from the cytosol to the mitochondrial matrix"
is_a: GO:0022857 ! transmembrane transporter activity
[Term]
@@ -125066,6 +127061,7 @@
name: organic anion transport
namespace: biological_process
def: "The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc]
+xref: Reactome:R-HSA-9955298 "SLC-mediated transport of organic anions"
is_a: GO:0006810 ! transport
[Term]
@@ -125154,6 +127150,7 @@
synonym: "bile acid transport" NARROW []
synonym: "bile salt transport" NARROW []
xref: Reactome:R-HSA-159418 "Recycling of bile acids and salts"
+xref: Reactome:R-HSA-9958517 "SLC-mediated bile acid transport"
is_a: GO:0006869 ! lipid transport
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
@@ -125493,6 +127490,7 @@
namespace: biological_process
def: "The directed movement of N-acetylglucosamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
is_a: GO:1901264 ! carbohydrate derivative transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0015765
@@ -125845,7 +127843,7 @@
id: GO:0015810
name: aspartate transmembrane transport
namespace: biological_process
-def: "The process in which aspartate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators, ISBN:0198506732]
+def: "The process in which aspartate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:curators, ISBN:0198506732]
synonym: "aspartate transport" BROAD []
synonym: "mitochondrial aspartate/glutamate transport" RELATED []
is_a: GO:0003333 ! amino acid transmembrane transport
@@ -125859,7 +127857,7 @@
id: GO:0015811
name: L-cystine transport
namespace: biological_process
-def: "The directed movement of L-cystine (also known as dicysteine) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
+def: "The directed movement of L-cystine (also known as dicysteine) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators, ISBN:0198506732]
is_a: GO:0000101 ! sulfur amino acid transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0015807 ! L-amino acid transport
@@ -125869,7 +127867,7 @@
id: GO:0015812
name: gamma-aminobutyric acid transport
namespace: biological_process
-def: "The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
+def: "The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators, ISBN:0198506732]
comment: See also the biological process term 'neurotransmitter transport ; GO:0006836'.
synonym: "4-aminobutanoate transport" EXACT []
synonym: "4-aminobutyrate transport" EXACT []
@@ -126047,7 +128045,7 @@
id: GO:0015830
name: diaminopimelate transport
namespace: biological_process
-def: "The directed movement of diaminopimelate, the anion of 2,6-diaminoheptanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
+def: "The directed movement of diaminopimelate, the anion of 2,6-diaminoheptanedioic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators, ISBN:0198506732]
is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:1901571 ! fatty acid derivative transport
@@ -126056,7 +128054,7 @@
id: GO:0015832
name: obsolete holin
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it represents a class of gene products.
synonym: "holin" EXACT []
is_obsolete: true
@@ -126105,6 +128103,7 @@
def: "The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai, ISBN:0198506732]
subset: goslim_pir
synonym: "amine/polyamine transport" RELATED []
+xref: Reactome:R-HSA-549127 "SLC-mediated transport of organic cations"
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -126215,7 +128214,7 @@
id: GO:0015853
name: adenine transport
namespace: biological_process
-def: "The directed movement of adenine, 6-aminopurine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
+def: "The directed movement of adenine, 6-aminopurine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators, ISBN:0198506732]
synonym: "adenine transmembrane transport" EXACT [GOC:mah]
is_a: GO:0006863 ! purine nucleobase transport
@@ -126223,7 +128222,7 @@
id: GO:0015854
name: guanine transport
namespace: biological_process
-def: "The directed movement of guanine, 2-amino-6-hydroxypurine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed movement of guanine, 2-amino-6-hydroxypurine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
is_a: GO:0006863 ! purine nucleobase transport
[Term]
@@ -126232,7 +128231,7 @@
namespace: biological_process
def: "The directed movement of pyrimidine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "pyrimidine base transmembrane transport" EXACT [GOC:mah]
-synonym: "pyrimidine base transport" EXACT [GOC:go_curators]
+synonym: "pyrimidine base transport" EXACT [GOC:curators]
synonym: "pyrimidine transmembrane transport" RELATED [GOC:mah]
synonym: "pyrimidine transport" RELATED []
is_a: GO:0015851 ! nucleobase transport
@@ -126241,7 +128240,7 @@
id: GO:0015856
name: cytosine transport
namespace: biological_process
-def: "The directed movement of cytosine, 4-amino-2-hydroxypyrimidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed movement of cytosine, 4-amino-2-hydroxypyrimidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
synonym: "cytosine transmembrane transport" EXACT [GOC:mah]
is_a: GO:0015855 ! pyrimidine nucleobase transport
@@ -126249,7 +128248,7 @@
id: GO:0015857
name: uracil transport
namespace: biological_process
-def: "The directed movement of uracil, 2,4-dioxopyrimidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed movement of uracil, 2,4-dioxopyrimidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
is_a: GO:0015855 ! pyrimidine nucleobase transport
[Term]
@@ -126284,14 +128283,14 @@
id: GO:0015861
name: cytidine transport
namespace: biological_process
-def: "The directed movement of cytidine, cytosine riboside, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed movement of cytidine, cytosine riboside, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
is_a: GO:0015864 ! pyrimidine nucleoside transport
[Term]
id: GO:0015862
name: uridine transmembrane transport
namespace: biological_process
-def: "The directed movement of uridine, uracil riboside, across a lipid bilayer, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed movement of uridine, uracil riboside, across a lipid bilayer, by means of some agent such as a transporter or pore." [GOC:curators]
is_a: GO:0015864 ! pyrimidine nucleoside transport
is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
is_a: GO:1901642 ! nucleoside transmembrane transport
@@ -126698,6 +128697,7 @@
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
synonym: "peroxisomal long-chain fatty acid import" EXACT []
synonym: "peroxisomal long-chain fatty acid uptake" EXACT [GOC:dph, GOC:tb]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015909 ! long-chain fatty acid transport
is_a: GO:0015919 ! peroxisomal membrane transport
is_a: GO:0032365 ! intracellular lipid transport
@@ -127084,7 +129084,7 @@
id: GO:0015945
name: methanol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent." [GOC:curators, ISBN:0198506732]
synonym: "methanol metabolism" EXACT []
is_a: GO:0034308 ! primary alcohol metabolic process
@@ -127566,6 +129566,8 @@
is_a: GO:0006779 ! porphyrin-containing compound biosynthetic process
is_a: GO:0015994 ! chlorophyll metabolic process
is_a: GO:0046148 ! pigment biosynthetic process
+property_value: skos:narrowMatch MetaCyc:CHLOROPHYLL-SYN
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0015996
@@ -127595,15 +129597,17 @@
[Term]
id: GO:0016002
-name: sulfite reductase activity
+name: obsolete obsolete sulfite reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hydrogen sulfide + acceptor + 3 H2O = sulfite + reduced acceptor." [GOC:curators]
+def: "OBSOLETE. Catalysis of the reaction: hydrogen sulfide + acceptor + 3 H2O = sulfite + reduced acceptor." [GOC:curators]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
synonym: "assimilatory sulfite reductase activity" EXACT []
synonym: "assimilatory-type sulfite reductase activity" EXACT []
synonym: "hydrogen-sulfide:(acceptor) oxidoreductase activity" EXACT []
synonym: "hydrogen-sulfide:acceptor oxidoreductase activity" EXACT []
synonym: "sulphite reductase activity" EXACT []
-is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0016004
@@ -127703,7 +129707,7 @@
id: GO:0016015
name: morphogen activity
namespace: molecular_function
-def: "Acts as a trigger for a pattern specification process when present at a specific concentration within a gradient." [GOC:go_curators]
+def: "Acts as a trigger for a pattern specification process when present at a specific concentration within a gradient." [GOC:curators]
is_a: GO:0048018 ! receptor ligand activity
[Term]
@@ -127781,7 +129785,7 @@
id: GO:0016025
name: obsolete proteasome endopeptidase regulator
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not represent a molecular function.
synonym: "proteasome endopeptidase regulator" EXACT []
is_obsolete: true
@@ -127791,7 +129795,7 @@
id: GO:0016026
name: obsolete proteasome endopeptidase core
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not represent a molecular function.
synonym: "proteasome endopeptidase core" EXACT []
is_obsolete: true
@@ -127896,7 +129900,7 @@
id: GO:0016037
name: light absorption
namespace: biological_process
-def: "The reception of a photon by a cell." [GOC:go_curators]
+def: "The reception of a photon by a cell." [GOC:curators]
synonym: "absorption of light" EXACT []
is_a: GO:0009987 ! cellular process
relationship: part_of GO:0009583 ! detection of light stimulus
@@ -127905,22 +129909,21 @@
id: GO:0016038
name: absorption of visible light
namespace: biological_process
-def: "The reception of a (visible light) photon by a cell, visible light being defined as having a wavelength within the range 380-780 nm." [GOC:go_curators, ISBN:0198506732]
+def: "The reception of a (visible light) photon by a cell, visible light being defined as having a wavelength within the range 380-780 nm." [GOC:curators, ISBN:0198506732]
is_a: GO:0016037 ! light absorption
[Term]
id: GO:0016039
name: absorption of UV light
namespace: biological_process
-def: "The reception of a (UV light) photon by a cell, UV light being defined as having a wavelength within the range 13.6-400 nm." [GOC:go_curators, ISBN:0198506732]
+def: "The reception of a (UV light) photon by a cell, UV light being defined as having a wavelength within the range 13.6-400 nm." [GOC:curators, ISBN:0198506732]
is_a: GO:0016037 ! light absorption
[Term]
id: GO:0016040
name: glutamate synthase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamate + NAD+ = 2-oxoglutarate + L-glutamine + H+ + NADH." [EC:1.4.1.14, RHEA:13753]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: 2 L-glutamate + NAD+ = 2-oxoglutarate + L-glutamine + H+ + NADH." [RHEA:13753]
synonym: "glutamate (reduced nicotinamide adenine dinucleotide) synthase" RELATED [EC:1.4.1.14]
synonym: "GOGAT activity" BROAD []
synonym: "L-glutamate synthase (NADH)" RELATED [EC:1.4.1.14]
@@ -127938,15 +129941,14 @@
property_value: skos:exactMatch EC:1.4.1.14
property_value: skos:exactMatch MetaCyc:GLUTAMATE-SYNTHASE-NADH-RXN
property_value: skos:exactMatch RHEA:13753
-property_value: skos:relatedMatch MetaCyc:GLUGLNSYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0016041
name: glutamate synthase (ferredoxin) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+. This is a two-step reaction: (a) L-glutamate + NH3 = L-glutamine + H2O, (b) L-glutamate + 2 oxidized ferredoxin + H2O = NH3 + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+." [EC:1.4.7.1]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+. This is a two-step reaction: (a) L-glutamate + NH4+ = L-glutamine + H2O, (b) L-glutamate + 2 oxidized ferredoxin + H2O = NH4+ + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+." [EC:1.4.7.1]
synonym: "ferredoxin-dependent glutamate synthase activity" RELATED [EC:1.4.7.1]
synonym: "ferredoxin-glutamate synthase activity" RELATED [EC:1.4.7.1]
synonym: "glutamate synthase (ferredoxin-dependent)" RELATED [EC:1.4.7.1]
@@ -127959,8 +129961,8 @@
property_value: skos:exactMatch EC:1.4.7.1
property_value: skos:exactMatch MetaCyc:GLUTAMATE-SYNTHASE-FERREDOXIN-RXN
property_value: skos:exactMatch RHEA:12128
-property_value: skos:relatedMatch MetaCyc:PWY-4341
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0016042
@@ -127968,7 +129970,7 @@
namespace: biological_process
alt_id: GO:0006724
alt_id: GO:0044240
-def: "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [GOC:curators]
synonym: "lipid breakdown" EXACT []
synonym: "lipid catabolism" EXACT []
synonym: "lipid degradation" EXACT []
@@ -128220,7 +130222,7 @@
id: GO:0016061
name: obsolete regulation of light-activated channel activity
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of light-activated channel activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of light-activated channel activity." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22455" xsd:anyURI
is_obsolete: true
@@ -128506,7 +130508,7 @@
id: GO:0016091
name: prenol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of prenols, isoprenoids of general formula (H-CH2-C(CH3)=CH-CH2-)n-OH, any primary monohydroxy alcohol whose carbon skeleton consists of two or more isoprenoid residues linked head to tail." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of prenols, isoprenoids of general formula (H-CH2-C(CH3)=CH-CH2-)n-OH, any primary monohydroxy alcohol whose carbon skeleton consists of two or more isoprenoid residues linked head to tail." [GOC:curators]
synonym: "prenol anabolism" EXACT []
synonym: "prenol biosynthesis" EXACT []
synonym: "prenol formation" EXACT []
@@ -128519,7 +130521,7 @@
id: GO:0016092
name: prenol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of prenols, isoprenoids of general formula (H-CH2-C(CH3)=CH-CH2-)n-OH, any primary monohydroxy alcohol whose carbon skeleton consists of two or more isoprenoid residues linked head to tail." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of prenols, isoprenoids of general formula (H-CH2-C(CH3)=CH-CH2-)n-OH, any primary monohydroxy alcohol whose carbon skeleton consists of two or more isoprenoid residues linked head to tail." [GOC:curators]
synonym: "prenol breakdown" EXACT []
synonym: "prenol catabolism" EXACT []
synonym: "prenol degradation" EXACT []
@@ -128540,7 +130542,7 @@
id: GO:0016094
name: polyprenol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans." [GOC:go_curators, PMID:11108713]
+def: "The chemical reactions and pathways resulting in the formation of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans." [GOC:curators, PMID:11108713]
synonym: "polyprenol anabolism" EXACT []
synonym: "polyprenol biosynthesis" EXACT []
synonym: "polyprenol formation" EXACT []
@@ -128553,7 +130555,7 @@
id: GO:0016095
name: polyprenol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans." [GOC:go_curators, Wikipedia:Polyprenol]
+def: "The chemical reactions and pathways resulting in the breakdown of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans." [GOC:curators, Wikipedia:Polyprenol]
synonym: "polyprenol breakdown" EXACT []
synonym: "polyprenol catabolism" EXACT []
synonym: "polyprenol degradation" EXACT []
@@ -128573,7 +130575,7 @@
id: GO:0016099
name: monoterpenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of monoterpenoid compounds, terpenoids having a C10 skeleton." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of monoterpenoid compounds, terpenoids having a C10 skeleton." [GOC:curators]
synonym: "monoterpenoid anabolism" EXACT []
synonym: "monoterpenoid biosynthesis" EXACT []
synonym: "monoterpenoid formation" EXACT []
@@ -128586,7 +130588,7 @@
id: GO:0016100
name: monoterpenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of monoterpenoid compounds, terpenoids having a C10 skeleton." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of monoterpenoid compounds, terpenoids having a C10 skeleton." [GOC:curators]
synonym: "monoterpenoid breakdown" EXACT []
synonym: "monoterpenoid catabolism" EXACT []
synonym: "monoterpenoid degradation" EXACT []
@@ -128634,7 +130636,7 @@
id: GO:0016104
name: triterpenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of triterpenoid compounds, terpenoids with six isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of triterpenoid compounds, terpenoids with six isoprene units." [GOC:curators]
synonym: "triterpene biosynthesis" NARROW []
synonym: "triterpene biosynthetic process" NARROW []
synonym: "triterpenoid anabolism" EXACT []
@@ -128648,7 +130650,7 @@
id: GO:0016105
name: triterpenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of triterpenoid compounds, terpenoids with six isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of triterpenoid compounds, terpenoids with six isoprene units." [GOC:curators]
synonym: "triterpene catabolic process" NARROW []
synonym: "triterpene catabolism" NARROW []
synonym: "triterpenoid breakdown" EXACT []
@@ -128661,7 +130663,7 @@
id: GO:0016106
name: sesquiterpenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units." [GOC:curators]
synonym: "sesquiterpenoid anabolism" EXACT []
synonym: "sesquiterpenoid biosynthesis" EXACT []
synonym: "sesquiterpenoid formation" EXACT []
@@ -128673,7 +130675,7 @@
id: GO:0016107
name: sesquiterpenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sesquiterpenoid compounds, terpenoids with three isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of sesquiterpenoid compounds, terpenoids with three isoprene units." [GOC:curators]
synonym: "sesquiterpenoid breakdown" EXACT []
synonym: "sesquiterpenoid catabolism" EXACT []
synonym: "sesquiterpenoid degradation" EXACT []
@@ -128696,7 +130698,7 @@
id: GO:0016109
name: tetraterpenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of tetraterpenoid compounds, terpenoids with eight isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of tetraterpenoid compounds, terpenoids with eight isoprene units." [GOC:curators]
synonym: "tetraterpene biosynthesis" NARROW []
synonym: "tetraterpene biosynthetic process" NARROW []
synonym: "tetraterpenoid anabolism" EXACT []
@@ -128709,7 +130711,7 @@
id: GO:0016110
name: tetraterpenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of tetraterpenoid compounds, terpenoids with eight isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of tetraterpenoid compounds, terpenoids with eight isoprene units." [GOC:curators]
synonym: "tetraterpene catabolic process" NARROW []
synonym: "tetraterpene catabolism" NARROW []
synonym: "tetraterpenoid breakdown" EXACT []
@@ -128733,7 +130735,7 @@
id: GO:0016112
name: polyterpenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of polyterpenoid compounds, terpenoids with more than eight isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of polyterpenoid compounds, terpenoids with more than eight isoprene units." [GOC:curators]
synonym: "polyterpene biosynthesis" NARROW []
synonym: "polyterpene biosynthetic process" NARROW []
synonym: "polyterpenoid anabolism" EXACT []
@@ -128746,7 +130748,7 @@
id: GO:0016113
name: polyterpenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of polyterpenoid compounds, terpenoids with more than eight isoprene units." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of polyterpenoid compounds, terpenoids with more than eight isoprene units." [GOC:curators]
synonym: "polyterpene catabolic process" NARROW []
synonym: "polyterpene catabolism" NARROW []
synonym: "polyterpenoid breakdown" EXACT []
@@ -128790,7 +130792,7 @@
id: GO:0016117
name: carotenoid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail." [GOC:curators]
synonym: "carotenoid anabolism" EXACT []
synonym: "carotenoid biosynthesis" EXACT []
synonym: "carotenoid formation" EXACT []
@@ -128804,7 +130806,7 @@
id: GO:0016118
name: carotenoid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail." [GOC:curators]
synonym: "carotenoid breakdown" EXACT []
synonym: "carotenoid catabolism" EXACT []
synonym: "carotenoid degradation" EXACT []
@@ -128823,7 +130825,7 @@
id: GO:0016120
name: carotene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids." [GOC:curators]
synonym: "carotene anabolism" EXACT []
synonym: "carotene biosynthesis" EXACT []
synonym: "carotene formation" EXACT []
@@ -128835,7 +130837,7 @@
id: GO:0016121
name: carotene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of carotenes, hydrocarbon carotenoids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of carotenes, hydrocarbon carotenoids." [GOC:curators]
synonym: "carotene breakdown" EXACT []
synonym: "carotene catabolism" EXACT []
synonym: "carotene degradation" EXACT []
@@ -128854,7 +130856,7 @@
id: GO:0016123
name: xanthophyll biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids." [GOC:curators]
synonym: "xanthophyll anabolism" EXACT []
synonym: "xanthophyll biosynthesis" EXACT []
synonym: "xanthophyll formation" EXACT []
@@ -128866,7 +130868,7 @@
id: GO:0016124
name: xanthophyll catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of xanthophylls, oxygen-containing carotenoids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of xanthophylls, oxygen-containing carotenoids." [GOC:curators]
synonym: "xanthophyll breakdown" EXACT []
synonym: "xanthophyll catabolism" EXACT []
synonym: "xanthophyll degradation" EXACT []
@@ -128886,7 +130888,7 @@
id: GO:0016126
name: sterol biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:curators]
synonym: "sterol anabolism" EXACT []
synonym: "sterol biosynthesis" EXACT []
synonym: "sterol formation" EXACT []
@@ -128899,7 +130901,7 @@
id: GO:0016127
name: sterol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule." [GOC:curators]
synonym: "sterol breakdown" EXACT []
synonym: "sterol catabolism" EXACT []
synonym: "sterol degradation" EXACT []
@@ -128920,7 +130922,7 @@
id: GO:0016129
name: phytosteroid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of phytosteroids, steroids that differ from animal steroids in having substitutions at C24 and/or a double bond at C22. Phytosteroids are so named because they occur in higher plants; some, notably ergosterol, are also found in fungi." [GOC:go_curators, GOC:mah, ISBN:0471331309]
+def: "The chemical reactions and pathways resulting in the formation of phytosteroids, steroids that differ from animal steroids in having substitutions at C24 and/or a double bond at C22. Phytosteroids are so named because they occur in higher plants; some, notably ergosterol, are also found in fungi." [GOC:curators, GOC:mah, ISBN:0471331309]
synonym: "phytosteroid anabolism" EXACT []
synonym: "phytosteroid biosynthesis" EXACT []
synonym: "phytosteroid formation" EXACT []
@@ -128931,7 +130933,7 @@
id: GO:0016130
name: phytosteroid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of phytosteroids, steroids that differ from animal steroids in having substitutions at C24 and/or a double bond at C22. Phytosteroids are so named because they occur in higher plants; some, notably ergosterol, are also found in fungi." [GOC:go_curators, GOC:mah]
+def: "The chemical reactions and pathways resulting in the breakdown of phytosteroids, steroids that differ from animal steroids in having substitutions at C24 and/or a double bond at C22. Phytosteroids are so named because they occur in higher plants; some, notably ergosterol, are also found in fungi." [GOC:curators, GOC:mah]
synonym: "phytosteroid breakdown" EXACT []
synonym: "phytosteroid catabolism" EXACT []
synonym: "phytosteroid degradation" EXACT []
@@ -128987,7 +130989,7 @@
id: GO:0016135
name: saponin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of saponins, glycosides of plants in which the aglycan (sapogenin) group is a terpene or steroid and the sugar group is a glucose, a galactose, a pentose, a methylpentose or an oligosaccharide. Saponins are powerful surfactant agents and membrane active; they are, hence, toxic to animals on injection." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of saponins, glycosides of plants in which the aglycan (sapogenin) group is a terpene or steroid and the sugar group is a glucose, a galactose, a pentose, a methylpentose or an oligosaccharide. Saponins are powerful surfactant agents and membrane active; they are, hence, toxic to animals on injection." [GOC:curators]
synonym: "saponin anabolism" EXACT []
synonym: "saponin biosynthesis" EXACT []
synonym: "saponin formation" EXACT []
@@ -128999,7 +131001,7 @@
id: GO:0016136
name: saponin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of saponins, glycosides of plants in which the aglycan (sapogenin) group is a terpene or steroid and the sugar group is a glucose, a galactose, a pentose, a methylpentose or an oligosaccharide. Saponins are powerful surfactant agents and membrane active; they are, hence, toxic to animals on injection." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of saponins, glycosides of plants in which the aglycan (sapogenin) group is a terpene or steroid and the sugar group is a glucose, a galactose, a pentose, a methylpentose or an oligosaccharide. Saponins are powerful surfactant agents and membrane active; they are, hence, toxic to animals on injection." [GOC:curators]
synonym: "saponin breakdown" EXACT []
synonym: "saponin catabolism" EXACT []
synonym: "saponin degradation" EXACT []
@@ -129022,7 +131024,7 @@
name: glycoside biosynthetic process
namespace: biological_process
alt_id: GO:0016141
-def: "The chemical reactions and pathways resulting in the formation of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound." [GOC:curators]
synonym: "glycoside anabolism" EXACT []
synonym: "glycoside biosynthesis" EXACT []
synonym: "glycoside formation" EXACT []
@@ -129040,7 +131042,7 @@
name: glycoside catabolic process
namespace: biological_process
alt_id: GO:0016142
-def: "The chemical reactions and pathways resulting in the breakdown of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound." [GOC:curators]
synonym: "glycoside breakdown" EXACT []
synonym: "glycoside catabolism" EXACT []
synonym: "glycoside degradation" EXACT []
@@ -129188,7 +131190,7 @@
xref: EC:4.2.1.49
xref: KEGG_REACTION:R02914
xref: MetaCyc:UROCANATE-HYDRATASE-RXN
-xref: Reactome:R-HSA-70903 "urocanate + H2O => 4-imidazolone-5-propionate"
+xref: Reactome:R-HSA-70903 "urocanate + H2O => 4-imidazolone-5-propanoate"
xref: RHEA:13101
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.49
@@ -129260,9 +131262,13 @@
xref: EC:2.4.1.13
xref: MetaCyc:SUCROSE-SYNTHASE-RXN
xref: RHEA:16241
+xref: RHEA:55080
+xref: RHEA:55092
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.13
property_value: skos:exactMatch RHEA:16241
+property_value: skos:narrowMatch RHEA:55080
+property_value: skos:narrowMatch RHEA:55092
[Term]
id: GO:0016158
@@ -129278,6 +131284,7 @@
synonym: "phytate 3-phosphatase activity" EXACT []
xref: EC:3.1.3.8
xref: MetaCyc:RXN0-1001
+xref: Reactome:R-HSA-1855225 "IP6 is dephosphorylated to I(1,2,4,5,6)P5 by MINPP1 in the ER lumen"
xref: RHEA:16989
is_a: GO:0004446 ! inositol hexakisphosphate phosphatase activity
property_value: skos:broadMatch EC:3.1.3.62
@@ -129487,7 +131494,7 @@
id: GO:0016174
name: NAD(P)H oxidase H2O2-forming activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + hydrogen peroxide." [EC:1.6.3.1, PMID:10401672, PMID:10601291, PMID:11822874]
+def: "Catalysis of the reaction: NAD(P)H + H+ + O2 = NAD(P)+ + H2O2." [EC:1.6.3.1, PMID:10401672, PMID:10601291, PMID:11822874]
synonym: "dual oxidase activity" RELATED [EC:1.6.3.1]
synonym: "NAD(P)H oxidase activity" BROAD []
synonym: "NAD(P)H:oxygen oxidoreductase activity" RELATED [EC:1.6.3.1]
@@ -129499,7 +131506,7 @@
synonym: "thyroid oxidase 2 activity" NARROW [EC:1.6.3.1]
synonym: "thyroid oxidase activity" NARROW [EC:1.6.3.1]
xref: EC:1.6.3.1
-xref: Reactome:R-HSA-5693681 "DUOX1,2 reduce O2 to H2O2"
+xref: Reactome:R-HSA-5693681 "DUOX1 reduces O2 to H2O2"
xref: Reactome:R-HSA-9698758 "FLT3 ITD- and NOX4-dependent H2O2 production"
xref: RHEA:11260
xref: RHEA:11264
@@ -129715,7 +131722,7 @@
id: GO:0016202
name: regulation of striated muscle tissue development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of striated muscle development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of striated muscle development." [GOC:curators]
is_a: GO:0048634 ! regulation of muscle organ development
is_a: GO:1901861 ! regulation of muscle tissue development
intersection_of: GO:0065007 ! biological regulation
@@ -129768,10 +131775,24 @@
xref: Reactome:R-HSA-175983 "COMT transfer CH3 from AdoMet to 3,4DHBNZ"
xref: Reactome:R-HSA-8955010 "LRTOMT transfers Met to DA, forming 3MT"
xref: RHEA:17877
+xref: RHEA:51268
+xref: RHEA:72243
+xref: RHEA:72247
+xref: RHEA:72251
+xref: RHEA:72255
+xref: RHEA:72259
+xref: RHEA:73719
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.6
property_value: skos:exactMatch RHEA:17877
+property_value: skos:narrowMatch RHEA:51268
+property_value: skos:narrowMatch RHEA:72243
+property_value: skos:narrowMatch RHEA:72247
+property_value: skos:narrowMatch RHEA:72251
+property_value: skos:narrowMatch RHEA:72255
+property_value: skos:narrowMatch RHEA:72259
+property_value: skos:narrowMatch RHEA:73719
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -129804,7 +131825,6 @@
xref: MetaCyc:4-COUMARATE--COA-LIGASE-RXN
xref: RHEA:19641
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.12
property_value: skos:exactMatch RHEA:19641
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -129813,8 +131833,10 @@
id: GO:0016208
name: AMP binding
namespace: molecular_function
-def: "Binding to AMP, adenosine monophosphate." [GOC:go_curators]
+def: "Binding to AMP, adenosine monophosphate." [GOC:curators]
xref: Reactome:R-HSA-380930 "Phosphorylated AMPK binds AMP"
+xref: Reactome:R-HSA-453342 "PYGM dimer, b form + 2 AMP => PYGM b dimer:AMP complex"
+xref: Reactome:R-HSA-453356 "PYGB dimer, b form + 2 AMP => PYGB b dimer:AMP complex"
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
is_a: GO:0043169 ! cation binding
@@ -129856,13 +131878,13 @@
id: GO:0016211
name: ammonia ligase activity
namespace: molecular_function
-def: "Catalysis of the ligation of ammonia (NH3) to another substance via a carbon-nitrogen bond with concomitant breakage of a diphosphate linkage, usually in a nucleoside triphosphate." [GOC:jl]
+def: "Catalysis of the ligation of ammonia (NH4+) to another substance via a carbon-nitrogen bond with concomitant breakage of a diphosphate linkage, usually in a nucleoside triphosphate." [GOC:jl]
is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28243" xsd:anyURI
[Term]
id: GO:0016212
-name: kynurenine-oxoglutarate transaminase activity
+name: L-kynurenine:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2-oxoglutarate + L-kynurenine = H2O + kynurenate + L-glutamate. The product 4-(2-aminophenyl)-2,4-dioxobutanoate is converted into kynurenate by a spontaneous reaction. Also acts on 3-hydroxykynurenine to form xanthurenate." [EC:2.6.1.7]
synonym: "kynurenine 2-oxoglutarate transaminase activity" RELATED [EC:2.6.1.7]
@@ -129870,14 +131892,15 @@
synonym: "kynurenine transaminase (cyclizing)" RELATED [EC:2.6.1.7]
synonym: "kynurenine--oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.7]
synonym: "kynurenine-oxoglutarate aminotransferase activity" EXACT []
+synonym: "kynurenine-oxoglutarate transaminase activity" EXACT []
synonym: "L-kynurenine aminotransferase activity" RELATED [EC:2.6.1.7]
synonym: "L-kynurenine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.7]
xref: EC:2.6.1.7
xref: MetaCyc:RXN-21858
xref: MetaCyc:RXN-21859
xref: Reactome:R-HSA-893583 "kynurenine + 2-oxoglutarate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + glutamate"
-xref: Reactome:R-HSA-893596 "PXLP-KYAT1 dimer transaminates L-KYN to AP-DOBu"
-xref: Reactome:R-HSA-901097 "kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL2]"
+xref: Reactome:R-HSA-893596 "PXLP-KYAT1 dimer transaminates L-KYN to KYNA"
+xref: Reactome:R-HSA-901097 "PXLP-KYAT3 (CCBL2) dimer transaminates L-KYN to KYNA"
xref: RHEA:65560
xref: RHEA:65884
is_a: GO:0008483 ! transaminase activity
@@ -129887,6 +131910,7 @@
property_value: skos:narrowMatch RHEA:65560
property_value: skos:narrowMatch RHEA:65884
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25811" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0016213
@@ -129955,11 +131979,12 @@
[Term]
id: GO:0016217
-name: N-ethylammeline chlorohydrolase activity
+name: obsolete N-ethylammeline chlorohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deethylsimazine + H2O = N-ethylammeline + chloride + H+." [MetaCyc:R465-RXN]
-xref: MetaCyc:R465-RXN
-is_a: GO:0019120 ! hydrolase activity, acting on halide bonds, in C-halide compounds
+def: "OBSOLETE. Catalysis of the reaction: deethylsimazine + H2O = N-ethylammeline + chloride + H+." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0016218
@@ -129987,7 +132012,7 @@
id: GO:0016223
name: beta-alanine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + 2-oxopropanoate = pyruvate + beta-alanine." [RHEA:14077]
+def: "Catalysis of the reaction: L-alanine + 3-oxopropanoate = beta-alanine + pyruvate." [RHEA:14077]
synonym: "beta-alanine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.18]
synonym: "beta-alanine-alpha-alanine transaminase activity" RELATED [EC:2.6.1.18]
synonym: "beta-alanine-pyruvate aminotransferase activity" EXACT []
@@ -129997,7 +132022,7 @@
xref: MetaCyc:2.6.1.18-RXN
xref: Reactome:R-HSA-909776 "beta-alanine + pyruvate => 3-oxopropanoate + alanine"
xref: RHEA:14077
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.18
property_value: skos:exactMatch RHEA:14077
@@ -130064,6 +132089,7 @@
def: "Catalysis of the synthesis of the HKK-1 carbohydrate epitope; adds a sulfate group to a precursor, GlcA-beta-(1->3)-Gal-beta-(1->4)-GlcNAc-beta-(1->R), forming sulfo-3GlcA-beta-(1->3)-Gal-beta-(1->4)-GlcNAc-beta-(1->R)." [PMID:9478973]
synonym: "HNK-1 sulphotransferase activity" EXACT []
xref: Reactome:R-HSA-6786048 "CHST10 transfers SO4(2-) from PAPS to GlcA-LacN on NCAM1"
+xref: Reactome:R-HSA-9940718 "CHST10 sulfates matriglycan chain"
is_a: GO:0008146 ! sulfotransferase activity
[Term]
@@ -130121,7 +132147,7 @@
id: GO:0016239
name: positive regulation of macroautophagy
namespace: biological_process
-def: "Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation." [GOC:go_curators, PMID:9412464]
+def: "Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation." [GOC:curators, PMID:9412464]
synonym: "activation of macroautophagy" NARROW []
synonym: "positive regulation of starvation-induced autophagy" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "stimulation of macroautophagy" NARROW []
@@ -130160,7 +132186,7 @@
id: GO:0016242
name: negative regulation of macroautophagy
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of macroautophagy." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of macroautophagy." [GOC:curators]
synonym: "down regulation of macroautophagy" EXACT []
synonym: "down-regulation of macroautophagy" EXACT []
synonym: "downregulation of macroautophagy" EXACT []
@@ -130304,25 +132330,28 @@
[Term]
id: GO:0016259
-name: selenocysteine metabolic process
+name: obsolete selenocysteine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins." [GOC:curators, ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "selenocysteine metabolism" EXACT []
xref: Reactome:R-HSA-2408522 "Selenoamino acid metabolism"
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0016260
+consider: GO:0016261
[Term]
id: GO:0016260
name: L-selenocysteine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins." [PMID:17880704]
synonym: "selenocysteine anabolism" EXACT []
synonym: "selenocysteine biosynthesis" EXACT []
synonym: "selenocysteine formation" EXACT []
synonym: "selenocysteine synthesis" EXACT []
xref: MetaCyc:PWY-6281
xref: MetaCyc:PWY0-901
-is_a: GO:0016259 ! selenocysteine metabolic process
is_a: GO:0042398 ! modified amino acid biosynthetic process
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
@@ -130332,13 +132361,13 @@
[Term]
id: GO:0016261
-name: selenocysteine catabolic process
+name: L-selenocysteine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of selenocysteine, an essential component of glutathione peroxidase and some other proteins." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of selenocysteine, an essential component of glutathione peroxidase and some other proteins." [PMID:12382038]
synonym: "selenocysteine breakdown" EXACT []
+synonym: "selenocysteine catabolic process" EXACT []
synonym: "selenocysteine catabolism" EXACT []
synonym: "selenocysteine degradation" EXACT []
-is_a: GO:0016259 ! selenocysteine metabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
@@ -130377,11 +132406,17 @@
xref: Reactome:R-HSA-1964505 "C1GALT1 transfers Galactose to the Tn antigen forming Core 1 glycoproteins (T antigens)"
xref: Reactome:R-HSA-6785524 "Defective C1GALT1C1 does not bind C1GALT1"
xref: RHEA:15621
+xref: RHEA:36763
+xref: RHEA:56196
+xref: RHEA:56200
is_a: GO:0035250 ! UDP-galactosyltransferase activity
is_a: GO:0048531 ! beta-1,3-galactosyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
property_value: skos:exactMatch EC:2.4.1.122
property_value: skos:exactMatch RHEA:15621
+property_value: skos:narrowMatch RHEA:36763
+property_value: skos:narrowMatch RHEA:56196
+property_value: skos:narrowMatch RHEA:56200
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30971" xsd:anyURI
[Term]
@@ -130663,9 +132698,11 @@
xref: Reactome:R-HSA-1483002 "DHAP is converted to 1-acyl GO3P by GNPAT"
xref: Reactome:R-HSA-75879 "palmitoyl-CoA + DHAP => 1-palmitoylglycerone phosphate + CoASH"
xref: RHEA:17657
+xref: RHEA:40715
is_a: GO:0016413 ! O-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.42
property_value: skos:exactMatch RHEA:17657
+property_value: skos:narrowMatch RHEA:40715
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -130675,10 +132712,40 @@
def: "Catalysis of the reaction: an acyl-CoA + H2O = a carboxylate + CoA + H+." [RHEA:70423]
synonym: "CoA hydrolase activity" BROAD []
xref: Reactome:R-HSA-193385 "Hydrolysis of choloyl-CoA to cholate and CoASH"
+xref: RHEA:19741
+xref: RHEA:28542
+xref: RHEA:31511
+xref: RHEA:40219
+xref: RHEA:45716
+xref: RHEA:46224
+xref: RHEA:49444
+xref: RHEA:59936
+xref: RHEA:66704
+xref: RHEA:70331
+xref: RHEA:70411
+xref: RHEA:70415
+xref: RHEA:70419
xref: RHEA:70423
+xref: RHEA:70427
+xref: RHEA:78267
is_a: GO:0016790 ! thiolester hydrolase activity
is_a: GO:0160215 ! deacylase activity
property_value: skos:exactMatch RHEA:70423
+property_value: skos:narrowMatch RHEA:19741
+property_value: skos:narrowMatch RHEA:28542
+property_value: skos:narrowMatch RHEA:31511
+property_value: skos:narrowMatch RHEA:40219
+property_value: skos:narrowMatch RHEA:45716
+property_value: skos:narrowMatch RHEA:46224
+property_value: skos:narrowMatch RHEA:49444
+property_value: skos:narrowMatch RHEA:59936
+property_value: skos:narrowMatch RHEA:66704
+property_value: skos:narrowMatch RHEA:70331
+property_value: skos:narrowMatch RHEA:70411
+property_value: skos:narrowMatch RHEA:70415
+property_value: skos:narrowMatch RHEA:70419
+property_value: skos:narrowMatch RHEA:70427
+property_value: skos:narrowMatch RHEA:78267
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26441" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -130751,7 +132818,14 @@
xref: MetaCyc:RXN-7902
xref: MetaCyc:RXN-9549
xref: Reactome:R-HSA-5655955 "OLAH hydrolyzes decanoyl-FASN dimer to DECA and FASN dimer"
+xref: RHEA:15057
+xref: RHEA:30115
+xref: RHEA:30119
+xref: RHEA:30123
+xref: RHEA:30131
+xref: RHEA:41932
xref: RHEA:44596
+xref: RHEA:63204
is_a: GO:0016790 ! thiolester hydrolase activity
property_value: skos:exactMatch MetaCyc:RXN-7902
property_value: skos:exactMatch RHEA:44596
@@ -130762,6 +132836,13 @@
property_value: skos:narrowMatch MetaCyc:3.1.2.14-RXN
property_value: skos:narrowMatch MetaCyc:RXN-10727
property_value: skos:narrowMatch MetaCyc:RXN-9549
+property_value: skos:narrowMatch RHEA:15057
+property_value: skos:narrowMatch RHEA:30115
+property_value: skos:narrowMatch RHEA:30119
+property_value: skos:narrowMatch RHEA:30123
+property_value: skos:narrowMatch RHEA:30131
+property_value: skos:narrowMatch RHEA:41932
+property_value: skos:narrowMatch RHEA:63204
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25677" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -130929,9 +133010,15 @@
xref: Reactome:R-HSA-3772436 "DVL-associated PIP5K1B phosphorylates PI4P to PI(4,5)P2"
xref: Reactome:R-HSA-8868066 "PIP5K1C phosphorylates PI(4)P to PI(4,5)P2"
xref: RHEA:14425
+xref: RHEA:40363
+xref: RHEA:40367
+xref: RHEA:65356
is_a: GO:0052742 ! phosphatidylinositol kinase activity
property_value: skos:exactMatch EC:2.7.1.68
property_value: skos:exactMatch RHEA:14425
+property_value: skos:narrowMatch RHEA:40363
+property_value: skos:narrowMatch RHEA:40367
+property_value: skos:narrowMatch RHEA:65356
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28336" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -130949,9 +133036,11 @@
xref: Reactome:R-HSA-1675776 "PI5P is phosphorylated to PI(4,5)P2 by PIP4K2 dimers at the plasma membrane"
xref: Reactome:R-HSA-6811522 "PI5P is phosphorylated to PI(4,5)P2 by PIP4K2 dimers in the nucleus"
xref: RHEA:12280
+xref: RHEA:55992
is_a: GO:0052742 ! phosphatidylinositol kinase activity
property_value: skos:exactMatch EC:2.7.1.149
property_value: skos:exactMatch RHEA:12280
+property_value: skos:narrowMatch RHEA:55992
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28336" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -131016,9 +133105,13 @@
xref: Reactome:R-HSA-202237 "Hydrolysis of PIP3 to PI(3,4)P2"
xref: Reactome:R-HSA-2317387 "PTEN cancer mutants do not dephosphorylate PIP3"
xref: RHEA:25017
+xref: RHEA:43552
+xref: RHEA:43560
is_a: GO:0034594 ! phosphatidylinositol trisphosphate phosphatase activity
property_value: skos:exactMatch EC:3.1.3.67
property_value: skos:exactMatch RHEA:25017
+property_value: skos:narrowMatch RHEA:43552
+property_value: skos:narrowMatch RHEA:43560
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -131092,7 +133185,7 @@
id: GO:0016323
name: basolateral plasma membrane
namespace: cellular_component
-def: "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:go_curators]
+def: "The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis." [GOC:curators]
is_a: GO:0098590 ! plasma membrane region
relationship: part_of GO:0009925 ! basal plasma membrane
@@ -131335,7 +133428,7 @@
id: GO:0016352
name: obsolete insecticide susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "insecticide susceptibility/resistance" EXACT []
is_obsolete: true
@@ -131345,7 +133438,7 @@
id: GO:0016353
name: obsolete carbamate susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "carbamate susceptibility/resistance" EXACT []
is_obsolete: true
@@ -131355,7 +133448,7 @@
id: GO:0016354
name: obsolete cyclodiene susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "cyclodiene susceptibility/resistance" EXACT []
is_obsolete: true
@@ -131375,7 +133468,7 @@
id: GO:0016356
name: obsolete organophosphorus susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "organophosphorus susceptibility/resistance" EXACT []
is_obsolete: true
@@ -131385,7 +133478,7 @@
id: GO:0016357
name: obsolete pyrethroid susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "pyrethroid susceptibility/resistance" EXACT []
is_obsolete: true
@@ -131403,7 +133496,7 @@
id: GO:0016360
name: sensory organ precursor cell fate determination
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into a sensory organ precursor cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into a sensory organ precursor cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
synonym: "sense organ precursor cell fate determination" EXACT [GOC:dph]
is_a: GO:0060582 ! cell fate determination involved in pattern specification
relationship: part_of GO:0008052 ! sensory organ boundary specification
@@ -131514,15 +133607,16 @@
xref: Reactome:R-HSA-159443 "benzoate + Coenzyme A + ATP => benzoyl-CoA + AMP + pyrophosphate"
xref: Reactome:R-HSA-159567 "ACSM2B-like proteins transform ST to ST-CoA"
xref: Reactome:R-HSA-177157 "phenylacetate + Coenzyme A + ATP => phenylacetyl-CoA + AMP + pyrophosphate"
-xref: Reactome:R-HSA-6798345 "PXLP-GCAT dimer ligates CoASH to 2A-3OB to form Gly and Ac-CoA"
xref: Reactome:R-HSA-9749971 "ACSM2B-like proteins transform 2,5-DHBA to 2,5-DHB-CoA"
-is_a: GO:0016877 ! ligase activity, forming carbon-sulfur bonds
+is_a: GO:0016878 ! acid-thiol ligase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31616" xsd:anyURI
[Term]
id: GO:0016406
name: carnitine O-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an acyl group to an oxygen atom on the carnitine molecule." [GOC:ai]
+xref: Reactome:R-HSA-200410 "CPT2 converts acylcarnitine to acyl-CoA"
is_a: GO:0008374 ! O-acyltransferase activity
[Term]
@@ -131581,9 +133675,27 @@
name: serine O-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a fatty acyl-CoA + L-seryl-[protein] = CoA + O-fatty acyl-L-seryl-[protein]." [RHEA:68272]
+xref: RHEA:59964
+xref: RHEA:59972
xref: RHEA:68272
+xref: RHEA:68276
+xref: RHEA:68280
+xref: RHEA:68284
+xref: RHEA:68288
+xref: RHEA:68292
+xref: RHEA:68296
+xref: RHEA:68300
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch RHEA:68272
+property_value: skos:narrowMatch RHEA:59964
+property_value: skos:narrowMatch RHEA:59972
+property_value: skos:narrowMatch RHEA:68276
+property_value: skos:narrowMatch RHEA:68280
+property_value: skos:narrowMatch RHEA:68284
+property_value: skos:narrowMatch RHEA:68288
+property_value: skos:narrowMatch RHEA:68292
+property_value: skos:narrowMatch RHEA:68296
+property_value: skos:narrowMatch RHEA:68300
[Term]
id: GO:0016413
@@ -131687,7 +133799,7 @@
name: tRNA (guanine) methyltransferase activity
namespace: molecular_function
alt_id: GO:0016424
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine in tRNA = S-adenosyl-L-homocysteine + tRNA containing methylguanine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine in tRNA = S-adenosyl-L-homocysteine + tRNA containing methylguanine." [GOC:curators]
synonym: "tRNA (guanosine) methyltransferase activity" EXACT []
is_a: GO:0008175 ! tRNA methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -131697,7 +133809,7 @@
id: GO:0016426
name: tRNA (adenine) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methyladenine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methyladenine." [GOC:curators]
synonym: "tRNA (adenine-C2-)-methyltransferase activity" BROAD []
is_a: GO:0008175 ! tRNA methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -131706,30 +133818,61 @@
id: GO:0016427
name: tRNA (cytidine) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methylcytosine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing methylcytosine." [GOC:curators]
synonym: "tRNA (cytosine) methyltransferase activity" EXACT []
is_a: GO:0008175 ! tRNA methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0016428
-name: tRNA (cytidine-5-)-methyltransferase activity
+name: tRNA (cytidine-N5)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a cytidine in tRNA + S-adenosyl-L-methionine = a 5-methylcytidine in tRNA + S-adenosyl-L-homocysteine + H+. This modification can occur on seversal residues, including cytidine(34), cytidine(40), cytidine(48), and cytidine(49)." [RHEA:61468]
+def: "Catalysis of the reaction: a cytidine in tRNA + S-adenosyl-L-methionine = a 5-methylcytidine in tRNA + S-adenosyl-L-homocysteine + H+. This modification can occur on several residues, including cytidine(34), cytidine(40), cytidine(48), and cytidine(49)." [RHEA:61468]
synonym: "S-adenosyl-L-methionine:tRNA (cytosine-5-)-methyltransferase activity" RELATED []
synonym: "transfer ribonucleate cytosine 5-methyltransferase activity" RELATED []
synonym: "transfer RNA cytosine 5-methyltransferase activity" RELATED []
+synonym: "tRNA (cytidine-5-)-methyltransferase activity" EXACT []
synonym: "tRNA (cytosine-5-)-methyltransferase activity" EXACT []
+xref: EC:2.1.1.202
xref: Reactome:R-HSA-6782388 "NSUN2 methylates cytidine-34, cytidine-48 of unspliced tRNA(Leu)(CAA)"
xref: Reactome:R-HSA-6782419 "TRDMT1 (DNMT2) methylates cytidine-38 of tRNA(Asp)"
xref: Reactome:R-HSA-6785409 "NSUN2 methylates cytidine-48 and cytidine-49 of tRNA(Asp)(GUC)"
xref: Reactome:R-HSA-6785438 "NSUN2 methylates cytidine-40, cytidine-48, cytidine-49, cytidine-50 of tRNA(GLY)(GCC)"
xref: Reactome:R-HSA-8932765 "NSUN6 methylates cytidine-72 in tRNA(Cys) and tRNA(Thr)"
+xref: RHEA:42940
+xref: RHEA:42944
+xref: RHEA:42948
+xref: RHEA:42952
+xref: RHEA:42956
+xref: RHEA:51160
+xref: RHEA:51164
+xref: RHEA:51172
+xref: RHEA:51180
+xref: RHEA:53076
+xref: RHEA:54136
+xref: RHEA:54140
xref: RHEA:61468
+xref: RHEA:61488
+xref: RHEA:61988
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
property_value: skos:exactMatch RHEA:61468
-property_value: skos:relatedMatch EC:2.1.1.202
+property_value: skos:narrowMatch EC:2.1.1.202
+property_value: skos:narrowMatch RHEA:42940
+property_value: skos:narrowMatch RHEA:42944
+property_value: skos:narrowMatch RHEA:42948
+property_value: skos:narrowMatch RHEA:42952
+property_value: skos:narrowMatch RHEA:42956
+property_value: skos:narrowMatch RHEA:51160
+property_value: skos:narrowMatch RHEA:51164
+property_value: skos:narrowMatch RHEA:51172
+property_value: skos:narrowMatch RHEA:51180
+property_value: skos:narrowMatch RHEA:53076
+property_value: skos:narrowMatch RHEA:54136
+property_value: skos:narrowMatch RHEA:54140
+property_value: skos:narrowMatch RHEA:61488
+property_value: skos:narrowMatch RHEA:61988
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24771" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26109" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -131754,20 +133897,15 @@
[Term]
id: GO:0016430
-name: tRNA (adenine-N6)-methyltransferase activity
+name: obsolete tRNA (adenine-N6)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N6-methyladenine." [EC:2.1.1.55]
+def: "OBSOLETE. Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N6-methyladenine." [EC:2.1.1.55]
+comment: This term was obsoleted because there is no evidence that this reaction exists, see PMID:33658722.
synonym: "S-adenosyl-L-methionine:tRNA (adenine-6-N-)-methyltransferase activity" RELATED [EC:2.1.1.55]
synonym: "S-adenosyl-L-methionine:tRNA (adenine-N6-)-methyltransferase activity" RELATED [EC:2.1.1.55]
synonym: "tRNA (adenine-N6-)-methyltransferase activity" EXACT []
-xref: EC:2.1.1.55
-xref: MetaCyc:TRNA-ADENINE-N6--METHYLTRANSFERASE-RXN
-xref: RHEA:16785
-is_a: GO:0008170 ! N-methyltransferase activity
-is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity
-property_value: skos:exactMatch EC:2.1.1.55
-property_value: skos:exactMatch RHEA:16785
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26109" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0016432
@@ -131777,11 +133915,13 @@
synonym: "S-adenosyl-L-methionine:tRNA-uridine 3-(3-amino-3-carboxypropyl)transferase activity" RELATED [EC:2.5.1.25]
xref: EC:2.5.1.25
xref: MetaCyc:RXN-21179
+xref: RHEA:12300
xref: RHEA:62432
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: skos:exactMatch EC:2.5.1.25
property_value: skos:exactMatch RHEA:62432
+property_value: skos:narrowMatch RHEA:12300
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30175" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -131789,14 +133929,14 @@
id: GO:0016433
name: rRNA (adenine) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine." [GOC:curators]
is_a: GO:0008649 ! rRNA methyltransferase activity
[Term]
id: GO:0016434
name: rRNA (cytosine) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylcytosine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methylcytosine." [GOC:curators]
is_a: GO:0008649 ! rRNA methyltransferase activity
[Term]
@@ -131811,7 +133951,7 @@
id: GO:0016436
name: rRNA (uridine) methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyluridine." [GOC:go-curators]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyluridine." [GOC:curators]
is_a: GO:0008649 ! rRNA methyltransferase activity
[Term]
@@ -132146,7 +134286,7 @@
id: GO:0016479
name: negative regulation of transcription by RNA polymerase I
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:curators]
synonym: "down regulation of transcription from RNA polymerase I promoter" EXACT []
synonym: "down-regulation of transcription from RNA polymerase I promoter" EXACT []
synonym: "downregulation of transcription from RNA polymerase I promoter" EXACT []
@@ -132163,7 +134303,7 @@
id: GO:0016480
name: negative regulation of transcription by RNA polymerase III
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase III." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase III." [GOC:curators]
synonym: "down regulation of transcription from RNA polymerase III promoter" EXACT []
synonym: "down-regulation of transcription from RNA polymerase III promoter" EXACT []
synonym: "downregulation of transcription from RNA polymerase III promoter" EXACT []
@@ -132216,6 +134356,7 @@
synonym: "protein maturation by peptide bond cleavage" EXACT [GOC:bf]
synonym: "protein maturation by peptide bond hydrolysis" EXACT [GOC:mah]
synonym: "protein maturation by proteolysis" RELATED [GOC:mah]
+xref: Reactome:R-HSA-159782 "Removal of aminoterminal propeptides from gamma-carboxylated proteins"
xref: Reactome:R-HSA-9033500 "TYSND1 cleaves peroxisomal proteins"
is_a: GO:0006508 ! proteolysis
is_a: GO:0051604 ! protein maturation
@@ -132235,7 +134376,7 @@
id: GO:0016487
name: farnesol metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving the sesquiterpenoid alcohol farnesol, 3,7,11-trimethyl-2,6,10,dodecatrien-1-ol." [GOC:go_curators]
+def: "The chemical reactions and pathways involving the sesquiterpenoid alcohol farnesol, 3,7,11-trimethyl-2,6,10,dodecatrien-1-ol." [GOC:curators]
synonym: "farnesol metabolism" EXACT []
is_a: GO:0006714 ! sesquiterpenoid metabolic process
is_a: GO:0016093 ! polyprenol metabolic process
@@ -132245,7 +134386,7 @@
id: GO:0016488
name: farnesol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of the sesquiterpenoid alcohol farnesol, 3,7,11-trimethyl-2,6,10,dodecatrien-1-ol." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of the sesquiterpenoid alcohol farnesol, 3,7,11-trimethyl-2,6,10,dodecatrien-1-ol." [GOC:curators]
synonym: "farnesol breakdown" EXACT []
synonym: "farnesol catabolism" EXACT []
synonym: "farnesol degradation" EXACT []
@@ -132280,15 +134421,11 @@
synonym: "redox activity" EXACT []
xref: EC:1.-.-.-
xref: Reactome:R-HSA-1614362 "SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases"
-xref: Reactome:R-HSA-209921 "Monoiodinated tyrosine can be deiodinated"
-xref: Reactome:R-HSA-209960 "Diiodinated tyrosine can be deiodinated"
xref: Reactome:R-HSA-2161612 "PGH2 is reduced to PGF2a by FAM213B"
xref: Reactome:R-HSA-265296 "Arachidonate is oxidised to 5S-HpETE by ALOX5"
xref: Reactome:R-HSA-266051 "5S-HpETE is dehydrated to LTA4 by ALOX5"
xref: Reactome:R-HSA-390425 "FAR1 reduces PalmCoA to HXOL"
xref: Reactome:R-HSA-390438 "FAR2 reduces PalmCoA to HXOL"
-xref: Reactome:R-HSA-5662660 "Dopachrome is transformed to DHICA by DCT"
-xref: Reactome:R-HSA-8878581 "TYRP1 oxidises DHICA to IQCA"
xref: Reactome:R-HSA-8936442 "MARC1,MARC2 reduce N-hydroxylated compounds"
xref: Reactome:R-HSA-9020249 "Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6"
xref: Reactome:R-HSA-9020260 "Hydroperoxy reductase reduces 7(S)-Hp-17(S)-HDHA to RvD5"
@@ -132473,10 +134610,60 @@
synonym: "long-chain-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity" BROAD []
xref: EC:1.1.1.211
xref: MetaCyc:1.1.1.211-RXN
+xref: RHEA:31159
+xref: RHEA:31167
+xref: RHEA:47428
+xref: RHEA:47440
+xref: RHEA:47456
xref: RHEA:52656
+xref: RHEA:78727
+xref: RHEA:78731
+xref: RHEA:78739
+xref: RHEA:82931
+xref: RHEA:82999
+xref: RHEA:83031
+xref: RHEA:83079
+xref: RHEA:83139
+xref: RHEA:83215
+xref: RHEA:83363
+xref: RHEA:83379
+xref: RHEA:83395
+xref: RHEA:84411
+xref: RHEA:84415
+xref: RHEA:84427
+xref: RHEA:84671
+xref: RHEA:84675
+xref: RHEA:84679
+xref: RHEA:84691
+xref: RHEA:85131
is_a: GO:0003857 ! (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.1.1.211
property_value: skos:exactMatch RHEA:52656
+property_value: skos:narrowMatch RHEA:31159
+property_value: skos:narrowMatch RHEA:31167
+property_value: skos:narrowMatch RHEA:47428
+property_value: skos:narrowMatch RHEA:47440
+property_value: skos:narrowMatch RHEA:47456
+property_value: skos:narrowMatch RHEA:78727
+property_value: skos:narrowMatch RHEA:78731
+property_value: skos:narrowMatch RHEA:78739
+property_value: skos:narrowMatch RHEA:82931
+property_value: skos:narrowMatch RHEA:82999
+property_value: skos:narrowMatch RHEA:83031
+property_value: skos:narrowMatch RHEA:83079
+property_value: skos:narrowMatch RHEA:83139
+property_value: skos:narrowMatch RHEA:83215
+property_value: skos:narrowMatch RHEA:83363
+property_value: skos:narrowMatch RHEA:83379
+property_value: skos:narrowMatch RHEA:83395
+property_value: skos:narrowMatch RHEA:84411
+property_value: skos:narrowMatch RHEA:84415
+property_value: skos:narrowMatch RHEA:84427
+property_value: skos:narrowMatch RHEA:84671
+property_value: skos:narrowMatch RHEA:84675
+property_value: skos:narrowMatch RHEA:84679
+property_value: skos:narrowMatch RHEA:84691
+property_value: skos:narrowMatch RHEA:85131
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30577" xsd:anyURI
@@ -132598,7 +134785,7 @@
id: GO:0016525
name: negative regulation of angiogenesis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis." [GOC:curators]
synonym: "down regulation of angiogenesis" EXACT []
synonym: "down-regulation of angiogenesis" EXACT []
synonym: "downregulation of angiogenesis" EXACT []
@@ -132839,6 +135026,7 @@
comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'.
synonym: "mRNA editing" NARROW [GOC:dph, GOC:hjd, GOC:tb]
xref: Reactome:R-HSA-75072 "mRNA Editing"
+xref: Reactome:R-HSA-9937008 "Mitochondrial mRNA modification"
is_a: GO:0009451 ! RNA modification
is_a: GO:0016071 ! mRNA metabolic process
@@ -133122,7 +135310,7 @@
id: GO:0016583
name: obsolete nucleosome modeling
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it has been replaced by more specific terms.
synonym: "nucleosome modeling" EXACT []
is_obsolete: true
@@ -133572,7 +135760,6 @@
def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor." [EC:1.3.-.-]
synonym: "oxidoreductase activity, acting on the CH-CH group of donors, other acceptors" NARROW []
xref: EC:1.3.-.-
-xref: Reactome:R-HSA-2995334 "COX15 transforms heme O to heme A"
xref: Reactome:R-HSA-9661710 "An unknown oxidase oxidises D-UBGN to UBN"
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.3.-.-
@@ -133584,7 +135771,6 @@
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP." [EC:1.3.1.-]
xref: EC:1.3.1.-
-xref: Reactome:R-HSA-4419979 "SRD5A3 reduces pPNOL to DCHOL"
xref: Reactome:R-HSA-4755572 "Defective SRD5A3 does not reduce pPNOL to DCHOL"
xref: Reactome:R-HSA-9661726 "An unknown reductase reduces D-UBGN to STBN"
xref: Reactome:R-HSA-9661745 "An unknown BILR reduces BIL to D-UBGN"
@@ -133837,6 +136023,7 @@
namespace: molecular_function
def: "Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces quinone or similar compound." [GOC:jl]
xref: EC:1.5.5.-
+xref: Reactome:R-HSA-70670 "PRODH oxidises L-Pro to 1PYR-5COOH"
is_a: GO:0016645 ! oxidoreductase activity, acting on the CH-NH group of donors
property_value: skos:exactMatch EC:1.5.5.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -134067,6 +136254,7 @@
def: "Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide." [GOC:jl]
synonym: "oxidoreductase activity, acting on sulphur group of donors, disulphide as acceptor" EXACT []
xref: EC:1.8.4.-
+xref: Reactome:R-HSA-9035484 "MPST and TXN2 enable the synthesis of disulfanide from CysS248-MPST"
is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
property_value: skos:exactMatch EC:1.8.4.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -134112,7 +136300,6 @@
synonym: "oxidoreductase activity, acting on haem group of donors" EXACT []
synonym: "oxidoreductase activity, acting on heme group of donors, other acceptors" NARROW []
xref: EC:1.9.-.-
-xref: Reactome:R-HSA-5340226 "CYGB dioxygenates NO"
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.9.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -134213,7 +136400,7 @@
id: GO:0016688
name: L-ascorbate peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ascorbate + hydrogen peroxide = dehydroascorbate + 2 H2O." [EC:1.11.1.11]
+def: "Catalysis of the reaction: L-ascorbate + H2O2 = dehydroascorbate + 2 H2O." [EC:1.11.1.11]
synonym: "ascorbate peroxidase activity" RELATED [EC:1.11.1.11]
synonym: "ascorbic acid peroxidase activity" RELATED [EC:1.11.1.11]
synonym: "L-ascorbate:hydrogen-peroxide oxidoreductase activity" RELATED [EC:1.11.1.11]
@@ -134231,7 +136418,7 @@
id: GO:0016689
name: manganese peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 Mn2+ + 2 H+ + hydrogen peroxide = 2 Mn3+ + 2 H2O." [EC:1.11.1.13]
+def: "Catalysis of the reaction: 2 Mn2+ + 2 H+ + H2O2 = 2 Mn3+ + 2 H2O." [EC:1.11.1.13]
synonym: "Mn(II):hydrogen-peroxide oxidoreductase activity" RELATED [EC:1.11.1.13]
synonym: "Mn-dependent (NADH-oxidizing) peroxidase activity" RELATED [EC:1.11.1.13]
synonym: "Mn-dependent peroxidase activity" RELATED [EC:1.11.1.13]
@@ -134461,6 +136648,7 @@
def: "Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor." [EC:1.14.-.-]
synonym: "oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, miscellaneous" NARROW []
xref: EC:1.14.-.-
+xref: Reactome:R-HSA-5333612 "MeSebGalNac is oxidatively cleaved to MeSeO2H and 2-acetamidoglucal"
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.14.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -134571,9 +136759,17 @@
xref: EC:1.14.14.82
xref: MetaCyc:FLAVONOID-3-MONOOXYGENASE-RXN
xref: RHEA:16337
+xref: RHEA:61096
+xref: RHEA:61112
+xref: RHEA:61124
+xref: RHEA:79895
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.14.82
property_value: skos:exactMatch RHEA:16337
+property_value: skos:narrowMatch RHEA:61096
+property_value: skos:narrowMatch RHEA:61112
+property_value: skos:narrowMatch RHEA:61124
+property_value: skos:narrowMatch RHEA:79895
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -134598,7 +136794,7 @@
xref: EC:1.14.14.-
xref: EC:1.14.14.1
xref: MetaCyc:UNSPECIFIC-MONOOXYGENASE-RXN
-xref: Reactome:R-HSA-194678 "CYP51A1 demethylates LNSOL"
+xref: Reactome:R-HSA-194678 "CYP51A1 demethylates LAN"
xref: Reactome:R-HSA-211966 "CYP2D6 4-hydroxylates debrisoquine"
xref: RHEA:17149
is_a: GO:0004497 ! monooxygenase activity
@@ -134929,6 +137125,7 @@
xref: EC:2.-.-.-
xref: Reactome:R-HSA-1483089 "PE is converted to PS by PTDSS2"
xref: Reactome:R-HSA-1483186 "PC is converted to PS by PTDSS1"
+xref: Reactome:R-HSA-5333607 "GSSeH combines with bGalNAc derivative to form GSSebGalNac"
xref: Reactome:R-HSA-5668414 "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK"
xref: Reactome:R-HSA-8868783 "TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248"
is_a: GO:0003824 ! catalytic activity
@@ -135168,11 +137365,14 @@
synonym: "uridine diphosphoglucose-cellulose glucosyltransferase activity" RELATED [EC:2.4.1.12]
xref: EC:2.4.1.12
xref: MetaCyc:CELLULOSE-SYNTHASE-UDP-FORMING-RXN
+xref: Reactome:R-HSA-9932210 "Bcs complex synthesizes cellulose from UDP-Glc"
xref: RHEA:19929
+xref: RHEA:63060
is_a: GO:0016759 ! cellulose synthase activity
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.12
property_value: skos:exactMatch RHEA:19929
+property_value: skos:narrowMatch RHEA:63060
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -135309,6 +137509,7 @@
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
subset: goslim_chembl
xref: EC:2.7.-.-
+xref: Reactome:R-HSA-9932322 "BcsG transfers pEtN from PE onto cellulose"
is_a: GO:0016740 ! transferase activity
property_value: skos:exactMatch EC:2.7.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135321,6 +137522,7 @@
subset: goslim_drosophila
xref: EC:2.7.1.-
xref: Reactome:R-HSA-2161193 "abacavir + AMP => abacavir monophosphate + adenosine"
+xref: Reactome:R-HSA-9941039 "FAM20B phosphorylates Xyl moiety"
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
property_value: skos:exactMatch EC:2.7.1.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135389,6 +137591,8 @@
xref: EC:2.7.8.-
xref: Reactome:R-HSA-162742 "(ethanolamineP) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI -> (ethanolamineP) mannose (a1-2) (ethanolamineP) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI"
xref: Reactome:R-HSA-163069 "mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + phosphatidylethanolamine -> (ethanolamineP) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI (acyl-GPI) + diacylglycerol"
+xref: Reactome:R-HSA-9940735 "FKTN transfers RboP to GalNAc-GlcNAc-ManP-DAG1"
+xref: Reactome:R-HSA-9940756 "FKRP dimer transfers RboP to matriglycan chain"
is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
property_value: skos:exactMatch EC:2.7.8.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135423,6 +137627,10 @@
xref: EC:2.8.1.-
xref: Reactome:R-HSA-1614618 "Persulfide sulfur is transferred onto sulfite"
xref: Reactome:R-HSA-6782264 "CTU1:CTU2:URM1 thiolates uridine-34 in tRNAs"
+xref: Reactome:R-HSA-9012721 "MPST transfers sulfur atom from 3MPYR to HSO3- to form S2O3(2-) and PYR"
+xref: Reactome:R-HSA-9013471 "MPST transfers sulfur from 3MPYR to HCN to form HSCN"
+xref: Reactome:R-HSA-9013533 "MPST transfers sulfur from sulfanegen to HCN to form HSCN"
+xref: Reactome:R-HSA-9034756 "MPST transfers sulfur atom from 3MPYR to form CysS248-MPST"
xref: Reactome:R-HSA-947538 "Transfer of sulfur from MOCS3-S-S onto MOCS2A"
is_a: GO:0016782 ! transferase activity, transferring sulphur-containing groups
property_value: skos:exactMatch EC:2.8.1.-
@@ -135439,10 +137647,6 @@
synonym: "mercaptopyruvate sulfurtransferase activity" EXACT []
xref: EC:2.8.1.2
xref: MetaCyc:MERCAPYSTRANS-RXN
-xref: Reactome:R-HSA-9012721 "MPST transfers sulfur atom from 3MPYR to HSO3- to form S2O3(2-) and PYR"
-xref: Reactome:R-HSA-9013471 "MPST transfers sulfur from 3MPYR to HCN to form HSCN"
-xref: Reactome:R-HSA-9013533 "MPST transfers sulfur from sulfanegen to HCN to form HSCN"
-xref: Reactome:R-HSA-9034756 "MPST transfers sulfur atom from 3MPYR to form CysS248-MPST"
xref: RHEA:21740
is_a: GO:0016783 ! sulfurtransferase activity
property_value: skos:exactMatch EC:2.8.1.2
@@ -135486,6 +137690,7 @@
xref: Reactome:R-HSA-6788295 "HDHD1:Mg2+ dephosphorylates PURIDP"
xref: Reactome:R-HSA-8938314 "ENPPs hydrolyse CoA-SH to PPANT, PAP"
xref: Reactome:R-HSA-8952137 "Phospholipid phosphatase 6 hydrolyses Presqualene diphosphate to presqualene monophosphate"
+xref: Reactome:R-HSA-9942295 "QNG1 hydrolyzes queuosine 5'-monophosphate yielding queuine and ribose 5'-monophosphate"
is_a: GO:0003824 ! catalytic activity
property_value: skos:exactMatch EC:3.-.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135535,6 +137740,7 @@
xref: Reactome:R-HSA-4419986 "Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL"
xref: Reactome:R-HSA-9636457 "SapM dephosphorylates PI3P"
xref: Reactome:R-HSA-9837419 "PANK4 hydrolyzes PPANT to pantetheine"
+xref: Reactome:R-HSA-9940993 "PXYLP1 dephosphorylates Xyl moiety"
is_a: GO:0042578 ! phosphoric ester hydrolase activity
property_value: skos:exactMatch EC:3.1.3.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25755" xsd:anyURI
@@ -135608,6 +137814,7 @@
xref: EC:3.2.-.-
xref: Reactome:R-HSA-1793176 "DS is cleaved from its proteoglycan"
xref: Reactome:R-HSA-2065233 "CS is cleaved from its proteoglycan"
+xref: Reactome:R-HSA-5333609 "MeSebGalNac is hydrolysed to MeSeH and bGalNac"
is_a: GO:0016787 ! hydrolase activity
property_value: skos:exactMatch EC:3.2.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135763,7 +137970,7 @@
namespace: molecular_function
def: "Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide." [EC:3.5.2.-]
xref: EC:3.5.2.-
-xref: Reactome:R-HSA-70906 "4-imidazolone-5-propionate + H2O => N-formiminoglutamate + 2H+"
+xref: Reactome:R-HSA-70906 "4-imidazolone-5-propanoate + H2O => N-formiminoglutamate"
is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
property_value: skos:exactMatch EC:3.5.2.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -135976,6 +138183,7 @@
xref: Reactome:R-HSA-6787757 "PXLP-K333-GADL1 decarboxylates acidic AAs"
xref: Reactome:R-HSA-6814165 "PXLP-K333-GADL1 decarboxylates CSA to HTAU"
xref: Reactome:R-HSA-71223 "2-amino-3-carboxymuconate semialdehyde => 2-aminomuconate semialdehyde + CO2"
+xref: Reactome:R-HSA-9856737 "Unknown enzyme(s) process 4-HMA to 4-Hbz"
is_a: GO:0016830 ! carbon-carbon lyase activity
property_value: skos:exactMatch EC:4.1.1.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136035,7 +138243,6 @@
def: "Catalysis of the cleavage of a carbon-oxygen bond by elimination of water." [EC:4.2.1.-]
xref: EC:4.2.1.-
xref: Reactome:R-HSA-2161659 "PGE2 is dehydrated to PGA2"
-xref: Reactome:R-HSA-9014627 "SDS dimers:PXLP dehydrate L-Thr to 2AA"
is_a: GO:0016835 ! carbon-oxygen lyase activity
property_value: skos:exactMatch EC:4.2.1.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136075,7 +138282,7 @@
id: GO:0016840
name: carbon-nitrogen lyase activity
namespace: molecular_function
-def: "Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH3, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99)." [EC:4.3.-.-]
+def: "Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH4+, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99)." [EC:4.3.-.-]
synonym: "other carbon-nitrogen lyase activity" NARROW []
xref: EC:4.3.-.-
is_a: GO:0016829 ! lyase activity
@@ -136152,6 +138359,8 @@
synonym: "carbon-sulphur lyase activity" EXACT []
xref: EC:4.4.-.-
xref: Reactome:R-HSA-1614567 "Excess homocysteine yields homolanthionine and H2S"
+xref: Reactome:R-HSA-1614591 "Excess cysteine yields lanthionine and H2S"
+xref: Reactome:R-HSA-1614614 "Cysteine is degraded to pyruvate and H2S"
is_a: GO:0016829 ! lyase activity
property_value: skos:exactMatch EC:4.4.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136161,7 +138370,7 @@
name: 1-aminocyclopropane-1-carboxylate synthase activity
namespace: molecular_function
alt_id: GO:0034100
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine + H+." [EC:4.4.1.14, RHEA:21744]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine + H+. 1-aminocyclopropane-1-carboxylate (ACC) is a direct precursor of ethylene biosynthesis." [RHEA:21744]
synonym: "1-aminocyclopropane-1-carboxylate synthetase activity" RELATED [EC:4.4.1.14]
synonym: "1-aminocyclopropane-1-carboxylic acid synthase activity" RELATED [EC:4.4.1.14]
synonym: "1-aminocyclopropanecarboxylate synthase activity" RELATED [EC:4.4.1.14]
@@ -136177,10 +138386,11 @@
xref: MetaCyc:4.4.1.14-RXN
xref: RHEA:21744
is_a: GO:0016846 ! carbon-sulfur lyase activity
-relationship: part_of GO:0042218 ! 1-aminocyclopropane-1-carboxylate biosynthetic process
+relationship: part_of GO:0009693 ! ethylene biosynthetic process
property_value: skos:exactMatch EC:4.4.1.14
property_value: skos:exactMatch RHEA:21744
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
[Term]
id: GO:0016848
@@ -136197,10 +138407,9 @@
name: phosphorus-oxygen lyase activity
namespace: molecular_function
def: "Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond." [GOC:jl]
-xref: EC:4.6.-.-
+xref: EC:4.6.1.-
is_a: GO:0016829 ! lyase activity
-property_value: skos:exactMatch EC:4.6.-.-
-property_value: skos:relatedMatch EC:4.6.1.-
+property_value: skos:exactMatch EC:4.6.1.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136272,7 +138481,7 @@
xref: EC:5.-.-.-
xref: Reactome:R-HSA-2161666 "PGA2 is isomerised to PGC2"
xref: Reactome:R-HSA-2161735 "PGC2 is isomerised to PGB2"
-xref: Reactome:R-HSA-6787623 "TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal"
+xref: Reactome:R-HSA-6787623 "GFUS dimer epimerises GDP-DHDMan to GDP-KDGal"
is_a: GO:0003824 ! catalytic activity
property_value: skos:exactMatch EC:5.-.-.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136382,6 +138591,7 @@
def: "Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor are the same molecule, one or more carbon-carbon double bonds in the molecule are rearranged, and no oxidized product appears." [EC:5.3.3.-, GOC:mah]
synonym: "intramolecular isomerase activity, transposing C=C bonds" EXACT []
xref: EC:5.3.3.-
+xref: Reactome:R-HSA-2161563 "PGJ2 is isomerised to delta12-PGJ2"
is_a: GO:0016860 ! intramolecular oxidoreductase activity
property_value: skos:exactMatch EC:5.3.3.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -136576,7 +138786,7 @@
id: GO:0016880
name: acid-ammonia (or amide) ligase activity
namespace: molecular_function
-def: "Catalysis of the ligation of an acid to ammonia (NH3) or an amide via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:jl, GOC:mah]
+def: "Catalysis of the ligation of an acid to ammonia (NH4+) or an amide via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate." [GOC:jl, GOC:mah]
synonym: "amide synthase activity" EXACT []
xref: EC:6.3.1.-
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
@@ -136681,6 +138891,9 @@
xref: Reactome:R-HSA-9668415 "VPS4 mediates disassembly of ESCRTIII subunits to promote sealing of holes in the nuclear envelope"
xref: Reactome:R-HSA-9706399 "RHOBTB3 hydrolyzes ATP"
xref: Reactome:R-HSA-9749350 "ATP-dependent release of CDT1 from the OCCM complex"
+xref: Reactome:R-HSA-9948300 "RQT complex:K63polyUb-80S ribosome dissociates yielding K63polyUb-40S subunit and 60S subunit:peptidyl-tRNA with nascent peptide"
+xref: Reactome:R-HSA-9949632 "VCP hexamer extracts K48 polyubiquitinated alanine-tailed nascent peptide from VCP hexamer:UFD1:NPLOC4:LTN1:NEMF:TCF25:60S ribosome subunit:K48polyUb-nascent peptide"
+xref: Reactome:R-HSA-9955731 "ABCE1:PELO:80S Ribosome:non-stop mRNA:peptidyl-tRNA with elongating peptide dissociates yielding ABCE1:40S ribosomal subunit, PELO, and 60S ribosomal subunit:peptidyl-tRNA with nascent peptide"
xref: RHEA:13065
is_a: GO:0017111 ! ribonucleoside triphosphate phosphatase activity
relationship: part_of GO:0140657 ! ATP-dependent activity
@@ -136808,6 +139021,7 @@
synonym: "exoribonuclease activity, producing 5'-phosphomonoesters" EXACT []
xref: EC:3.1.13.-
xref: Reactome:R-HSA-429860 "DCP1-DCP2 complex decaps mRNA"
+xref: Reactome:R-HSA-9946784 "DENV mRNA is decapped"
is_a: GO:0004532 ! RNA exonuclease activity
property_value: skos:exactMatch EC:3.1.13.-
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
@@ -136939,6 +139153,23 @@
xref: MetaCyc:RXN-8882
xref: MetaCyc:STEROL-GLUCOSYLTRANSFERASE-RXN
xref: RHEA:22724
+xref: RHEA:61812
+xref: RHEA:61816
+xref: RHEA:61820
+xref: RHEA:61824
+xref: RHEA:61828
+xref: RHEA:61832
+xref: RHEA:61836
+xref: RHEA:61840
+xref: RHEA:61844
+xref: RHEA:61848
+xref: RHEA:61852
+xref: RHEA:61888
+xref: RHEA:61940
+xref: RHEA:61944
+xref: RHEA:66276
+xref: RHEA:66280
+xref: RHEA:66284
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.173
property_value: skos:exactMatch MetaCyc:STEROL-GLUCOSYLTRANSFERASE-RXN
@@ -136951,6 +139182,23 @@
property_value: skos:narrowMatch MetaCyc:RXN-16975
property_value: skos:narrowMatch MetaCyc:RXN-8875
property_value: skos:narrowMatch MetaCyc:RXN-8882
+property_value: skos:narrowMatch RHEA:61812
+property_value: skos:narrowMatch RHEA:61816
+property_value: skos:narrowMatch RHEA:61820
+property_value: skos:narrowMatch RHEA:61824
+property_value: skos:narrowMatch RHEA:61828
+property_value: skos:narrowMatch RHEA:61832
+property_value: skos:narrowMatch RHEA:61836
+property_value: skos:narrowMatch RHEA:61840
+property_value: skos:narrowMatch RHEA:61844
+property_value: skos:narrowMatch RHEA:61848
+property_value: skos:narrowMatch RHEA:61852
+property_value: skos:narrowMatch RHEA:61888
+property_value: skos:narrowMatch RHEA:61940
+property_value: skos:narrowMatch RHEA:61944
+property_value: skos:narrowMatch RHEA:66276
+property_value: skos:narrowMatch RHEA:66280
+property_value: skos:narrowMatch RHEA:66284
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25771" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -137242,6 +139490,8 @@
xref: KEGG_REACTION:R01178
xref: MetaCyc:RXN-13449
xref: RHEA:24004
+xref: RHEA:31287
+xref: RHEA:43456
xref: RHEA:47196
xref: UM-BBD_reactionID:r0013
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
@@ -137250,6 +139500,8 @@
property_value: skos:exactMatch MetaCyc:RXN-13449
property_value: skos:exactMatch RHEA:47196
property_value: skos:narrowMatch RHEA:24004
+property_value: skos:narrowMatch RHEA:31287
+property_value: skos:narrowMatch RHEA:43456
property_value: skos:narrowMatch UM-BBD_reactionID:r0013
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23273" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25073" xsd:anyURI
@@ -137284,7 +139536,7 @@
subset: goslim_pir
synonym: "IGF binding protein complex" EXACT []
is_a: GO:0036454 ! growth factor complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0016943
@@ -137484,8 +139736,7 @@
xref: MetaCyc:RXN0-1141
xref: MetaCyc:RXN0-5098
xref: RHEA:49288
-is_a: GO:0016779 ! nucleotidyltransferase activity
-is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
+is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:6.3.1.20
property_value: skos:exactMatch MetaCyc:RXN-17127
@@ -137493,6 +139744,7 @@
property_value: skos:narrowMatch MetaCyc:RXN0-1141
property_value: skos:narrowMatch MetaCyc:RXN0-5098
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31616" xsd:anyURI
[Term]
id: GO:0016980
@@ -137613,7 +139865,7 @@
id: GO:0016990
name: arginine deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3." [EC:3.5.3.6]
+def: "Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH4+." [RHEA:19597]
synonym: "arginine dihydrolase activity" RELATED [EC:3.5.3.6]
synonym: "citrulline iminase activity" RELATED [EC:3.5.3.6]
synonym: "L-arginine deiminase activity" RELATED [EC:3.5.3.6]
@@ -137740,7 +139992,7 @@
name: cell wall macromolecule catabolic process
namespace: biological_process
alt_id: GO:0044039
-def: "The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall." [GOC:curators]
synonym: "cell wall breakdown" RELATED [GOC:mah]
synonym: "cell wall catabolism" RELATED [GOC:mah]
synonym: "cell wall degradation" RELATED [GOC:mah]
@@ -137763,7 +140015,7 @@
id: GO:0017000
name: antibiotic biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:curators]
subset: goslim_metagenomics
synonym: "antibiotic anabolism" EXACT []
synonym: "antibiotic biosynthesis" EXACT []
@@ -137776,7 +140028,7 @@
id: GO:0017001
name: antibiotic catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:curators]
synonym: "antibiotic breakdown" EXACT []
synonym: "antibiotic catabolism" EXACT []
synonym: "antibiotic degradation" EXACT []
@@ -138095,11 +140347,38 @@
xref: Reactome:R-HSA-1606602 "ASAH1 hydrolyzes ceramide"
xref: Reactome:R-HSA-428205 "ACER2 hydrolyzes ceramide (Golgi)"
xref: Reactome:R-HSA-428231 "ACER1 hydrolyzes ceramide (endoplasmic reticulum)"
+xref: Reactome:R-HSA-428262 "ACER3 hydrolyzes phytoceramide"
xref: RHEA:20856
+xref: RHEA:38891
+xref: RHEA:41267
+xref: RHEA:41275
+xref: RHEA:41279
+xref: RHEA:41283
+xref: RHEA:41287
+xref: RHEA:41291
+xref: RHEA:41295
+xref: RHEA:41299
+xref: RHEA:45092
+xref: RHEA:45348
+xref: RHEA:45356
+xref: RHEA:58484
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.23
property_value: skos:exactMatch MetaCyc:CERAMIDASE-RXN
property_value: skos:exactMatch RHEA:20856
+property_value: skos:narrowMatch RHEA:38891
+property_value: skos:narrowMatch RHEA:41267
+property_value: skos:narrowMatch RHEA:41275
+property_value: skos:narrowMatch RHEA:41279
+property_value: skos:narrowMatch RHEA:41283
+property_value: skos:narrowMatch RHEA:41287
+property_value: skos:narrowMatch RHEA:41291
+property_value: skos:narrowMatch RHEA:41295
+property_value: skos:narrowMatch RHEA:41299
+property_value: skos:narrowMatch RHEA:45092
+property_value: skos:narrowMatch RHEA:45348
+property_value: skos:narrowMatch RHEA:45356
+property_value: skos:narrowMatch RHEA:58484
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27364" xsd:anyURI
[Term]
@@ -138179,8 +140458,6 @@
def: "OBSOLETE. Catalysis of the reaction: sphingosine + ATP = sphingosine 1-phosphate + ADP." [RHEA:35847]
comment: This term was obsoleted because it represents a specific substrate of sphingosine kinase activity ; GO:0008481.
synonym: "sphingosine kinase activity" BROAD []
-xref: Reactome:R-HSA-5218845 "p-SPHK1 phosphorylates sphingosine to sphingosine 1-phosphate"
-xref: Reactome:R-HSA-9625814 "SPHK1 phosphorylates sphingosine in response to E2 stimulation"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30243" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008481
@@ -138229,7 +140506,7 @@
id: GO:0017055
name: negative regulation of RNA polymerase II transcription preinitiation complex assembly
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:curators]
synonym: "down regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
synonym: "down-regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
synonym: "downregulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
@@ -138255,11 +140532,10 @@
synonym: "nuclear pore activity" RELATED []
synonym: "nucleocytoplasmic transporter activity" EXACT []
xref: Reactome:R-HSA-1176059 "Translocation of Influenza A virus nonstructural protein 1 (NS1A) into the nucleus"
-xref: Reactome:R-HSA-170796 "NPC transports GCK1:GKRP from cytosol to nucleoplasm"
+xref: Reactome:R-HSA-170796 "NPC transports GCK1:GCKR from cytosol to nucleoplasm"
xref: Reactome:R-HSA-192627 "Viral mRNA Export"
xref: Reactome:R-HSA-192925 "Export of Spliced Viral mRNA"
xref: Reactome:R-HSA-5252041 "NPC transports Hikeshi:HSP70s:ATP from cytosol to nucleoplasm"
-xref: Reactome:R-HSA-5578744 "Importin-8 imports AGO2:miRNA into the nucleus"
xref: Reactome:R-HSA-5661474 "Defective NPC does not transport GCK1:GKRP from cytosol to nucleoplasm"
xref: Reactome:R-HSA-6783483 "tRNA:XPOT:RAN:GTP translocates from the nucleus to the cytosol"
is_a: GO:0005198 ! structural molecule activity
@@ -138281,7 +140557,7 @@
xref: EC:3.1.1.31
xref: KEGG_REACTION:R02035
xref: MetaCyc:6PGLUCONOLACT-RXN
-xref: Reactome:R-HSA-71296 "D-glucono-1,5-lactone 6-phosphate + H2O => 6-phospho-D-gluconate"
+xref: Reactome:R-HSA-71296 "PGLS hydrolyzes D-glucono-1,5-lactone 6-phosphate"
xref: RHEA:12556
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.31
@@ -138292,7 +140568,7 @@
id: GO:0017058
name: FH1 domain binding
namespace: molecular_function
-def: "Binding to a FH1 domain of a protein, a proline-rich domain, usually located in front of a FH2 domain." [GOC:go_curators]
+def: "Binding to a FH1 domain of a protein, a proline-rich domain, usually located in front of a FH2 domain." [GOC:curators]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -138345,10 +140621,14 @@
xref: Reactome:R-HSA-9603986 "FUT3 transfers Fuc to Type 1 chains to form LeA"
xref: RHEA:23628
xref: RHEA:48824
+xref: RHEA:62844
+xref: RHEA:62848
is_a: GO:0008417 ! fucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.65
property_value: skos:exactMatch RHEA:23628
property_value: skos:narrowMatch RHEA:48824
+property_value: skos:narrowMatch RHEA:62844
+property_value: skos:narrowMatch RHEA:62848
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30384" xsd:anyURI
@@ -138586,9 +140866,13 @@
xref: EC:2.4.1.152
xref: MetaCyc:GALACTOSIDE-3-FUCOSYLTRANSFERASE-RXN
xref: RHEA:14257
+xref: RHEA:62828
+xref: RHEA:82143
is_a: GO:0046920 ! alpha-(1->3)-fucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.152
property_value: skos:exactMatch RHEA:14257
+property_value: skos:narrowMatch RHEA:62828
+property_value: skos:narrowMatch RHEA:82143
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -138641,7 +140925,7 @@
id: GO:0017088
name: obsolete X-Pro dipeptidyl-peptidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the hydrolysis of the terminal bond of Xaa-Pro-Xaa motifs to release unblocked, N-terminal dipeptides from substrates including Ala-Pro-para-nitroanilide and (sequentially, at the second, fourth and sixth bonds) of the motif Tyr-Pro-Phe-Pro-Gly-Pro-Ile." [GOC:curator]
+def: "OBSOLETE. Catalysis of the hydrolysis of the terminal bond of Xaa-Pro-Xaa motifs to release unblocked, N-terminal dipeptides from substrates including Ala-Pro-para-nitroanilide and (sequentially, at the second, fourth and sixth bonds) of the motif Tyr-Pro-Phe-Pro-Gly-Pro-Ile." [GOC:curators]
comment: This term was made obsolete because it represents a gene product.
synonym: "X-Pro dipeptidyl-peptidase activity" EXACT []
synonym: "Xaa-Pro dipeptidyl-peptidase activity" EXACT []
@@ -138763,10 +141047,20 @@
xref: MetaCyc:RXN-13451
xref: Reactome:R-HSA-548831 "TECR,TECRL dehydrogenate TOD-CoA to ST-CoA"
xref: RHEA:19181
+xref: RHEA:47232
+xref: RHEA:48216
+xref: RHEA:48220
+xref: RHEA:83051
+xref: RHEA:83291
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
property_value: skos:exactMatch EC:1.3.8.9
property_value: skos:exactMatch MetaCyc:RXN-13451
property_value: skos:exactMatch RHEA:19181
+property_value: skos:narrowMatch RHEA:47232
+property_value: skos:narrowMatch RHEA:48216
+property_value: skos:narrowMatch RHEA:48220
+property_value: skos:narrowMatch RHEA:83051
+property_value: skos:narrowMatch RHEA:83291
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23273" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23497" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
@@ -138873,6 +141167,7 @@
xref: Reactome:R-HSA-5651782 "FEN1 bound to POLB cleaves displaced DNA strand (flap)"
xref: Reactome:R-HSA-5687664 "FEN1 cleaves displaced ssDNA flaps during MMEJ"
xref: Reactome:R-HSA-69152 "Removal of remaining Flap"
+xref: Reactome:R-HSA-9914870 "MGME1 cleaves 5' DNA flap from nascent mitochondrial DNA"
is_a: GO:0016888 ! DNA endonuclease activity, producing 5'-phosphomonoesters
is_a: GO:0048256 ! flap endonuclease activity
@@ -138942,9 +141237,13 @@
xref: Reactome:R-HSA-8851494 "NTPDase7 hydrolyzes nucleoside triphosphates"
xref: Reactome:R-HSA-8851538 "NTPDase8 hydrolyzes nucleoside triphosphates"
xref: RHEA:23680
+xref: RHEA:64900
+xref: RHEA:65580
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.15
property_value: skos:exactMatch RHEA:23680
+property_value: skos:narrowMatch RHEA:64900
+property_value: skos:narrowMatch RHEA:65580
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21232" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23401" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -139018,14 +141317,15 @@
[Term]
id: GO:0017119
-name: Golgi transport complex
+name: COG complex
namespace: cellular_component
def: "A multisubunit tethering complex of the CATCHR family (complexes associated with tethering containing helical rods) that has a role in tethering vesicles to the Golgi prior to fusion. Composed of 8 subunits COG1-8." [GOC:krc, PMID:11980916, PMID:20972446, PMID:9792665]
-synonym: "COG complex" EXACT []
synonym: "conserved oligomeric Golgi complex" EXACT []
+synonym: "Golgi transport complex" EXACT []
synonym: "Sec34/35 complex" NARROW []
is_a: GO:0099023 ! vesicle tethering complex
relationship: part_of GO:0005794 ! Golgi apparatus
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31397" xsd:anyURI
[Term]
id: GO:0017120
@@ -139066,7 +141366,7 @@
id: GO:0017124
name: SH3 domain binding
namespace: molecular_function
-def: "Binding to a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins." [GOC:go_curators, Pfam:PF00018]
+def: "Binding to a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins." [GOC:curators, Pfam:PF00018]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -139095,8 +141395,7 @@
namespace: molecular_function
def: "Catalysis of the movement of phospholipids from one membrane bilayer leaflet to the other, by an ATP-independent mechanism." [GOC:cjm, PMID:20043909, PMID:20302864]
comment: Nomenclature note. Scramblases are ATP-independent, non-selective, translocases inducing non-specific transbilayer movements across the membrane. Flippases and floppases are ATP-dependent transbilayer lipid translocators. According to an extensively used, though not universal, nomenclature, they catalyze lipid transfer towards the inward monolayer (flippases) or towards the outward monolayer (floppases).
-is_a: GO:0005548 ! phospholipid transporter activity
-is_a: GO:0140303 ! intramembrane lipid transporter activity
+is_a: GO:0140303 ! intramembrane lipid carrier activity
relationship: part_of GO:0017121 ! plasma membrane phospholipid scrambling
[Term]
@@ -139192,7 +141491,7 @@
id: GO:0017139
name: obsolete arsenate sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "arsenate sensitivity/resistance" EXACT []
is_obsolete: true
@@ -139202,7 +141501,7 @@
id: GO:0017141
name: obsolete antibiotic susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "antibiotic susceptibility/resistance" EXACT []
is_obsolete: true
@@ -139212,7 +141511,7 @@
id: GO:0017142
name: obsolete toxin susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "toxin susceptibility/resistance" EXACT []
is_obsolete: true
@@ -139347,7 +141646,7 @@
id: GO:0017156
name: calcium-ion regulated exocytosis
namespace: biological_process
-def: "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels." [GOC:go_curators]
+def: "The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels." [GOC:curators]
comment: Note that the calcium regulated exocytosis pathway can be leaky: some level of exocytosis via this pathway occurs spontaneously. This phenomenon underlies spontaneous neurotransmitter release from presynapses. This phenomenon is distinct from the unregulated, calcium independent exocytosis pathway.
synonym: "calcium ion-dependent exocytosis" EXACT []
is_a: GO:0045055 ! regulated exocytosis
@@ -139356,7 +141655,7 @@
id: GO:0017157
name: regulation of exocytosis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of exocytosis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of exocytosis." [GOC:curators]
is_a: GO:0060627 ! regulation of vesicle-mediated transport
is_a: GO:1903530 ! regulation of secretion by cell
intersection_of: GO:0065007 ! biological regulation
@@ -139367,7 +141666,7 @@
id: GO:0017158
name: regulation of calcium ion-dependent exocytosis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:curators]
is_a: GO:1903305 ! regulation of regulated secretory pathway
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0017156 ! calcium-ion regulated exocytosis
@@ -139603,7 +141902,7 @@
id: GO:0017179
name: obsolete peptidyl-diphthine metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving peptidyl-diphthine, a modified histidine residue." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving peptidyl-diphthine, a modified histidine residue." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "peptidyl-diphthine metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25694" xsd:anyURI
@@ -139613,7 +141912,7 @@
id: GO:0017180
name: obsolete protein histidyl modification to diphthine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of peptidyl-diphthine from other compounds, including peptidyl-histidine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of peptidyl-diphthine from other compounds, including peptidyl-histidine." [GOC:curators]
comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "peptidyl-diphthine anabolism from peptidyl-histidine" EXACT []
synonym: "peptidyl-diphthine biosynthetic process from peptidyl-histidine" EXACT []
@@ -139626,7 +141925,7 @@
id: GO:0017181
name: obsolete peptidyl-diphthine catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of peptidyl-diphthine, a modified histidine residue." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of peptidyl-diphthine, a modified histidine residue." [GOC:curators]
comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "peptidyl-diphthine breakdown" EXACT []
synonym: "peptidyl-diphthine catabolism" EXACT []
@@ -139638,7 +141937,7 @@
id: GO:0017182
name: obsolete peptidyl-diphthamide metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving peptidyl-diphthamide, a modified histidine residue." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving peptidyl-diphthamide, a modified histidine residue." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "peptidyl-diphthamide metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25694" xsd:anyURI
@@ -139661,7 +141960,7 @@
id: GO:0017184
name: obsolete peptidyl-diphthamide catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of peptidyl-diphthamide, a modified histidine residue." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of peptidyl-diphthamide, a modified histidine residue." [GOC:curators]
comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "peptidyl-diphthamide breakdown" EXACT []
synonym: "peptidyl-diphthamide catabolism" EXACT []
@@ -139715,7 +142014,7 @@
xref: EC:2.3.1.17
xref: KEGG_REACTION:R00487
xref: MetaCyc:ASPARTATE-N-ACETYLTRANSFERASE-RXN
-xref: Reactome:R-HSA-8954468 "NAT8L transfers acetyl group from Ac-CoA to L-Asp, forming NAA"
+xref: Reactome:R-HSA-8954468 "NAT8L transfers acetyl group from Ac-CoA to L-Asp, forming NAASP"
xref: RHEA:14165
is_a: GO:0140085 ! L-amino-acid N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.17
@@ -141677,14 +143976,13 @@
namespace: biological_process
def: "The alteration of an amino acid residue in a peptide." [GOC:mah]
subset: gocheck_do_not_annotate
-subset: goslim_yeast
is_a: GO:0036211 ! protein modification process
[Term]
id: GO:0018194
name: peptidyl-alanine modification
namespace: biological_process
-def: "The modification of peptidyl-alanine." [GOC:go_curators]
+def: "The modification of peptidyl-alanine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141692,7 +143990,7 @@
id: GO:0018195
name: peptidyl-arginine modification
namespace: biological_process
-def: "The modification of peptidyl-arginine." [GOC:go_curators]
+def: "The modification of peptidyl-arginine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141700,7 +143998,7 @@
id: GO:0018196
name: obsolete peptidyl-asparagine modification
namespace: biological_process
-def: "OBSOLETE. The modification of peptidyl-asparagine." [GOC:go_curators]
+def: "OBSOLETE. The modification of peptidyl-asparagine." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23829" xsd:anyURI
is_obsolete: true
@@ -141717,7 +144015,7 @@
id: GO:0018198
name: peptidyl-cysteine modification
namespace: biological_process
-def: "The modification of peptidyl-cysteine." [GOC:go_curators]
+def: "The modification of peptidyl-cysteine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141725,7 +144023,7 @@
id: GO:0018199
name: peptidyl-glutamine modification
namespace: biological_process
-def: "The modification of peptidyl-glutamine." [GOC:go_curators]
+def: "The modification of peptidyl-glutamine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141733,7 +144031,7 @@
id: GO:0018200
name: peptidyl-glutamic acid modification
namespace: biological_process
-def: "The modification of peptidyl-glutamic acid." [GOC:go_curators]
+def: "The modification of peptidyl-glutamic acid." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141741,7 +144039,7 @@
id: GO:0018201
name: peptidyl-glycine modification
namespace: biological_process
-def: "The modification of peptidyl-glycine." [GOC:go_curators]
+def: "The modification of peptidyl-glycine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141757,7 +144055,7 @@
id: GO:0018203
name: peptidyl-isoleucine modification
namespace: biological_process
-def: "The modification of peptidyl-isoleucine." [GOC:go_curators]
+def: "The modification of peptidyl-isoleucine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141765,7 +144063,7 @@
id: GO:0018204
name: peptidyl-leucine modification
namespace: biological_process
-def: "The modification of peptidyl-leucine." [GOC:go_curators]
+def: "The modification of peptidyl-leucine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141773,7 +144071,7 @@
id: GO:0018205
name: peptidyl-lysine modification
namespace: biological_process
-def: "The modification of peptidyl-lysine." [GOC:go_curators]
+def: "The modification of peptidyl-lysine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141781,7 +144079,7 @@
id: GO:0018206
name: peptidyl-methionine modification
namespace: biological_process
-def: "The modification of peptidyl-methionine." [GOC:go_curators]
+def: "The modification of peptidyl-methionine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141789,7 +144087,7 @@
id: GO:0018207
name: peptidyl-phenylalanine modification
namespace: biological_process
-def: "The modification of peptidyl-phenylalanine." [GOC:go_curators]
+def: "The modification of peptidyl-phenylalanine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141797,7 +144095,7 @@
id: GO:0018208
name: peptidyl-proline modification
namespace: biological_process
-def: "The modification of peptidyl-proline." [GOC:go_curators]
+def: "The modification of peptidyl-proline." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141805,7 +144103,7 @@
id: GO:0018209
name: peptidyl-serine modification
namespace: biological_process
-def: "The modification of peptidyl-serine." [GOC:go_curators]
+def: "The modification of peptidyl-serine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141813,7 +144111,7 @@
id: GO:0018210
name: peptidyl-threonine modification
namespace: biological_process
-def: "The modification of peptidyl-threonine." [GOC:go_curators]
+def: "The modification of peptidyl-threonine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141829,7 +144127,7 @@
id: GO:0018212
name: peptidyl-tyrosine modification
namespace: biological_process
-def: "The modification of peptidyl-tyrosine." [GOC:go_curators]
+def: "The modification of peptidyl-tyrosine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -141837,7 +144135,7 @@
id: GO:0018213
name: peptidyl-valine modification
namespace: biological_process
-def: "The modification of peptidyl-valine." [GOC:go_curators]
+def: "The modification of peptidyl-valine." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0018193 ! peptidyl-amino acid modification
@@ -142392,15 +144690,6 @@
def: "OBSOLETE. Catalysis of the reaction: ATP + biotin + protein = AMP + diphosphate + biotin-protein." [GOC:mah]
comment: The reason for obsoletion is this term is an unnecessary grouping term.
synonym: "biotin-apoprotein ligase activity" EXACT []
-xref: Reactome:R-HSA-2993447 "HLCS biotinylates 6x(PCCA:PCCB)"
-xref: Reactome:R-HSA-2993799 "HLCS biotinylates 6xMCCC1:6xMCCC2"
-xref: Reactome:R-HSA-2993802 "HLCS biotinylates PC:Mn2+"
-xref: Reactome:R-HSA-2993814 "HLCS biotinylates ACACA:Mn2+"
-xref: Reactome:R-HSA-3323184 "Defective HLCS does not biotinylate ACACA:Mn2+"
-xref: Reactome:R-HSA-4167511 "HLCS biotinylates ACACB"
-xref: Reactome:R-HSA-9035987 "Defective HLCS does not biotinylate 6xMCCC1:6xMCCC2"
-xref: Reactome:R-HSA-9035988 "Defective HLCS does not biotinylate PC:Mn2+"
-xref: Reactome:R-HSA-9035990 "Defective HLCS does not biotinylate 6x(PCCA:PCCB)"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28107" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004077
@@ -142479,9 +144768,6 @@
def: "OBSOLETE. The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification." [GOC:jsg]
comment: The reason for obsoletion is that this term is equivalent to protein N-linked glycosylation.
synonym: "protein amino acid N-linked glycosylation via asparagine" EXACT [GOC:bf]
-xref: Reactome:R-HSA-162699 "Synthesis of dolichyl-phosphate mannose"
-xref: Reactome:R-HSA-446203 "Asparagine N-linked glycosylation"
-xref: Reactome:R-HSA-480985 "Synthesis of dolichyl-phosphate-glucose"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30880" xsd:anyURI
is_obsolete: true
replaced_by: GO:0006487
@@ -143952,10 +146238,92 @@
synonym: "short chain beta-ketoacetyl(acetoacetyl)-CoA reductase activity" RELATED [EC:1.1.1.36]
xref: EC:1.1.1.36
xref: RHEA:22256
+xref: RHEA:39151
+xref: RHEA:39163
+xref: RHEA:39171
+xref: RHEA:39183
+xref: RHEA:39195
+xref: RHEA:39207
+xref: RHEA:39219
+xref: RHEA:39231
+xref: RHEA:39243
+xref: RHEA:39255
+xref: RHEA:39299
+xref: RHEA:39311
+xref: RHEA:39323
+xref: RHEA:39335
+xref: RHEA:39339
+xref: RHEA:39359
+xref: RHEA:39371
+xref: RHEA:39383
+xref: RHEA:39395
+xref: RHEA:39407
+xref: RHEA:39419
+xref: RHEA:39435
+xref: RHEA:39447
+xref: RHEA:39459
+xref: RHEA:39471
+xref: RHEA:39483
+xref: RHEA:39495
+xref: RHEA:39507
+xref: RHEA:39519
+xref: RHEA:39531
+xref: RHEA:39543
+xref: RHEA:39555
+xref: RHEA:39575
+xref: RHEA:39587
+xref: RHEA:39599
+xref: RHEA:39611
+xref: RHEA:39623
+xref: RHEA:39635
+xref: RHEA:45796
+xref: RHEA:45844
+xref: RHEA:45848
xref: UM-BBD_reactionID:r0202
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.36
property_value: skos:exactMatch RHEA:22256
+property_value: skos:narrowMatch RHEA:39151
+property_value: skos:narrowMatch RHEA:39163
+property_value: skos:narrowMatch RHEA:39171
+property_value: skos:narrowMatch RHEA:39183
+property_value: skos:narrowMatch RHEA:39195
+property_value: skos:narrowMatch RHEA:39207
+property_value: skos:narrowMatch RHEA:39219
+property_value: skos:narrowMatch RHEA:39231
+property_value: skos:narrowMatch RHEA:39243
+property_value: skos:narrowMatch RHEA:39255
+property_value: skos:narrowMatch RHEA:39299
+property_value: skos:narrowMatch RHEA:39311
+property_value: skos:narrowMatch RHEA:39323
+property_value: skos:narrowMatch RHEA:39335
+property_value: skos:narrowMatch RHEA:39339
+property_value: skos:narrowMatch RHEA:39359
+property_value: skos:narrowMatch RHEA:39371
+property_value: skos:narrowMatch RHEA:39383
+property_value: skos:narrowMatch RHEA:39395
+property_value: skos:narrowMatch RHEA:39407
+property_value: skos:narrowMatch RHEA:39419
+property_value: skos:narrowMatch RHEA:39435
+property_value: skos:narrowMatch RHEA:39447
+property_value: skos:narrowMatch RHEA:39459
+property_value: skos:narrowMatch RHEA:39471
+property_value: skos:narrowMatch RHEA:39483
+property_value: skos:narrowMatch RHEA:39495
+property_value: skos:narrowMatch RHEA:39507
+property_value: skos:narrowMatch RHEA:39519
+property_value: skos:narrowMatch RHEA:39531
+property_value: skos:narrowMatch RHEA:39543
+property_value: skos:narrowMatch RHEA:39555
+property_value: skos:narrowMatch RHEA:39575
+property_value: skos:narrowMatch RHEA:39587
+property_value: skos:narrowMatch RHEA:39599
+property_value: skos:narrowMatch RHEA:39611
+property_value: skos:narrowMatch RHEA:39623
+property_value: skos:narrowMatch RHEA:39635
+property_value: skos:narrowMatch RHEA:45796
+property_value: skos:narrowMatch RHEA:45844
+property_value: skos:narrowMatch RHEA:45848
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25814" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -143984,9 +146352,17 @@
xref: EC:1.1.1.90
xref: MetaCyc:ARYL-ALCOHOL-DEHYDROGENASE-RXN
xref: RHEA:12076
+xref: RHEA:64696
+xref: RHEA:65044
+xref: RHEA:65048
+xref: RHEA:65052
is_a: GO:0004022 ! alcohol dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.1.1.90
property_value: skos:exactMatch RHEA:12076
+property_value: skos:narrowMatch RHEA:64696
+property_value: skos:narrowMatch RHEA:65044
+property_value: skos:narrowMatch RHEA:65048
+property_value: skos:narrowMatch RHEA:65052
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27136" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -144403,7 +146779,7 @@
id: GO:0018488
name: aryl-aldehyde oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an aromatic aldehyde + O2 + H2O = an aromatic acid + hydrogen peroxide." [EC:1.2.3.9]
+def: "Catalysis of the reaction: an aromatic aldehyde + O2 + H2O = an aromatic carboxylate + H2O2 + H+." [RHEA:18569]
synonym: "aryl-aldehyde:oxygen oxidoreductase activity" RELATED [EC:1.2.3.9]
xref: EC:1.2.3.9
xref: MetaCyc:ARYL-ALDEHYDE-OXIDASE-RXN
@@ -144411,6 +146787,12 @@
xref: MetaCyc:RXN-8090
xref: MetaCyc:RXN-8091
xref: RHEA:18569
+xref: RHEA:58960
+xref: RHEA:58968
+xref: RHEA:58972
+xref: RHEA:58992
+xref: RHEA:58996
+xref: RHEA:59008
xref: UM-BBD_reactionID:r0145
is_a: GO:0004031 ! aldehyde oxidase activity
property_value: skos:exactMatch EC:1.2.3.9
@@ -144418,6 +146800,12 @@
property_value: skos:narrowMatch MetaCyc:RXN-8089
property_value: skos:narrowMatch MetaCyc:RXN-8090
property_value: skos:narrowMatch MetaCyc:RXN-8091
+property_value: skos:narrowMatch RHEA:58960
+property_value: skos:narrowMatch RHEA:58968
+property_value: skos:narrowMatch RHEA:58972
+property_value: skos:narrowMatch RHEA:58992
+property_value: skos:narrowMatch RHEA:58996
+property_value: skos:narrowMatch RHEA:59008
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -144953,7 +147341,7 @@
id: GO:0018527
name: cyclohexylamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohexylamine + O2 + H2O = cyclohexanone + NH3 + hydrogen peroxide." [PMID:18451, RHEA:18433]
+def: "Catalysis of the reaction: cyclohexylamine + O2 + H2O = cyclohexanone + H2O2 + NH4+." [PMID:18451, RHEA:18433]
synonym: "cyclohexylamine:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.12]
xref: EC:1.4.3.12
xref: MetaCyc:CYCLOHEXYLAMINE-OXIDASE-RXN
@@ -145001,7 +147389,7 @@
xref: MetaCyc:R-6-HYDROXYNICOTINE-OXIDASE-RXN
xref: RHEA:10012
xref: UM-BBD_reactionID:r0477
-is_a: GO:0019116 ! hydroxy-nicotine oxidase activity
+is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.5.3.6
property_value: skos:exactMatch RHEA:10012
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -145021,7 +147409,7 @@
xref: MetaCyc:S-6-HYDROXYNICOTINE-OXIDASE-RXN
xref: RHEA:11880
xref: UM-BBD_reactionID:r0478
-is_a: GO:0019116 ! hydroxy-nicotine oxidase activity
+is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.5.3.5
property_value: skos:exactMatch RHEA:11880
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -145190,7 +147578,6 @@
def: "OBSOLETE. Catalysis of the removal of one or more nitrite (NO2-) groups from nitroglycerin or a derivative." [GOC:curators]
comment: This term was obsoleted because there is no evidence that this specific reaction exists.
synonym: "NG reductase activity" EXACT []
-xref: Reactome:R-HSA-9620103 "ALDH2 transforms GTN to NO"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28261" xsd:anyURI
is_obsolete: true
@@ -145207,7 +147594,7 @@
id: GO:0018549
name: methanethiol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: methanethiol + O2 + H2O = formaldehyde + hydrogen sulfide + hydrogen peroxide." [EC:1.8.3.4]
+def: "Catalysis of the reaction: methanethiol + O2 + H2O = hydrogen sulfide + formaldehyde + H2O2 + H+." [RHEA:11812]
synonym: "(MM)-oxidase activity" RELATED [EC:1.8.3.4]
synonym: "methanethiol:oxygen oxidoreductase activity" RELATED [EC:1.8.3.4]
synonym: "methyl mercaptan oxidase activity" RELATED [EC:1.8.3.4]
@@ -145965,7 +148352,7 @@
id: GO:0018618
name: anthranilate 1,2-dioxygenase (deaminating, decarboxylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: anthranilate + NADPH + H+ + O2 = catechol + CO2 + NADP+ + NH3." [EC:1.14.12.1]
+def: "Catalysis of the reaction: anthranilate + NAD(P)H + O2 + 3 H+ = catechol + NH4+ + CO2 + NAD(P)+." [EC:1.14.12.1]
synonym: "AntA" RELATED []
synonym: "AntB" RELATED []
synonym: "AntC" RELATED []
@@ -146117,10 +148504,12 @@
synonym: "2-chlorobenzoate,NADH:oxygen oxidoreductase (1,2-hydroxylating, dechlorinating, decarboxylating)" RELATED [EC:1.14.12.13]
xref: EC:1.14.12.13
xref: MetaCyc:RXN-13706
+xref: RHEA:21652
xref: RHEA:53736
is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
property_value: skos:exactMatch EC:1.14.12.13
property_value: skos:exactMatch RHEA:53736
+property_value: skos:narrowMatch RHEA:21652
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30179" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -147278,30 +149667,30 @@
[Term]
id: GO:0018711
-name: benzoyl acetate-CoA thiolase activity
+name: obsolete benzoyl acetate-CoA thiolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzoyl acetyl-CoA + CoA = acetyl-CoA + benzoyl-CoA." [UM-BBD_reactionID:r0243]
-xref: MetaCyc:RXN-2006
-xref: UM-BBD_reactionID:r0243
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+def: "OBSOLETE. Catalysis of the reaction: benzoyl acetyl-CoA + CoA = acetyl-CoA + benzoyl-CoA." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018712
-name: 3-hydroxybutyryl-CoA thiolase activity
+name: obsolete 3-hydroxybutyryl-CoA thiolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-5-oxohexanoyl-CoA + CoASH = 3-hydroxybutyryl-CoA + acetyl-CoA." [UM-BBD_reactionID:r0010]
-xref: MetaCyc:R7-RXN
-xref: UM-BBD_reactionID:r0010
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+def: "OBSOLETE. Catalysis of the reaction: 3-hydroxy-5-oxohexanoyl-CoA + CoASH = 3-hydroxybutyryl-CoA + acetyl-CoA." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018713
-name: 3-ketopimelyl-CoA thiolase activity
+name: obsolete 3-ketopimelyl-CoA thiolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-ketopimeloyl-CoA + CoA = glutaryl-CoA + acetyl-CoA." [UM-BBD_reactionID:r0197]
-xref: MetaCyc:RXN-8032
-xref: UM-BBD_reactionID:r0197
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+def: "OBSOLETE. Catalysis of the reaction: 3-ketopimeloyl-CoA + CoA = glutaryl-CoA + acetyl-CoA." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018715
@@ -147341,12 +149730,18 @@
[Term]
id: GO:0018719
-name: 6-aminohexanoate transaminase activity
+name: 6-aminohexanoate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-aminohexanoate + alpha-ketoglutarate = glutamate + 6-oxohexanoate." [UM-BBD_reactionID:r0449]
+def: "Catalysis of the reaction: 6-aminohexanoate + 2-oxoglutarate = 6-oxohexanoate + L-glutamate." [RHEA:58200]
+synonym: "6-aminohexanoate aminotransferase activity" EXACT []
+xref: EC:2.6.1.116
xref: MetaCyc:R562-RXN
+xref: RHEA:58200
xref: UM-BBD_reactionID:r0449
is_a: GO:0008483 ! transaminase activity
+property_value: skos:exactMatch EC:2.6.1.116
+property_value: skos:exactMatch RHEA:58200
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0018720
@@ -147681,7 +150076,7 @@
id: GO:0018750
name: biuret amidohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: biuret + H2O = urea + CO2 + NH3." [EC:3.5.1.84]
+def: "Catalysis of the reaction: biuret + H2O = urea-1-carboxylate + NH4+." [RHEA:17525]
xref: EC:3.5.1.84
xref: RHEA:17525
xref: UM-BBD_reactionID:r0846
@@ -147701,12 +150096,12 @@
[Term]
id: GO:0018752
-name: epsilon-caprolactam lactamase activity
+name: obsolete epsilon-caprolactam lactamase activity
namespace: molecular_function
-def: "Catalysis of the reaction: epsilon-caprolactam + H2O = H+ + 6-aminohexanoate." [UM-BBD_reactionID:r0448]
-xref: MetaCyc:R561-RXN
-xref: UM-BBD_reactionID:r0448
-is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
+def: "OBSOLETE. Catalysis of the reaction: epsilon-caprolactam + H2O = H+ + 6-aminohexanoate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018753
@@ -147725,40 +150120,49 @@
[Term]
id: GO:0018754
-name: ammelide aminohydrolase activity
+name: obsolete ammelide aminohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ammelide + H2O = cyanuric acid + NH3." [PMID:1991731]
+def: "OBSOLETE. Catalysis of the reaction: ammelide + H2O = cyanuric acid + NH4+." [PMID:1991731]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: MetaCyc:RXN-8017
-is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018755
-name: 2-chloro-4-hydroxy-6-amino-1,3,5-triazine aminohydrolase activity
+name: obsolete 2-chloro-4-hydroxy-6-amino-1,3,5-triazine aminohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-chloro-4-hydroxy-6-amino-1,3,5-triazine + OH- = 2,4-dihydroxy-6-amino-1,3,5-triazine + Cl-." [UM-BBD_reactionID:r1414]
-xref: UM-BBD_reactionID:r1414
-is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
+def: "OBSOLETE. Catalysis of the reaction: 2-chloro-4-hydroxy-6-amino-1,3,5-triazine + OH- = 2,4-dihydroxy-6-amino-1,3,5-triazine + Cl-." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018756
name: ammeline aminohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ammeline + H2O = ammelide + NH3." [PMID:1991731]
+def: "Catalysis of the reaction: ammeline + H2O = ammelide + NH4+. Also converts melamine to ammeline." [EC:3.5.4.45, PMID:1991731]
+xref: EC:3.5.4.45
xref: MetaCyc:RXN-8016
+xref: RHEA:26197
xref: RHEA:26201
is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
-property_value: skos:exactMatch RHEA:26201
+property_value: skos:exactMatch EC:3.5.4.45
+property_value: skos:narrowMatch RHEA:26197
+property_value: skos:narrowMatch RHEA:26201
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0018757
-name: deisopropylhydroxyatrazine aminohydrolase activity
+name: obsolete deisopropylhydroxyatrazine aminohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: deisopropylhydroxyatrazine + H2O = NH3 + 2,4-dihydroxy-6-(N'-ethyl)amino-1,3,5-triazine." [UM-BBD_reactionID:r0121]
+def: "OBSOLETE. Catalysis of the reaction: deisopropylhydroxyatrazine + H2O = NH4+ + 2,4-dihydroxy-6-(N'-ethyl)amino-1,3,5-triazine." [UM-BBD_reactionID:r0121]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: KEGG_REACTION:R05574
xref: UM-BBD_reactionID:r0121
-is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018758
@@ -147826,7 +150230,7 @@
id: GO:0018762
name: aliphatic nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: R-CN + H2O = R-COOH + NH3." [EC:3.5.5.7]
+def: "Catalysis of the reaction: an aliphatic nitrile + 2 H2O = a carboxylate + NH4+." [RHEA:46188]
synonym: "aliphatic nitrile aminohydrolase activity" RELATED [EC:3.5.5.7]
xref: EC:3.5.5.7
xref: MetaCyc:3.5.5.7-RXN
@@ -147886,13 +150290,12 @@
[Term]
id: GO:0018766
-name: dihydrophloroglucinol hydrolase activity
+name: obsolete dihydrophloroglucinol hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dihydrophloroglucinol + OH- = 3-hydroxy-5-oxohexanoate." [UM-BBD_reactionID:r0008]
-xref: KEGG_REACTION:R07831
-xref: MetaCyc:R6-RXN
-xref: UM-BBD_reactionID:r0008
-is_a: GO:0016823 ! hydrolase activity, acting on carbon-carbon bonds, in ketonic substances
+def: "OBSOLETE. Catalysis of the reaction: dihydrophloroglucinol + OH- = 3-hydroxy-5-oxohexanoate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018767
@@ -147954,12 +150357,12 @@
[Term]
id: GO:0018772
-name: trioxoheptanoate hydrolase activity
+name: obsolete trioxoheptanoate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4,6-trioxoheptanoate + H2O = acetylpyruvate + acetate." [MetaCyc:R306-RXN, UM-BBD_reactionID:r0094]
-xref: MetaCyc:R306-RXN
-xref: UM-BBD_reactionID:r0094
-is_a: GO:0016823 ! hydrolase activity, acting on carbon-carbon bonds, in ketonic substances
+def: "OBSOLETE. Catalysis of the reaction: 2,4,6-trioxoheptanoate + H2O = acetylpyruvate + acetate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018773
@@ -148119,11 +150522,15 @@
xref: EC:3.8.1.3
xref: MetaCyc:HALOACETATE-DEHALOGENASE-RXN
xref: RHEA:11044
+xref: RHEA:25189
+xref: RHEA:30051
xref: UM-BBD_enzymeID:r0004
xref: UM-BBD_enzymeID:r1028
is_a: GO:0019120 ! hydrolase activity, acting on halide bonds, in C-halide compounds
property_value: skos:exactMatch EC:3.8.1.3
property_value: skos:exactMatch RHEA:11044
+property_value: skos:narrowMatch RHEA:25189
+property_value: skos:narrowMatch RHEA:30051
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -148423,12 +150830,12 @@
[Term]
id: GO:0018811
-name: cyclohex-1-ene-1-carboxyl-CoA hydratase activity
+name: obsolete cyclohex-1-ene-1-carboxyl-CoA hydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclohex-1-ene-1-carboxyl-CoA + H2O = 2-hydroxycyclohexane-1-carboxyl-CoA." [MetaCyc:R266-RXN, UM-BBD_reactionID:r0191]
-xref: MetaCyc:R266-RXN
-xref: UM-BBD_reactionID:r0191
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: cyclohex-1-ene-1-carboxyl-CoA + H2O = 2-hydroxycyclohexane-1-carboxyl-CoA." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018812
@@ -148447,6 +150854,11 @@
xref: Reactome:R-HSA-8957389 "RPP14 (HTD2) dehydrates 3HA-CoA to t2E-CoA"
xref: RHEA:16105
xref: RHEA:33767
+xref: RHEA:35347
+xref: RHEA:35355
+xref: RHEA:35359
+xref: RHEA:46348
+xref: RHEA:46352
xref: RHEA:52664
xref: RHEA:71647
is_a: GO:0004300 ! enoyl-CoA hydratase activity
@@ -148455,6 +150867,11 @@
property_value: skos:narrowMatch EC:4.2.1.74
property_value: skos:narrowMatch MetaCyc:ENOYL-COA-HYDRAT-RXN
property_value: skos:narrowMatch RHEA:16105
+property_value: skos:narrowMatch RHEA:35347
+property_value: skos:narrowMatch RHEA:35355
+property_value: skos:narrowMatch RHEA:35359
+property_value: skos:narrowMatch RHEA:46348
+property_value: skos:narrowMatch RHEA:46352
property_value: skos:narrowMatch RHEA:52664
property_value: skos:narrowMatch RHEA:71647
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24738" xsd:anyURI
@@ -148496,12 +150913,12 @@
[Term]
id: GO:0018815
-name: 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon hydratase-aldolase activity
+name: obsolete 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon hydratase-aldolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon + H2O = 2-oxobut-3-enanoate + 2,5,6-trihydroxy-3-methylpyridine." [MetaCyc:RXN-645, UM-BBD_reactionID:r0051]
-xref: MetaCyc:RXN-645
-xref: UM-BBD_reactionID:r0051
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon + H2O = 2-oxobut-3-enanoate + 2,5,6-trihydroxy-3-methylpyridine." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018816
@@ -148599,9 +151016,29 @@
xref: EC:4.2.1.84
xref: MetaCyc:NITRILE-HYDRATASE-RXN
xref: RHEA:12673
+xref: RHEA:85603
+xref: RHEA:85607
+xref: RHEA:85611
+xref: RHEA:85643
+xref: RHEA:85647
+xref: RHEA:85651
+xref: RHEA:85655
+xref: RHEA:85671
+xref: RHEA:85691
+xref: RHEA:85695
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.84
property_value: skos:exactMatch RHEA:12673
+property_value: skos:narrowMatch RHEA:85603
+property_value: skos:narrowMatch RHEA:85607
+property_value: skos:narrowMatch RHEA:85611
+property_value: skos:narrowMatch RHEA:85643
+property_value: skos:narrowMatch RHEA:85647
+property_value: skos:narrowMatch RHEA:85651
+property_value: skos:narrowMatch RHEA:85655
+property_value: skos:narrowMatch RHEA:85671
+property_value: skos:narrowMatch RHEA:85691
+property_value: skos:narrowMatch RHEA:85695
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -148657,7 +151094,7 @@
id: GO:0018826
name: methionine gamma-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-methionine = methanethiol + NH3 + 2-oxobutanoate." [EC:4.4.1.11, RHEA:23800]
+def: "Catalysis of the reaction: L-methionine + H2O = methanethiol + 2-oxobutanoate + NH4+." [RHEA:23800]
synonym: "L-methioninase activity" RELATED [EC:4.4.1.11]
synonym: "L-methionine gamma-lyase activity" RELATED [EC:4.4.1.11]
synonym: "L-methionine methanethiol-lyase (deaminating)" RELATED [EC:4.4.1.11]
@@ -148981,21 +151418,18 @@
xref: RHEA:33419
xref: UM-BBD_reactionID:r0429
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.38
property_value: skos:exactMatch RHEA:33419
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0018856
-name: benzoyl acetate-CoA ligase activity
+name: obsolete benzoyl acetate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-oxo-3-phenylpropionate + CoA + ATP = AMP + diphosphate + benzoyl acetyl-CoA." [UM-BBD_reactionID:r0242]
-xref: KEGG_REACTION:R05452
-xref: SABIO-RK:5058
-xref: UM-BBD_reactionID:r0242
-is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
+def: "OBSOLETE. Catalysis of the reaction: 3-oxo-3-phenylpropionate + CoA + ATP = AMP + diphosphate + benzoyl acetyl-CoA." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0018857
@@ -149021,7 +151455,6 @@
xref: RHEA:10132
xref: UM-BBD_reactionID:r0189
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.25
property_value: skos:exactMatch RHEA:10132
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -149042,7 +151475,6 @@
xref: RHEA:23116
xref: UM-BBD_reactionID:r0156
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.27
property_value: skos:exactMatch RHEA:23116
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -149064,7 +151496,6 @@
xref: RHEA:10828
xref: UM-BBD_reactionID:r0341
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.32
property_value: skos:exactMatch RHEA:10828
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -149081,7 +151512,6 @@
xref: RHEA:23220
xref: UM-BBD_reactionID:r0139
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.33
property_value: skos:exactMatch RHEA:23220
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -149170,24 +151600,28 @@
[Term]
id: GO:0018870
-name: anaerobic 2-aminobenzoate metabolic process
+name: obsolete anaerobic 2-aminobenzoate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 2-aminobenzoate, a derivative of benzoic acid with an NH2 group attached to C2, that occurs in the absence of oxygen." [GOC:ai]
-synonym: "anaerobic 2-aminobenzoate metabolism" EXACT []
-xref: UM-BBD_pathwayID:abz
-is_a: GO:0043420 ! anthranilate metabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 2-aminobenzoate, a derivative of benzoic acid with an NH2 group attached to C2, that occurs in the absence of oxygen." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+synonym: "anaerobic 2-aminobenzoate metabolism" BROAD []
+synonym: "anthranilate catabolic process" BROAD []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0043421
[Term]
id: GO:0018871
-name: 1-aminocyclopropane-1-carboxylate metabolic process
+name: obsolete 1-aminocyclopropane-1-carboxylate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving 1-aminocyclopropane-1-carboxylate, the anion of 1-aminocyclopropane-1-carboxylic acid, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [UM-BBD_pathwayID:acp]
+def: "OBSOLETE. The chemical reactions and pathways involving 1-aminocyclopropane-1-carboxylate, the anion of 1-aminocyclopropane-1-carboxylic acid, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "1-aminocyclopropane-1-carboxylate metabolism" EXACT []
synonym: "ACP metabolic process" EXACT []
synonym: "ACP metabolism" EXACT []
-xref: UM-BBD_pathwayID:acp
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+consider: GO:0042217
[Term]
id: GO:0018872
@@ -150233,11 +152667,9 @@
synonym: "thiocyanate metabolism" EXACT []
synonym: "thiocyanic acid metabolic process" EXACT []
synonym: "thiocyanic acid metabolism" EXACT []
-xref: MetaCyc:P581-PWY
xref: UM-BBD_pathwayID:thc
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
-is_a: GO:0006805 ! xenobiotic metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0018970
@@ -150501,7 +152933,7 @@
id: GO:0018997
name: obsolete electron transfer carrier
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because the parent terms cover its function.
synonym: "electron transfer carrier" EXACT []
is_obsolete: true
@@ -150952,10 +153384,6 @@
synonym: "viral host defence evasion" NARROW []
synonym: "viral host defense evasion" NARROW []
synonym: "viral regulation of antiviral response" EXACT []
-xref: Reactome:R-HSA-164938 "Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters"
-xref: Reactome:R-HSA-164944 "Nef and signal transduction"
-xref: Reactome:R-HSA-168305 "Inhibition of Interferon Synthesis"
-xref: Reactome:R-HSA-169131 "Inhibition of PKR"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23043" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25016" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29236" xsd:anyURI
@@ -151016,8 +153444,6 @@
synonym: "regulation of cellular process in host by virus" EXACT []
synonym: "regulation of host cellular process by virus" EXACT []
synonym: "viral host cell process manipulation" EXACT []
-xref: Reactome:R-HSA-168276 "NS1 Mediated Effects on Host Pathways"
-xref: Reactome:R-HSA-9833110 "RSV-host interactions"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26621" xsd:anyURI
is_obsolete: true
replaced_by: GO:0044068
@@ -151626,6 +154052,7 @@
def: "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule." [GOC:ai]
xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1"
xref: Reactome:R-HSA-162914 "Myristoylation of Nef"
+xref: Reactome:R-HSA-9919009 "NMT1 interacts with E"
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
@@ -151638,10 +154065,24 @@
xref: EC:1.2.1.29
xref: MetaCyc:ARYL-ALDEHYDE-DEHYDROGENASE-RXN
xref: RHEA:11804
+xref: RHEA:19693
+xref: RHEA:36311
+xref: RHEA:57936
+xref: RHEA:80363
+xref: RHEA:80367
+xref: RHEA:80371
+xref: RHEA:80375
xref: UM-BBD_reactionID:r0394
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.2.1.29
property_value: skos:exactMatch RHEA:11804
+property_value: skos:narrowMatch RHEA:19693
+property_value: skos:narrowMatch RHEA:36311
+property_value: skos:narrowMatch RHEA:57936
+property_value: skos:narrowMatch RHEA:80363
+property_value: skos:narrowMatch RHEA:80367
+property_value: skos:narrowMatch RHEA:80371
+property_value: skos:narrowMatch RHEA:80375
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -151657,10 +154098,12 @@
[Term]
id: GO:0019112
-name: phenanthrol glycosyltransferase activity
+name: obsolete phenanthrol glycosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phenanthrol + glucose = phenanthryl-beta-D-glucopyranoside + H2O." [GOC:ai]
-is_a: GO:0016758 ! hexosyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: phenanthrol + glucose = phenanthryl-beta-D-glucopyranoside + H2O." [GOC:ai]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019113
@@ -151696,11 +154139,14 @@
[Term]
id: GO:0019116
-name: hydroxy-nicotine oxidase activity
+name: obsolete hydroxy-nicotine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-hydroxynicotine + H2O + O2 = 1-(6-hydroxypyrid-3-yl)-4-(methylamino)butan-1-one + hydrogen peroxide." [GOC:jl, PMID:16095622]
-is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
+def: "OBSOLETE. Catalysis of the reaction: 6-hydroxynicotine + H2O + O2 = 1-(6-hydroxypyrid-3-yl)-4-(methylamino)butan-1-one + hydrogen peroxide." [GOC:jl, PMID:16095622]
+comment: This term was obsoleted because it is an unnecessary grouping term.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
+is_obsolete: true
+consider: GO:0018530
+consider: GO:0018531
[Term]
id: GO:0019117
@@ -151927,10 +154373,12 @@
xref: MetaCyc:2.7.1.145-RXN
xref: Reactome:R-HSA-74207 "dA, dG, or dI + ATP => dAMP, dGMP, or dIMP + ADP (DGUOK)"
xref: RHEA:12140
+xref: RHEA:28206
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
relationship: part_of GO:0009157 ! deoxyribonucleoside monophosphate biosynthetic process
property_value: skos:exactMatch EC:2.7.1.145
property_value: skos:exactMatch RHEA:12140
+property_value: skos:narrowMatch RHEA:28206
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27917" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -151954,7 +154402,6 @@
namespace: molecular_function
alt_id: GO:0046420
def: "Catalysis of the reaction: N6-dimethylallyladenine + acceptor + H2O = adenine + 3-methylbut-2-enal + reduced electron acceptor." [EC:1.5.99.12]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "6-N-dimethylallyladenine:acceptor oxidoreductase activity" RELATED [EC:1.5.99.12]
synonym: "cytokinin oxidase activity" RELATED []
synonym: "N6-dimethylallyladenine:(acceptor) oxidoreductase activity" RELATED [EC:1.5.99.12]
@@ -151966,8 +154413,8 @@
property_value: skos:exactMatch EC:1.5.99.12
property_value: skos:exactMatch MetaCyc:1.5.99.12-RXN
property_value: skos:exactMatch RHEA:13625
-property_value: skos:relatedMatch MetaCyc:PWY-2841
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0019140
@@ -152118,7 +154565,7 @@
id: GO:0019148
name: D-cysteine desulfhydrase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-cysteine + H2O = sulfide + NH3 + pyruvate." [EC:4.4.1.15]
+def: "Catalysis of the reaction: D-cysteine + H2O = hydrogen sulfide + pyruvate + NH4+ + H+." [RHEA:11268]
synonym: "D-cysteine lyase activity" RELATED [EC:4.4.1.15]
synonym: "D-cysteine sulfide-lyase (deaminating)" RELATED [EC:4.4.1.15]
synonym: "D-cysteine sulfide-lyase (deaminating; pyruvate-forming)" RELATED [EC:4.4.1.15]
@@ -152134,7 +154581,7 @@
id: GO:0019149
name: 3-chloro-D-alanine dehydrochlorinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-chloro-D-alanine + H2O = pyruvate + chloride + NH3." [EC:4.5.1.2]
+def: "Catalysis of the reaction: 3-chloro-D-alanine + H2O = chloride + pyruvate + NH4+ + H+." [RHEA:18873]
synonym: "3-chloro-D-alanine chloride-lyase (deaminating)" RELATED [EC:4.5.1.2]
synonym: "3-chloro-D-alanine chloride-lyase (deaminating; pyruvate-forming)" RELATED [EC:4.5.1.2]
synonym: "beta-chloro-D-alanine dehydrochlorinase activity" RELATED [EC:4.5.1.2]
@@ -152283,6 +154730,7 @@
synonym: "mannokinase (phosphorylating)" RELATED [EC:2.7.1.7]
xref: EC:2.7.1.7
xref: MetaCyc:MANNKIN-RXN
+xref: Reactome:R-HSA-8931653 "POMK 6-phosphorylates mannose in GalNAc-GlcNAc-Man-DAG1"
xref: Reactome:R-HSA-9909159 "HK1 phosphorylates Mannose to Man6P"
xref: RHEA:11028
is_a: GO:0004396 ! hexokinase activity
@@ -152294,7 +154742,7 @@
id: GO:0019159
name: nicotinamide-nucleotide amidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + H2O = beta-nicotinate D-ribonucleotide + NH3." [EC:3.5.1.42]
+def: "Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + H2O = nicotinate beta-D-ribonucleotide + NH4+." [RHEA:12400]
synonym: "nicotinamide mononucleotide amidohydrolase activity" RELATED [EC:3.5.1.42]
synonym: "nicotinamide mononucleotide deamidase activity" RELATED [EC:3.5.1.42]
synonym: "nicotinamide-D-ribonucleotide amidohydrolase activity" RELATED [EC:3.5.1.42]
@@ -152330,29 +154778,36 @@
[Term]
id: GO:0019161
-name: diamine transaminase activity
+name: diamine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an alpha,omega-diamine + 2-oxoglutarate = an omega-aminoaldehyde + L-glutamate." [EC:2.6.1.29]
+def: "Catalysis of the reaction: an alpha,omega-diamine + 2-oxoglutarate = an omega-aminoaldehyde + L-glutamate." [RHEA:18217]
synonym: "amine transaminase activity" RELATED [EC:2.6.1.29]
synonym: "amine-ketoacid transaminase activity" RELATED [EC:2.6.1.29]
synonym: "diamine aminotransferase activity" EXACT []
+synonym: "diamine transaminase activity" BROAD []
synonym: "diamine-ketoglutaric transaminase activity" RELATED [EC:2.6.1.29]
synonym: "diamine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.29]
xref: EC:2.6.1.29
xref: MetaCyc:DIAMTRANSAM-RXN
xref: RHEA:18217
+xref: RHEA:23816
+xref: RHEA:61624
is_a: GO:0008483 ! transaminase activity
property_value: skos:exactMatch EC:2.6.1.29
property_value: skos:exactMatch RHEA:18217
+property_value: skos:narrowMatch RHEA:23816
+property_value: skos:narrowMatch RHEA:61624
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0019162
-name: pyridoxamine-oxaloacetate transaminase activity
+name: pyridoxamine:oxaloacetate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: oxaloacetate + pyridoxamine = L-aspartate + pyridoxal." [EC:2.6.1.31, RHEA:10844]
+def: "Catalysis of the reaction: oxaloacetate + pyridoxamine = L-aspartate + pyridoxal." [RHEA:10844]
synonym: "pyridoxamine--oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.31]
synonym: "pyridoxamine-oxaloacetate aminotransferase activity" EXACT []
+synonym: "pyridoxamine-oxaloacetate transaminase activity" EXACT []
synonym: "pyridoxamine:oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.31]
xref: EC:2.6.1.31
xref: KEGG_REACTION:R01713
@@ -152362,17 +154817,19 @@
property_value: skos:exactMatch EC:2.6.1.31
property_value: skos:exactMatch RHEA:10844
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0019163
-name: pyridoxamine-phosphate transaminase activity
+name: pyridoxamine-phosphate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + 2-oxoglutarate = pyridoxal 5'-phosphate + D-glutamate." [EC:2.6.1.54]
+def: "Catalysis of the reaction: pyridoxamine 5'-phosphate + 2-oxoglutarate = pyridoxal 5'-phosphate + D-glutamate." [RHEA:15877]
synonym: "pyridoxamine 5'-phosphate transaminase activity" RELATED [EC:2.6.1.54]
synonym: "pyridoxamine 5'-phosphate-alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.54]
synonym: "pyridoxamine phosphate aminotransferase activity" RELATED [EC:2.6.1.54]
synonym: "pyridoxamine-5'-phosphate:2-oxoglutarate aminotransferase (D-glutamate-forming)" RELATED [EC:2.6.1.54]
synonym: "pyridoxamine-phosphate aminotransferase activity" EXACT []
+synonym: "pyridoxamine-phosphate transaminase activity" BROAD []
xref: EC:2.6.1.54
xref: MetaCyc:PYRDAMPTRANS-RXN
xref: RHEA:15877
@@ -152380,6 +154837,7 @@
property_value: skos:exactMatch EC:2.6.1.54
property_value: skos:exactMatch RHEA:15877
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0019164
@@ -152438,9 +154896,79 @@
xref: Reactome:R-HSA-6809810 "PECR reduces 2E-phytenoyl-CoA to phytanoyl-CoA"
xref: Reactome:R-HSA-8952873 "MECR dimer reduces tdec2-CoA to DEC-CoA"
xref: RHEA:33763
+xref: RHEA:35351
+xref: RHEA:35363
+xref: RHEA:35367
+xref: RHEA:36143
+xref: RHEA:39179
+xref: RHEA:39191
+xref: RHEA:39203
+xref: RHEA:39215
+xref: RHEA:39227
+xref: RHEA:39239
+xref: RHEA:39251
+xref: RHEA:39263
+xref: RHEA:39275
+xref: RHEA:39307
+xref: RHEA:39319
+xref: RHEA:39331
+xref: RHEA:39347
+xref: RHEA:39355
+xref: RHEA:39367
+xref: RHEA:39379
+xref: RHEA:39391
+xref: RHEA:39403
+xref: RHEA:39415
+xref: RHEA:39427
+xref: RHEA:39443
+xref: RHEA:39455
+xref: RHEA:39467
+xref: RHEA:39479
+xref: RHEA:39491
+xref: RHEA:39503
+xref: RHEA:39515
+xref: RHEA:39527
+xref: RHEA:39539
+xref: RHEA:39551
+xref: RHEA:39563
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.38
property_value: skos:exactMatch RHEA:33763
+property_value: skos:narrowMatch RHEA:35351
+property_value: skos:narrowMatch RHEA:35363
+property_value: skos:narrowMatch RHEA:35367
+property_value: skos:narrowMatch RHEA:36143
+property_value: skos:narrowMatch RHEA:39179
+property_value: skos:narrowMatch RHEA:39191
+property_value: skos:narrowMatch RHEA:39203
+property_value: skos:narrowMatch RHEA:39215
+property_value: skos:narrowMatch RHEA:39227
+property_value: skos:narrowMatch RHEA:39239
+property_value: skos:narrowMatch RHEA:39251
+property_value: skos:narrowMatch RHEA:39263
+property_value: skos:narrowMatch RHEA:39275
+property_value: skos:narrowMatch RHEA:39307
+property_value: skos:narrowMatch RHEA:39319
+property_value: skos:narrowMatch RHEA:39331
+property_value: skos:narrowMatch RHEA:39347
+property_value: skos:narrowMatch RHEA:39355
+property_value: skos:narrowMatch RHEA:39367
+property_value: skos:narrowMatch RHEA:39379
+property_value: skos:narrowMatch RHEA:39391
+property_value: skos:narrowMatch RHEA:39403
+property_value: skos:narrowMatch RHEA:39415
+property_value: skos:narrowMatch RHEA:39427
+property_value: skos:narrowMatch RHEA:39443
+property_value: skos:narrowMatch RHEA:39455
+property_value: skos:narrowMatch RHEA:39467
+property_value: skos:narrowMatch RHEA:39479
+property_value: skos:narrowMatch RHEA:39491
+property_value: skos:narrowMatch RHEA:39503
+property_value: skos:narrowMatch RHEA:39515
+property_value: skos:narrowMatch RHEA:39527
+property_value: skos:narrowMatch RHEA:39539
+property_value: skos:narrowMatch RHEA:39551
+property_value: skos:narrowMatch RHEA:39563
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -152451,10 +154979,18 @@
synonym: "2-octaprenylphenol hydroxylase activity" NARROW []
xref: EC:1.14.13.240
xref: MetaCyc:RXN-18459
+xref: RHEA:27790
xref: RHEA:55892
+xref: RHEA:56112
+xref: RHEA:56116
+xref: RHEA:56120
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.13.240
property_value: skos:exactMatch RHEA:55892
+property_value: skos:narrowMatch RHEA:27790
+property_value: skos:narrowMatch RHEA:56112
+property_value: skos:narrowMatch RHEA:56116
+property_value: skos:narrowMatch RHEA:56120
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI
[Term]
@@ -152487,9 +155023,25 @@
xref: EC:4.2.1.59
xref: MetaCyc:3-HYDROXYDECANOYL-ACP-DEHYDR-RXN
xref: RHEA:13097
+xref: RHEA:41808
+xref: RHEA:41828
+xref: RHEA:41844
+xref: RHEA:41860
+xref: RHEA:41876
+xref: RHEA:41892
+xref: RHEA:41908
+xref: RHEA:41924
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.59
property_value: skos:exactMatch RHEA:13097
+property_value: skos:narrowMatch RHEA:41808
+property_value: skos:narrowMatch RHEA:41828
+property_value: skos:narrowMatch RHEA:41844
+property_value: skos:narrowMatch RHEA:41860
+property_value: skos:narrowMatch RHEA:41876
+property_value: skos:narrowMatch RHEA:41892
+property_value: skos:narrowMatch RHEA:41908
+property_value: skos:narrowMatch RHEA:41924
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -152560,10 +155112,11 @@
[Term]
id: GO:0019179
-name: dTDP-4-amino-4,6-dideoxy-D-glucose transaminase activity
+name: dTDP-4-amino-4,6-dideoxy-D-glucose:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-4-amino-4,6-dideoxy-D-glucose + 2-oxoglutarate = dTDP-4-dehydro-6-deoxy-D-glucose + L-glutamate." [EC:2.6.1.33]
+def: "Catalysis of the reaction: dTDP-4-amino-4,6-dideoxy-D-glucose + 2-oxoglutarate = dTDP-4-dehydro-6-deoxy-D-glucose + L-glutamate." [RHEA:19085]
synonym: "dTDP-4-amino-4,6-dideoxy-D-glucose aminotransferase activity" EXACT []
+synonym: "dTDP-4-amino-4,6-dideoxy-D-glucose transaminase activity" EXACT []
synonym: "dTDP-4-amino-4,6-dideoxy-D-glucose:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.33]
synonym: "TDP-4-keto-6-deoxy-D-glucose transaminase activity" RELATED [EC:2.6.1.33]
synonym: "TDP-4-oxo-6-deoxy-D-glucose transaminase activity" RELATED [EC:2.6.1.33]
@@ -152578,14 +155131,16 @@
property_value: skos:exactMatch EC:2.6.1.33
property_value: skos:exactMatch RHEA:19085
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0019180
-name: dTDP-4-amino-4,6-dideoxygalactose transaminase activity
+name: dTDP-4-amino-4,6-dideoxygalactose:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + dTDP-4-amino-4,6-dideoxy-D-galactose = L-glutamate + dTDP-4-dehydro-6-deoxy-D-galactose." [EC:2.6.1.59, RHEA:10368]
+def: "Catalysis of the reaction: dTDP-4-amino-4,6-dideoxy-alpha-D-galactose + 2-oxoglutarate = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + L-glutamate." [RHEA:10368]
synonym: "dTDP-4,6-dideoxy-D-galactose:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.59]
synonym: "dTDP-4-amino-4,6-dideoxygalactose aminotransferase activity" RELATED [EC:2.6.1.59]
+synonym: "dTDP-4-amino-4,6-dideoxygalactose transaminase activity" EXACT []
synonym: "dTDP-fucosamine aminotransferase activity" EXACT []
synonym: "thymidine diphosphate 4-keto-6-deoxy-D-glucose transaminase activity" RELATED [EC:2.6.1.59]
synonym: "thymidine diphosphoaminodideoxygalactose aminotransferase activity" RELATED [EC:2.6.1.59]
@@ -152597,6 +155152,7 @@
property_value: skos:exactMatch EC:2.6.1.59
property_value: skos:exactMatch RHEA:10368
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0019181
@@ -152721,7 +155277,6 @@
name: carbohydrate kinase activity
namespace: molecular_function
def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a carbohydrate substrate molecule." [GOC:jl]
-xref: Reactome:R-HSA-8931653 "POMK 6-phosphorylates Mannose in GalNAc-GlcNAc-Man-DAG1"
is_a: GO:0016301 ! kinase activity
[Term]
@@ -152807,6 +155362,7 @@
name: kinase inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of a kinase." [GOC:mah]
+xref: Reactome:R-HSA-170824 "glucokinase (GCK1) + glucokinase regulatory protein (GKRP) <=> GCK1:GKRP complex"
is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0019207 ! kinase regulator activity
relationship: negatively_regulates GO:0016301 ! kinase activity
@@ -152816,6 +155372,11 @@
name: phosphatase activator activity
namespace: molecular_function
def: "Binds to and increases the activity of a phosphatase." [GOC:ai]
+xref: Reactome:R-HSA-6809238 "MTMR7 binds MTMR9"
+xref: Reactome:R-HSA-6809254 "MTMR8 binds MTMR9"
+xref: Reactome:R-HSA-6809309 "MTMR6 binds MTMR9"
+xref: Reactome:R-HSA-6809680 "MTMR12 binds MTM1"
+xref: Reactome:R-HSA-6809793 "MTMR2 binds SBF2"
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0019208 ! phosphatase regulator activity
relationship: positively_regulates GO:0016791 ! phosphatase activity
@@ -152863,7 +155424,7 @@
id: GO:0019216
name: regulation of lipid metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:curators]
synonym: "regulation of lipid metabolism" EXACT []
xref: Reactome:R-HSA-2426168 "Activation of gene expression by SREBF (SREBP)"
xref: Reactome:R-HSA-400206 "Regulation of lipid metabolism by PPARalpha"
@@ -152877,7 +155438,7 @@
name: regulation of fatty acid metabolic process
namespace: biological_process
alt_id: GO:0006632
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:curators]
synonym: "regulation of fatty acid metabolism" EXACT []
is_a: GO:0010565 ! regulation of ketone metabolic process
is_a: GO:0019216 ! regulation of lipid metabolic process
@@ -152890,7 +155451,7 @@
id: GO:0019218
name: regulation of steroid metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:curators]
synonym: "regulation of steroid metabolism" EXACT []
is_a: GO:0019216 ! regulation of lipid metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -152901,19 +155462,21 @@
id: GO:0019219
name: regulation of nucleobase-containing compound metabolic process
namespace: biological_process
-def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators]
+def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:curators]
+subset: gocheck_do_not_annotate
synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT []
is_a: GO:0080090 ! regulation of primary metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006139 ! nucleobase-containing compound metabolic process
relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
[Term]
id: GO:0019220
name: obsolete regulation of phosphate metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "regulation of phosphate metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30570" xsd:anyURI
@@ -152939,7 +155502,7 @@
name: regulation of metabolic process
namespace: biological_process
alt_id: GO:0044246
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_metagenomics
synonym: "regulation of metabolism" EXACT []
@@ -153068,10 +155631,9 @@
id: GO:0019239
name: deaminase activity
namespace: molecular_function
-def: "Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH3/NH2R)." [GOC:jl]
+def: "Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH4+/NH2R)." [GOC:jl]
subset: goslim_pir
xref: Reactome:R-HSA-74241 "ADA catalyzes the deamination of (deoxy)adenosine"
-xref: Reactome:R-HSA-9014641 "HRSP12 deaminates 2AA to 2OBUTA"
xref: Reactome:R-HSA-9734745 "Defective ADA does not deaminate (deoxy)adenosine"
xref: Reactome:R-HSA-9754964 "ADA deamidates RBV"
is_a: GO:0016810 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
@@ -153094,7 +155656,7 @@
id: GO:0019241
name: L-citrulline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of L-citrulline." [GOC:curators]
synonym: "citrulline breakdown" EXACT []
synonym: "citrulline catabolism" EXACT []
synonym: "citrulline degradation" EXACT []
@@ -153103,6 +155665,7 @@
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0019242
@@ -153136,40 +155699,43 @@
[Term]
id: GO:0019244
-name: lactate biosynthetic process from pyruvate
+name: pyruvate fermentation to lactate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lactate from other compounds, including pyruvate." [GOC:go_curators]
+def: "The anaerobic chemical reactions and pathways resulting in the breakdown of pyruvate into lactate." [GOC:curators]
synonym: "lactate anabolism from pyruvate" EXACT []
+synonym: "lactate biosynthetic process from pyruvate" EXACT []
synonym: "lactate formation from pyruvate" EXACT []
synonym: "lactate synthesis from pyruvate" EXACT []
-synonym: "pyruvate fermentation to lactate" EXACT []
-is_a: GO:0006090 ! pyruvate metabolic process
-is_a: GO:0019249 ! lactate biosynthetic process
-relationship: has_part GO:0004457 ! lactate dehydrogenase activity
+is_a: GO:0006089 ! lactate metabolic process
+is_a: GO:0019660 ! pyruvate fermentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019245
-name: D(-)-lactate biosynthetic process from pyruvate
+name: pyruvate fermentation to D(-)-lactate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of D(-)-lactate from other compounds, including pyruvate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of D(-)-lactate from other compounds, including pyruvate." [GOC:curators]
synonym: "D(-)-lactate anabolism from pyruvate" EXACT []
+synonym: "D(-)-lactate biosynthetic process from pyruvate" EXACT []
synonym: "D(-)-lactate formation from pyruvate" EXACT []
synonym: "D(-)-lactate synthesis from pyruvate" EXACT []
-is_a: GO:0019244 ! lactate biosynthetic process from pyruvate
-relationship: has_part GO:0008720 ! D-lactate dehydrogenase (NAD+) activity
+xref: MetaCyc:PWY-8274
+is_a: GO:0019244 ! pyruvate fermentation to lactate
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019246
-name: L(+)-lactate biosynthetic process from pyruvate
+name: pyruvate fermentation to L(+)-lactate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L(+)-lactate from other compounds, including pyruvate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of L(+)-lactate from other compounds, including pyruvate." [GOC:curators]
synonym: "L(+)-lactate anabolism from pyruvate" EXACT []
+synonym: "L(+)-lactate biosynthetic process from pyruvate" EXACT []
synonym: "L(+)-lactate formation from pyruvate" EXACT []
synonym: "L(+)-lactate synthesis from pyruvate" EXACT []
synonym: "S-lactate biosynthetic process from pyruvate" EXACT []
xref: MetaCyc:PWY-5481
-is_a: GO:0019244 ! lactate biosynthetic process from pyruvate
-relationship: has_part GO:0004459 ! L-lactate dehydrogenase (NAD+) activity
+is_a: GO:0019244 ! pyruvate fermentation to lactate
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019247
@@ -153195,7 +155761,7 @@
id: GO:0019249
name: lactate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid." [GOC:curators]
synonym: "lactate anabolism" EXACT []
synonym: "lactate biosynthesis" EXACT []
synonym: "lactate formation" EXACT []
@@ -153207,7 +155773,7 @@
id: GO:0019250
name: aerobic cobalamin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the presence of oxygen." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the presence of oxygen." [GOC:curators]
synonym: "aerobic cobalamin anabolism" EXACT []
synonym: "aerobic cobalamin biosynthesis" EXACT []
synonym: "aerobic cobalamin formation" EXACT []
@@ -153225,7 +155791,7 @@
id: GO:0019251
name: anaerobic cobalamin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the absence of oxygen." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12) in the absence of oxygen." [GOC:curators]
synonym: "anaerobic cobalamin anabolism" EXACT []
synonym: "anaerobic cobalamin biosynthesis" EXACT []
synonym: "anaerobic cobalamin formation" EXACT []
@@ -153236,8 +155802,9 @@
synonym: "cobalamin biosynthetic process, anaerobic" EXACT []
synonym: "vitamin B12 biosynthesis, anaerobic" EXACT []
synonym: "vitamin B12 biosynthetic process, anaerobic" EXACT []
-xref: MetaCyc:COBALSYN-PWY
+xref: MetaCyc:PWY-5507
is_a: GO:0009236 ! cobalamin biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019252
@@ -153268,7 +155835,7 @@
id: GO:0019254
name: carnitine metabolic process, CoA-linked
namespace: biological_process
-def: "The chemical reactions and pathways involving carnitine, where metabolism is linked to CoA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving carnitine, where metabolism is linked to CoA." [GOC:curators]
synonym: "carnitine metabolism, CoA-linked" EXACT []
xref: MetaCyc:CARNMET-PWY
is_a: GO:0009437 ! carnitine metabolic process
@@ -153322,13 +155889,17 @@
synonym: "4NT catabolic process" EXACT []
synonym: "4NT catabolism" EXACT []
xref: MetaCyc:P421-PWY
+xref: MetaCyc:PWY-5644
is_a: GO:0046263 ! nitrotoluene catabolic process
+property_value: skos:narrowMatch MetaCyc:P421-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5644
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019260
name: 1,2-dichloroethane catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 1,2-dichloroethane, a major commodity chemical used, for example, in the manufacture of vinyl chloride." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of 1,2-dichloroethane, a major commodity chemical used, for example, in the manufacture of vinyl chloride." [GOC:curators]
synonym: "1,2-dichloroethane breakdown" EXACT []
synonym: "1,2-dichloroethane catabolism" EXACT []
synonym: "1,2-dichloroethane degradation" EXACT []
@@ -153361,6 +155932,7 @@
is_a: GO:0006054 ! N-acetylneuraminate metabolic process
is_a: GO:0046348 ! amino sugar catabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
[Term]
id: GO:0019263
@@ -153376,62 +155948,63 @@
[Term]
id: GO:0019264
-name: glycine biosynthetic process from L-serine
+name: obsolete glycine biosynthetic process from L-serine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycine from L-serine." [MetaCyc:GLYSYN-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine." [MetaCyc:GLYSYN-PWY]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "glycine anabolism from serine" EXACT []
synonym: "glycine formation from serine" EXACT []
synonym: "glycine synthesis from serine" EXACT []
-xref: MetaCyc:GLYSYN-PWY
-is_a: GO:0006545 ! glycine biosynthetic process
-is_a: GO:0006563 ! L-serine metabolic process
-property_value: skos:exactMatch MetaCyc:GLYSYN-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30758" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006545
[Term]
id: GO:0019265
-name: glycine biosynthetic process, by transamination of glyoxylate
+name: obsolete glycine biosynthetic process, by transamination of glyoxylate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycine by the transamination of glyoxylate." [GOC:go_curators, MetaCyc:GLYSYN-ALA-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine by the transamination of glyoxylate." [GOC:curators, MetaCyc:GLYSYN-ALA-PWY]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "glycine anabolism, by transamination of glyoxylate" EXACT []
synonym: "glycine formation, by transamination of glyoxylate" EXACT []
synonym: "glycine synthesis, by transamination of glyoxylate" EXACT []
-xref: MetaCyc:GLYSYN-ALA-PWY
-is_a: GO:0006545 ! glycine biosynthetic process
-property_value: skos:exactMatch MetaCyc:GLYSYN-ALA-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006545
[Term]
id: GO:0019266
-name: L-asparagine biosynthetic process from oxaloacetate
+name: obsolete L-asparagine biosynthetic process from oxaloacetate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of asparagine from other compounds, including oxaloacetate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine from other compounds, including oxaloacetate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific pathway and is out of scope for GO.
synonym: "asparagine anabolism from oxaloacetate" EXACT []
synonym: "asparagine formation from oxaloacetate" EXACT []
synonym: "asparagine synthesis from oxaloacetate" EXACT []
-xref: MetaCyc:ASPARAGINE-BIOSYNTHESIS
-is_a: GO:0006107 ! oxaloacetate metabolic process
-is_a: GO:0043649 ! dicarboxylic acid catabolic process
-is_a: GO:0070981 ! L-asparagine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070981
[Term]
id: GO:0019267
-name: L-asparagine biosynthetic process from L-cysteine
+name: obsolete L-asparagine biosynthetic process from L-cysteine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-asparagine from other compounds, including L-cysteine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-asparagine from other compounds, including L-cysteine." [GOC:curators]
+comment: This term was obsoleted because it is too specific and is outside the scope of GO.
synonym: "asparagine anabolism from cysteine" EXACT []
synonym: "asparagine formation from cysteine" EXACT []
synonym: "asparagine synthesis from cysteine" EXACT []
-xref: MetaCyc:ASPSYNII-PWY
-is_a: GO:0046439 ! L-cysteine metabolic process
-is_a: GO:0070981 ! L-asparagine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070981
[Term]
id: GO:0019268
name: obsolete glutamate biosynthetic process, using glutamate dehydrogenase (NAD(P)+)
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, catalyzed by the enzyme glutamate dehydrogenase (NADP+)." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, catalyzed by the enzyme glutamate dehydrogenase (NADP+)." [GOC:curators]
comment: This term was made obsolete because it represents a molecular function.
synonym: "glutamate anabolism, using glutamate dehydrogenase (NAD(P)+)" EXACT []
synonym: "glutamate biosynthetic process, using glutamate dehydrogenase (NAD(P)+)" EXACT []
@@ -153444,7 +156017,7 @@
id: GO:0019269
name: obsolete glutamate biosynthetic process, using glutamate synthase (NADPH)
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, catalyzed by the enzyme glutamate synthase (NADPH)." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, catalyzed by the enzyme glutamate synthase (NADPH)." [GOC:curators]
comment: This term was made obsolete because it refers to a molecular function.
synonym: "glutamate anabolism, using glutamate synthase (NADPH)" EXACT []
synonym: "glutamate biosynthetic process, using glutamate synthase (NADPH)" EXACT []
@@ -153475,23 +156048,23 @@
[Term]
id: GO:0019272
-name: L-alanine biosynthetic process from pyruvate
+name: obsolete L-alanine biosynthetic process from pyruvate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of alanine from other compounds, including pyruvate." [GOC:go_curators, MetaCyc:ALANINE-SYN2-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of alanine from other compounds, including pyruvate." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "L-alanine anabolism from pyruvate" EXACT []
synonym: "L-alanine formation from pyruvate" EXACT []
synonym: "L-alanine synthesis from pyruvate" EXACT []
-xref: MetaCyc:ALANINE-SYN2-PWY
-is_a: GO:0006090 ! pyruvate metabolic process
-is_a: GO:0042852 ! L-alanine biosynthetic process
-property_value: skos:exactMatch MetaCyc:ALANINE-SYN2-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042852
[Term]
id: GO:0019273
name: obsolete L-alanine biosynthetic process via ornithine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-alanine, via the intermediate ornithine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-alanine, via the intermediate ornithine." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this process exists in vivo.
synonym: "L-alanine anabolism via ornithine" EXACT []
synonym: "L-alanine formation via ornithine" EXACT []
@@ -153517,15 +156090,18 @@
synonym: "UDP-N-acetylgalactosamine biosynthesis" EXACT []
synonym: "UDP-N-acetylgalactosamine formation" EXACT []
synonym: "UDP-N-acetylgalactosamine synthesis" EXACT []
+xref: MetaCyc:PWY-5512
xref: MetaCyc:PWY-5514
xref: MetaCyc:PWY-8013
is_a: GO:0009226 ! nucleotide-sugar biosynthetic process
is_a: GO:0019276 ! UDP-N-acetylgalactosamine metabolic process
is_a: GO:0046349 ! amino sugar biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-5512
property_value: skos:narrowMatch MetaCyc:PWY-5514
property_value: skos:narrowMatch MetaCyc:PWY-8013
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0019278
@@ -153541,69 +156117,74 @@
[Term]
id: GO:0019279
-name: L-methionine biosynthetic process from L-homoserine via cystathionine
+name: obsolete L-methionine biosynthetic process from L-homoserine via cystathionine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-methionine from L-homoserine, via the intermediate cystathionine." [MetaCyc:HOMOSER-METSYN-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from L-homoserine, via the intermediate cystathionine." [MetaCyc:HOMOSER-METSYN-PWY]
+comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
synonym: "L-methionine anabolism from L-homoserine via cystathionine" EXACT [GOC:mah]
synonym: "L-methionine formation from L-homoserine via cystathionine" EXACT [GOC:mah]
synonym: "L-methionine synthesis from L-homoserine via cystathionine" EXACT [GOC:mah]
synonym: "methionine biosynthetic process from L-homoserine via cystathionine" EXACT [GOC:mah]
-xref: MetaCyc:HOMOSER-METSYN-PWY
-is_a: GO:0009092 ! L-homoserine metabolic process
-is_a: GO:0071265 ! L-methionine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29576" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071266
[Term]
id: GO:0019280
-name: L-methionine biosynthetic process from L-homoserine via O-acetyl-L-homoserine
+name: obsolete L-methionine biosynthetic process from L-homoserine via O-acetyl-L-homoserine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of methionine from L-homoserine, via the intermediate O-acetyl-L-homoserine using sulfur from hydrogen sulfide assimilation." [MetaCyc:HSERMETANA-PWY]
-xref: MetaCyc:HSERMETANA-PWY
-is_a: GO:0009092 ! L-homoserine metabolic process
-is_a: GO:0071265 ! L-methionine biosynthetic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of methionine from L-homoserine, via the intermediate O-acetyl-L-homoserine using sulfur from hydrogen sulfide assimilation." [MetaCyc:HSERMETANA-PWY]
+comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29576" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30025" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071266
[Term]
id: GO:0019281
-name: L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine
+name: obsolete L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-methionine from other compounds, including homoserine, via the intermediates O-succinyl-L-homoserine and cystathionine." [MetaCyc:MET-SAM-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from other compounds, including homoserine, via the intermediates O-succinyl-L-homoserine and cystathionine." [GOC:curators]
+comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
synonym: "L-methionine anabolism from homoserine via O-succinyl-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "L-methionine formation from homoserine via O-succinyl-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "L-methionine synthesis from homoserine via O-succinyl-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine" EXACT [GOC:mah]
-xref: MetaCyc:MET-SAM-PWY
-is_a: GO:0019279 ! L-methionine biosynthetic process from L-homoserine via cystathionine
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071266
[Term]
id: GO:0019283
-name: L-methionine biosynthetic process from L-homoserine via O-phospho-L-homoserine and cystathionine
+name: obsolete L-methionine biosynthetic process from L-homoserine via O-phospho-L-homoserine and cystathionine
namespace: biological_process
-def: "he chemical reactions and pathways resulting in the formation of L-methionine from L-homoserine, via the intermediates O-phospho-L-homoserine and cystathionine." [GOC:go_curators, MetaCyc:PWY-702]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from L-homoserine, via the intermediates O-phospho-L-homoserine and cystathionine." [GOC:curators, MetaCyc:PWY-702]
+comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
synonym: "L-methionine formation from O-phospho-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "L-methionine synthesis from O-phospho-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "methionine biosynthetic process from O-phospho-L-homoserine and cystathionine" EXACT [GOC:mah]
-xref: MetaCyc:PWY-702
-is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
-is_a: GO:0009092 ! L-homoserine metabolic process
-is_a: GO:0019637 ! organophosphate metabolic process
-is_a: GO:0071266 ! 'de novo' L-methionine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29576" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071266
[Term]
id: GO:0019284
-name: L-methionine salvage from S-adenosylmethionine
+name: obsolete L-methionine salvage from S-adenosylmethionine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine." [GOC:go_curators, GOC:vw, PMID:31950558]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine." [GOC:curators, GOC:vw, PMID:31950558]
+comment: This term was obsoleted because it was not clearly defined and usage has been inconsistent.
synonym: "L-methionine formation from S-adenosylmethionine" EXACT [GOC:mah]
synonym: "L-methionine synthesis from S-adenosylmethionine" EXACT [GOC:mah]
-is_a: GO:0071267 ! L-methionine salvage
-relationship: part_of GO:0033353 ! S-adenosylmethionine cycle
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29900" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+consider: GO:0033353
+consider: GO:0071267
[Term]
id: GO:0019285
@@ -153630,7 +156211,7 @@
id: GO:0019286
name: glycine betaine biosynthetic process from glycine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycine betaine from other compounds, including glycine." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of glycine betaine from other compounds, including glycine." [GOC:curators]
synonym: "glycine betaine anabolism from glycine" EXACT []
synonym: "glycine betaine formation from glycine" EXACT []
synonym: "glycine betaine synthesis from glycine" EXACT []
@@ -153644,7 +156225,7 @@
id: GO:0019287
name: isopentenyl diphosphate biosynthetic process, mevalonate pathway
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, via the intermediate mevalonate. This pathway converts acetate, in the form of acetyl-CoA, to isopentenyl diphosphate (IPP), the fundamental unit in isoprenoid biosynthesis, through a series of mevalonate intermediates." [GOC:go_curators, MetaCyc:PWY-922]
+def: "The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, via the intermediate mevalonate. This pathway converts acetate, in the form of acetyl-CoA, to isopentenyl diphosphate (IPP), the fundamental unit in isoprenoid biosynthesis, through a series of mevalonate intermediates." [GOC:curators, MetaCyc:PWY-922]
synonym: "Ac-MVA pathway" EXACT [PMID:14517367]
synonym: "acetate-mevalonate pathway" EXACT [PMID:14517367]
synonym: "isopentenyl diphosphate anabolism, mevalonate pathway" EXACT []
@@ -153660,7 +156241,7 @@
id: GO:0019288
name: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate." [GOC:go_curators, MetaCyc:NONMEVIPP-PWY, PMID:18948055]
+def: "The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate." [GOC:curators, MetaCyc:NONMEVIPP-PWY, PMID:18948055]
synonym: "isopentenyl diphosphate anabolism, mevalonate-independent pathway" EXACT []
synonym: "isopentenyl diphosphate biosynthesis, mevalonate-independent" EXACT []
synonym: "isopentenyl diphosphate biosynthesis, non-mevalonate pathway" EXACT []
@@ -153717,31 +156298,33 @@
[Term]
id: GO:0019292
-name: L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate
+name: obsolete L-tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-tyrosine from other compounds, including chorismate, via the intermediate 4-hydroxyphenylpyruvate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-tyrosine from other compounds, including chorismate, via the intermediate 4-hydroxyphenylpyruvate." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "L-tyrosine anabolism from chorismate via 4-hydroxyphenylpyruvate" EXACT []
synonym: "L-tyrosine biosynthetic process from chorismate via p-hydroxyphenylpyruvate" EXACT []
synonym: "L-tyrosine formation from chorismate via 4-hydroxyphenylpyruvate" EXACT []
synonym: "L-tyrosine synthesis from chorismate via 4-hydroxyphenylpyruvate" EXACT []
synonym: "tyrosine biosynthetic process from chorismate via 4-hydroxyphenylpyruvate" BROAD []
-xref: MetaCyc:TYRSYN
-is_a: GO:0006571 ! L-tyrosine biosynthetic process
-is_a: GO:0046417 ! chorismate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006571
[Term]
id: GO:0019293
-name: L-tyrosine biosynthetic process, by oxidation of phenylalanine
+name: obsolete L-tyrosine biosynthetic process, by oxidation of phenylalanine
namespace: biological_process
-alt_id: GO:0019291
-def: "The conversion of phenylalanine to tyrosine." [PMID:4004813]
+def: "OBSOLETE. The conversion of phenylalanine to tyrosine." [PMID:4004813]
+comment: The reason for obsoletion is that this term represents a GO-CAM model
synonym: "L-tyrosine biosynthesis IV" EXACT []
synonym: "tyrosine anabolism, by oxidation of phenylalanine" EXACT []
synonym: "tyrosine formation, by oxidation of phenylalanine" EXACT []
synonym: "tyrosine synthesis, by oxidation of phenylalanine" EXACT []
-xref: MetaCyc:PWY-6134
-is_a: GO:0006571 ! L-tyrosine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20583" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006571
[Term]
id: GO:0019294
@@ -153770,14 +156353,18 @@
synonym: "coenzyme M formation" EXACT []
synonym: "coenzyme M synthesis" EXACT []
xref: MetaCyc:P261-PWY
+xref: MetaCyc:PWY-6643
is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
+property_value: skos:narrowMatch MetaCyc:P261-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6643
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019296
name: obsolete coenzyme M metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving coenzyme M (2-thioethansulfonate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving coenzyme M (2-thioethansulfonate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "coenzyme M metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -153787,7 +156374,7 @@
id: GO:0019297
name: obsolete coenzyme B metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving coenzyme B (7-mercaptoheptanoylthreonine phosphate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving coenzyme B (7-mercaptoheptanoylthreonine phosphate), a coenzyme involved in the utilization of methane by methanogenic prokaryotes." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "coenzyme B metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
@@ -153836,8 +156423,14 @@
synonym: "rhamnose breakdown" EXACT []
synonym: "rhamnose catabolism" EXACT []
synonym: "rhamnose degradation" EXACT []
+xref: MetaCyc:PWY-6713
+xref: MetaCyc:PWY-6714
xref: MetaCyc:RHAMCAT-PWY
is_a: GO:0019320 ! hexose catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6713
+property_value: skos:narrowMatch MetaCyc:PWY-6714
+property_value: skos:narrowMatch MetaCyc:RHAMCAT-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019302
@@ -153865,13 +156458,13 @@
[Term]
id: GO:0019304
-name: anaerobic rhamnose catabolic process
+name: obsolete anaerobic rhamnose catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose, that occurs in the absence of oxygen." [GOC:ai]
-synonym: "anaerobic rhamnose breakdown" EXACT []
-synonym: "anaerobic rhamnose catabolism" EXACT []
-synonym: "anaerobic rhamnose degradation" EXACT []
-is_a: GO:0019301 ! rhamnose catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose, that occurs in the absence of oxygen." [GOC:ai]
+comment: The reason for obsoletion is that this term lacks annotations or supporting evidence, and the MetaCyc pathways for L-rhamnose degradation are not described as anaerobic.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31652" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019301
[Term]
id: GO:0019305
@@ -153937,7 +156530,7 @@
id: GO:0019310
name: inositol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms." [GOC:curators]
synonym: "inositol breakdown" EXACT []
synonym: "inositol catabolism" EXACT []
synonym: "inositol degradation" EXACT []
@@ -153946,8 +156539,12 @@
synonym: "vitamin Bh catabolic process" EXACT []
synonym: "vitamin Bh catabolism" EXACT []
xref: MetaCyc:P562-PWY
+xref: MetaCyc:PWY-7241
is_a: GO:0006020 ! inositol metabolic process
is_a: GO:0046174 ! polyol catabolic process
+property_value: skos:narrowMatch MetaCyc:P562-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-7241
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019311
@@ -154013,15 +156610,13 @@
[Term]
id: GO:0019317
-name: fucose catabolic process
+name: obsolete fucose catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fucose (6-deoxygalactose)." [GOC:jl]
-synonym: "fucose breakdown" EXACT []
-synonym: "fucose catabolism" EXACT []
-synonym: "fucose degradation" EXACT []
-xref: MetaCyc:FUCCAT-PWY
-is_a: GO:0006004 ! fucose metabolic process
-is_a: GO:0019320 ! hexose catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fucose (6-deoxygalactose)." [GOC:jl]
+comment: The reason for obsoletion is that this term is redundant with its more specific child term GO:0042355 'L-fucose catabolic process'. The existing annotations appear to be specific for L-fucose based on the protein names.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31652" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042355
[Term]
id: GO:0019318
@@ -154191,10 +156786,15 @@
def: "The reduction of nitrate to dinitrogen by four reduction reactions: nitrate reduced to nitrite, then to nitric oxide, then to nitrous oxide, and finally to dinitrogen." [MetaCyc:DENITRIFICATION-PWY]
xref: kegg.module:M00529
xref: MetaCyc:DENITRIFICATION-PWY
+xref: MetaCyc:PWY-6748
+xref: MetaCyc:PWY-7084
is_a: GO:0071941 ! nitrogen cycle metabolic process
-relationship: has_part GO:0008940 ! nitrate reductase activity
relationship: has_part GO:0050304 ! nitrous-oxide reductase activity
+property_value: skos:narrowMatch MetaCyc:DENITRIFICATION-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6748
+property_value: skos:narrowMatch MetaCyc:PWY-7084
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27221" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019334
@@ -154219,8 +156819,9 @@
synonym: "3-methylquinoline catabolism" NARROW []
synonym: "3-methylquinoline degradation" NARROW []
synonym: "quinaldine catabolic process" NARROW []
-xref: MetaCyc:PWY-721 {comment="skos:narrowMatch"}
+xref: MetaCyc:PWY-721
is_a: GO:0042178 ! xenobiotic catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-721
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27606" xsd:anyURI
[Term]
@@ -154231,9 +156832,9 @@
synonym: "phenol-containing compound breakdown" EXACT []
synonym: "phenol-containing compound catabolism" EXACT []
synonym: "phenol-containing compound degradation" EXACT []
-xref: MetaCyc:PHENOLDEG-PWY
is_a: GO:0009056 ! catabolic process
is_a: GO:0018958 ! phenol-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019337
@@ -154253,7 +156854,7 @@
id: GO:0019338
name: pentachlorophenol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pentachlorophenol, a chlorinated insecticide and fungicide used primarily to protect timber from fungal rot and wood boring insects. Pentachlorophenol is significantly toxic to mammals, plants, and many microorganisms." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of pentachlorophenol, a chlorinated insecticide and fungicide used primarily to protect timber from fungal rot and wood boring insects. Pentachlorophenol is significantly toxic to mammals, plants, and many microorganisms." [GOC:curators]
synonym: "pentachlorophenol breakdown" EXACT []
synonym: "pentachlorophenol catabolism" EXACT []
synonym: "pentachlorophenol degradation" EXACT []
@@ -154317,47 +156918,63 @@
[Term]
id: GO:0019343
-name: L-cysteine biosynthetic process via L-cystathionine
+name: obsolete L-cysteine biosynthetic process via L-cystathionine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate L-cystathionine." [GOC:go_curators, MetaCyc:HOMOCYSDEGR-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate L-cystathionine." [GOC:curators]
+comment: This term was obsoleted because it is too specific and is outside the scope of GO.
synonym: "cysteine anabolism via cystathionine" EXACT []
synonym: "cysteine formation via cystathionine" EXACT []
synonym: "cysteine synthesis via cystathionine" EXACT []
-xref: MetaCyc:HOMOCYSDEGR-PWY
-is_a: GO:0019344 ! L-cysteine biosynthetic process
-property_value: skos:exactMatch MetaCyc:HOMOCYSDEGR-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019344
[Term]
id: GO:0019344
name: L-cysteine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid." [GOC:curators]
synonym: "cysteine anabolism" EXACT []
synonym: "cysteine biosynthesis" EXACT []
synonym: "cysteine formation" EXACT []
synonym: "cysteine synthesis" EXACT []
+xref: MetaCyc:CYSTSYN-PWY
+xref: MetaCyc:HOMOCYSDEGR-PWY
+xref: MetaCyc:PWY-6308
+xref: MetaCyc:PWY-7289
+xref: MetaCyc:PWY-7870
+xref: MetaCyc:PWY-8009
+xref: MetaCyc:PWY-8010
+xref: MetaCyc:PWY-I9
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
-is_a: GO:0046439 ! L-cysteine metabolic process
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:CYSTSYN-PWY
+property_value: skos:narrowMatch MetaCyc:HOMOCYSDEGR-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6308
+property_value: skos:narrowMatch MetaCyc:PWY-7289
+property_value: skos:narrowMatch MetaCyc:PWY-7870
+property_value: skos:narrowMatch MetaCyc:PWY-8009
+property_value: skos:narrowMatch MetaCyc:PWY-8010
+property_value: skos:narrowMatch MetaCyc:PWY-I9
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0019345
-name: L-cysteine biosynthetic process via S-sulfo-L-cysteine
+name: obsolete L-cysteine biosynthetic process via S-sulfo-L-cysteine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate S-sulfo-L-cysteine." [MetaCyc:PWY-7289]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate S-sulfo-L-cysteine." [GOC:curators]
+comment: This term was obsoleted because it is too specific and is outside the scope of GO.
synonym: "cysteine anabolism via S-sulfo-L-cysteine" EXACT []
synonym: "cysteine biosynthesis via S-sulpho-L-cysteine" EXACT []
synonym: "cysteine biosynthetic process via S-sulpho-L-cysteine" EXACT []
synonym: "cysteine formation via S-sulfo-L-cysteine" EXACT []
synonym: "cysteine synthesis via S-sulfo-L-cysteine" EXACT []
-xref: MetaCyc:PWY-7289
-is_a: GO:0019344 ! L-cysteine biosynthetic process
-property_value: skos:exactMatch MetaCyc:PWY-7289
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019344
[Term]
id: GO:0019346
@@ -154369,8 +156986,9 @@
xref: MetaCyc:PWY-801
xref: Reactome:R-HSA-1614603 "Cysteine formation from homocysteine"
xref: Wikipedia:Transsulfuration_pathway
-is_a: GO:0046439 ! L-cysteine metabolic process
is_a: GO:0050667 ! homocysteine metabolic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
@@ -154444,7 +157062,7 @@
id: GO:0019352
name: protoporphyrinogen IX biosynthetic process from glycine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glycine." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glycine." [GOC:curators]
synonym: "protoporphyrinogen IX anabolism from glycine" EXACT []
synonym: "protoporphyrinogen IX formation from glycine" EXACT []
synonym: "protoporphyrinogen IX synthesis from glycine" EXACT []
@@ -154482,7 +157100,7 @@
id: GO:0019356
name: obsolete nicotinate nucleotide biosynthetic process from tryptophan
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of nicotinate nucleotide from other compounds, including tryptophan." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of nicotinate nucleotide from other compounds, including tryptophan." [GOC:curators]
comment: The reason for obsoletion is that this term is essentially equivalent to 'de novo' NAD+ biosynthetic process from L-tryptophan.
synonym: "nicotinate nucleotide anabolism from tryptophan" EXACT []
synonym: "nicotinate nucleotide formation from tryptophan" EXACT []
@@ -154495,7 +157113,7 @@
id: GO:0019357
name: nicotinate nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid)." [GOC:curators]
synonym: "nicotinate nucleotide anabolism" EXACT []
synonym: "nicotinate nucleotide biosynthesis" EXACT []
synonym: "nicotinate nucleotide formation" EXACT []
@@ -154506,7 +157124,7 @@
id: GO:0019358
name: nicotinate nucleotide salvage
namespace: biological_process
-def: "The generation of nicotinate nucleotide without de novo synthesis." [GOC:go_curators]
+def: "The generation of nicotinate nucleotide without de novo synthesis." [GOC:curators]
synonym: "nicotinate nucleotide biosynthesis, salvage pathway" EXACT []
synonym: "nicotinate nucleotide biosynthetic process, salvage pathway" EXACT []
xref: MetaCyc:PWY3O-224
@@ -154519,7 +157137,7 @@
id: GO:0019359
name: nicotinamide nucleotide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinamide." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinamide." [GOC:curators]
synonym: "nicotinamide nucleotide anabolism" EXACT []
synonym: "nicotinamide nucleotide biosynthesis" EXACT []
synonym: "nicotinamide nucleotide formation" EXACT []
@@ -154531,7 +157149,7 @@
id: GO:0019360
name: nicotinamide nucleotide biosynthetic process from niacinamide
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotide from other compounds, including niacinamide." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of nicotinamide nucleotide from other compounds, including niacinamide." [GOC:curators]
synonym: "nicotinamide nucleotide anabolism from niacinamide" EXACT []
synonym: "nicotinamide nucleotide formation from niacinamide" EXACT []
synonym: "nicotinamide nucleotide synthesis from niacinamide" EXACT []
@@ -154605,8 +157223,8 @@
name: fatty acid elongation, unsaturated fatty acid
namespace: biological_process
def: "Elongation of a fatty acid chain into which one or more C-C double bonds have been introduced." [GOC:mah]
-xref: MetaCyc:PWY0-862
is_a: GO:0030497 ! fatty acid elongation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019369
@@ -154628,7 +157246,7 @@
id: GO:0019370
name: leukotriene biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid." [GOC:curators]
synonym: "leukotriene anabolism" EXACT []
synonym: "leukotriene biosynthesis" EXACT []
synonym: "leukotriene formation" EXACT []
@@ -154682,8 +157300,13 @@
synonym: "galactolipid biosynthesis" EXACT []
synonym: "galactolipid formation" EXACT []
synonym: "galactolipid synthesis" EXACT []
+xref: MetaCyc:PWY-401
+xref: MetaCyc:PWY-7666
is_a: GO:0009247 ! glycolipid biosynthetic process
is_a: GO:0019374 ! galactolipid metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-401
+property_value: skos:narrowMatch MetaCyc:PWY-7666
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019376
@@ -154700,7 +157323,7 @@
id: GO:0019377
name: glycolipid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide)." [GOC:curators]
synonym: "glycolipid breakdown" EXACT []
synonym: "glycolipid catabolism" EXACT []
synonym: "glycolipid degradation" EXACT []
@@ -154755,7 +157378,7 @@
id: GO:0019382
name: carbon tetrachloride catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of carbon tetrachloride, a toxic, carcinogenic compound which is used as a general solvent in industrial degreasing operations. It is also used as grain fumigant and a chemical intermediate in the production of refrigerants." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of carbon tetrachloride, a toxic, carcinogenic compound which is used as a general solvent in industrial degreasing operations. It is also used as grain fumigant and a chemical intermediate in the production of refrigerants." [GOC:curators]
synonym: "carbon tetrachloride breakdown" EXACT []
synonym: "carbon tetrachloride catabolism" EXACT []
synonym: "carbon tetrachloride degradation" EXACT []
@@ -154899,14 +157522,13 @@
[Term]
id: GO:0019394
-name: glucarate catabolic process
+name: obsolete glucarate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glucarate, the anion of glucaric acid." [ISBN:0198506732]
-synonym: "glucarate breakdown" EXACT []
-synonym: "glucarate catabolism" EXACT []
-synonym: "glucarate degradation" EXACT []
-xref: MetaCyc:GLUCARDEG-PWY
-is_a: GO:0019579 ! aldaric acid catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glucarate, the anion of glucaric acid." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term is redundant with its more specific child term GO:0042838 'D-glucarate catabolic process'. The existing annotations are specific for D-glucarate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31652" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042838
[Term]
id: GO:0019395
@@ -155078,7 +157700,7 @@
id: GO:0019409
name: aerobic respiration, using ammonia as electron donor
namespace: biological_process
-def: "The metabolic process in which ammonia (NH3) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite." [MetaCyc:AMMOXID-PWY]
+def: "The metabolic process in which ammonia (NH4+) is oxidized to nitrite (NO2) in the presence of oxygen; enzymatic reactions convert ammonia to hydrazine, and hydrazine to nitrite." [MetaCyc:AMMOXID-PWY]
synonym: "aerobic ammonia oxidation to nitrite via hydrazine" EXACT [GOC:mah]
synonym: "nitrification" RELATED []
xref: MetaCyc:AMMOXID-PWY
@@ -155117,7 +157739,7 @@
id: GO:0019413
name: acetate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of acetate, the anion of acetic acid." [GOC:curators]
synonym: "acetate anabolism" EXACT []
synonym: "acetate biosynthesis" EXACT []
synonym: "acetate formation" EXACT []
@@ -155138,7 +157760,7 @@
id: GO:0019415
name: acetate biosynthetic process from carbon monoxide
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide." [GOC:curators]
synonym: "acetate anabolism from carbon monoxide" EXACT []
synonym: "acetate formation from carbon monoxide" EXACT []
synonym: "acetate synthesis from carbon monoxide" EXACT []
@@ -155147,11 +157769,20 @@
[Term]
id: GO:0019416
-name: polythionate oxidation
+name: thiosulfate oxidation
namespace: biological_process
def: "The chemical reactions and pathways resulting in the conversion of thiosulfate to tetrathionate, using cytochrome c as an electron acceptor." [MetaCyc:THIOSULFOX-PWY]
+synonym: "polythionate oxidation" EXACT []
+xref: MetaCyc:PWY-5296
+xref: MetaCyc:PWY-5303
+xref: MetaCyc:PWY-6677
xref: MetaCyc:THIOSULFOX-PWY
is_a: GO:0006790 ! sulfur compound metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5296
+property_value: skos:narrowMatch MetaCyc:PWY-5303
+property_value: skos:narrowMatch MetaCyc:PWY-6677
+property_value: skos:narrowMatch MetaCyc:THIOSULFOX-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019417
@@ -155204,10 +157835,14 @@
id: GO:0019422
name: disproportionation of elemental sulfur
namespace: biological_process
-def: "The process in which sulfur compounds with an intermediate oxidation state serve as both electron donors and electron acceptors in an energy-generating redox process. The reaction takes place anaerobically, in light and in the absence of CO2." [MetaCyc:P203-PWY]
+def: "The process in which sulfur compounds with an intermediate oxidation state serve as both electron donors and electron acceptors in an energy-generating redox process." [MetaCyc:P203-PWY]
synonym: "disproportionation of elemental sulphur" EXACT []
xref: MetaCyc:P203-PWY
+xref: MetaCyc:PWY-5302
is_a: GO:0006790 ! sulfur compound metabolic process
+property_value: skos:narrowMatch MetaCyc:P203-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5302
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019423
@@ -155246,22 +157881,23 @@
[Term]
id: GO:0019427
-name: acetyl-CoA biosynthetic process from acetate
+name: obsolete acetyl-CoA biosynthetic process from acetate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate." [MetaCyc:ACETATEUTIL-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from acetate, either directly or via acetylphosphate." [MetaCyc:ACETATEUTIL-PWY]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "acetate utilization" RELATED []
synonym: "acetyl-CoA anabolism from acetate" EXACT []
synonym: "acetyl-CoA formation from acetate" EXACT []
synonym: "acetyl-CoA synthesis from acetate" EXACT []
-xref: MetaCyc:ACETATEUTIL-PWY
-is_a: GO:0006083 ! acetate metabolic process
-is_a: GO:0006085 ! acetyl-CoA biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31666" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006085
[Term]
id: GO:0019428
name: allantoin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of allantoin, (2,5-dioxo-4-imidazolidinyl)urea." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of allantoin, (2,5-dioxo-4-imidazolidinyl)urea." [GOC:curators]
synonym: "allantoin anabolism" EXACT []
synonym: "allantoin biosynthesis" EXACT []
synonym: "allantoin formation" EXACT []
@@ -155282,9 +157918,13 @@
synonym: "fluorene metabolic process" NARROW []
synonym: "fluorene metabolism" EXACT []
xref: MetaCyc:FLUORENE-DEG-9-ONE-PWY
+xref: MetaCyc:PWY-1381
xref: UM-BBD_pathwayID:flu
is_a: GO:0042178 ! xenobiotic catabolic process
is_a: GO:0120253 ! hydrocarbon catabolic process
+property_value: skos:narrowMatch MetaCyc:FLUORENE-DEG-9-ONE-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-1381
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019430
@@ -155301,25 +157941,18 @@
[Term]
id: GO:0019431
-name: acetyl-CoA biosynthetic process from ethanol
+name: obsolete acetyl-CoA biosynthetic process from ethanol
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA from ethanol via acetaldehyde." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from ethanol via acetaldehyde." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "acetyl-CoA anabolism from ethanol" EXACT []
synonym: "acetyl-CoA formation from ethanol" EXACT []
synonym: "acetyl-CoA synthesis from ethanol" EXACT []
-xref: MetaCyc:ETOH-ACETYLCOA-ANA-PWY
-xref: MetaCyc:PWY66-161
-xref: MetaCyc:PWY66-162
-xref: MetaCyc:PWY66-21
-is_a: GO:0006067 ! ethanol metabolic process
-is_a: GO:0006085 ! acetyl-CoA biosynthetic process
-is_a: GO:0006091 ! generation of precursor metabolites and energy
-property_value: skos:narrowMatch MetaCyc:ETOH-ACETYLCOA-ANA-PWY
-property_value: skos:narrowMatch MetaCyc:PWY66-161
-property_value: skos:narrowMatch MetaCyc:PWY66-162
-property_value: skos:narrowMatch MetaCyc:PWY66-21
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27260" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31666" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006085
[Term]
id: GO:0019432
@@ -155409,7 +158042,7 @@
id: GO:0019440
name: obsolete L-tryptophan catabolic process to indole-3-acetate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including indole-3-acetate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including indole-3-acetate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "tryptophan breakdown to indole-3-acetate" EXACT []
synonym: "tryptophan catabolic process to IAA" EXACT []
@@ -155426,7 +158059,7 @@
id: GO:0019441
name: obsolete L-tryptophan catabolic process to L-kynurenine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including L-kynurenine." [GOC:go_curators, PMID:31704347]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including L-kynurenine." [GOC:curators, PMID:31704347]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "tryptophan breakdown to kynurenine" EXACT []
synonym: "tryptophan catabolic process to kynurenine" EXACT []
@@ -155440,7 +158073,7 @@
id: GO:0019442
name: obsolete L-tryptophan catabolic process to acetyl-CoA
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including acetyl-CoA." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including acetyl-CoA." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "tryptophan breakdown to acetyl-CoA" EXACT []
synonym: "tryptophan catabolic process to acetyl-CoA" EXACT []
@@ -155467,7 +158100,7 @@
id: GO:0019444
name: obsolete L-tryptophan catabolic process to catechol
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including catechol." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tryptophan into other compounds, including catechol." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "tryptophan breakdown to catechol" EXACT []
synonym: "tryptophan catabolic process to catechol" EXACT []
@@ -155480,7 +158113,7 @@
id: GO:0019445
name: obsolete L-tyrosine catabolic process to fumarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tyrosine into other compounds, including fumarate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-tyrosine into other compounds, including fumarate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "tyrosine breakdown to fumarate" EXACT []
synonym: "tyrosine degradation to fumarate" EXACT []
@@ -155492,7 +158125,7 @@
id: GO:0019446
name: obsolete tyrosine catabolic process to phosphoenolpyruvate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of tyrosine into other compounds, including phosphoenolpyruvate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of tyrosine into other compounds, including phosphoenolpyruvate." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this is a real process.
synonym: "tyrosine breakdown to phosphoenolpyruvate" EXACT []
synonym: "tyrosine degradation to phosphoenolpyruvate" EXACT []
@@ -155500,21 +158133,21 @@
[Term]
id: GO:0019447
-name: D-cysteine catabolic process
+name: obsolete D-cysteine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-cysteine, (S)-2-amino-3-mercaptopropanoic acid, which occurs naturally in firefly luciferin." [PMID:11527960]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-cysteine, (S)-2-amino-3-mercaptopropanoic acid, which occurs naturally in firefly luciferin." [PMID:11527960]
+comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-cysteine.
synonym: "D-cysteine breakdown" EXACT []
synonym: "D-cysteine catabolism" EXACT []
synonym: "D-cysteine degradation" EXACT []
-is_a: GO:0000098 ! sulfur amino acid catabolic process
-is_a: GO:0006534 ! cysteine metabolic process
-is_a: GO:0019478 ! D-amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019448
name: L-cysteine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [GOC:jsg, GOC:mah]
+def: "The chemical reactions and pathways resulting in the breakdown of L-cysteine." [GOC:curators]
synonym: "L-cysteine breakdown" EXACT []
synonym: "L-cysteine catabolism" EXACT []
synonym: "L-cysteine degradation" EXACT []
@@ -155522,19 +158155,19 @@
xref: MetaCyc:LCYSDEG-PWY
xref: MetaCyc:PWY-5329
is_a: GO:0000098 ! sulfur amino acid catabolic process
-is_a: GO:0046439 ! L-cysteine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:CYSTEINE-DEG-PWY
property_value: skos:narrowMatch MetaCyc:LCYSDEG-PWY
property_value: skos:narrowMatch MetaCyc:PWY-5329
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0019449
name: obsolete L-cysteine catabolic process to hypotaurine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including hypotaurine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including hypotaurine." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown to hypotaurine" EXACT []
synonym: "L-cysteine degradation to hypotaurine" EXACT []
@@ -155546,7 +158179,7 @@
id: GO:0019450
name: obsolete L-cysteine catabolic process to pyruvate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including pyruvate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including pyruvate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown to pyruvate" EXACT []
synonym: "L-cysteine degradation to pyruvate" EXACT []
@@ -155556,37 +158189,33 @@
[Term]
id: GO:0019451
-name: L-cysteine catabolic process to pyruvate, using cysteine dioxygenase
+name: obsolete L-cysteine catabolic process to pyruvate, using cysteine dioxygenase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown into pyruvate of L-cystine, catalyzed by the enzyme cysteine dioxygenase (EC:1.13.11.20)." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown into pyruvate of L-cystine, catalyzed by the enzyme cysteine dioxygenase (EC:1.13.11.20)." [GOC:jl]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown to pyruvate, using cysteine dioxygenase" EXACT []
synonym: "L-cysteine degradation to pyruvate, using cysteine dioxygenase" EXACT []
-is_a: GO:0006090 ! pyruvate metabolic process
-is_a: GO:0019448 ! L-cysteine catabolic process
-relationship: has_part GO:0017172 ! cysteine dioxygenase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019448
[Term]
id: GO:0019452
-name: taurine biosynthetic process from L-cysteine
+name: obsolete taurine biosynthetic process from L-cysteine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of taurine (2-aminoethanesulfonic acid) from L-cysteine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of taurine (2-aminoethanesulfonic acid) from L-cysteine." [GOC:curators]
+comment: This term was obsoleted because it is too specific and is outside the scope of GO.
synonym: "L-cysteine breakdown to taurine" EXACT []
synonym: "L-cysteine degradation to taurine" EXACT []
-xref: MetaCyc:PWY-5331
-xref: MetaCyc:PWY-7850
-xref: MetaCyc:PWY-8359
-is_a: GO:0042412 ! taurine biosynthetic process
-is_a: GO:0046439 ! L-cysteine metabolic process
-property_value: skos:narrowMatch MetaCyc:PWY-5331
-property_value: skos:narrowMatch MetaCyc:PWY-7850
-property_value: skos:narrowMatch MetaCyc:PWY-8359
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042412
[Term]
id: GO:0019453
name: obsolete L-cysteine catabolic process via cystine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine, via the intermediate cystine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine, via the intermediate cystine." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown via cystine" EXACT []
synonym: "L-cysteine degradation via cystine" EXACT []
@@ -155596,40 +158225,46 @@
[Term]
id: GO:0019454
-name: L-cysteine catabolic process via cystine, using glutathione-cystine transhydrogenase
+name: obsolete L-cysteine catabolic process via cystine, using glutathione-cystine transhydrogenase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme glutathione-cystine transhydrogenase." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme glutathione-cystine transhydrogenase." [GOC:jl]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown via cystine, using glutathione-cystine transhydrogenase" EXACT []
synonym: "L-cysteine degradation via cystine, using glutathione-cystine transhydrogenase" EXACT []
-is_a: GO:0019448 ! L-cysteine catabolic process
-relationship: has_part GO:0047141 ! glutathione-cystine transhydrogenase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019448
[Term]
id: GO:0019455
-name: L-cysteine catabolic process via cystine, using cystine reductase
+name: obsolete L-cysteine catabolic process via cystine, using cystine reductase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cystine reductase." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cystine reductase." [GOC:jl]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown via cystine, using cystine reductase" EXACT []
synonym: "L-cysteine degradation via cystine, using cystine reductase" EXACT []
-is_a: GO:0019448 ! L-cysteine catabolic process
-relationship: has_part GO:0050456 ! L-cystine reductase (NADH) activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019448
[Term]
id: GO:0019456
-name: L-cysteine catabolic process via cystine, using cysteine transaminase
+name: obsolete L-cysteine catabolic process via cystine, using cysteine transaminase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cysteine transaminase." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cysteine transaminase." [GOC:jl]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-cysteine breakdown via cystine, using cysteine transaminase" EXACT []
synonym: "L-cysteine degradation via cystine, using cysteine transaminase" EXACT []
-is_a: GO:0019448 ! L-cysteine catabolic process
-relationship: has_part GO:0047801 ! L-cysteine transaminase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22538" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019448
[Term]
id: GO:0019457
name: obsolete L-methionine catabolic process to succinyl-CoA
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine into other compounds, including succinyl-CoA." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine into other compounds, including succinyl-CoA." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "methionine breakdown to succinyl-CoA" EXACT []
synonym: "methionine degradation to succinyl-CoA" EXACT []
@@ -155641,7 +158276,7 @@
id: GO:0019458
name: obsolete L-methionine catabolic process via 2-oxobutanoate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine, via the intermediate 2-oxobutanoate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-methionine, via the intermediate 2-oxobutanoate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "methionine breakdown via 2-oxobutanoate" EXACT []
synonym: "methionine degradation via 2-oxobutanoate" EXACT []
@@ -155653,7 +158288,7 @@
id: GO:0019460
name: obsolete glutamine catabolic process to fumarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamine into other compounds, including fumarate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamine into other compounds, including fumarate." [GOC:curators]
comment: The reason for obsoletion is that this term is the same as the parent term.
synonym: "glutamate catabolic process to fumarate" NARROW [GOC:bf, GOC:jl]
synonym: "glutamine breakdown to fumarate" EXACT []
@@ -155692,7 +158327,7 @@
id: GO:0019463
name: obsolete glycine catabolic process to creatine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glycine into other compounds, including creatine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glycine into other compounds, including creatine." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "glycine breakdown to creatine" EXACT []
synonym: "glycine degradation to creatine" EXACT []
@@ -155714,7 +158349,7 @@
id: GO:0019465
name: obsolete aspartate transamidation
namespace: biological_process
-def: "OBSOLETE. The exchange of the amino group of aspartate, the anion derived from aspartic acid, for another amino group." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The exchange of the amino group of aspartate, the anion derived from aspartic acid, for another amino group." [GOC:curators, ISBN:0198506732]
comment: The reason for obsoletion is that this term represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28786" xsd:anyURI
@@ -155722,26 +158357,30 @@
[Term]
id: GO:0019466
-name: L-ornithine catabolic process via proline
+name: obsolete L-ornithine catabolic process via proline
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-ornithine, via the intermediate proline." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-ornithine, via the intermediate proline." [GOC:curators]
+comment: This term was obsoleted because it represents a variant pathway of L-ornithine degradation and is out of scope for GO.
synonym: "ornithine breakdown via proline" EXACT []
synonym: "ornithine degradation via proline" EXACT []
-xref: MetaCyc:ORN-AMINOPENTANOATE-CAT-PWY
-is_a: GO:0006593 ! L-ornithine catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006593
[Term]
id: GO:0019467
-name: L-ornithine catabolic process, by decarboxylation
+name: obsolete L-ornithine catabolic process, by decarboxylation
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-ornithine by decarboxylation." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-ornithine by decarboxylation." [GOC:curators]
+comment: This term was obsoleted because it represents a variant pathway of L-ornithine degradation and is out of scope for GO.
synonym: "ornithine breakdown, by decarboxylation" EXACT []
synonym: "ornithine degradation, by decarboxylation" EXACT []
xref: MetaCyc:ORNDEG-PWY
-is_a: GO:0006593 ! L-ornithine catabolic process
-relationship: has_part GO:0016831 ! carboxy-lyase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006593
[Term]
id: GO:0019468
@@ -155771,7 +158410,7 @@
id: GO:0019470
name: trans-4-hydroxy-L-proline catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of trans-4-hydroxy-L-proline, C5H9NO3, a derivative of the amino acid proline." [GOC:ai]
+def: "The chemical reactions and pathways resulting in the breakdown of trans-4-hydroxy-L-proline." [GOC:curators]
synonym: "4-hydroxyproline breakdown" EXACT []
synonym: "4-hydroxyproline catabolism" EXACT []
synonym: "4-hydroxyproline degradation" EXACT []
@@ -155784,6 +158423,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-5159
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0019471
@@ -155797,22 +158437,22 @@
[Term]
id: GO:0019472
-name: 4-hydroxyproline biosynthetic process
+name: obsolete 4-hydroxyproline biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline." [GOC:ai]
+comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
synonym: "4-hydroxyproline anabolism" EXACT []
synonym: "4-hydroxyproline biosynthesis" EXACT []
synonym: "4-hydroxyproline formation" EXACT []
synonym: "4-hydroxyproline synthesis" EXACT []
-is_a: GO:0042398 ! modified amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
-is_a: GO:1901607 ! alpha-amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019473
name: obsolete L-lysine catabolic process to glutarate, by acetylation
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including glutarate, by acetylation." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including glutarate, by acetylation." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-lysine breakdown to glutarate, by acetylation" EXACT []
synonym: "L-lysine degradation to glutarate, by acetylation" EXACT []
@@ -155824,7 +158464,7 @@
id: GO:0019474
name: obsolete L-lysine catabolic process to acetyl-CoA
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-lysine breakdown to acetyl-CoA" EXACT []
synonym: "L-lysine degradation to acetyl-CoA" EXACT []
@@ -155852,20 +158492,21 @@
[Term]
id: GO:0019476
-name: D-lysine catabolic process
+name: obsolete D-lysine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-lysine, the D-enantiomer of lysine; i.e. (2R)-2,6-diaminohexanoic acid." [GOC:ai, GOC:jsg, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-lysine, the D-enantiomer of lysine; i.e. (2R)-2,6-diaminohexanoic acid." [GOC:ai, GOC:jsg, GOC:mah]
+comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-lysine.
synonym: "D-lysine breakdown" EXACT []
synonym: "D-lysine catabolism" EXACT []
synonym: "D-lysine degradation" EXACT []
-is_a: GO:0006553 ! lysine metabolic process
-is_a: GO:0019478 ! D-amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019477
name: L-lysine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-lysine, the L-enantiomer of (S)-2,6-diaminohexanoic acid." [GOC:go_curators, GOC:jsg, GOC:mah]
+def: "The chemical reactions and pathways resulting in the breakdown of L-lysine." [GOC:curators]
synonym: "L-lysine breakdown" EXACT []
synonym: "L-lysine catabolism" EXACT []
synonym: "L-lysine degradation" EXACT []
@@ -155874,10 +158515,12 @@
xref: MetaCyc:PWY-5280
xref: MetaCyc:PWY-5283
xref: MetaCyc:PWY-5298
+xref: MetaCyc:PWY-5311
+xref: MetaCyc:PWY-5314
+xref: MetaCyc:PWY-5324
xref: MetaCyc:PWY-6328
xref: MetaCyc:PWY0-461
xref: MetaCyc:PWY66-425
-is_a: GO:0006553 ! lysine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:LYSDEGII-PWY
@@ -155885,10 +158528,15 @@
property_value: skos:narrowMatch MetaCyc:PWY-5280
property_value: skos:narrowMatch MetaCyc:PWY-5283
property_value: skos:narrowMatch MetaCyc:PWY-5298
+property_value: skos:narrowMatch MetaCyc:PWY-5311
+property_value: skos:narrowMatch MetaCyc:PWY-5314
+property_value: skos:narrowMatch MetaCyc:PWY-5324
property_value: skos:narrowMatch MetaCyc:PWY-6328
property_value: skos:narrowMatch MetaCyc:PWY0-461
property_value: skos:narrowMatch MetaCyc:PWY66-425
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0019478
@@ -155926,7 +158574,7 @@
id: GO:0019481
name: obsolete L-alanine catabolic process, by transamination
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-alanine by transamination." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-alanine by transamination." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-alanine breakdown, by transamination" EXACT []
synonym: "L-alanine degradation, by transamination" EXACT []
@@ -155952,15 +158600,26 @@
synonym: "beta-alanine biosynthesis" EXACT []
synonym: "beta-alanine formation" EXACT []
synonym: "beta-alanine synthesis" EXACT []
+xref: MetaCyc:PWY-3941
+xref: MetaCyc:PWY-3981
+xref: MetaCyc:PWY-3982
+xref: MetaCyc:PWY-5155
+xref: MetaCyc:PWY-5760
is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0019482 ! beta-alanine metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-3941
+property_value: skos:narrowMatch MetaCyc:PWY-3981
+property_value: skos:narrowMatch MetaCyc:PWY-3982
+property_value: skos:narrowMatch MetaCyc:PWY-5155
+property_value: skos:narrowMatch MetaCyc:PWY-5760
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
[Term]
id: GO:0019484
name: beta-alanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins." [GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of beta-alanine." [GOC:curators]
synonym: "beta-alanine breakdown" EXACT []
synonym: "beta-alanine catabolism" EXACT []
synonym: "beta-alanine degradation" EXACT []
@@ -155974,25 +158633,31 @@
property_value: skos:narrowMatch MetaCyc:PWY-1781
property_value: skos:narrowMatch MetaCyc:PWY-8120
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0019485
-name: beta-alanine catabolic process to L-alanine
+name: obsolete beta-alanine catabolic process to L-alanine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including L-alanine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including L-alanine." [GOC:curators]
+comment: This term was obsoleted because it represents a variant pathway of beta-alanine degradation and is out of scope for GO.
synonym: "beta-alanine breakdown to L-alanine" EXACT []
synonym: "beta-alanine degradation to L-alanine" EXACT []
-is_a: GO:0019484 ! beta-alanine catabolic process
-is_a: GO:0042851 ! L-alanine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019484
[Term]
id: GO:0019486
-name: beta-alanine catabolic process to mevalonate semialdehyde, by transamination
+name: obsolete beta-alanine catabolic process to mevalonate semialdehyde, by transamination
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including mevalonate semialdehyde, by transamination." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of beta-alanine into other compounds, including mevalonate semialdehyde, by transamination." [GOC:curators]
+comment: This term was obsoleted because it represents a variant pathway of beta-alanine degradation and is out of scope for GO.
synonym: "beta-alanine breakdown to mevalonate semialdehyde, by transamination" EXACT []
synonym: "beta-alanine degradation to mevalonate semialdehyde, by transamination" EXACT []
-is_a: GO:0019484 ! beta-alanine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019484
[Term]
id: GO:0019487
@@ -156056,19 +158721,21 @@
[Term]
id: GO:0019492
-name: L-proline salvage
+name: obsolete L-proline salvage
namespace: biological_process
-def: "Any process which produces L-proline from derivatives of it, without de novo synthesis." [GOC:jl]
+def: "OBSOLETE. Any process which produces L-proline from derivatives of it, without de novo synthesis." [GOC:jl]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "proline cycling" EXACT []
-is_a: GO:0043102 ! amino acid salvage
-is_a: GO:0055129 ! L-proline biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30816" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0055129
[Term]
id: GO:0019493
name: obsolete L-arginine catabolic process to L-proline
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-proline." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-proline." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "arginine breakdown to proline" EXACT []
synonym: "arginine degradation to proline" EXACT []
@@ -156080,7 +158747,7 @@
id: GO:0019495
name: obsolete proline catabolic process to 2-oxoglutarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including 2-oxoglutarate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including 2-oxoglutarate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "proline breakdown to 2-oxoglutarate" EXACT []
synonym: "proline catabolic process to 2-ketoglutarate" EXACT []
@@ -156168,24 +158835,23 @@
[Term]
id: GO:0019503
-name: L-proline betaine biosynthetic process
+name: obsolete L-proline betaine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [GOC:ai, PMID:14367364]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [GOC:ai, PMID:14367364]
+comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
synonym: "stachydrine anabolism" EXACT []
synonym: "stachydrine biosynthesis" EXACT []
synonym: "stachydrine biosynthetic process" EXACT []
synonym: "stachydrine formation" EXACT []
synonym: "stachydrine synthesis" EXACT []
-is_a: GO:0006578 ! amino-acid betaine biosynthetic process
-is_a: GO:0009821 ! alkaloid biosynthetic process
-is_a: GO:0170034 ! L-amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019504
name: L-proline betaine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of stachydrine, N-methylproline methylbetaine, the betaine derivative of L-proline." [PMID:10689197, PMID:1804402, PMID:24520058]
+def: "The chemical reactions and pathways resulting in the breakdown of L-proline betaine (stachydrine)." [PMID:10689197, PMID:1804402, PMID:24520058]
synonym: "stachydrine breakdown" EXACT []
synonym: "stachydrine catabolic process" EXACT []
synonym: "stachydrine catabolism" EXACT []
@@ -156200,6 +158866,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-8109
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23577" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0019505
@@ -156248,41 +158915,37 @@
synonym: "2,5-dihydroxypyridine utilization" RELATED []
synonym: "maleamate pathway" EXACT []
synonym: "pyridine-2,5-diol catabolic process to fumarate" EXACT []
-xref: MetaCyc:PWY-722
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
is_obsolete: true
replaced_by: GO:1901848
[Term]
id: GO:0019509
-name: L-methionine salvage from methylthioadenosine
+name: obsolete L-methionine salvage from methylthioadenosine
namespace: biological_process
-def: "The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine." [GOC:jl, MetaCyc:PWY-4361, PMID:19946895]
+def: "OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine." [GOC:jl, PMID:19946895]
+comment: This term was obsoleted because it represents a specific pathway beyond the specificity of GO.
synonym: "methionine recycling" NARROW []
synonym: "methionine regeneration" NARROW []
synonym: "methionine salvage from methylthioadenosine" EXACT [GOC:mah]
synonym: "methionine salvage pathway" EXACT []
-xref: MetaCyc:PWY-4361
-xref: MetaCyc:PWY-6753
-xref: MetaCyc:PWY-6754
-xref: MetaCyc:PWY-6756
xref: Reactome:R-HSA-1237112 "Methionine salvage pathway"
-is_a: GO:0071267 ! L-methionine salvage
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31318" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0033353
[Term]
id: GO:0019510
-name: S-adenosylhomocysteine catabolic process
+name: obsolete S-adenosylhomocysteine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of S-adenosylhomocysteine, forming homocysteine and then methionine." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of S-adenosylhomocysteine, forming homocysteine and then methionine." [ISBN:0198506732]
+comment: The reason for obsoletion is that the terms represent molecular functions and not biological processes.
synonym: "S-adenosylhomocysteine breakdown" EXACT []
synonym: "S-adenosylhomocysteine catabolism" EXACT []
synonym: "S-adenosylhomocysteine degradation" EXACT []
-is_a: GO:0042219 ! modified amino acid catabolic process
-is_a: GO:0044273 ! sulfur compound catabolic process
-is_a: GO:0046130 ! purine ribonucleoside catabolic process
-is_a: GO:0046498 ! S-adenosylhomocysteine metabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15179" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019511
@@ -156298,7 +158961,7 @@
id: GO:0019512
name: lactose catabolic process via tagatose-6-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate." [GOC:curators]
synonym: "lactose breakdown via tagatose-6-phosphate" EXACT []
synonym: "lactose degradation via tagatose-6-phosphate" EXACT []
xref: MetaCyc:LACTOSECAT-PWY
@@ -156329,7 +158992,7 @@
id: GO:0019515
name: lactose catabolic process via UDP-galactose
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate UDP-galactose." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate UDP-galactose." [GOC:curators]
synonym: "lactose breakdown via UDP-galactose" EXACT []
synonym: "lactose degradation via UDP-galactose" EXACT []
is_a: GO:0005990 ! lactose catabolic process
@@ -156493,9 +159156,17 @@
synonym: "taurine breakdown" EXACT []
synonym: "taurine catabolism" EXACT []
synonym: "taurine degradation" EXACT []
+xref: MetaCyc:PWY-1263
+xref: MetaCyc:PWY-1264
+xref: MetaCyc:PWY0-981
xref: MetaCyc:TAURINEDEG-PWY
is_a: GO:0019530 ! taurine metabolic process
is_a: GO:0046306 ! alkanesulfonate catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-1263
+property_value: skos:narrowMatch MetaCyc:PWY-1264
+property_value: skos:narrowMatch MetaCyc:PWY0-981
+property_value: skos:narrowMatch MetaCyc:TAURINEDEG-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019530
@@ -156623,7 +159294,7 @@
id: GO:0019541
name: propionate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving propionate, the anion derived from propionic (propanoic) acid, a carboxylic acid important in the energy metabolism of ruminants." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving propionate, the anion derived from propionic (propanoic) acid, a carboxylic acid important in the energy metabolism of ruminants." [GOC:curators, ISBN:0198506732]
synonym: "propanoate metabolic process" EXACT []
synonym: "propanoate metabolism" EXACT []
synonym: "propionate metabolism" EXACT []
@@ -156633,7 +159304,7 @@
id: GO:0019542
name: propionate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of propionate, the anion derived from propionic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of propionate, the anion derived from propionic acid." [GOC:curators]
synonym: "propionate anabolism" EXACT []
synonym: "propionate biosynthesis" EXACT []
synonym: "propionate formation" EXACT []
@@ -156645,18 +159316,23 @@
id: GO:0019543
name: propionate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of propionate, the anion derived from propionic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of propionate, the anion derived from propionic acid." [GOC:curators]
synonym: "propionate breakdown" EXACT []
synonym: "propionate catabolism" EXACT []
synonym: "propionate degradation" EXACT []
+xref: MetaCyc:PWY-5747
+xref: MetaCyc:PWY0-42
is_a: GO:0019541 ! propionate metabolic process
is_a: GO:0019626 ! short-chain fatty acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5747
+property_value: skos:narrowMatch MetaCyc:PWY0-42
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31668" xsd:anyURI
[Term]
id: GO:0019544
name: obsolete L-arginine catabolic process to L-glutamate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-glutamate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including L-glutamate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "arginine breakdown to glutamate" EXACT []
synonym: "arginine degradation to glutamate" EXACT []
@@ -156669,7 +159345,7 @@
id: GO:0019545
name: obsolete L-arginine catabolic process to succinate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including succinate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-arginine into other compounds, including succinate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "arginine breakdown to succinate" EXACT []
synonym: "arginine degradation to succinate" EXACT []
@@ -156692,7 +159368,7 @@
id: GO:0019547
name: obsolete arginine catabolic process to ornithine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "arginine breakdown to ornithine" EXACT []
synonym: "arginine degradation to ornithine" EXACT []
@@ -156704,7 +159380,7 @@
id: GO:0019548
name: obsolete arginine catabolic process to spermine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including spermine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including spermine." [GOC:curators]
comment: The reason for obsoletion is that this term was added in error.
synonym: "arginine breakdown to spermine" EXACT []
synonym: "arginine degradation to spermine" EXACT []
@@ -156716,7 +159392,7 @@
id: GO:0019549
name: obsolete glutamate catabolic process to succinate via succinate semialdehyde
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into succinate, that includes the conversion of 4-aminobutyrate to succinate semialdehyde by the pyruvate-dependent gamma aminobutyrate (GABA) transaminase." [GOC:bf, GOC:go_curators, MetaCyc:PWY-4321]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into succinate, that includes the conversion of 4-aminobutyrate to succinate semialdehyde by the pyruvate-dependent gamma aminobutyrate (GABA) transaminase." [GOC:bf, GOC:curators, MetaCyc:PWY-4321]
comment: The reason for obsoletion is that this term was added in error (unnecessary specificity, these are steps in a single pathway)
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28355" xsd:anyURI
is_obsolete: true
@@ -156726,7 +159402,7 @@
id: GO:0019550
name: obsolete L-glutamate catabolic process to aspartate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including aspartate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including aspartate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate breakdown to aspartate" EXACT []
synonym: "glutamate degradation to aspartate" EXACT []
@@ -156738,7 +159414,7 @@
id: GO:0019551
name: obsolete glutamate catabolic process to 2-oxoglutarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including 2-oxoglutarate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including 2-oxoglutarate." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "glutamate breakdown to 2-oxoglutarate" EXACT []
synonym: "glutamate catabolic process to 2-ketoglutarate" EXACT []
@@ -156754,35 +159430,34 @@
[Term]
id: GO:0019552
-name: L-glutamate fermentation via 2-hydroxyglutarate
+name: obsolete L-glutamate fermentation via 2-hydroxyglutarate
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate 2-hydroxyglutarate, yielding acetyl-CoA and butanoate. Acetyl-CoA can be further converted into acetate, releasing one ATP molecule." [PMID:17166837]
+def: "OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate 2-hydroxyglutarate, yielding acetyl-CoA and butanoate. Acetyl-CoA can be further converted into acetate, releasing one ATP molecule." [PMID:17166837]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-glutamate catabolic process via 2-hydroxyglutarate" EXACT []
-xref: MetaCyc:P162-PWY
-is_a: GO:0006538 ! L-glutamate catabolic process
-is_a: GO:0019665 ! amino acid fermentation
-property_value: skos:narrowMatch MetaCyc:P162-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0033508
[Term]
id: GO:0019553
-name: L-glutamate fermentation via L-citramalate
+name: obsolete L-glutamate fermentation via L-citramalate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate L-citramalate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate, via the intermediate L-citramalate." [GOC:curators]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate breakdown via L-citramalate" EXACT []
synonym: "glutamate degradation via L-citramalate" EXACT []
synonym: "L-glutamate catabolic process via L-citramalate" EXACT []
-xref: MetaCyc:GLUDEG-II-PWY
-is_a: GO:0006538 ! L-glutamate catabolic process
-is_a: GO:0019665 ! amino acid fermentation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0033508
[Term]
id: GO:0019554
name: obsolete glutamate catabolic process to oxaloacetate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including oxaloacetate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including oxaloacetate." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this function/process/component exists.
synonym: "glutamate breakdown to oxaloacetate" EXACT []
synonym: "glutamate degradation to oxaloacetate" EXACT []
@@ -156793,7 +159468,7 @@
id: GO:0019555
name: obsolete L-glutamate catabolic process to ornithine
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including ornithine." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including ornithine." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate breakdown to ornithine" EXACT []
synonym: "glutamate degradation to ornithine" EXACT []
@@ -156805,7 +159480,7 @@
id: GO:0019556
name: obsolete L-histidine catabolic process to glutamate and formamide
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formamide." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formamide." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "histidine breakdown to glutamate and formamide" EXACT []
synonym: "histidine catabolic process to glutamate and formamide" BROAD []
@@ -156818,7 +159493,7 @@
id: GO:0019557
name: obsolete L-histidine catabolic process to glutamate and formate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "histidine breakdown to glutamate and formate" EXACT []
synonym: "histidine catabolic process to glutamate and formate" BROAD []
@@ -156831,7 +159506,7 @@
id: GO:0019558
name: obsolete L-histidine catabolic process to 2-oxoglutarate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including 2-oxoglutarate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including 2-oxoglutarate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "histidine breakdown to 2-oxoglutarate" EXACT []
synonym: "histidine catabolic process to 2-ketoglutarate" EXACT []
@@ -156850,7 +159525,7 @@
id: GO:0019559
name: obsolete L-histidine catabolic process to imidazol-5-yl-lactate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including imidazol-5-yl-lactate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including imidazol-5-yl-lactate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "histidine breakdown to imidazol-5-yl-lactate" EXACT []
synonym: "histidine degradation to imidazol-5-yl-lactate" EXACT []
@@ -156862,7 +159537,7 @@
id: GO:0019560
name: obsolete L-histidine catabolic process to hydantoin-5-propionate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including hydantoin-5-propionate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including hydantoin-5-propionate." [GOC:curators]
comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "histidine breakdown to hydantoin-5-propionate" EXACT []
synonym: "histidine degradation to hydantoin-5-propionate" EXACT []
@@ -156884,7 +159559,7 @@
id: GO:0019562
name: obsolete L-phenylalanine catabolic process to phosphoenolpyruvate
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-phenylalanine into other compounds, including phosphoenolpyruvate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-phenylalanine into other compounds, including phosphoenolpyruvate." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this is a real process.
synonym: "phenylalanine breakdown to phosphoenolpyruvate" EXACT []
synonym: "phenylalanine degradation to phosphoenolpyruvate" EXACT []
@@ -156894,14 +159569,17 @@
id: GO:0019563
name: glycerol catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids." [GOC:curators, ISBN:0198506732]
synonym: "glycerol breakdown" EXACT []
synonym: "glycerol catabolism" EXACT []
synonym: "glycerol degradation" EXACT []
xref: MetaCyc:GLYCEROL-DEG
+xref: MetaCyc:GLYCEROLMETAB-PWY
is_a: GO:0006071 ! glycerol metabolic process
is_a: GO:0019405 ! alditol catabolic process
+property_value: skos:narrowMatch MetaCyc:GLYCEROLMETAB-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019564
@@ -156953,7 +159631,7 @@
id: GO:0019569
name: L-arabinose catabolic process to D-xylulose 5-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate." [GOC:curators]
synonym: "L-arabinose breakdown to xylulose 5-phosphate" EXACT []
synonym: "L-arabinose degradation to xylulose 5-phosphate" EXACT []
xref: MetaCyc:ARABCAT-PWY
@@ -156965,7 +159643,7 @@
id: GO:0019570
name: L-arabinose catabolic process to 2-oxoglutarate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-arabinose into other compounds, including 2-oxoglutarate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-arabinose into other compounds, including 2-oxoglutarate." [GOC:curators]
synonym: "L-arabinose breakdown to 2-oxoglutarate" EXACT []
synonym: "L-arabinose catabolic process to 2-ketoglutarate" EXACT []
synonym: "L-arabinose catabolic process to alpha-ketoglutarate" EXACT []
@@ -157002,7 +159680,7 @@
id: GO:0019573
name: D-arabinose catabolic process to D-xylulose 5-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-arabinose to form D-xylulose 5-phosphate. D-arabinose is converted into D-ribulose, which is phosphorylated to D-ribulose-5-phosphate, which is isomerized to give D-xylulose-5-phosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of D-arabinose to form D-xylulose 5-phosphate. D-arabinose is converted into D-ribulose, which is phosphorylated to D-ribulose-5-phosphate, which is isomerized to give D-xylulose-5-phosphate." [GOC:curators]
synonym: "D-arabinose breakdown to xylulose 5-phosphate" EXACT []
synonym: "D-arabinose degradation to xylulose 5-phosphate" EXACT []
xref: MetaCyc:DARABCAT-PWY
@@ -157012,23 +159690,18 @@
[Term]
id: GO:0019574
-name: sucrose catabolic process via 3'-ketosucrose
+name: obsolete sucrose catabolic process via 3'-ketosucrose
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds via the conversion of sucrose to 3'-ketosucrose. 3'-ketosucrose is hydrolyzed to 3-ketoglucose and fructose, and the 3-ketoglucose is then be converted to glucose." [GOC:bf, GOC:dgf, MetaCyc:SUCROSEUTIL2-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose, which proceeds via the conversion of sucrose to 3'-ketosucrose. 3'-ketosucrose is hydrolyzed to 3-ketoglucose and fructose, and the 3-ketoglucose is then be converted to glucose." [GOC:bf, GOC:dgf, MetaCyc:SUCROSEUTIL2-PWY]
+comment: This term was obsoleted because it represents a specific pathway out of scope for GO.
synonym: "sucrose breakdown, using glucoside 3-dehydrogenase" EXACT []
synonym: "sucrose catabolic process to D-glucose" EXACT [GOC:bf, MetaCyc:SUCROSEUTIL2-PWY]
synonym: "sucrose catabolic process, using glucoside 3-dehydrogenase" EXACT [GOC:bf, MetaCyc:SUCROSEUTIL2-PWY]
synonym: "sucrose catabolism, using glucoside 3-dehydrogenase" EXACT []
synonym: "sucrose degradation, using glucoside 3-dehydrogenase" EXACT []
-xref: MetaCyc:SUCROSEUTIL2-PWY
-is_a: GO:0005987 ! sucrose catabolic process
-is_a: GO:0006006 ! glucose metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
-is_a: GO:0019637 ! organophosphate metabolic process
-is_a: GO:1901135 ! carbohydrate derivative metabolic process
-relationship: has_part GO:0008865 ! fructokinase activity
-relationship: has_part GO:0033757 ! glucoside 3-dehydrogenase activity
-relationship: has_part GO:0048258 ! 3-ketoglucose-reductase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0005987
[Term]
id: GO:0019575
@@ -157098,7 +159771,9 @@
synonym: "galactarate metabolism" EXACT []
synonym: "mucic acid metabolic process" EXACT []
synonym: "mucic acid metabolism" EXACT []
+is_a: GO:0005975 ! carbohydrate metabolic process
is_a: GO:0043648 ! dicarboxylic acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0019583
@@ -157126,8 +159801,9 @@
name: glucuronate metabolic process
namespace: biological_process
alt_id: GO:0019699
-def: "The chemical reactions and pathways involving glucuronate, any salt or ester of glucuronic acid, the uronic acid formally derived from glucose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving glucuronate, any salt or ester of glucuronic acid, the uronic acid formally derived from glucose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:curators, ISBN:0198506732]
synonym: "glucuronate metabolism" EXACT []
+xref: Reactome:R-HSA-156588 "Glucuronidation"
xref: Wikipedia:Glucuronic_acid
is_a: GO:0032787 ! monocarboxylic acid metabolic process
@@ -157183,11 +159859,14 @@
synonym: "mannitol breakdown" EXACT []
synonym: "mannitol catabolism" EXACT []
synonym: "mannitol degradation" EXACT []
+xref: MetaCyc:MANNIDEG-PWY
xref: MetaCyc:PWY-3861
is_a: GO:0019407 ! hexitol catabolic process
is_a: GO:0019594 ! mannitol metabolic process
+property_value: skos:narrowMatch MetaCyc:MANNIDEG-PWY
property_value: skos:narrowMatch MetaCyc:PWY-3861
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0019593
@@ -157225,7 +159904,7 @@
id: GO:0019596
name: mandelate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic." [GOC:curators]
synonym: "mandelate breakdown" EXACT []
synonym: "mandelate catabolism" EXACT []
synonym: "mandelate degradation" EXACT []
@@ -157236,7 +159915,7 @@
id: GO:0019597
name: (R)-mandelate catabolic process to benzoate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (R)-mandelate into other compounds, including benzoate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of (R)-mandelate into other compounds, including benzoate." [GOC:curators]
synonym: "(R)-mandelate breakdown to benzoate" EXACT []
synonym: "(R)-mandelate degradation to benzoate" EXACT []
is_a: GO:0018874 ! benzoate metabolic process
@@ -157247,7 +159926,7 @@
id: GO:0019598
name: (R)-mandelate catabolic process to catechol
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of (R)-mandelate into other compounds, including catechol." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of (R)-mandelate into other compounds, including catechol." [GOC:curators]
synonym: "(R)-mandelate breakdown to catechol" EXACT []
synonym: "(R)-mandelate degradation to catechol" EXACT []
is_a: GO:0009713 ! catechol-containing compound biosynthetic process
@@ -157330,7 +160009,11 @@
synonym: "alpha-ketobutyrate catabolic process" EXACT []
synonym: "alpha-ketobutyrate catabolism" EXACT []
xref: MetaCyc:2OXOBUTYRATECAT-PWY
+xref: MetaCyc:PWY-5130
is_a: GO:0019626 ! short-chain fatty acid catabolic process
+property_value: skos:narrowMatch MetaCyc:2OXOBUTYRATECAT-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5130
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019607
@@ -157341,9 +160024,13 @@
synonym: "phenylethylamine catabolism" EXACT []
synonym: "phenylethylamine degradation" EXACT []
xref: MetaCyc:2PHENDEG-PWY
+xref: MetaCyc:PWY-6534
is_a: GO:0042402 ! biogenic amine catabolic process
is_a: GO:0042443 ! phenylethylamine metabolic process
is_a: GO:1901161 ! primary amino compound catabolic process
+property_value: skos:narrowMatch MetaCyc:2PHENDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6534
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019608
@@ -157354,9 +160041,19 @@
synonym: "nicotine catabolism" EXACT []
synonym: "nicotine degradation" EXACT []
xref: MetaCyc:P181-PWY
+xref: MetaCyc:PWY-6993
+xref: MetaCyc:PWY-7128
+xref: MetaCyc:PWY66-201
+xref: MetaCyc:PWY66-221
xref: UM-BBD_pathwayID:nic
is_a: GO:0009056 ! catabolic process
is_a: GO:0018933 ! nicotine metabolic process
+property_value: skos:narrowMatch MetaCyc:P181-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6993
+property_value: skos:narrowMatch MetaCyc:PWY-7128
+property_value: skos:narrowMatch MetaCyc:PWY66-201
+property_value: skos:narrowMatch MetaCyc:PWY66-221
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019609
@@ -157413,7 +160110,7 @@
id: GO:0019614
name: catechol-containing compound catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." [GOC:curators]
synonym: "catechol breakdown" RELATED []
synonym: "catechol catabolic process" RELATED []
synonym: "catechol catabolism" RELATED []
@@ -157429,8 +160126,12 @@
synonym: "catechol breakdown, ortho-cleavage" EXACT []
synonym: "catechol degradation, ortho-cleavage" EXACT []
xref: MetaCyc:CATECHOL-ORTHO-CLEAVAGE-PWY
+xref: MetaCyc:PWY-5417
is_a: GO:0019614 ! catechol-containing compound catabolic process
is_a: GO:0042952 ! beta-ketoadipate pathway
+property_value: skos:narrowMatch MetaCyc:CATECHOL-ORTHO-CLEAVAGE-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5417
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019616
@@ -157440,7 +160141,15 @@
synonym: "catechol breakdown, meta-cleavage" EXACT []
synonym: "catechol degradation, meta-cleavage" EXACT []
xref: MetaCyc:P183-PWY
+xref: MetaCyc:PWY-5415
+xref: MetaCyc:PWY-5419
+xref: MetaCyc:PWY-5420
is_a: GO:0019614 ! catechol-containing compound catabolic process
+property_value: skos:narrowMatch MetaCyc:P183-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5415
+property_value: skos:narrowMatch MetaCyc:PWY-5419
+property_value: skos:narrowMatch MetaCyc:PWY-5420
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019617
@@ -157497,7 +160206,7 @@
id: GO:0019621
name: creatinine catabolic process to formate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of creatinine into other compounds, including formate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of creatinine into other compounds, including formate." [GOC:curators]
synonym: "creatinine breakdown to formate" EXACT []
synonym: "creatinine degradation to formate" EXACT []
xref: MetaCyc:CRNFORCAT-PWY
@@ -157589,12 +160298,15 @@
[Term]
id: GO:0019629
-name: propionate catabolic process, 2-methylcitrate cycle
+name: obsolete propionate catabolic process, 2-methylcitrate cycle
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle." [GOC:curators]
+comment: The reason for obsoletion is that the meaning of the term is too narrow.
synonym: "propionate breakdown, 2-methylcitrate cycle" EXACT []
synonym: "propionate degradation, 2-methylcitrate cycle" EXACT []
-is_a: GO:0019543 ! propionate catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31668" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019543
[Term]
id: GO:0019630
@@ -157618,8 +160330,12 @@
synonym: "quinate degradation" EXACT []
synonym: "quinic acid catabolic process" EXACT []
synonym: "quinic acid catabolism" EXACT []
+xref: MetaCyc:PWY-6416
xref: MetaCyc:QUINATEDEG-PWY
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6416
+property_value: skos:narrowMatch MetaCyc:QUINATEDEG-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019632
@@ -157633,13 +160349,17 @@
id: GO:0019633
name: shikimate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid." [GOC:curators]
synonym: "shikimate breakdown" EXACT []
synonym: "shikimate catabolism" EXACT []
synonym: "shikimate degradation" EXACT []
+xref: MetaCyc:PWY-6419
xref: MetaCyc:SHIKIMATEDEG-PWY
is_a: GO:0019632 ! shikimate metabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6419
+property_value: skos:narrowMatch MetaCyc:SHIKIMATEDEG-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019634
@@ -157664,8 +160384,14 @@
synonym: "ciliatine catabolic process" EXACT []
synonym: "ciliatine catabolism" EXACT []
xref: MetaCyc:PHOSPHONOTASE-PWY
+xref: MetaCyc:PWY-6832
+xref: MetaCyc:PWY-7447
is_a: GO:0006793 ! phosphorus metabolic process
is_a: GO:1901161 ! primary amino compound catabolic process
+property_value: skos:narrowMatch MetaCyc:PHOSPHONOTASE-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6832
+property_value: skos:narrowMatch MetaCyc:PWY-7447
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019636
@@ -157723,7 +160449,7 @@
id: GO:0019640
name: D-glucuronate catabolic process to D-xylulose 5-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-glucuronate into D-xylulose 5-phosphate." [GOC:go_curators, PMID:27189775]
+def: "The chemical reactions and pathways resulting in the breakdown of D-glucuronate into D-xylulose 5-phosphate." [GOC:curators, PMID:27189775]
synonym: "glucuronate breakdown to xylulose 5-phosphate" EXACT []
synonym: "glucuronate catabolic process to xylulose 5-phosphate" EXACT []
synonym: "glucuronate degradation to xylulose 5-phosphate" EXACT []
@@ -157773,9 +160499,11 @@
synonym: "NADH-O2 electron transport" NARROW []
synonym: "succinate-O2 electron transport" NARROW []
synonym: "ubiquinone-8-O2 electron transport" NARROW []
+xref: MetaCyc:PWY-3781
is_a: GO:0009060 ! aerobic respiration
is_a: GO:0022904 ! respiratory electron transport chain
relationship: part_of GO:0006119 ! oxidative phosphorylation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019647
@@ -157854,7 +160582,7 @@
name: purine fermentation
namespace: biological_process
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of purine nucleobases, yielding acetate and CO2." [GOC:mah]
-synonym: "anaerobic purine base catabolic process" EXACT [GOC:go_curators]
+synonym: "anaerobic purine base catabolic process" EXACT [GOC:curators]
synonym: "anaerobic purine base catabolism" EXACT []
synonym: "anaerobic purine catabolic process" RELATED []
synonym: "anaerobic purine nucleobase catabolic process" EXACT []
@@ -157876,9 +160604,25 @@
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of acetate, yielding energy in the form of ATP." [GOC:jl, MetaCyc:P142-PWY]
synonym: "acetate fermentation" RELATED []
xref: MetaCyc:P142-PWY
+xref: MetaCyc:PWY-5482
+xref: MetaCyc:PWY-5483
+xref: MetaCyc:PWY-5485
+xref: MetaCyc:PWY-5537
+xref: MetaCyc:PWY-5538
+xref: MetaCyc:PWY-5600
+xref: MetaCyc:PWY-5768
is_a: GO:0006083 ! acetate metabolic process
is_a: GO:0019660 ! pyruvate fermentation
+property_value: skos:narrowMatch MetaCyc:P142-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5482
+property_value: skos:narrowMatch MetaCyc:PWY-5483
+property_value: skos:narrowMatch MetaCyc:PWY-5485
+property_value: skos:narrowMatch MetaCyc:PWY-5537
+property_value: skos:narrowMatch MetaCyc:PWY-5538
+property_value: skos:narrowMatch MetaCyc:PWY-5600
+property_value: skos:narrowMatch MetaCyc:PWY-5768
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019655
@@ -157895,28 +160639,35 @@
synonym: "glucose catabolic process to ethanol" RELATED [GOC:dph]
synonym: "glucose fermentation to ethanol" EXACT []
synonym: "glycolytic fermentation to ethanol" RELATED []
-xref: MetaCyc:Pyruvate-Ethanol-Fermentation
+xref: MetaCyc:PWY-5480
+xref: MetaCyc:PWY-5486
+xref: MetaCyc:PWY-6587
xref: Wikipedia:Ethanol_fermentation
is_a: GO:0006067 ! ethanol metabolic process
is_a: GO:0019660 ! pyruvate fermentation
+property_value: skos:narrowMatch MetaCyc:PWY-5480
+property_value: skos:narrowMatch MetaCyc:PWY-5486
+property_value: skos:narrowMatch MetaCyc:PWY-6587
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23284" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019656
-name: heterolactic fermentation
+name: obsolete heterolactic fermentation
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the enzymatic breakdown of D-glucose to D-lactate and ethanol, yielding energy in the form of adenosine triphosphate (ATP) at the rate of one ATP per glucose molecule." [GOC:jl, MetaCyc:P122-PWY]
+def: "OBSOLETE. The anaerobic chemical reactions and pathways resulting in the enzymatic breakdown of D-glucose to D-lactate and ethanol, yielding energy in the form of adenosine triphosphate (ATP) at the rate of one ATP per glucose molecule." [GOC:jl]
+comment: The reason for obsoletion is that the term is not needed for fermentation process starting with pyruvate.
synonym: "glucose catabolic process to D-lactate and ethanol" RELATED []
synonym: "glucose fermentation to D-lactate and ethanol" EXACT []
synonym: "heterofermentation" EXACT []
synonym: "heterofermentative lactate fermentation" EXACT []
synonym: "heterofermentative pathway" EXACT []
synonym: "heterolactate fermentation" EXACT []
-xref: MetaCyc:P122-PWY
-is_a: GO:0006067 ! ethanol metabolic process
-is_a: GO:0019659 ! glucose catabolic process to lactate
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019244
[Term]
id: GO:0019657
@@ -157935,28 +160686,31 @@
[Term]
id: GO:0019658
-name: glucose fermentation to lactate and acetate
+name: bifid shunt
namespace: biological_process
def: "The anaerobic chemical reactions and pathways resulting in the breakdown of glucose to lactate and acetate, yielding energy in the form of ATP." [MetaCyc:P124-PWY]
synonym: "bifidum pathway" EXACT []
synonym: "glucose catabolic process to lactate and acetate" BROAD []
+synonym: "glucose fermentation to lactate and acetate" EXACT []
xref: MetaCyc:P124-PWY
+is_a: GO:0006007 ! glucose catabolic process
is_a: GO:0006083 ! acetate metabolic process
-is_a: GO:0019659 ! glucose catabolic process to lactate
+is_a: GO:0006089 ! lactate metabolic process
+is_a: GO:0006113 ! fermentation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31217" xsd:anyURI
[Term]
id: GO:0019659
-name: glucose catabolic process to lactate
+name: obsolete glucose catabolic process to lactate
namespace: biological_process
-def: "The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, and possibly ethanol, yielding energy in the form of adenosine triphosphate (ATP)." [GOC:jl]
-subset: gocheck_do_not_annotate
+def: "OBSOLETE. The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, and possibly ethanol, yielding energy in the form of adenosine triphosphate (ATP)." [GOC:jl]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
synonym: "glucose fermentation to lactate" EXACT []
synonym: "lactate fermentation" EXACT []
xref: Wikipedia:Lactic_acid_fermentation
-is_a: GO:0006007 ! glucose catabolic process
-is_a: GO:0006089 ! lactate metabolic process
-is_a: GO:0006113 ! fermentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31217" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019660
@@ -157964,27 +160718,28 @@
namespace: biological_process
def: "The fermentation process resulting in the oxygen-independent conversion of pyruvate to reduced end products (e.g., lactate, ethanol, and acetate), accompanied by the concomitant oxidation of NADH to NAD." [GOC:curators]
synonym: "glycolytic fermentation" RELATED []
-xref: MetaCyc:Pyruvate-Degradation
is_a: GO:0006113 ! fermentation
is_a: GO:0042867 ! pyruvate catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
[Term]
id: GO:0019661
-name: homolactic fermentation
+name: obsolete homolactic fermentation
namespace: biological_process
-def: "The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, via canonical glycolysis, yielding energy in the form of adenosine triphosphate (ATP)." [GOC:jl]
+def: "OBSOLETE. The anaerobic enzymatic chemical reactions and pathways resulting in the breakdown of glucose to lactate, via canonical glycolysis, yielding energy in the form of adenosine triphosphate (ATP)." [GOC:jl]
+comment: The reason for obsoletion is that the term is not needed for fermentation process starting with pyruvate.
synonym: "glucose catabolic process to lactate via pyruvate" RELATED []
synonym: "glucose fermentation to lactate via pyruvate" RELATED []
synonym: "homofermentation" EXACT []
synonym: "homofermentative lactate fermentation" EXACT []
synonym: "homofermentative pathway" EXACT []
synonym: "homolactate fermentation" EXACT []
-xref: MetaCyc:ANAEROFRUCAT-PWY
-is_a: GO:0019659 ! glucose catabolic process to lactate
-relationship: has_part GO:0019246 ! L(+)-lactate biosynthetic process from pyruvate
-relationship: has_part GO:0061621 ! canonical glycolysis
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019244
[Term]
id: GO:0019662
@@ -158022,7 +160777,7 @@
id: GO:0019665
name: amino acid fermentation
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids to ammonia, CO2, H2, acetate and short chain fatty acids, under anoxic conditions." [GOC:curators, GOC:jl]
+def: "The anaerobic chemical reactions and pathways resulting in the breakdown of amino acids to ammonia, CO2, H2, acetate and short chain fatty acids, under anoxic conditions." [PMID:38821505]
synonym: "anaerobic amino acid catabolic process" EXACT []
is_a: GO:0006113 ! fermentation
is_a: GO:0009063 ! amino acid catabolic process
@@ -158042,7 +160797,7 @@
id: GO:0019667
name: L-alanine fermentation
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the breakdown of L-alanine, yielding acetylCoA. AcetylCoA can be further converted to ATP." [GOC:jl]
+def: "The anaerobic chemical reactions and pathways resulting in the breakdown of L-alanine, yielding acetylCoA. AcetylCoA can be further converted to ATP." [GOC:jl, PMID:38821505]
synonym: "anaerobic L-alanine catabolic process" EXACT []
xref: MetaCyc:PROPFERM-PWY
xref: MetaCyc:PWY-8188
@@ -158093,13 +160848,11 @@
name: obsolete glutamate catabolic process via mesaconate and citramalate
namespace: biological_process
def: "OBSOLETE. The anaerobic chemical reactions and pathways resulting in the breakdown of glutamate via the intermediates mesaconate and S-citramalate, yielding energy in the form of ATP." [GOC:rynl]
-comment: The reason for obsoletion is that this term is an unnecessary grouping term.
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate fermentation via mesaconate and citramalate" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28390" xsd:anyURI
is_obsolete: true
-consider: GO:0019553
consider: GO:0033508
-consider: GO:0033509
[Term]
id: GO:0019672
@@ -158135,7 +160888,6 @@
synonym: "oxidized NAD metabolism" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide metabolic process" EXACT []
synonym: "oxidized nicotinamide adenine dinucleotide metabolism" EXACT []
-xref: Reactome:R-HSA-196807 "Nicotinate metabolism"
is_a: GO:0006163 ! purine nucleotide metabolic process
is_a: GO:0046496 ! nicotinamide nucleotide metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21577" xsd:anyURI
@@ -158167,7 +160919,7 @@
xref: MetaCyc:PWY-6963
xref: MetaCyc:PWY-6964
is_a: GO:0006536 ! glutamate metabolic process
-is_a: GO:0006541 ! glutamine metabolic process
+is_a: GO:0006541 ! L-glutamine metabolic process
is_a: GO:0019740 ! nitrogen utilization
property_value: skos:narrowMatch MetaCyc:AMMASSIM-PWY
property_value: skos:narrowMatch MetaCyc:PWY-3282
@@ -158201,7 +160953,6 @@
synonym: "reduced NAD catabolism" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide catabolic process" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide catabolism" EXACT []
-xref: MetaCyc:NAD-BIOSYNTHESIS-II
is_a: GO:0006195 ! purine nucleotide catabolic process
is_a: GO:0019364 ! pyridine nucleotide catabolic process
is_a: GO:0019674 ! NAD+ metabolic process
@@ -158211,21 +160962,27 @@
[Term]
id: GO:0019678
-name: propionate metabolic process, methylmalonyl pathway
+name: obsolete propionate metabolic process, methylmalonyl pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving propionate that occur in the methylmalonyl pathway." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving propionate that occur in the methylmalonyl pathway." [GOC:curators]
+comment: The reason for obsoletion is that the meaning of the term is too narrow.
+synonym: "methylmalonyl pathway" EXACT []
+synonym: "propanoyl CoA degradation" EXACT []
synonym: "propionate metabolism, methylmalonyl pathway" EXACT []
-xref: MetaCyc:PROPIONMET-PWY
-is_a: GO:0019541 ! propionate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31668" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:1902859
[Term]
id: GO:0019679
-name: propionate metabolic process, methylcitrate cycle
+name: obsolete propionate metabolic process, methylcitrate cycle
namespace: biological_process
-def: "The chemical reactions and pathways involving propionate that occur in the methylcitrate cycle." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving propionate that occur in the methylcitrate cycle." [GOC:curators]
+comment: The reason for obsoletion is that the meaning of the term is too narrow.
synonym: "propionate metabolism, methylcitrate cycle" EXACT []
-xref: MetaCyc:PWY0-42
-is_a: GO:0019541 ! propionate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31668" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019543
[Term]
id: GO:0019680
@@ -158291,9 +161048,13 @@
def: "The light reactions of photosynthesis, which take place in photosystems II and I. Light energy is harvested and used to power the transfer of electrons among a series of electron donors and acceptors. The final electron acceptor is NADP+, which is reduced to NADPH. NADPH generated from light reactions is used in sugar synthesis in dark reactions. Light reactions also generate a proton motive force across the thylakoid membrane, and the proton gradient is used to synthesize ATP. There are two chemical reactions involved in the light reactions: water oxidation in photosystem II, and NADP reduction in photosystem I." [PMID:15746074]
synonym: "photolysis" RELATED []
xref: MetaCyc:PWY-101
+xref: MetaCyc:PWY2PN3-7
xref: Wikipedia:Photolysis#Photolysis_in_photosynthesis
is_a: GO:0006091 ! generation of precursor metabolites and energy
relationship: part_of GO:0015979 ! photosynthesis
+property_value: skos:narrowMatch MetaCyc:PWY-101
+property_value: skos:narrowMatch MetaCyc:PWY2PN3-7
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019685
@@ -158315,7 +161076,7 @@
id: GO:0019687
name: pyruvate biosynthetic process from acetate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyruvate from other compounds, including acetate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of pyruvate from other compounds, including acetate." [GOC:curators]
synonym: "pyruvate anabolism from acetate" EXACT []
synonym: "pyruvate formation from acetate" EXACT []
synonym: "pyruvate synthesis from acetate" EXACT []
@@ -158406,9 +161167,13 @@
synonym: "xylitol degradation to xylulose 5-phosphate" EXACT []
synonym: "xylitol utilization" RELATED []
xref: MetaCyc:LARABITOLUTIL-PWY
+xref: MetaCyc:PWY-8393
is_a: GO:0051160 ! xylitol catabolic process
is_a: GO:0051167 ! D-xylulose 5-phosphate metabolic process
+property_value: skos:narrowMatch MetaCyc:LARABITOLUTIL-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-8393
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28597" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019698
@@ -158419,9 +161184,17 @@
synonym: "D-galacturonate catabolism" EXACT []
synonym: "D-galacturonate degradation" EXACT []
xref: MetaCyc:GALACTUROCAT-PWY
+xref: MetaCyc:PWY-6486
+xref: MetaCyc:PWY-6491
+xref: MetaCyc:PWY-8391
is_a: GO:0046365 ! monosaccharide catabolic process
is_a: GO:0046396 ! D-galacturonate metabolic process
is_a: GO:0046397 ! galacturonate catabolic process
+property_value: skos:narrowMatch MetaCyc:GALACTUROCAT-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6486
+property_value: skos:narrowMatch MetaCyc:PWY-6491
+property_value: skos:narrowMatch MetaCyc:PWY-8391
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019700
@@ -158523,6 +161296,8 @@
name: protein-cysteine S-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an acyl group to a sulfur atom on the cysteine of a protein molecule." [GOC:ai, RHEA:63372]
+xref: Reactome:R-HSA-158832 "The acetyl group from acetyl-CoA is transferred to NAT2"
+xref: Reactome:R-HSA-174959 "The acetyl group from acetyl-CoA is transferred to NAT1"
xref: RHEA:63372
is_a: GO:0016417 ! S-acyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -158566,7 +161341,7 @@
id: GO:0019711
name: obsolete peptidyl-beta-carboxyaspartic acid biosynthetic process from peptidyl-aspartic acid
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of peptidyl-beta-carboxyaspartic acid from other compounds, including peptidyl-aspartic acid." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of peptidyl-beta-carboxyaspartic acid from other compounds, including peptidyl-aspartic acid." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-beta-carboxyaspartic acid anabolism from peptidyl-aspartic acid" EXACT []
synonym: "peptidyl-beta-carboxyaspartic acid formation from peptidyl-aspartic acid" EXACT []
@@ -158751,7 +161526,7 @@
namespace: biological_process
alt_id: GO:0006960
alt_id: GO:0019735
-def: "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." [GOC:go_curators, GOC:mtg_sensu]
+def: "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." [GOC:curators, GOC:mtg_sensu]
xref: Reactome:R-HSA-6803157 "Antimicrobial peptides"
is_a: GO:0006959 ! humoral immune response
is_a: GO:0140546 ! defense response to symbiont
@@ -158762,7 +161537,7 @@
namespace: biological_process
alt_id: GO:0006961
alt_id: GO:0019733
-def: "An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu]
+def: "An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0019730 ! antimicrobial humoral response
is_a: GO:0042742 ! defense response to bacterium
@@ -158772,7 +161547,7 @@
namespace: biological_process
alt_id: GO:0006966
alt_id: GO:0019734
-def: "An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu]
+def: "An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0019730 ! antimicrobial humoral response
is_a: GO:0050832 ! defense response to fungus
@@ -158861,7 +161636,7 @@
id: GO:0019747
name: regulation of isoprenoid metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving isoprenoids." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving isoprenoids." [GOC:curators]
synonym: "regulation of isoprenoid metabolism" EXACT []
is_a: GO:0019216 ! regulation of lipid metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -158872,7 +161647,7 @@
id: GO:0019748
name: secondary metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:curators]
subset: goslim_chembl
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_pir
@@ -158914,9 +161689,11 @@
name: carboxylic acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [ISBN:0198506732]
+subset: gocheck_do_not_annotate
synonym: "carboxylic acid metabolism" EXACT []
xref: Reactome:R-HSA-389661 "Glyoxylate metabolism and glycine degradation"
is_a: GO:0043436 ! oxoacid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31063" xsd:anyURI
[Term]
id: GO:0019755
@@ -159109,8 +161886,7 @@
name: proteasome core complex, alpha-subunit complex
namespace: cellular_component
def: "The proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex. An example of this component is found in Mus musculus." [GOC:jl, GOC:mtg_sensu, GOC:rb, PMID:10854779]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005622 ! intracellular anatomical structure
+is_a: GO:0140535 ! intracellular protein-containing complex
relationship: part_of GO:0005839 ! proteasome core complex
[Term]
@@ -159197,6 +161973,7 @@
namespace: molecular_function
def: "Catalysis of the activation of the small ubiquitin-related modifier ISG15, through the formation of an ATP-dependent high-energy thiolester bond." [GOC:mah]
synonym: "UBE1L" NARROW []
+xref: Reactome:R-HSA-1169397 "Activation of ISG15 by UBA7 E1 enzyme"
is_a: GO:0008641 ! ubiquitin-like modifier activating enzyme activity
[Term]
@@ -159450,6 +162227,8 @@
xref: Reactome:R-HSA-6804468 "PIAS1 SUMOylates SP3 with SUMO2"
xref: Reactome:R-HSA-6804485 "PIAS1 SUMOylates L3MBTL2 with SUMO2"
xref: Reactome:R-HSA-8956365 "ZBED1 (DREF) SUMOylates CHD3 with SUMO1"
+xref: Reactome:R-HSA-9920126 "UBC9 SUMOylates NS5"
+xref: Reactome:R-HSA-9926476 "UBE2I sumoylates MITF-M"
is_a: GO:0019787 ! ubiquitin-like protein transferase activity
[Term]
@@ -159668,11 +162447,13 @@
synonym: "N-acyl-L-aspartate amidohydrolase activity" RELATED [EC:3.5.1.15]
xref: EC:3.5.1.15
xref: MetaCyc:ASPARTOACYLASE-RXN
-xref: Reactome:R-HSA-5691507 "ASPA deacetylates NAA to acetate and L-aspartate"
+xref: Reactome:R-HSA-5691507 "ASPA deacetylates NAASP to acetate and L-aspartate"
xref: RHEA:10872
+xref: RHEA:59408
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.15
property_value: skos:exactMatch RHEA:10872
+property_value: skos:narrowMatch RHEA:59408
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -159882,7 +162663,7 @@
id: GO:0019830
name: obsolete cadmium sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "cadmium sensitivity/resistance" EXACT []
is_obsolete: true
@@ -159892,7 +162673,7 @@
id: GO:0019831
name: obsolete chromate sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "chromate sensitivity/resistance" EXACT []
is_obsolete: true
@@ -159902,7 +162683,7 @@
id: GO:0019832
name: obsolete mercuric sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "mercuric sensitivity/resistance" EXACT []
is_obsolete: true
@@ -159961,7 +162742,7 @@
id: GO:0019837
name: obsolete herbicide susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "herbicide susceptibility/resistance" EXACT []
is_obsolete: true
@@ -160117,7 +162898,7 @@
id: GO:0019854
name: L-ascorbic acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of L-ascorbic acid; L-ascorbic acid ionizes to give L-ascorbate, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate, which is required as a cofactor in the oxidation of prolyl residues to hydroxyprolyl, and other reactions." [GOC:curators]
synonym: "ascorbate catabolic process" EXACT []
synonym: "ascorbate catabolism" EXACT []
synonym: "L-ascorbic acid breakdown" EXACT []
@@ -160125,18 +162906,29 @@
synonym: "L-ascorbic acid degradation" EXACT []
synonym: "vitamin C catabolic process" EXACT []
synonym: "vitamin C catabolism" EXACT []
+xref: MetaCyc:PWY-6704
+xref: MetaCyc:PWY-6959
+xref: MetaCyc:PWY-6960
+xref: MetaCyc:PWY-6961
xref: MetaCyc:PWY0-301
is_a: GO:0019852 ! L-ascorbic acid metabolic process
is_a: GO:0042365 ! water-soluble vitamin catabolic process
is_a: GO:0046365 ! monosaccharide catabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901335 ! lactone catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6704
+property_value: skos:narrowMatch MetaCyc:PWY-6959
+property_value: skos:narrowMatch MetaCyc:PWY-6960
+property_value: skos:narrowMatch MetaCyc:PWY-6961
+property_value: skos:narrowMatch MetaCyc:PWY0-301
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0019855
name: calcium channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a calcium channel." [GOC:mah]
+xref: Reactome:R-HSA-400046 "L-type Calcium Channels close in pancreatic beta cells"
is_a: GO:0005246 ! calcium channel regulator activity
is_a: GO:0008200 ! ion channel inhibitor activity
relationship: negatively_regulates GO:0005262 ! calcium channel activity
@@ -160145,10 +162937,10 @@
id: GO:0019856
name: pyrimidine nucleobase biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases." [GOC:curators]
synonym: "pyrimidine base anabolism" EXACT []
synonym: "pyrimidine base biosynthesis" EXACT []
-synonym: "pyrimidine base biosynthetic process" EXACT [GOC:go_curators]
+synonym: "pyrimidine base biosynthetic process" EXACT [GOC:curators]
synonym: "pyrimidine base formation" EXACT []
synonym: "pyrimidine base synthesis" EXACT []
is_a: GO:0006206 ! pyrimidine nucleobase metabolic process
@@ -160179,7 +162971,7 @@
id: GO:0019859
name: thymine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:go_curators]
+def: "The chemical reactions and pathways involving thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:curators]
synonym: "thymine metabolism" EXACT []
is_a: GO:0006206 ! pyrimidine nucleobase metabolic process
@@ -160187,7 +162979,7 @@
id: GO:0019860
name: uracil metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:curators]
synonym: "uracil metabolism" EXACT []
is_a: GO:0006206 ! pyrimidine nucleobase metabolic process
@@ -160246,7 +163038,7 @@
id: GO:0019867
name: outer membrane
namespace: cellular_component
-def: "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites." [GOC:go_curators]
+def: "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites." [GOC:curators]
subset: goslim_metagenomics
is_a: GO:0016020 ! membrane
@@ -160264,6 +163056,8 @@
name: potassium channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a potassium channel." [GOC:mah]
+xref: Reactome:R-HSA-381644 "ER calcium channels open in response to activated PKA"
+xref: Reactome:R-HSA-381713 "Potassium voltage-gated channels close in reponse to PKA"
is_a: GO:0008200 ! ion channel inhibitor activity
is_a: GO:0015459 ! potassium channel regulator activity
relationship: negatively_regulates GO:0005267 ! potassium channel activity
@@ -160294,7 +163088,7 @@
id: GO:0019873
name: obsolete tellurium sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "tellurium sensitivity/resistance" EXACT []
is_obsolete: true
@@ -160344,22 +163138,24 @@
[Term]
id: GO:0019877
-name: diaminopimelate biosynthetic process
+name: obsolete diaminopimelate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls." [GOC:ma, ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls." [GOC:ma, ISBN:0198547684]
+comment: This term was obsoleted because it represents an intermediate in L-leucine biosynthesis.
synonym: "diaminopimelate anabolism" EXACT []
synonym: "diaminopimelate biosynthesis" EXACT []
synonym: "diaminopimelate formation" EXACT []
synonym: "diaminopimelate synthesis" EXACT []
-is_a: GO:0008652 ! amino acid biosynthetic process
-is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
-is_a: GO:1901570 ! fatty acid derivative biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+consider: GO:0009098
[Term]
id: GO:0019878
-name: L-lysine biosynthetic process via aminoadipic acid
+name: obsolete L-lysine biosynthetic process via aminoadipic acid
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-lysine by the aminoadipic pathway." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-lysine by the aminoadipic pathway." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine anabolism via aminoadipic acid" EXACT []
synonym: "lysine biosynthesis, aminoadipic acid pathway" EXACT []
synonym: "lysine biosynthesis, aminoadipic pathway" EXACT []
@@ -160367,8 +163163,10 @@
synonym: "lysine biosynthetic process, aminoadipic pathway" EXACT []
synonym: "lysine formation via aminoadipic acid" EXACT []
synonym: "lysine synthesis via aminoadipic acid" EXACT []
-is_a: GO:0009085 ! L-lysine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0019879
@@ -160386,7 +163184,7 @@
id: GO:0019880
name: obsolete bacteriocin susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "bacteriocin susceptibility/resistance" EXACT []
is_obsolete: true
@@ -160396,7 +163194,7 @@
id: GO:0019881
name: obsolete streptomycin susceptibility/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "streptomycin susceptibility/resistance" EXACT []
is_obsolete: true
@@ -160498,7 +163296,7 @@
id: GO:0019889
name: pteridine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving pteridine, pyrazino(2,3-dipyrimidine), the parent structure of pterins and the pteroyl group." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving pteridine, pyrazino(2,3-dipyrimidine), the parent structure of pterins and the pteroyl group." [GOC:curators, ISBN:0198506732]
synonym: "pteridine metabolism" EXACT []
is_a: GO:0042558 ! pteridine-containing compound metabolic process
@@ -160608,7 +163406,7 @@
id: GO:0019904
name: protein domain specific binding
namespace: molecular_function
-def: "Binding to a specific domain of a protein." [GOC:go_curators]
+def: "Binding to a specific domain of a protein." [GOC:curators]
subset: goslim_chembl
synonym: "protein domain-specific binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -160621,12 +163419,9 @@
alt_id: GO:0030349
alt_id: GO:0050430
alt_id: GO:0051535
-def: "Binding to a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse." [ISBN:0198506732]
-synonym: "syntaxin-13 binding" NARROW []
-synonym: "syntaxin-2 binding" NARROW []
-synonym: "syntaxin-5 binding" NARROW []
-synonym: "syntaxin-6 binding" NARROW []
+def: "Binding to a syntaxin, a SNAP receptor involved in the docking of vesicles." [ISBN:0198506732]
is_a: GO:0000149 ! SNARE binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31404" xsd:anyURI
[Term]
id: GO:0019907
@@ -160686,7 +163481,7 @@
name: obsolete cyclin-dependent protein kinase activating kinase activity
namespace: molecular_function
alt_id: GO:0019913
-def: "OBSOLETE. Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein; increases the activity of a cyclin-dependent protein kinase (CDK)." [GOC:go_curators]
+def: "OBSOLETE. Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein; increases the activity of a cyclin-dependent protein kinase (CDK)." [GOC:curators]
comment: The reason for obsoletion is that the term is s kinase+ substrate, but covers a number of unrelated kinases.
synonym: "CAK" EXACT []
synonym: "cdk-activating kinase activity" EXACT []
@@ -160765,7 +163560,7 @@
id: GO:0019920
name: obsolete peptidyl-1-thioglycine biosynthetic process, internal
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of internal peptidyl-1-thioglycine, which has an internal C=S bond, instead of an internal C=O bond, in the peptide." [GOC:go_curators, PMID:10660523, RESID:AA0265]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of internal peptidyl-1-thioglycine, which has an internal C=S bond, instead of an internal C=O bond, in the peptide." [GOC:curators, PMID:10660523, RESID:AA0265]
comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-1-thioglycine anabolism, internal" EXACT []
synonym: "peptidyl-1-thioglycine formation, internal" EXACT []
@@ -160777,7 +163572,7 @@
id: GO:0019921
name: obsolete peptidyl-1-thioglycine biosynthetic process, carboxy-terminal
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of carboxy-terminal peptidyl-1-thioglycine, which has a carboxy-terminal thiocarboxy-C(=O)-SH bond." [GOC:go_curators, PMID:10660523, RESID:AA0265]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of carboxy-terminal peptidyl-1-thioglycine, which has a carboxy-terminal thiocarboxy-C(=O)-SH bond." [GOC:curators, PMID:10660523, RESID:AA0265]
comment: This term was obsoleted because it represents a molecular function.
synonym: "peptidyl-1-thioglycine anabolism, carboxy-terminal" EXACT []
synonym: "peptidyl-1-thioglycine formation, carboxy-terminal" EXACT []
@@ -160982,7 +163777,7 @@
id: GO:0019941
name: modification-dependent protein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein." [GOC:curators]
synonym: "modification-dependent protein breakdown" EXACT []
synonym: "modification-dependent protein catabolism" EXACT []
synonym: "modification-dependent protein degradation" EXACT []
@@ -161287,7 +164082,7 @@
id: GO:0019987
name: obsolete negative regulation of anti-apoptosis
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of anti-apoptosis." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of anti-apoptosis." [GOC:curators, GOC:mtg_apoptosis]
comment: This term was made obsolete because it was ill-defined.
synonym: "down regulation of anti-apoptosis" EXACT []
synonym: "down-regulation of anti-apoptosis" EXACT []
@@ -161542,7 +164337,7 @@
id: GO:0020027
name: hemoglobin metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving hemoglobin, including its uptake and utilization." [GOC:go_curators, GOC:jl]
+def: "The chemical reactions and pathways involving hemoglobin, including its uptake and utilization." [GOC:curators, GOC:jl]
synonym: "haemoglobin metabolic process" EXACT []
synonym: "haemoglobin metabolism" EXACT []
synonym: "hemoglobin metabolism" EXACT []
@@ -161629,6 +164424,7 @@
namespace: molecular_function
def: "Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring." [GOC:ai]
synonym: "haem binding" EXACT []
+xref: Reactome:R-HSA-9661419 "ALB binds extracellular heme"
is_a: GO:0046906 ! tetrapyrrole binding
[Term]
@@ -167050,7 +169846,7 @@
id: GO:0022825
name: obsolete copper-exporting ATPase activity
namespace: molecular_function
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it was a placeholder during work on transporter terms, and was not defined.
synonym: "copper-exporting ATPase activity" EXACT []
is_obsolete: true
@@ -167248,8 +170044,9 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + glucose(out) = protein histidine + glucose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "glucose PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0055056 ! D-glucose transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022856
@@ -167257,8 +170054,9 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sorbitol(out) = protein histidine + sorbitol phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "sorbitol PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015576 ! sorbitol transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022857
@@ -167278,12 +170076,26 @@
synonym: "uptake permease activity" RELATED []
synonym: "uptake transmembrane transporter activity" RELATED []
xref: Reactome:R-HSA-1236947 "Egress of internalized antigen to the cytosol via sec61"
+xref: Reactome:R-HSA-2142859 "Growing HA is extruded from the cell by ABCC5"
+xref: Reactome:R-HSA-2161500 "abacavir [extracellular] => abacavir [cytosol]"
xref: Reactome:R-HSA-429036 "SLC2A9 transports Fru, Glc, urate"
xref: Reactome:R-HSA-434650 "MATEs mediate extrusion of xenobiotics"
+xref: Reactome:R-HSA-549129 "OCT1 transports organic cations into hepatic cells"
+xref: Reactome:R-HSA-549279 "OCT2 mediates tubular uptake of organic cations in the kidney"
+xref: Reactome:R-HSA-549304 "OCT3 mediates renal clearance of organic cations"
+xref: Reactome:R-HSA-549322 "OCT1 transports organic cations out of hepatic cells"
+xref: Reactome:R-HSA-561041 "OAT1,2,3 transport organic anions with antiport of dicarboxylic acids"
+xref: Reactome:R-HSA-561054 "OCT2 mediates tubular secretion of organic cations in the kidney"
+xref: Reactome:R-HSA-561072 "OCT3 mediates renal uptake of organic cations"
xref: Reactome:R-HSA-5638209 "Defective SLC2A9 does not transport Fru, Glc, urate"
xref: Reactome:R-HSA-5671707 "Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA"
xref: Reactome:R-HSA-6784434 "An unknown carrier transports cytosolic glyoxylate to the peroxisome"
xref: Reactome:R-HSA-6784436 "An unknown carrier transports mitochondrial glyoxylate to the cytosol"
+xref: Reactome:R-HSA-8954513 "NAASP translocates from mitochondrial matrix to cytosol"
+xref: Reactome:R-HSA-9794270 "SLCO1A2 transports Cipro(1+) into the cytosol"
+xref: Reactome:R-HSA-9794523 "SLC22A1 transports Cipro into renal cell"
+xref: Reactome:R-HSA-9794830 "SLC22A8 transports Cipro into renal cell"
+xref: Reactome:R-HSA-9795207 "SLC22A1 transports Cipro into hepatic cell"
is_a: GO:0005215 ! transporter activity
relationship: part_of GO:0055085 ! transmembrane transport
@@ -167337,17 +170149,23 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + lactose(out) = protein histidine + lactose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "lactose PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015155 ! lactose transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022870
name: protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity
namespace: molecular_function
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + mannose(out) = protein histidine + mannose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane according to the reaction: D-mannose(out) + N(pros)-phospho-L-histidyl-[protein] = D-mannose 6-phosphate(in) + L-histidyl-[protein]. This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, RHEA:49232]
synonym: "mannose PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+xref: EC:2.7.1.191
+xref: RHEA:49232
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015578 ! mannose transmembrane transporter activity
+property_value: skos:exactMatch EC:2.7.1.191
+property_value: skos:exactMatch RHEA:49232
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022871
@@ -167358,13 +170176,14 @@
xref: EC:2.7.1.206
xref: MetaCyc:RXN-15094
xref: RHEA:49296
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0055056 ! D-glucose transmembrane transporter activity
property_value: skos:exactMatch EC:2.7.1.206
-property_value: skos:narrowMatch RHEA:49296
+property_value: skos:exactMatch RHEA:49296
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17289" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022872
@@ -167372,8 +170191,9 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + mannitol(out) = protein histidine + mannitol phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "mannitol PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015575 ! mannitol transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022873
@@ -167382,16 +170202,22 @@
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + maltose(out) = protein histidine + maltose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "maltose PTS transporter activity" EXACT []
is_a: GO:0005363 ! maltose transmembrane transporter activity
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022874
name: protein-N(PI)-phosphohistidine-cellobiose phosphotransferase system transporter activity
namespace: molecular_function
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + cellobiose(out) = protein histidine + cellobiose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane according to the reaction: D-cellobiose(out) + N(pros)-phospho-L-histidyl-[protein] = 6-phospho-beta-D-glucosyl-(1->4)-D-glucose(in) + L-histidyl-[protein]. This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, RHEA:49292]
synonym: "cellobiose PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+xref: EC:2.7.1.205
+xref: RHEA:49292
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0019191 ! cellobiose transmembrane transporter activity
+property_value: skos:exactMatch EC:2.7.1.205
+property_value: skos:exactMatch RHEA:49292
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022875
@@ -167399,8 +170225,9 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + galactitol(out) = protein histidine + galactitol phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "galactitol PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015577 ! galactitol transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022876
@@ -167408,8 +170235,9 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + galactosamine(out) = protein histidine + galactosamine phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "galactosamine PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0019196 ! galactosamine transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022877
@@ -167418,7 +170246,8 @@
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + fructose(out) = protein histidine + fructose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "fructose PTS transporter activity" EXACT []
is_a: GO:0005353 ! fructose transmembrane transporter activity
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022878
@@ -167426,12 +170255,15 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sucrose(out) = protein histidine + sucrose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "sucrose PTS transporter activity" EXACT []
+xref: EC:2.7.1.211
xref: MetaCyc:SUCROSEPHOSPHO-RXN
xref: RHEA:49236
is_a: GO:0008515 ! sucrose transmembrane transporter activity
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: skos:exactMatch EC:2.7.1.211
property_value: skos:exactMatch RHEA:49236
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022879
@@ -167439,18 +170271,24 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + trehalose(out) = protein histidine + trehalose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "trehalose PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015574 ! trehalose transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022880
name: protein-N(PI)-phosphohistidine-N-acetylglucosamine phosphotransferase system transporter activity
namespace: molecular_function
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + N-acetylglucosamine(out) = protein histidine + N-acetylglucosamine phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane by the reaction: N(pros)-phospho-L-histidyl-[protein] + N-acetyl-D-glucosamine(out) = L-histidyl-[protein] + N-acetyl-D-glucosamine 6-phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, RHEA:49240]
synonym: "N-acetylglucosamine PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+xref: EC:2.7.1.193
+xref: RHEA:49240
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015572 ! N-acetylglucosamine transmembrane transporter activity
+property_value: skos:exactMatch EC:2.7.1.193
+property_value: skos:exactMatch RHEA:49240
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27517" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022881
@@ -167458,18 +170296,19 @@
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + N-acetylgalactosamine(out) = protein histidine + N-acetylgalactosamine phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
synonym: "N-acetylgalactosamine PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
is_a: GO:0015571 ! N-acetylgalactosamine transmembrane transporter activity
is_a: GO:0055056 ! D-glucose transmembrane transporter activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022882
name: protein-N(PI)-phosphohistidine-beta-glucoside phosphotransferase system transporter activity
namespace: molecular_function
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + beta-glucoside(out) = protein histidine + beta-glucoside phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, ISBN:0815340729]
+def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + beta-glucoside(out) = protein histidine + beta-glucoside phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:mtg_transport, PMID:19251853]
synonym: "beta-glucoside PTS transporter activity" EXACT []
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
-is_a: GO:0015573 ! beta-glucoside transmembrane transporter activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
id: GO:0022883
@@ -168279,6 +171118,7 @@
synonym: "divalent metal ion transport" NARROW []
synonym: "heavy metal ion transport" NARROW []
synonym: "metal ion export" NARROW []
+xref: Reactome:R-HSA-425410 "Metal ion SLC transporters"
is_a: GO:0006812 ! monoatomic cation transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23033" xsd:anyURI
created_by: mah
@@ -168785,9 +171625,11 @@
synonym: "methylamine dehydrogenase activity" RELATED []
synonym: "primary-amine dehydrogenase activity" BROAD []
synonym: "primary-amine:acceptor oxidoreductase (deaminating)" RELATED []
+xref: RHEA:21916
xref: RHEA:51128
is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
property_value: skos:exactMatch RHEA:51128
+property_value: skos:narrowMatch RHEA:21916
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21650" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -168801,9 +171643,11 @@
xref: EC:1.4.9.2
xref: MetaCyc:ARALKYLAMINE-DEHYDROGENASE-RXN
xref: RHEA:47796
+xref: RHEA:57128
is_a: GO:0052877 ! oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor
property_value: skos:exactMatch EC:1.4.9.2
property_value: skos:exactMatch RHEA:47796
+property_value: skos:narrowMatch RHEA:57128
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -168904,7 +171748,7 @@
id: GO:0030068
name: obsolete lytic viral life cycle
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because more specific terms were created.
synonym: "lytic viral life cycle" EXACT []
is_obsolete: true
@@ -169105,7 +171949,7 @@
id: GO:0030092
name: obsolete regulation of flagellum assembly
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the formation of a flagellum." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the formation of a flagellum." [GOC:curators]
comment: This term was made obsolete because microtubule-based flagellum (GO:0009434) and motile cilium (GO:0031514), as referenced by this term, were determined to be equivalent and merged. When a merge for this term was considered, it was noticed that both eukaryotic and prokaryotic proteins are annotated to it because its meaning had been ambiguous so obsoletion was considered safest.
synonym: "regulation of flagella assembly" RELATED [GOC:mah]
synonym: "regulation of flagella biogenesis" RELATED []
@@ -169179,7 +172023,7 @@
name: lymphocyte differentiation
namespace: biological_process
alt_id: GO:0046650
-def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:go_curators]
+def: "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [CL:0000542, GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "lymphocyte cell differentiation" EXACT []
synonym: "lymphocyte development" RELATED [GOC:add]
@@ -169199,7 +172043,7 @@
id: GO:0030100
name: regulation of endocytosis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of endocytosis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of endocytosis." [GOC:curators]
is_a: GO:0051128 ! regulation of cellular component organization
is_a: GO:0060627 ! regulation of vesicle-mediated transport
intersection_of: GO:0065007 ! biological regulation
@@ -169559,7 +172403,7 @@
id: GO:0030139
name: endocytic vesicle
namespace: cellular_component
-def: "A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting." [GOC:go_curators, PMID:19696797]
+def: "A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting." [GOC:curators, PMID:19696797]
synonym: "endocytotic transport vesicle" EXACT []
synonym: "endocytotic vesicle" EXACT []
xref: NIF_Subcellular:sao1362520468
@@ -169627,6 +172471,7 @@
synonym: "uridine diphosphoacetylglucosamine-alpha-mannoside beta1->6-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.155]
xref: EC:2.4.1.155
xref: MetaCyc:2.4.1.155-RXN
+xref: Reactome:R-HSA-8932427 "MGAT5B transfers GlcNAc from UDP-GlcNAc to GlcNAc-Man-DAG1"
xref: Reactome:R-HSA-9696980 "Spike trimer glycoside chains get additional branches"
xref: Reactome:R-HSA-975916 "Addition of GlcNAc to position 5 by MGAT5"
xref: RHEA:16921
@@ -169710,6 +172555,7 @@
synonym: "mitochondrial matrix protein import" EXACT []
synonym: "mitochondrial translocation" BROAD []
synonym: "protein transport into mitochondrial matrix" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0070585 ! protein localization to mitochondrion
is_a: GO:0071806 ! protein transmembrane transport
is_a: GO:0072594 ! establishment of protein localization to organelle
@@ -169870,6 +172716,7 @@
subset: goslim_generic
subset: goslim_pombe
subset: goslim_prokaryote
+subset: goslim_yeast
synonym: "cellular protein breakdown" EXACT []
synonym: "cellular protein catabolic process" EXACT []
synonym: "cellular protein catabolism" EXACT []
@@ -169897,7 +172744,7 @@
id: GO:0030165
name: PDZ domain binding
namespace: molecular_function
-def: "Binding to a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC:go_curators, Pfam:PF00595]
+def: "Binding to a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC:curators, Pfam:PF00595]
synonym: "DHR-domain binding" EXACT []
synonym: "GLGF-domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -169923,6 +172770,7 @@
synonym: "proteoglycan breakdown" EXACT []
synonym: "proteoglycan catabolism" EXACT []
synonym: "proteoglycan degradation" EXACT []
+xref: Reactome:R-HSA-2024101 "CS/DS degradation"
is_a: GO:0006029 ! proteoglycan metabolic process
is_a: GO:0006516 ! glycoprotein catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29745" xsd:anyURI
@@ -169979,7 +172827,7 @@
id: GO:0030173
name: obsolete integral component of Golgi membrane
namespace: cellular_component
-def: "OBSOLETE. The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:go_curators]
+def: "OBSOLETE. The component of the Golgi membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:curators]
comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "Golgi integral membrane protein" RELATED []
synonym: "integral to Golgi membrane" NARROW []
@@ -170031,7 +172879,7 @@
name: positive regulation of Wnt signaling pathway
namespace: biological_process
alt_id: GO:0045811
-def: "Any process that activates or increases the frequency, rate or extent of Wnt signal transduction." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of Wnt signal transduction." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of frizzled signaling pathway" NARROW []
synonym: "activation of Wnt receptor signaling pathway" NARROW []
synonym: "positive regulation of frizzled signaling pathway" EXACT []
@@ -170058,7 +172906,7 @@
name: negative regulation of Wnt signaling pathway
namespace: biological_process
alt_id: GO:0045810
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of frizzled signaling pathway" EXACT []
synonym: "down regulation of Wnt receptor signaling pathway" EXACT []
synonym: "down-regulation of frizzled signaling pathway" EXACT []
@@ -170346,6 +173194,7 @@
synonym: "heparan sulphate proteoglycan metabolic process" EXACT []
synonym: "heparan sulphate proteoglycan metabolism" EXACT []
synonym: "heparin proteoglycan metabolic process" RELATED []
+xref: Reactome:R-HSA-1638091 "Heparan sulfate/heparin (HS-GAG) metabolism"
is_a: GO:0006029 ! proteoglycan metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29294" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29745" xsd:anyURI
@@ -170380,7 +173229,6 @@
synonym: "chondroitin sulfate metabolism" EXACT []
synonym: "chondroitin sulphate metabolic process" EXACT []
synonym: "chondroitin sulphate metabolism" EXACT []
-xref: Reactome:R-HSA-1793185 "Chondroitin sulfate/dermatan sulfate metabolism"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28977" xsd:anyURI
is_obsolete: true
replaced_by: GO:0050654
@@ -170412,7 +173260,6 @@
synonym: "chondroitin sulfate synthesis" EXACT []
synonym: "chondroitin sulphate biosynthesis" EXACT []
synonym: "chondroitin sulphate biosynthetic process" EXACT []
-xref: Reactome:R-HSA-2022870 "Chondroitin sulfate biosynthesis"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28977" xsd:anyURI
is_obsolete: true
@@ -170453,7 +173300,6 @@
synonym: "dermatan sulfate synthesis" EXACT []
synonym: "dermatan sulphate biosynthesis" EXACT []
synonym: "dermatan sulphate biosynthetic process" EXACT []
-xref: Reactome:R-HSA-2022923 "Dermatan sulfate biosynthesis"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28977" xsd:anyURI
is_obsolete: true
@@ -170531,7 +173377,6 @@
synonym: "hyaluronan biosynthesis" EXACT []
synonym: "hyaluronan formation" EXACT []
synonym: "hyaluronan synthesis" EXACT []
-xref: Reactome:R-HSA-2142850 "Hyaluronan biosynthesis and export"
is_a: GO:0006024 ! glycosaminoglycan biosynthetic process
is_a: GO:0030212 ! hyaluronan metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29745" xsd:anyURI
@@ -170545,7 +173390,7 @@
synonym: "hyaluronan catabolism" EXACT []
synonym: "hyaluronan degradation" EXACT []
xref: MetaCyc:PWY-7645
-xref: Reactome:R-HSA-2160916 "Hyaluronan uptake and degradation"
+xref: Reactome:R-HSA-2160916 "Hyaluronan degradation"
is_a: GO:0006027 ! glycosaminoglycan catabolic process
is_a: GO:0030212 ! hyaluronan metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI
@@ -170581,6 +173426,7 @@
synonym: "T lymphocyte differentiation" EXACT []
synonym: "T-cell differentiation" EXACT []
synonym: "T-lymphocyte differentiation" EXACT []
+xref: Reactome:R-HSA-9945266 "Differentiation of T cells"
is_a: GO:0030098 ! lymphocyte differentiation
is_a: GO:0042110 ! T cell activation
@@ -171207,14 +174053,14 @@
id: GO:0030274
name: LIM domain binding
namespace: molecular_function
-def: "Binding to a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions." [GOC:go_curators, Pfam:PF00412]
+def: "Binding to a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions." [GOC:curators, Pfam:PF00412]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0030275
name: LRR domain binding
namespace: molecular_function
-def: "Binding to a LRR domain (leucine rich repeats) of a protein." [GOC:go_curators, Pfam:PF00560]
+def: "Binding to a LRR domain (leucine rich repeats) of a protein." [GOC:curators, Pfam:PF00560]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -171236,7 +174082,7 @@
id: GO:0030278
name: regulation of ossification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:curators]
synonym: "regulation of bone biosynthesis" EXACT []
synonym: "regulation of bone formation" EXACT []
is_a: GO:0051239 ! regulation of multicellular organismal process
@@ -171248,7 +174094,7 @@
id: GO:0030279
name: negative regulation of ossification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:curators]
synonym: "down regulation of ossification" EXACT []
synonym: "down-regulation of ossification" EXACT []
synonym: "downregulation of ossification" EXACT []
@@ -171291,7 +174137,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: testosterone + NAD(P)+ = androst-4-ene-3,17-dione + NAD(P)H + H+." [EC:1.1.1.51]
comment: This term was obsoleted because it is an unnecessary grouing class.
-xref: Reactome:R-HSA-193064 "HSD17B3-like proteins reducde ANDST to TEST"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28298" xsd:anyURI
is_obsolete: true
consider: GO:0047035
@@ -171311,7 +174156,7 @@
id: GO:0030285
name: obsolete integral component of synaptic vesicle membrane
namespace: cellular_component
-def: "OBSOLETE. The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators]
+def: "OBSOLETE. The component of the synaptic vesicle membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:curators, GOC:dos]
comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to synaptic vesicle membrane" NARROW []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23424" xsd:anyURI
@@ -171504,7 +174349,7 @@
id: GO:0030307
name: positive regulation of cell growth
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate, extent or direction of cell growth." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate, extent or direction of cell growth." [GOC:curators]
synonym: "activation of cell growth" NARROW []
synonym: "stimulation of cell growth" NARROW []
synonym: "up regulation of cell growth" EXACT []
@@ -171521,7 +174366,7 @@
id: GO:0030308
name: negative regulation of cell growth
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth." [GOC:curators]
synonym: "down regulation of cell growth" EXACT []
synonym: "down-regulation of cell growth" EXACT []
synonym: "downregulation of cell growth" EXACT []
@@ -171568,7 +174413,7 @@
id: GO:0030312
name: external encapsulating structure
namespace: cellular_component
-def: "A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space." [GOC:go_curators]
+def: "A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space." [GOC:curators]
comment: The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
subset: goslim_chembl
subset: goslim_drosophila
@@ -171576,7 +174421,8 @@
subset: goslim_pir
subset: goslim_plant
is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0071944 ! cell periphery
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0030313
@@ -171746,11 +174592,13 @@
name: DNA damage response, signal transduction by p53 class mediator
namespace: biological_process
alt_id: GO:0006976
-def: "A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage." [GOC:go_curators]
+def: "A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage." [GOC:curators]
synonym: "DNA damage response, activation of p53" RELATED []
synonym: "p53 signaling pathway" RELATED [GOC:mah, GOC:vk]
synonym: "p53-mediated DNA damage response" BROAD []
synonym: "TP53 signaling pathway" RELATED [GOC:mah, GOC:vk]
+xref: Reactome:R-HSA-6791312 "TP53 Regulates Transcription of Cell Cycle Genes"
+xref: Reactome:R-HSA-69563 "p53-Dependent G1 DNA Damage Response"
is_a: GO:0042770 ! signal transduction in response to DNA damage
is_a: GO:0072331 ! signal transduction by p53 class mediator
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26003" xsd:anyURI
@@ -171775,7 +174623,7 @@
id: GO:0030334
name: regulation of cell migration
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cell migration." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of cell migration." [GOC:curators]
is_a: GO:2000145 ! regulation of cell motility
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0016477 ! cell migration
@@ -171785,7 +174633,7 @@
id: GO:0030335
name: positive regulation of cell migration
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cell migration." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cell migration." [GOC:curators]
synonym: "activation of cell migration" NARROW []
synonym: "stimulation of cell migration" NARROW []
synonym: "up regulation of cell migration" EXACT []
@@ -171801,7 +174649,7 @@
id: GO:0030336
name: negative regulation of cell migration
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." [GOC:curators]
synonym: "down regulation of cell migration" EXACT []
synonym: "down-regulation of cell migration" EXACT []
synonym: "downregulation of cell migration" EXACT []
@@ -171854,9 +174702,13 @@
xref: EC:3.1.1.67
xref: MetaCyc:FATTY-ACYL-ETHYL-ESTER-SYNTHASE-RXN
xref: RHEA:16641
+xref: RHEA:50132
+xref: RHEA:50316
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.67
property_value: skos:exactMatch RHEA:16641
+property_value: skos:narrowMatch RHEA:50132
+property_value: skos:narrowMatch RHEA:50316
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -172576,26 +175428,28 @@
id: GO:0030418
name: nicotianamine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nicotianamine, 2(S),3'2(S),3''(S)-N-(N-(3-amino-3-carboxypropyl)-3-amino-3-carboxypropyl)-azetidine-2-carboxylic acid." [GOC:mah, PMID:10069850]
+def: "The chemical reactions and pathways resulting in the formation of nicotianamine." [GOC:curators, PMID:10069850]
synonym: "nicotianamine anabolism" EXACT []
synonym: "nicotianamine biosynthesis" EXACT []
synonym: "nicotianamine formation" EXACT []
synonym: "nicotianamine synthesis" EXACT []
+xref: MetaCyc:PWY-5957
is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0042401 ! biogenic amine biosynthetic process
is_a: GO:0072351 ! tricarboxylic acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
[Term]
id: GO:0030419
-name: nicotianamine catabolic process
+name: obsolete nicotianamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of nicotianamine, 2(S),3'2(S),3''(S)-N-(N-(3-amino-3-carboxypropyl)-3-amino-3-carboxypropyl)-azetidine-2-carboxylic acid." [GOC:mah, PMID:10069850]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of nicotianamine, 2(S),3'2(S),3''(S)-N-(N-(3-amino-3-carboxypropyl)-3-amino-3-carboxypropyl)-azetidine-2-carboxylic acid." [GOC:mah, PMID:10069850]
+comment: This term was obsoleted because there is no evidence that a specific pathway for nicotianamine degradation exists.
synonym: "nicotianamine breakdown" EXACT []
synonym: "nicotianamine catabolism" EXACT []
synonym: "nicotianamine degradation" EXACT []
-is_a: GO:0009063 ! amino acid catabolic process
-is_a: GO:0042402 ! biogenic amine catabolic process
-is_a: GO:0072352 ! tricarboxylic acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0030420
@@ -172698,7 +175552,7 @@
synonym: "L-kynurenine hydrolase activity" RELATED [EC:3.7.1.3]
xref: EC:3.7.1.3
xref: MetaCyc:KYNURENINASE-RXN
-xref: Reactome:R-HSA-71217 "3-hydroxykynurenine + H2O => 3-hydroxyanthranilate + alanine"
+xref: Reactome:R-HSA-71217 "3-hydroxykynurenine + H2O => 3-hydroxyanthranilate + alanine + H+"
xref: RHEA:16813
xref: RHEA:25143
is_a: GO:0016823 ! hydrolase activity, acting on carbon-carbon bonds, in ketonic substances
@@ -172860,7 +175714,7 @@
id: GO:0030445
name: yeast-form cell wall
namespace: cellular_component
-def: "The wall surrounding a cell of a dimorphic fungus growing in the single-cell budding yeast form, in contrast to the filamentous or hyphal form." [GOC:mah, GOC:mcc]
+def: "The wall surrounding a cell of a dimorphic fungus growing in the single-cell budding yeast form, in contrast to the filamentous or hyphal form." [GOC:mah, GOC:mcc, PMID:36266346]
comment: See also the Fungal Anatomy Ontology term 'vegetative cell ; FAO:0000032'.
is_a: GO:0009277 ! fungal-type cell wall
@@ -172868,7 +175722,7 @@
id: GO:0030446
name: hyphal cell wall
namespace: cellular_component
-def: "The cell wall surrounding a fungal hypha." [GOC:mah]
+def: "The cell wall surrounding a fungal hypha." [GOC:mah, PMID:36266346]
comment: See also the Fungal Anatomy Ontology term 'hypha ; FAO:0001001'.
is_a: GO:0009277 ! fungal-type cell wall
@@ -172899,7 +175753,7 @@
id: GO:0030449
name: regulation of complement activation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of complement activation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of complement activation." [GOC:curators]
synonym: "regulation of complement cascade" EXACT [GOC:add]
xref: Reactome:R-HSA-977606 "Regulation of Complement cascade"
is_a: GO:0002697 ! regulation of immune effector process
@@ -172912,7 +175766,7 @@
id: GO:0030450
name: regulation of complement activation, classical pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the classical pathway of complement activation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the classical pathway of complement activation." [GOC:curators]
synonym: "regulation of complement cascade, classical pathway" EXACT [GOC:add]
is_a: GO:0002923 ! regulation of humoral immune response mediated by circulating immunoglobulin
is_a: GO:0030449 ! regulation of complement activation
@@ -172924,7 +175778,7 @@
id: GO:0030451
name: regulation of complement activation, alternative pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the alternative pathway of complement activation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the alternative pathway of complement activation." [GOC:curators]
synonym: "regulation of complement cascade, alternative pathway" EXACT [GOC:add]
is_a: GO:0030449 ! regulation of complement activation
is_a: GO:0045088 ! regulation of innate immune response
@@ -172996,7 +175850,7 @@
id: GO:0030463
name: obsolete cell aging (sensu Fungi)
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because it does not describe a biological process that is distinct from 'cell aging'.
synonym: "cell aging (sensu Fungi)" EXACT []
is_obsolete: true
@@ -173015,7 +175869,7 @@
id: GO:0030465
name: obsolete autophagic death (sensu Fungi)
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because a more correct term has been created.
synonym: "autophagic death (sensu Fungi)" EXACT []
is_obsolete: true
@@ -173234,7 +176088,7 @@
id: GO:0030495
name: bacteriochlorophyll catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of bacteriochlorophyll, any of the chlorophylls of photosynthetic bacteria. They differ structurally from the chlorophylls of higher plants." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of bacteriochlorophyll, any of the chlorophylls of photosynthetic bacteria. They differ structurally from the chlorophylls of higher plants." [GOC:curators]
synonym: "bacteriochlorophyll breakdown" EXACT []
synonym: "bacteriochlorophyll catabolism" EXACT []
synonym: "bacteriochlorophyll degradation" EXACT []
@@ -173260,7 +176114,7 @@
id: GO:0030500
name: regulation of bone mineralization
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of bone mineralization." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of bone mineralization." [GOC:curators]
is_a: GO:0030278 ! regulation of ossification
is_a: GO:0070167 ! regulation of biomineral tissue development
intersection_of: GO:0065007 ! biological regulation
@@ -173271,7 +176125,7 @@
id: GO:0030501
name: positive regulation of bone mineralization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of bone mineralization." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of bone mineralization." [GOC:curators]
synonym: "activation of bone mineralization" NARROW []
synonym: "stimulation of bone mineralization" NARROW []
synonym: "up regulation of bone mineralization" EXACT []
@@ -173288,7 +176142,7 @@
id: GO:0030502
name: negative regulation of bone mineralization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone mineralization." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone mineralization." [GOC:curators]
synonym: "down regulation of bone mineralization" EXACT []
synonym: "down-regulation of bone mineralization" EXACT []
synonym: "downregulation of bone mineralization" EXACT []
@@ -173307,7 +176161,6 @@
def: "OBSOLETE. Enables the transfer of inorganic diphosphate across a membrane." [PMID:11326272]
comment: The reason for obsoletion is that this term was an unnecessary and confusing grouping term.
synonym: "inorganic pyrophosphate transporter activity" EXACT []
-xref: Reactome:R-HSA-5226964 "ANKH transports PPi from cytosol to extracellular region"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0022857
@@ -173394,7 +176247,7 @@
id: GO:0030511
name: positive regulation of transforming growth factor beta receptor signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity." [GOC:curators]
synonym: "activation of transforming growth factor beta receptor signaling pathway" NARROW []
synonym: "positive regulation of TGF-beta receptor signaling pathway" EXACT []
synonym: "positive regulation of TGFbeta receptor signaling pathway" EXACT []
@@ -173434,7 +176287,7 @@
name: positive regulation of BMP signaling pathway
namespace: biological_process
alt_id: GO:0090098
-def: "Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity." [GOC:curators]
synonym: "activation of BMP signaling pathway" NARROW []
synonym: "positive regulation of BMP receptor signaling pathway" RELATED []
synonym: "positive regulation of BMP signalling pathway" EXACT []
@@ -173460,7 +176313,7 @@
name: negative regulation of BMP signaling pathway
namespace: biological_process
alt_id: GO:0090099
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway." [GOC:curators]
synonym: "down regulation of BMP signaling pathway" EXACT []
synonym: "down-regulation of BMP signaling pathway" EXACT []
synonym: "downregulation of BMP signaling pathway" EXACT []
@@ -173492,7 +176345,7 @@
id: GO:0030516
name: regulation of axon extension
namespace: biological_process
-def: "Any process that modulates the rate, direction or extent of axon extension." [GOC:go_curators]
+def: "Any process that modulates the rate, direction or extent of axon extension." [GOC:curators]
is_a: GO:0048638 ! regulation of developmental growth
is_a: GO:0061387 ! regulation of extent of cell growth
intersection_of: GO:0065007 ! biological regulation
@@ -173663,7 +176516,7 @@
id: GO:0030535
name: obsolete adult feeding behavior (sensu Insecta)
namespace: biological_process
-def: "OBSOLETE. Feeding behavior in a fully developed and mature organism, as described in insects." [GOC:go_curators, GOC:jid]
+def: "OBSOLETE. Feeding behavior in a fully developed and mature organism, as described in insects." [GOC:curators, GOC:jid]
comment: This term was made obsolete because there is no clear difference between the sensu Insecta term and the generic term.
synonym: "adult feeding behavior (sensu Insecta)" EXACT []
is_obsolete: true
@@ -174017,7 +176870,7 @@
name: bile acid catabolic process
namespace: biological_process
alt_id: GO:0019613
-def: "The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:curators]
synonym: "bile acid 7alpha-dehydroxylation pathway" NARROW []
synonym: "bile acid breakdown" EXACT []
synonym: "bile acid catabolism" EXACT []
@@ -174082,7 +176935,7 @@
id: GO:0030579
name: obsolete ubiquitin-dependent SMAD protein catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome." [GOC:curators]
comment: The reason for obsoletion is that the substrate should be captured as the input.
synonym: "ubiquitin-dependent SMAD protein breakdown" EXACT []
synonym: "ubiquitin-dependent SMAD protein catabolism" EXACT []
@@ -174632,7 +177485,6 @@
synonym: "D-alanine formation" EXACT []
synonym: "D-alanine synthesis" EXACT []
is_a: GO:0006523 ! alanine biosynthetic process
-is_a: GO:0046436 ! D-alanine metabolic process
is_a: GO:0046437 ! D-amino acid biosynthetic process
[Term]
@@ -174728,13 +177580,13 @@
[Term]
id: GO:0030641
-name: regulation of cellular pH
+name: obsolete regulation of cellular pH
namespace: biological_process
-def: "Any process involved in the maintenance of an internal equilibrium of hydrogen ions (protons) within a cell or between a cell and its external environment." [GOC:dph, GOC:mah, GOC:tb]
-synonym: "cellular hydrogen ion homeostasis" EXACT [GOC:dph, GOC:tb]
-synonym: "proton homeostasis" EXACT []
-is_a: GO:0006885 ! regulation of pH
-is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
+def: "OBSOLETE. Any process involved in the maintenance of an internal equilibrium of hydrogen ions (protons) within a cell or between a cell and its external environment." [GOC:dph, GOC:mah, GOC:tb]
+comment: The reason for obsoletion is that this term is equivalent to 'regulation of intracellular pH' (GO:0051453). The terms 'cellular pH' and 'intracellular pH' refer to the same concept, and GO:0051453 is the more appropriate term with a proper logical definition.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0051453
[Term]
id: GO:0030642
@@ -175056,6 +177908,12 @@
synonym: "protein recruiting activity" RELATED []
synonym: "protein-containing complex scaffold activity" BROAD []
synonym: "protein-protein adaptor" NARROW []
+xref: Reactome:R-HSA-3780997 "PPP1R3C binds to glycogen:GYG2:GYS2"
+xref: Reactome:R-HSA-3781001 "EPM2A dimer binds PPP1R3C:phosphoglycogen-GYG1 complex"
+xref: Reactome:R-HSA-3781021 "EPM2A dimer binds PPP1R3C:phosphoglycogen-GYG2 complex"
+xref: Reactome:R-HSA-3781023 "PPP1R3C binds to glycogen:GYG1:GYS1"
+xref: Reactome:R-HSA-8871366 "p-Y389,400-RUFY1 binds RAB4A:GTP, RAB5:GTP, RAB14:GTP"
+xref: Reactome:R-HSA-8871376 "p-Y389,400-RUFY1 binds PI3P"
is_a: GO:0060090 ! molecular adaptor activity
relationship: has_part GO:0005515 ! protein binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18655" xsd:anyURI
@@ -175504,7 +178362,7 @@
id: GO:0030716
name: oocyte fate determination
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into an oocyte cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into an oocyte cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
synonym: "oocyte cell fate determination" EXACT []
is_a: GO:0001709 ! cell fate determination
@@ -175630,7 +178488,6 @@
xref: Reactome:R-HSA-5694494 "AACS ligates CoA-SH to ACA, forming ACA-CoA"
xref: RHEA:16117
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.16
property_value: skos:exactMatch RHEA:16117
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -175777,7 +178634,7 @@
id: GO:0030738
name: tyramine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tyramine = N-methyltyramine + S-adenosyl-L-homocysteine + H+." [EC:2.1.1.27, RHEA:14865]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + tyramine = N-methyltyramine + S-adenosyl-L-homocysteine + H+." [RHEA:14865]
synonym: "DIB O-methyltransferase (3,5-diiodo-4-hydroxy-benzoic acid)" RELATED [EC:2.1.1.27]
synonym: "S-adenosyl-L-methionine:tyramine N-methyltransferase activity" RELATED [EC:2.1.1.27]
synonym: "S-adenosyl-methionine:tyramine N-methyltransferase activity" RELATED [EC:2.1.1.27]
@@ -175852,15 +178709,16 @@
id: GO:0030742
name: GTP-dependent protein binding
namespace: molecular_function
-def: "Binding to a protein or protein complex when at least one of the interacting partners is in the GTP-bound state." [GOC:go_curators, GOC:krc]
+def: "Binding to a protein or protein complex when at least one of the interacting partners is in the GTP-bound state." [GOC:curators, GOC:krc]
comment: This term may be used to annotate both partners in a GTP-dependent binding interaction, both the GTP-bound protein and the protein(s) which interact with it.
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0030743
-name: 23S rRNA (adenosine(1067)-2'-O)-methyltransferase activity
+name: 23S rRNA (adenosine(1067)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: adenosine(1067) in 23S rRNA + S-adenosyl-L-methionine = 2'-O-methyladenosine(1067) in 23S rRNA + H+ + S-adenosyl-L-homocysteine." [EC:2.1.1.230]
+synonym: "23S rRNA (adenosine(1067)-2'-O)-methyltransferase activity" EXACT []
synonym: "ribosomal ribonucleate adenosine 2'-methyltransferase activity" RELATED [EC:2.1.1.230]
synonym: "RNA-pentose methylase activity" RELATED []
synonym: "rRNA adenosine 2'-methylase activity" RELATED [EC:2.1.1.230]
@@ -176020,10 +178878,14 @@
synonym: "S-adenosyl-L-methionine:bergaptolO-methyltransferase activity" RELATED [EC:2.1.1.69]
xref: EC:2.1.1.69
xref: MetaCyc:RXN-8448
+xref: RHEA:11808
xref: RHEA:18861
+xref: RHEA:24894
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.69
property_value: skos:exactMatch RHEA:18861
+property_value: skos:narrowMatch RHEA:11808
+property_value: skos:narrowMatch RHEA:24894
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30155" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -176329,7 +179191,7 @@
id: GO:0030772
name: tryptophan 2-C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine(1+) + L-tryptophan = S-adenosyl-L-homocysteine + L-2-methyltryptophan + H+." [EC:2.1.1.106, RHEA:17321]
+def: "Catalysis of the reaction: L-tryptophan + S-adenosyl-L-methionine = 2-methyl-L-tryptophan + S-adenosyl-L-homocysteine + H+." [RHEA:17321]
synonym: "S-adenosyl-L-methionine:L-tryptophan 2-C-methyltransferase activity" RELATED [EC:2.1.1.106]
synonym: "S-adenosylmethionine:tryptophan 2-methyltransferase activity" RELATED [EC:2.1.1.106]
synonym: "tryptophan 2-methyltransferase activity" RELATED [EC:2.1.1.106]
@@ -176488,10 +179350,18 @@
synonym: "tetrahydroprotoberberine cis-N-methyltransferase activity" RELATED [EC:2.1.1.122]
xref: EC:2.1.1.122
xref: MetaCyc:RXN-23969
+xref: RHEA:12805
+xref: RHEA:75975
+xref: RHEA:76047
+xref: RHEA:76051
xref: RHEA:76067
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.122
property_value: skos:exactMatch RHEA:76067
+property_value: skos:narrowMatch RHEA:12805
+property_value: skos:narrowMatch RHEA:75975
+property_value: skos:narrowMatch RHEA:76047
+property_value: skos:narrowMatch RHEA:76051
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30156" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -176551,9 +179421,11 @@
xref: EC:2.1.1.128
xref: MetaCyc:2.1.1.128-RXN
xref: RHEA:19941
+xref: RHEA:31907
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.128
property_value: skos:exactMatch RHEA:19941
+property_value: skos:narrowMatch RHEA:31907
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -179376,12 +182248,12 @@
synonym: "negative regulation of septation initiation network" EXACT []
synonym: "negative regulation of septation initiation signaling cascade" RELATED [GOC:signaling]
synonym: "negative regulation of septation initiation signalling" EXACT []
-is_a: GO:0010974 ! negative regulation of division septum assembly
is_a: GO:0031029 ! regulation of septation initiation signaling
is_a: GO:0051058 ! negative regulation of small GTPase mediated signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0031028 ! septation initiation signaling
relationship: negatively_regulates GO:0031028 ! septation initiation signaling
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31584" xsd:anyURI
[Term]
id: GO:0031031
@@ -179396,7 +182268,6 @@
synonym: "up regulation of septation initiation signaling" EXACT []
synonym: "up-regulation of septation initiation signaling" EXACT []
synonym: "upregulation of septation initiation signaling" EXACT []
-is_a: GO:0010973 ! positive regulation of division septum assembly
is_a: GO:0031029 ! regulation of septation initiation signaling
is_a: GO:0051057 ! positive regulation of small GTPase mediated signal transduction
intersection_of: GO:0065007 ! biological regulation
@@ -180003,12 +182874,14 @@
name: organelle membrane
namespace: cellular_component
def: "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle." [GOC:dos, GOC:mah]
+subset: gocheck_do_not_annotate
synonym: "intracellular membrane" RELATED [NIF_Subcellular:sao830981606]
xref: NIF_Subcellular:sao830981606
is_a: GO:0016020 ! membrane
intersection_of: GO:0016020 ! membrane
intersection_of: part_of GO:0043227 ! membrane-bounded organelle
relationship: part_of GO:0043227 ! membrane-bounded organelle
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31446" xsd:anyURI
[Term]
id: GO:0031091
@@ -180792,8 +183665,9 @@
synonym: "phosphatidylinositol degradation" EXACT []
synonym: "PtdIns catabolic process" EXACT []
synonym: "PtdIns catabolism" EXACT []
-is_a: GO:0046475 ! glycerophospholipid catabolic process
+is_a: GO:0009056 ! catabolic process
is_a: GO:0046488 ! phosphatidylinositol metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0031162
@@ -181066,6 +183940,8 @@
name: phosphatidylcholine binding
namespace: molecular_function
def: "Binding to a phosphatidylcholine, a glycophospholipid in which a phosphatidyl group is esterified to the hydroxyl group of choline." [GOC:mah, ISBN:0198506732]
+xref: Reactome:R-HSA-8873794 "PCTP binds PC"
+xref: Reactome:R-HSA-8873923 "STARD10 binds LPCAT1 and PC"
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043169 ! cation binding
is_a: GO:0050997 ! quaternary ammonium group binding
@@ -181376,24 +184252,26 @@
id: GO:0031240
name: external side of cell outer membrane
namespace: cellular_component
-def: "The side of the outer membrane that is opposite to the side that faces the periplasm of the cell." [GOC:mlg, GOC:mtg_sensu]
+def: "The leaflet of the outer membrane that is opposite to the side that faces the periplasm of the cell, including any protein embedded in, attached to, or peripherally associated with it." [GOC:mlg, GOC:mtg_sensu]
comment: In GO, 'external side' still refers to part of the membrane and does not refer to components beyond (outside of) the membrane.
synonym: "external leaflet of cell outer membrane" EXACT [GOC:ab]
synonym: "external side of outer membrane" RELATED []
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0009279 ! cell outer membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0031241
name: periplasmic side of cell outer membrane
namespace: cellular_component
-def: "The side (leaflet) of the outer membrane that faces the periplasm of the cell." [GOC:mlg, GOC:mtg_sensu]
+def: "The leaflet of a outer cell membrane that faces the periplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:mlg, GOC:mtg_sensu]
comment: In GO, 'internal side' still refers to part of the membrane and does not refer to components beyond (inside of) the membrane.
synonym: "internal leaflet of cell outer membrane" EXACT [GOC:ab]
synonym: "internal side of cell outer membrane" EXACT []
synonym: "internal side of outer membrane" EXACT []
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0009279 ! cell outer membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0031242
@@ -182004,7 +184882,7 @@
synonym: "T-cell co-stimulation" EXACT []
synonym: "T-cell costimulation" EXACT []
synonym: "T-lymphocyte costimulation" EXACT []
-xref: Reactome:R-HSA-388841 "Costimulation by the CD28 family"
+xref: Reactome:R-HSA-388841 "Regulation of T cell activation by CD28 family"
is_a: GO:0031294 ! lymphocyte costimulation
is_a: GO:0050870 ! positive regulation of T cell activation
@@ -182055,9 +184933,10 @@
[Term]
id: GO:0031299
-name: taurine-pyruvate aminotransferase activity
+name: taurine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + taurine = L-alanine + sulfoacetaldehyde." [PMID:11082195, RHEA:10420]
+def: "Catalysis of the reaction: taurine + pyruvate = sulfoacetaldehyde + L-alanine." [PMID:11082195, RHEA:10420]
+synonym: "taurine-pyruvate aminotransferase activity" EXACT []
synonym: "taurine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.77]
synonym: "Tpa" RELATED [EC:2.6.1.77]
xref: EC:2.6.1.77
@@ -182068,6 +184947,7 @@
property_value: skos:exactMatch EC:2.6.1.77
property_value: skos:exactMatch RHEA:10420
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0031300
@@ -182370,7 +185250,6 @@
synonym: "up regulation of cellular metabolic process" EXACT []
synonym: "up-regulation of cellular metabolic process" EXACT []
synonym: "upregulation of cellular metabolic process" EXACT []
-xref: Reactome:R-HSA-163765 "ChREBP activates metabolic gene expression"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI
is_obsolete: true
@@ -183202,8 +186081,7 @@
name: bursicon neuropeptide hormone complex
namespace: cellular_component
def: "A neuropeptide hormone secreted by the central nervous system of insects that stimulates the tanning and sclerotization of the adult cuticle following eclosion. The active hormone consists of an obligate heterodimer of the alpha and beta subunits." [GOC:rc]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0031396
@@ -183251,7 +186129,6 @@
name: regulation of protein modification process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." [GOC:mah, GOC:tb]
-subset: goslim_yeast
is_a: GO:0051246 ! regulation of protein metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0036211 ! protein modification process
@@ -184421,7 +187298,6 @@
synonym: "chromatin silencing at pericentric region" RELATED [GOC:mah]
synonym: "heterochromatic silencing at centromere" EXACT []
synonym: "pericentric heterochromatin assembly" EXACT []
-is_a: GO:0140462 ! pericentric heterochromatin organization
is_a: GO:0140719 ! constitutive heterochromatin formation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18954" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19112" xsd:anyURI
@@ -184842,9 +187718,12 @@
xref: Reactome:R-HSA-1234177 "Cytosolic PHD2,3 hydroxylates proline residues on HIF1A"
xref: Reactome:R-HSA-1234179 "Cytosolic PHD2,3 hydroxylates proline residues on EPAS1 (HIF2A)"
xref: Reactome:R-HSA-1234181 "Nuclear PHD1,3 hydroxylates proline residues on HIF1A"
+xref: Reactome:R-HSA-9918779 "Proline hydroxylases hydroxylate Polyprotein"
+xref: RHEA:48936
xref: RHEA:63484
is_a: GO:0031543 ! peptidyl-proline dioxygenase activity
property_value: skos:exactMatch RHEA:63484
+property_value: skos:narrowMatch RHEA:48936
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -188675,9 +191554,23 @@
synonym: "short-chain fatty acid activation" RELATED []
synonym: "short-chain fatty-acid-CoA ligase activity" EXACT [GOC:bf]
synonym: "short-chain-fatty-acid-CoA ligase activity" EXACT []
+xref: RHEA:46168
+xref: RHEA:46172
+xref: RHEA:46176
+xref: RHEA:46184
xref: RHEA:52860
+xref: RHEA:66988
+xref: RHEA:66992
+xref: RHEA:66996
is_a: GO:0120515 ! fatty acid-CoA ligase activity
property_value: skos:exactMatch RHEA:52860
+property_value: skos:narrowMatch RHEA:46168
+property_value: skos:narrowMatch RHEA:46172
+property_value: skos:narrowMatch RHEA:46176
+property_value: skos:narrowMatch RHEA:46184
+property_value: skos:narrowMatch RHEA:66988
+property_value: skos:narrowMatch RHEA:66992
+property_value: skos:narrowMatch RHEA:66996
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23296" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26439" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
@@ -188694,10 +191587,24 @@
synonym: "medium-chain-fatty-acid-CoA ligase activity" EXACT []
xref: EC:6.2.1.2
xref: Reactome:R-HSA-8875013 "ACSM3,ACSM6 ligate CoA to BUT"
+xref: RHEA:33623
+xref: RHEA:33631
+xref: RHEA:43740
+xref: RHEA:44080
+xref: RHEA:44088
+xref: RHEA:44228
xref: RHEA:48340
+xref: RHEA:54952
is_a: GO:0120515 ! fatty acid-CoA ligase activity
property_value: skos:exactMatch EC:6.2.1.2
property_value: skos:exactMatch RHEA:48340
+property_value: skos:narrowMatch RHEA:33623
+property_value: skos:narrowMatch RHEA:33631
+property_value: skos:narrowMatch RHEA:43740
+property_value: skos:narrowMatch RHEA:44080
+property_value: skos:narrowMatch RHEA:44088
+property_value: skos:narrowMatch RHEA:44228
+property_value: skos:narrowMatch RHEA:54952
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14783" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18967" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23497" xsd:anyURI
@@ -188717,9 +191624,17 @@
xref: Reactome:R-HSA-5696007 "ACSF3 ligates CoA-SH to VLCFA"
xref: Reactome:R-HSA-8875077 "SLC27A3 ligates CoA-SH to VLCFA"
xref: Reactome:R-HSA-9914143 "SLC27A2-mediated ligation of peroxisomal fatty acid and CoASH"
+xref: RHEA:33639
+xref: RHEA:43748
xref: RHEA:54536
+xref: RHEA:83111
+xref: RHEA:83403
is_a: GO:0120515 ! fatty acid-CoA ligase activity
property_value: skos:exactMatch RHEA:54536
+property_value: skos:narrowMatch RHEA:33639
+property_value: skos:narrowMatch RHEA:43748
+property_value: skos:narrowMatch RHEA:83111
+property_value: skos:narrowMatch RHEA:83403
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26439" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -189029,7 +191944,7 @@
id: GO:0031992
name: energy transducer activity
namespace: molecular_function
-def: "The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell." [GOC:go_curators]
+def: "The biological transducer activity that accepts energy and converts it to another form, often by transfer to another molecule within the cell." [GOC:curators]
subset: goslim_pir
synonym: "light harvesting activity" RELATED []
synonym: "photon capture" RELATED []
@@ -189384,7 +192299,9 @@
synonym: "up regulation of insulin secretion" EXACT []
synonym: "up-regulation of insulin secretion" EXACT []
synonym: "upregulation of insulin secretion" EXACT []
+xref: Reactome:R-HSA-381676 "Glucagon-like Peptide-1 (GLP1) regulates insulin secretion"
xref: Reactome:R-HSA-399997 "Acetylcholine regulates insulin secretion"
+xref: Reactome:R-HSA-400451 "Free fatty acids regulate insulin secretion"
is_a: GO:0050714 ! positive regulation of protein secretion
is_a: GO:0050796 ! regulation of insulin secretion
is_a: GO:0090277 ! positive regulation of peptide hormone secretion
@@ -189621,9 +192538,15 @@
synonym: "diphosphatidylglycerol biosynthesis" RELATED []
synonym: "diphosphatidylglycerol biosynthetic process" RELATED []
xref: MetaCyc:PWY-5269
+xref: MetaCyc:PWY-5668
+xref: MetaCyc:PWY0-1545
xref: Reactome:R-HSA-1483076 "Synthesis of CL"
is_a: GO:0006655 ! phosphatidylglycerol biosynthetic process
is_a: GO:0032048 ! cardiolipin metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5269
+property_value: skos:narrowMatch MetaCyc:PWY-5668
+property_value: skos:narrowMatch MetaCyc:PWY0-1545
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0032050
@@ -189644,6 +192567,7 @@
name: bile acid binding
namespace: molecular_function
def: "Binding to a bile acid, a steroid carboxylic acids occurring in bile." [GOC:rph]
+xref: Reactome:R-HSA-8873850 "STARD5 binds DCA, LCA"
is_a: GO:0033293 ! monocarboxylic acid binding
[Term]
@@ -191450,8 +194374,10 @@
synonym: "glucosaminyl-phosphotidylinositol O-acyltransferase activity" EXACT []
synonym: "GPI-inositol acyltransferase" RELATED []
xref: RHEA:60496
+xref: RHEA:83759
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch RHEA:60496
+property_value: skos:narrowMatch RHEA:83759
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30693" xsd:anyURI
[Term]
@@ -191488,17 +194414,17 @@
[Term]
id: GO:0032220
-name: plasma membrane fusion involved in cytogamy
+name: obsolete plasma membrane fusion involved in cytogamy
namespace: biological_process
alt_id: GO:0070872
-def: "The joining of two or more lipid bilayer membranes that surround cells, that contributes to cytogamy." [GOC:mah, PMID:29134248]
+def: "OBSOLETE. The joining of two or more lipid bilayer membranes that surround cells, that contributes to cytogamy." [GOC:mah, PMID:29134248]
+comment: precomposed term, represents a GO-CAM model.
synonym: "plasma membrane fusion during cytogamy" RELATED [GOC:dph, GOC:tb]
synonym: "plasma membrane organization involved in conjugation with cellular fusion" EXACT []
-is_a: GO:0045026 ! plasma membrane fusion
-intersection_of: GO:0045026 ! plasma membrane fusion
-intersection_of: part_of GO:0000755 ! cytogamy
-relationship: part_of GO:0000755 ! cytogamy
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16258" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
+is_obsolete: true
+consider: GO:0140253
created_by: mah
creation_date: 2009-08-20T02:24:56Z
@@ -191989,10 +194915,12 @@
name: methylation
namespace: biological_process
def: "The process in which a methyl group is covalently attached to a molecule." [GOC:mah]
+subset: gocheck_obsoletion_candidate
subset: goslim_chembl
xref: Reactome:R-HSA-156581 "Methylation"
xref: Wikipedia:Methylation
is_a: GO:0008152 ! metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27423" xsd:anyURI
[Term]
id: GO:0032260
@@ -192054,6 +194982,7 @@
def: "Binding to phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position." [GOC:bf, PMID:10209156, PMID:11395417, PMID:11557775]
synonym: "phosphatidylinositol 3-phosphate binding" EXACT []
synonym: "PtdIns-3-P binding" EXACT []
+xref: Reactome:R-HSA-8870489 "PLEKHA4,(5,6) bind PI3P"
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
[Term]
@@ -192539,8 +195468,7 @@
namespace: cellular_component
def: "A stable heterodimer of angiogenin and placental ribonuclease inhibitor; interaction between angiogenin and PRI prevents angiogenin binding to its receptor to stimulate angiogenesis." [PMID:2706246, PMID:3470787]
synonym: "angiogenin-placental ribonuclease inhibitor complex" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0032322
@@ -193032,13 +195960,14 @@
[Term]
id: GO:0032361
-name: pyridoxal phosphate catabolic process
+name: pyridoxal 5'-phosphate catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6." [GOC:mah]
is_a: GO:0042820 ! vitamin B6 catabolic process
-is_a: GO:0042822 ! pyridoxal phosphate metabolic process
+is_a: GO:0042822 ! pyridoxal 5'-phosphate metabolic process
is_a: GO:0046185 ! aldehyde catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0032362
@@ -194344,7 +197273,7 @@
id: GO:0032473
name: cytoplasmic side of mitochondrial outer membrane
namespace: cellular_component
-def: "The external (cytoplasmic) face of the mitochondrial outer membrane." [GOC:mah]
+def: "The leaflet of the mitochondrial outer membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:mah]
comment: In GO, 'external side' still refers to part of the membrane and does not refer to components beyond (outside of) the membrane.
synonym: "cytosolic side of mitochondrial outer membrane" EXACT []
synonym: "external leaflet of mitochondrial outer membrane" EXACT [GOC:ab]
@@ -194352,6 +197281,7 @@
synonym: "external side of mitochondrial outer membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0005741 ! mitochondrial outer membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0032474
@@ -195038,7 +197968,7 @@
id: GO:0032543
name: mitochondrial translation
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:curators]
subset: goslim_yeast
synonym: "mitochondrial protein anabolism" EXACT []
synonym: "mitochondrial protein biosynthesis" EXACT []
@@ -195057,7 +197987,7 @@
id: GO:0032544
name: plastid translation
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of a protein in a plastid. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the plastid has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:curators]
synonym: "plastid protein anabolism" EXACT []
synonym: "plastid protein biosynthesis" EXACT []
synonym: "plastid protein formation" EXACT []
@@ -195089,7 +198019,6 @@
namespace: molecular_function
def: "Binding to a purine deoxyribonucleoside, a compound consisting of a purine base linked to deoxyribose." [GOC:mah]
is_a: GO:0001883 ! purine nucleoside binding
-is_a: GO:0032546 ! deoxyribonucleoside binding
[Term]
id: GO:0032548
@@ -195097,7 +198026,6 @@
namespace: molecular_function
def: "Binding to a pyrimidine deoxyribonucleoside, a compound consisting of a pyrimidine base linked to deoxyribose." [GOC:mah]
is_a: GO:0001884 ! pyrimidine nucleoside binding
-is_a: GO:0032546 ! deoxyribonucleoside binding
[Term]
id: GO:0032549
@@ -195127,8 +198055,8 @@
name: deoxyribonucleotide binding
namespace: molecular_function
def: "Binding to a deoxyribonucleotide, any compound consisting of a deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
-is_a: GO:0000166 ! nucleotide binding
-is_a: GO:0097367 ! carbohydrate derivative binding
+is_a: GO:0005488 ! binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0032553
@@ -195144,7 +198072,7 @@
namespace: molecular_function
def: "Binding to a purine deoxyribonucleotide, any compound consisting of a purine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0017076 ! purine nucleotide binding
-is_a: GO:0032552 ! deoxyribonucleotide binding
+is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:0032555
@@ -195160,7 +198088,7 @@
namespace: molecular_function
def: "Binding to a pyrimidine deoxyribonucleotide, any compound consisting of a pyrimidine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0019103 ! pyrimidine nucleotide binding
-is_a: GO:0032552 ! deoxyribonucleotide binding
+is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:0032557
@@ -198701,6 +201629,7 @@
name: lead ion binding
namespace: molecular_function
def: "Binding to lead (Pb) ions." [GOC:mah]
+xref: Reactome:R-HSA-190141 "ALAD binds to Pb2+"
is_a: GO:0046872 ! metal ion binding
[Term]
@@ -199397,64 +202326,34 @@
[Term]
id: GO:0032847
-name: regulation of cellular pH reduction
+name: obsolete regulation of cellular pH reduction
namespace: biological_process
-def: "Any process that modulates the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
-synonym: "regulation of cell pH reduction" EXACT []
-synonym: "regulation of cellular acidification" EXACT []
-synonym: "regulation of intracellular acidification" RELATED []
-synonym: "regulation of intracellular pH reduction" EXACT []
-synonym: "regulation of reduction of cellular pH" EXACT []
-synonym: "regulation of reduction of pH in cell" EXACT []
-is_a: GO:0050789 ! regulation of biological process
-is_a: GO:0051453 ! regulation of intracellular pH
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0051452 ! intracellular pH reduction
-relationship: regulates GO:0051452 ! intracellular pH reduction
+def: "OBSOLETE. Any process that modulates the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
+comment: This term was obsoleted because it represents 'regulation of regulation', which is redundant with direct pH regulation terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+consider: GO:0051452
+consider: GO:0051454
[Term]
id: GO:0032848
-name: negative regulation of cellular pH reduction
+name: obsolete negative regulation of cellular pH reduction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
-synonym: "down regulation of cellular pH reduction" EXACT []
-synonym: "down-regulation of cellular pH reduction" EXACT []
-synonym: "downregulation of cellular pH reduction" EXACT []
-synonym: "inhibition of cellular pH reduction" NARROW []
-synonym: "negative regulation of cell pH reduction" EXACT []
-synonym: "negative regulation of cellular acidification" EXACT []
-synonym: "negative regulation of intracellular acidification" RELATED []
-synonym: "negative regulation of intracellular pH reduction" EXACT []
-synonym: "negative regulation of reduction of cellular pH" EXACT []
-synonym: "negative regulation of reduction of pH in cell" EXACT []
-is_a: GO:0032847 ! regulation of cellular pH reduction
-is_a: GO:0048519 ! negative regulation of biological process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0051452 ! intracellular pH reduction
-relationship: negatively_regulates GO:0051452 ! intracellular pH reduction
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
+comment: This term was obsoleted because it represents 'regulation of regulation', which is redundant with direct pH regulation terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0051454
[Term]
id: GO:0032849
-name: positive regulation of cellular pH reduction
+name: obsolete positive regulation of cellular pH reduction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
-synonym: "activation of cellular pH reduction" NARROW []
-synonym: "positive regulation of cell pH reduction" EXACT []
-synonym: "positive regulation of cellular acidification" EXACT []
-synonym: "positive regulation of intracellular acidification" RELATED []
-synonym: "positive regulation of intracellular pH reduction" EXACT []
-synonym: "positive regulation of reduction of cellular pH" EXACT []
-synonym: "positive regulation of reduction of pH in cell" EXACT []
-synonym: "stimulation of cellular pH reduction" NARROW []
-synonym: "up regulation of cellular pH reduction" EXACT []
-synonym: "up-regulation of cellular pH reduction" EXACT []
-synonym: "upregulation of cellular pH reduction" EXACT []
-is_a: GO:0032847 ! regulation of cellular pH reduction
-is_a: GO:0048518 ! positive regulation of biological process
-is_a: GO:0051452 ! intracellular pH reduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0051452 ! intracellular pH reduction
-relationship: positively_regulates GO:0051452 ! intracellular pH reduction
+def: "OBSOLETE. Any process that activates or increases the frequency, rate, or extent of a process that reduces the internal pH of a cell." [GOC:mah]
+comment: This term was obsoleted because it represents 'regulation of regulation', which is redundant with direct pH regulation terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0051452
[Term]
id: GO:0032865
@@ -200861,6 +203760,7 @@
synonym: "amino acid efflux from vacuole" EXACT []
synonym: "vacuolar amino acid export" EXACT []
is_a: GO:0003333 ! amino acid transmembrane transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
[Term]
@@ -200870,6 +203770,7 @@
def: "The directed movement of amino acids into the vacuole across the vacuolar membrane." [GOC:mah]
synonym: "vacuolar amino acid import" EXACT []
is_a: GO:0003333 ! amino acid transmembrane transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
[Term]
@@ -200892,7 +203793,8 @@
xref: Reactome:R-HSA-1307803 "TIMM22 inserts proteins into inner membrane"
xref: Reactome:R-HSA-9902096 "COX18 inserts nascent MT-CO2 in COX20:TMEM77"
xref: Reactome:R-HSA-9906955 "MT-ND4 is translated"
-is_a: GO:0140597 ! protein carrier chaperone
+xref: Reactome:R-HSA-9926981 "Bam complex inserts Hbp into outer membrane"
+is_a: GO:0140597 ! protein carrier activity
relationship: part_of GO:0090150 ! establishment of protein localization to membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16976" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20414" xsd:anyURI
@@ -202130,13 +205032,14 @@
[Term]
id: GO:0033094
-name: putrescine--2-oxoglutarate transaminase activity
+name: putrescine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: putrescine + 2-oxoglutarate = L-glutamate + 1-pyrroline + H2O. The enzymatic part of the reaction produces 4-aminobutanal that spontaneously cyclizes to form 1-pyrroline." [EC:2.6.1.82, GOC:mlg, RHEA:12268]
+def: "Catalysis of the reaction: putrescine + 2-oxoglutarate = L-glutamate + 1-pyrroline + H2O. The enzymatic part of the reaction produces 4-aminobutanal that spontaneously cyclizes to form 1-pyrroline." [EC:2.6.1.82, RHEA:12268]
synonym: "butane-1,4-diamine:2-oxoglutarate aminotransferase activity" RELATED []
synonym: "PAT activity" RELATED []
synonym: "putrescine aminotransferase activity" BROAD [EC:2.6.1.82]
synonym: "putrescine transaminase activity" BROAD []
+synonym: "putrescine--2-oxoglutarate transaminase activity" EXACT []
synonym: "putrescine-alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.82]
synonym: "putrescine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.82]
synonym: "putrescine:alpha-ketoglutarate aminotransferase activity" RELATED [EC:2.6.1.82]
@@ -202149,6 +205052,7 @@
property_value: skos:exactMatch RHEA:12268
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25992" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0033095
@@ -203091,9 +205995,11 @@
xref: Reactome:R-HSA-429786 "SGMS2 transfers phosphocholine onto ceramide"
xref: Reactome:R-HSA-429798 "SGMS1 transfers phosphocholine onto ceramide"
xref: RHEA:18765
+xref: RHEA:43320
is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
property_value: skos:exactMatch EC:2.7.8.27
property_value: skos:exactMatch RHEA:18765
+property_value: skos:narrowMatch RHEA:43320
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -203164,7 +206070,7 @@
id: GO:0033196
name: tryparedoxin peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tryparedoxin + hydrogen peroxide = tryparedoxin disulfide + H2O." [GOC:mah, PMID:32388269]
+def: "Catalysis of the reaction: tryparedoxin + H2O2 = tryparedoxin disulfide + H2O." [GOC:mah, PMID:32388269]
synonym: "TXNPx activity" EXACT []
xref: MetaCyc:1.11.1.15-RXN
is_a: GO:0004601 ! peroxidase activity
@@ -204258,7 +207164,7 @@
id: GO:0033300
name: dehydroascorbic acid transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of dehydroascorbate, 5-(1,2-dihydroxyethyl)furan-2,3,4(5H)-trione, from one side of a membrane to the other." [GOC:go_curators]
+def: "Enables the transfer of dehydroascorbate, 5-(1,2-dihydroxyethyl)furan-2,3,4(5H)-trione, from one side of a membrane to the other." [GOC:curators]
synonym: "dehydroascorbate transporter activity" EXACT []
synonym: "dehydroascorbic acid transporter activity" RELATED []
xref: Reactome:R-HSA-198818 "SLC2A1,3 transports DeHA from extracellular region to cytosol"
@@ -204366,8 +207272,14 @@
synonym: "chlorophyll a catabolism" EXACT []
synonym: "chlorophyll a degradation" EXACT []
xref: MetaCyc:PWY-5098
+xref: MetaCyc:PWY-6927
+xref: MetaCyc:PWY-7164
is_a: GO:0015996 ! chlorophyll catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5098
+property_value: skos:narrowMatch MetaCyc:PWY-6927
+property_value: skos:narrowMatch MetaCyc:PWY-7164
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0033311
@@ -204614,9 +207526,13 @@
synonym: "ent-kaurene formation" EXACT []
synonym: "ent-kaurene synthesis" EXACT []
xref: MetaCyc:PWY-5032
+xref: MetaCyc:PWY-6653
is_a: GO:0033331 ! ent-kaurene metabolic process
is_a: GO:0046246 ! terpene biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-5032
+property_value: skos:narrowMatch MetaCyc:PWY-6653
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0033333
@@ -204808,14 +207724,18 @@
[Term]
id: GO:0033353
-name: S-adenosylmethionine cycle
+name: L-methionine cycle
namespace: biological_process
-def: "A cyclic series of interconversions involving S-adenosylmethionine, S-adenosyl-L-homocysteine, L-cysteine, and L-methionine. Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of methionine." [GOC:mah, MetaCyc:PWY-5041]
+def: "A cyclic series of interconversions involving S-adenosyl-L-homocysteine, L-homocysteine, L-methionine and S-adenosyl-L-methionine (SAM). Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of L-methionine." [PMID:31950558, PMID:39394448]
synonym: "activated methyl cycle" EXACT []
+synonym: "S-adenosylmethionine cycle" EXACT []
synonym: "SAM cycle" EXACT []
xref: MetaCyc:PWY-5041
+xref: MetyaCyc:PWY-6151
is_a: GO:0046500 ! S-adenosylmethionine metabolic process
-relationship: has_part GO:0008898 ! S-adenosylmethionine-homocysteine S-methyltransferase activity
+property_value: skos:narrowMatch MetaCyc:PWY-5041
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31318" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0033354
@@ -204829,7 +207749,7 @@
id: GO:0033355
name: ascorbate glutathione cycle
namespace: biological_process
-def: "A cyclic series of interconversions involving L-ascorbate and glutathione that scavenges hydrogen peroxide and reduces it to water, with concomitant oxidation of NADPH." [GOC:mah, MetaCyc:PWY-2261]
+def: "A cyclic series of interconversions involving L-ascorbate and glutathione that scavenges H2O2 and reduces it to water, with concomitant oxidation of NADPH." [GOC:mah, MetaCyc:PWY-2261]
synonym: "hydrogen peroxide detoxification" RELATED []
xref: MetaCyc:PWY-2261
is_a: GO:0006749 ! glutathione metabolic process
@@ -204875,61 +207795,65 @@
[Term]
id: GO:0033359
-name: L-lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate
+name: obsolete L-lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and N-succinyl-2-amino-6-ketopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah, MetaCyc:DAPLYSINESYN-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and N-succinyl-2-amino-6-ketopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine anabolism via diaminopimelate and N-succinyl-2-amino-6-ketopimelate" EXACT []
synonym: "lysine biosynthesis via diaminopimelic acid and N-succinyl-2-amino-6-ketopimelate" EXACT []
synonym: "lysine biosynthetic process via diaminopimelic acid and N-succinyl-2-amino-6-ketopimelate" EXACT []
synonym: "lysine formation via diaminopimelate and N-succinyl-2-amino-6-ketopimelate" EXACT []
synonym: "lysine synthesis via diaminopimelate and N-succinyl-2-amino-6-ketopimelate" EXACT []
-xref: MetaCyc:DAPLYSINESYN-PWY
-is_a: GO:0009089 ! L-lysine biosynthetic process via diaminopimelate
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0033360
-name: L-lysine biosynthetic process via diaminopimelate and L-2-acetamido-6-oxoheptanedioate
+name: obsolete L-lysine biosynthetic process via diaminopimelate and L-2-acetamido-6-oxoheptanedioate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and L-2-acetamido-6-oxoheptanedioate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah, MetaCyc:PWY-2941]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and L-2-acetamido-6-oxoheptanedioate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine anabolism via diaminopimelate and L-2-acetamido-6-oxoheptanedioate" EXACT []
synonym: "lysine biosynthesis via diaminopimelic acid and L-2-acetamido-6-oxoheptanedioate" EXACT []
synonym: "lysine biosynthetic process via diaminopimelic acid and L-2-acetamido-6-oxoheptanedioate" EXACT []
synonym: "lysine formation via diaminopimelate and L-2-acetamido-6-oxoheptanedioate" EXACT []
synonym: "lysine synthesis via diaminopimelate and L-2-acetamido-6-oxoheptanedioate" EXACT []
-xref: MetaCyc:PWY-2941
-is_a: GO:0009089 ! L-lysine biosynthetic process via diaminopimelate
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0033361
-name: L-lysine biosynthetic process via diaminopimelate, dehydrogenase pathway
+name: obsolete L-lysine biosynthetic process via diaminopimelate, dehydrogenase pathway
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in a single enzymatic step." [GOC:mah, GOC:pr, MetaCyc:PWY-2942]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in a single enzymatic step." [GOC:mah, GOC:pr]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine anabolism via diaminopimelate, dehydrogenase pathway" EXACT []
synonym: "lysine biosynthesis via diaminopimelic acid, dehydrogenase pathway" EXACT []
synonym: "lysine formation via diaminopimelate, dehydrogenase pathway" EXACT []
synonym: "lysine synthesis via diaminopimelate, dehydrogenase pathway" EXACT []
-xref: MetaCyc:PWY-2942
-is_a: GO:0009089 ! L-lysine biosynthetic process via diaminopimelate
-relationship: has_part GO:0047850 ! diaminopimelate dehydrogenase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0033362
-name: L-lysine biosynthetic process via diaminopimelate, diaminopimelate-aminotransferase pathway
+name: obsolete L-lysine biosynthetic process via diaminopimelate, diaminopimelate-aminotransferase pathway
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in two enzymatic steps." [GOC:mah, GOC:pr, MetaCyc:PWY-5097]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in two enzymatic steps." [GOC:mah, GOC:pr]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine anabolism via diaminopimelate, diaminopimelate-aminotransferase pathway" EXACT []
synonym: "lysine biosynthesis via diaminopimelate, diaminopimelate-aminotransferase pathway" EXACT []
synonym: "lysine formation via diaminopimelate, diaminopimelate-aminotransferase pathway" EXACT []
synonym: "lysine synthesis via diaminopimelate, diaminopimelate-aminotransferase pathway" EXACT []
-xref: MetaCyc:PWY-5097
-is_a: GO:0009089 ! L-lysine biosynthetic process via diaminopimelate
-relationship: has_part GO:0008837 ! diaminopimelate epimerase activity
-relationship: has_part GO:0010285 ! L,L-diaminopimelate aminotransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0033363
@@ -205199,14 +208123,17 @@
synonym: "geranylgeranyl diphosphate biosynthesis" EXACT []
synonym: "geranylgeranyl diphosphate formation" EXACT []
synonym: "geranylgeranyl diphosphate synthesis" EXACT []
+xref: MetaCyc:PWY-5120
xref: MetaCyc:PWY-5121
xref: MetaCyc:PWY-5910
is_a: GO:0008654 ! phospholipid biosynthetic process
is_a: GO:0016114 ! terpenoid biosynthetic process
is_a: GO:0033385 ! geranylgeranyl diphosphate metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5120
property_value: skos:narrowMatch MetaCyc:PWY-5121
property_value: skos:narrowMatch MetaCyc:PWY-5910
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0033387
@@ -205296,38 +208223,44 @@
[Term]
id: GO:0033394
-name: beta-alanine biosynthetic process via 1,3 diaminopropane
+name: obsolete beta-alanine biosynthetic process via 1,3 diaminopropane
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 1,3 diaminopropane." [GOC:mah, MetaCyc:PWY-3981]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 1,3 diaminopropane." [GOC:mah]
+comment: The reason for merging is that this term represents a GO-CAM model.
synonym: "beta-alanine anabolism via 1,3 diaminopropane" EXACT []
synonym: "beta-alanine biosynthesis via 1,3 diaminopropane" EXACT []
synonym: "beta-alanine formation via 1,3 diaminopropane" EXACT []
synonym: "beta-alanine synthesis via 1,3 diaminopropane" EXACT []
-xref: MetaCyc:PWY-3981
-is_a: GO:0019483 ! beta-alanine biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019483
[Term]
id: GO:0033395
-name: beta-alanine biosynthetic process via 3-hydroxypropionate
+name: obsolete beta-alanine biosynthetic process via 3-hydroxypropionate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-hydroxypropionate." [GOC:mah, MetaCyc:PWY-3941]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-hydroxypropionate." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "beta-alanine anabolism via 3-hydroxypropionate" EXACT []
synonym: "beta-alanine biosynthesis via 3-hydroxypropionate" EXACT []
synonym: "beta-alanine formation via 3-hydroxypropionate" EXACT []
synonym: "beta-alanine synthesis via 3-hydroxypropionate" EXACT []
-xref: MetaCyc:PWY-3941
-is_a: GO:0019483 ! beta-alanine biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019483
[Term]
id: GO:0033396
-name: beta-alanine biosynthetic process via 3-ureidopropionate
+name: obsolete beta-alanine biosynthetic process via 3-ureidopropionate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-ureidopropionate." [GOC:mah, MetaCyc:PWY-3982]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of beta-alanine via the intermediate 3-ureidopropionate." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "beta-alanine anabolism via 3-ureidopropionate" EXACT []
synonym: "beta-alanine formation via 3-ureidopropionate" EXACT []
synonym: "beta-alanine synthesis via 3-ureidopropionate" EXACT []
-xref: MetaCyc:PWY-3982
-is_a: GO:0019483 ! beta-alanine biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019483
[Term]
id: GO:0033397
@@ -206180,7 +209113,11 @@
synonym: "UDP-D-galacturonate formation" EXACT []
synonym: "UDP-D-galacturonate synthesis" EXACT []
xref: MetaCyc:PWY-4
+xref: MetaCyc:PWY-4861
is_a: GO:0009226 ! nucleotide-sugar biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-4
+property_value: skos:narrowMatch MetaCyc:PWY-4861
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0033481
@@ -206290,7 +209227,6 @@
synonym: "cholesterol formation via desmosterol" EXACT []
synonym: "cholesterol synthesis via desmosterol" EXACT []
xref: MetaCyc:PWY66-4
-xref: Reactome:R-HSA-6807047 "Cholesterol biosynthesis via desmosterol"
is_a: GO:0006695 ! cholesterol biosynthetic process
[Term]
@@ -206303,7 +209239,6 @@
synonym: "cholesterol formation via lathosterol" EXACT []
synonym: "cholesterol synthesis via lathosterol" EXACT []
xref: MetaCyc:PWY66-341
-xref: Reactome:R-HSA-6807062 "Cholesterol biosynthesis via lathosterol"
is_a: GO:0006695 ! cholesterol biosynthetic process
[Term]
@@ -206505,31 +209440,44 @@
[Term]
id: GO:0033508
-name: L-glutamate catabolic process to pyruvate
+name: L-glutamate fermentation
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-glutamate into pyruvate." [MetaCyc:PWY-5087]
+def: "The anaerobic chemical reactions and pathways resulting in the breakdown of L-glutamate, yielding energy in the form of ATP." [PMID:38821505]
synonym: "glutamate breakdown to butyrate" EXACT []
synonym: "glutamate degradation to butyrate" EXACT []
+synonym: "L-glutamate catabolic process to pyruvate" NARROW []
+synonym: "L-glutamate fermentation to propionate" NARROW []
+synonym: "L-glutamate fermentation to pyruvate" NARROW []
+synonym: "L-glutamate fermentation via 2-hydroxyglutarate" NARROW []
+synonym: "L-glutamate fermentation via L-citramalate" NARROW []
+xref: MetaCyc:GLUDEG-II-PWY
+xref: MetaCyc:P162-PWY
xref: MetaCyc:PWY-5087
+xref: MetaCyc:PWY-5088
+xref: MetaCyc:PWY-8190
is_a: GO:0006090 ! pyruvate metabolic process
is_a: GO:0006538 ! L-glutamate catabolic process
is_a: GO:0019665 ! amino acid fermentation
+property_value: skos:narrowMatch MetaCyc:GLUDEG-II-PWY
+property_value: skos:narrowMatch MetaCyc:P162-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5087
+property_value: skos:narrowMatch MetaCyc:PWY-5088
+property_value: skos:narrowMatch MetaCyc:PWY-8190
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31218" xsd:anyURI
[Term]
id: GO:0033509
-name: L-glutamate fermentation to propionate
+name: obsolete L-glutamate fermentation to propionate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including propionate." [GOC:mah, MetaCyc:PWY-5088]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-glutamate into other compounds, including propionate." [GOC:mah]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "glutamate breakdown to propionate" EXACT []
synonym: "glutamate degradation to propionate" EXACT []
synonym: "L-glutamate catabolic process to propionate" EXACT []
-xref: MetaCyc:PWY-5088
-is_a: GO:0006538 ! L-glutamate catabolic process
-is_a: GO:0019541 ! propionate metabolic process
-is_a: GO:0019665 ! amino acid fermentation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0033508
[Term]
id: GO:0033510
@@ -206555,34 +209503,40 @@
[Term]
id: GO:0033512
-name: L-lysine catabolic process to acetyl-CoA via L-saccharopine
+name: obsolete L-lysine catabolic process to acetyl-CoA via L-saccharopine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-saccharopine." [GOC:mah, MetaCyc:LYSINE-DEG1-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-saccharopine." [GOC:mah, MetaCyc:LYSINE-DEG1-PWY]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-lysine breakdown to acetyl-CoA via saccharopine" EXACT []
synonym: "L-lysine degradation to acetyl-CoA via saccharopine" EXACT []
-is_a: GO:0006084 ! acetyl-CoA metabolic process
-is_a: GO:0019477 ! L-lysine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019477
[Term]
id: GO:0033513
-name: L-lysine catabolic process to acetyl-CoA via 5-aminopentanamide
+name: obsolete L-lysine catabolic process to acetyl-CoA via 5-aminopentanamide
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate 5-aminopentanamide." [GOC:mah, MetaCyc:PWY-5280]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate 5-aminopentanamide." [GOC:mah, MetaCyc:PWY-5280]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-lysine breakdown to acetyl-CoA via 5-aminopentanamide" EXACT []
synonym: "L-lysine degradation to acetyl-CoA via 5-aminopentanamide" EXACT []
-is_a: GO:0006084 ! acetyl-CoA metabolic process
-is_a: GO:0019477 ! L-lysine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019477
[Term]
id: GO:0033514
-name: L-lysine catabolic process to acetyl-CoA via L-pipecolate
+name: obsolete L-lysine catabolic process to acetyl-CoA via L-pipecolate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-pipecolate." [GOC:mah, MetaCyc:PWY66-425]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-pipecolate." [GOC:mah, MetaCyc:PWY66-425]
+comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
synonym: "L-lysine breakdown to acetyl-CoA via L-pipecolate" EXACT []
synonym: "L-lysine degradation to acetyl-CoA via L-pipecolate" EXACT []
-is_a: GO:0006084 ! acetyl-CoA metabolic process
-is_a: GO:0019477 ! L-lysine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019477
[Term]
id: GO:0033515
@@ -206607,7 +209561,7 @@
synonym: "L-methionine synthesis from homoserine via O-phospho-L-homoserine and cystathionine" EXACT [GOC:mah]
synonym: "methionine biosynthetic process from homoserine via O-phospho-L-homoserine and cystathionine" EXACT [GOC:mah]
is_obsolete: true
-replaced_by: GO:0019283
+replaced_by: GO:0071266
[Term]
id: GO:0033517
@@ -207058,10 +210012,12 @@
xref: Reactome:R-HSA-9701565 "HDACs deacetylate p-STAT3 dimers"
xref: Reactome:R-HSA-9825772 "SIRT1 deacetylates HINT1 dimer"
xref: Reactome:R-HSA-9841847 "SIRT3 deacetylates Ac-K272,K290-FOXO3"
+xref: RHEA:21548
xref: RHEA:58108
is_a: GO:0019213 ! deacetylase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:58108
+property_value: skos:narrowMatch RHEA:21548
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22833" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27528" xsd:anyURI
@@ -207169,7 +210125,7 @@
name: lactoferrin transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of lactoferrin from one side of a membrane to the other." [GOC:mlg]
-is_a: GO:0008320 ! protein transmembrane transporter activity
+is_a: GO:0008320 ! transmembrane protein transporter activity
relationship: part_of GO:0033571 ! lactoferrin transport
[Term]
@@ -207316,46 +210272,47 @@
[Term]
id: GO:0033584
-name: L-tyrosine biosynthetic process from chorismate via L-arogenate
+name: obsolete L-tyrosine biosynthetic process from chorismate via L-arogenate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-tyrosine from other compounds, including chorismate, via the intermediate L-arogenate." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-tyrosine from other compounds, including chorismate, via the intermediate L-arogenate." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "L-tyrosine anabolism from chorismate via L-arogenate" EXACT []
synonym: "L-tyrosine formation from chorismate via L-arogenate" EXACT []
synonym: "L-tyrosine synthesis from chorismate via L-arogenate" EXACT []
synonym: "tyrosine biosynthetic process from chorismate via L-arogenate" BROAD []
-xref: MetaCyc:PWY-3461
-is_a: GO:0006571 ! L-tyrosine biosynthetic process
-is_a: GO:0009095 ! aromatic amino acid family biosynthetic process, prephenate pathway
-is_a: GO:0046417 ! chorismate metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31091" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006571
[Term]
id: GO:0033585
-name: L-phenylalanine biosynthetic process from chorismate via phenylpyruvate
+name: obsolete L-phenylalanine biosynthetic process from chorismate via phenylpyruvate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate phenylpyruvate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate phenylpyruvate." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "L-phenylalanine anabolism from chorismate via phenylpyruvate" EXACT []
synonym: "L-phenylalanine biosynthesis from chorismate via phenylpyruvate" EXACT []
synonym: "L-phenylalanine formation from chorismate via phenylpyruvate" EXACT []
synonym: "L-phenylalanine synthesis from chorismate via phenylpyruvate" EXACT []
-xref: MetaCyc:PHESYN
-is_a: GO:0009094 ! L-phenylalanine biosynthetic process
-is_a: GO:0046417 ! chorismate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009094
[Term]
id: GO:0033586
-name: L-phenylalanine biosynthetic process from chorismate via L-arogenate
+name: obsolete L-phenylalanine biosynthetic process from chorismate via L-arogenate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate L-arogenate." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-phenylalanine from other compounds, including chorismate, via the intermediate L-arogenate." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "L-phenylalanine anabolism from chorismate via L-arogenate" EXACT []
synonym: "L-phenylalanine biosynthesis from chorismate via L-arogenate" EXACT []
synonym: "L-phenylalanine formation from chorismate via L-arogenate" EXACT []
synonym: "L-phenylalanine synthesis from chorismate via L-arogenate" EXACT []
-xref: MetaCyc:PWY-3462
-is_a: GO:0009094 ! L-phenylalanine biosynthetic process
-is_a: GO:0009095 ! aromatic amino acid family biosynthetic process, prephenate pathway
-is_a: GO:0046417 ! chorismate metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31091" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009094
[Term]
id: GO:0033588
@@ -208450,7 +211407,7 @@
id: GO:0033692
name: obsolete cellular polysaccharide biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides, polymers of many (typically more than 10) monosaccharide residues linked glycosidically, occurring at the level of an individual cell." [GOC:curators]
comment: This term was obsoleted because it is not different from its parent, polysaccharide biosynthetic process ; GO:0000271.
synonym: "cellular glycan biosynthesis" EXACT []
synonym: "cellular glycan biosynthetic process" EXACT []
@@ -208758,7 +211715,7 @@
id: GO:0033713
name: choline:oxygen 1-oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: choline + O2 = betaine aldehyde + hydrogen peroxide." [EC:1.1.3.17, RHEA:13505]
+def: "Catalysis of the reaction: choline + O2 = betaine aldehyde + H2O2." [EC:1.1.3.17, RHEA:13505]
synonym: "choline oxidase activity" BROAD [EC:1.1.3.17]
xref: EC:1.1.3.17
xref: MetaCyc:CHOLINE-OXIDASE-RXN
@@ -208780,9 +211737,13 @@
xref: KEGG_REACTION:R02277
xref: MetaCyc:SECONDARY-ALCOHOL-OXIDASE-RXN
xref: RHEA:23180
+xref: RHEA:68964
+xref: RHEA:68968
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.1.3.18
property_value: skos:exactMatch RHEA:23180
+property_value: skos:narrowMatch RHEA:68964
+property_value: skos:narrowMatch RHEA:68968
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -208803,7 +211764,7 @@
id: GO:0033716
name: nucleoside oxidase (hydrogen peroxide-forming) activity
namespace: molecular_function
-def: "Catalysis of the reactions: adenosine + 2 O2 = 9-riburonosyladenine + 2 hydrogen peroxide." [EC:1.1.3.39, RHEA:15489]
+def: "Catalysis of the reaction: adenosine + 2 O2 + H2O = 9-riburonosyladenine + 2 H2O2 + H+." [RHEA:15489]
comment: Two other reactions might be associated with this activity: (1a) adenosine + O2 = 5'-dehydroadenosine + hydrogen peroxide, and (1b) 5'-dehydroadenosine + O2 = 9-riburonosyladenine + hydrogen peroxide.
synonym: "nucleoside:oxygen 5'-oxidoreductase (hydrogen peroxide-forming) activity" RELATED [EC:1.1.3.39]
xref: EC:1.1.3.39
@@ -208906,9 +211867,45 @@
xref: EC:1.2.1.4
xref: MetaCyc:ALDEHYDE-DEHYDROGENASE-NADP+-RXN
xref: RHEA:11888
+xref: RHEA:28410
+xref: RHEA:30803
+xref: RHEA:34215
+xref: RHEA:47928
+xref: RHEA:60680
+xref: RHEA:60684
+xref: RHEA:60716
+xref: RHEA:60728
+xref: RHEA:60732
+xref: RHEA:60736
+xref: RHEA:60740
+xref: RHEA:62248
+xref: RHEA:68412
+xref: RHEA:72535
+xref: RHEA:72539
+xref: RHEA:76671
+xref: RHEA:80823
+xref: RHEA:81423
is_a: GO:0004030 ! aldehyde dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.2.1.4
property_value: skos:exactMatch RHEA:11888
+property_value: skos:narrowMatch RHEA:28410
+property_value: skos:narrowMatch RHEA:30803
+property_value: skos:narrowMatch RHEA:34215
+property_value: skos:narrowMatch RHEA:47928
+property_value: skos:narrowMatch RHEA:60680
+property_value: skos:narrowMatch RHEA:60684
+property_value: skos:narrowMatch RHEA:60716
+property_value: skos:narrowMatch RHEA:60728
+property_value: skos:narrowMatch RHEA:60732
+property_value: skos:narrowMatch RHEA:60736
+property_value: skos:narrowMatch RHEA:60740
+property_value: skos:narrowMatch RHEA:62248
+property_value: skos:narrowMatch RHEA:68412
+property_value: skos:narrowMatch RHEA:72535
+property_value: skos:narrowMatch RHEA:72539
+property_value: skos:narrowMatch RHEA:76671
+property_value: skos:narrowMatch RHEA:80823
+property_value: skos:narrowMatch RHEA:81423
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29544" xsd:anyURI
[Term]
@@ -209491,10 +212488,12 @@
xref: EC:1.14.20.5
xref: MetaCyc:RXN-8000
xref: RHEA:10448
+xref: RHEA:32755
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
relationship: part_of GO:0051553 ! flavone biosynthetic process
property_value: skos:exactMatch EC:1.14.20.5
property_value: skos:exactMatch RHEA:10448
+property_value: skos:narrowMatch RHEA:32755
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -209676,9 +212675,13 @@
xref: KEGG_REACTION:R07198
xref: MetaCyc:RXN-19645
xref: RHEA:57584
+xref: RHEA:57592
+xref: RHEA:57596
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: skos:exactMatch EC:1.14.14.162
property_value: skos:exactMatch RHEA:57584
+property_value: skos:narrowMatch RHEA:57592
+property_value: skos:narrowMatch RHEA:57596
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25989" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -209693,10 +212696,16 @@
xref: EC:1.14.14.81
xref: MetaCyc:RXN-13192
xref: RHEA:55448
+xref: RHEA:61104
+xref: RHEA:61108
+xref: RHEA:61120
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.14.81
property_value: skos:exactMatch MetaCyc:RXN-13192
property_value: skos:exactMatch RHEA:55448
+property_value: skos:narrowMatch RHEA:61104
+property_value: skos:narrowMatch RHEA:61108
+property_value: skos:narrowMatch RHEA:61120
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
[Term]
@@ -209710,9 +212719,13 @@
xref: EC:1.14.14.90
xref: MetaCyc:RXN-11846
xref: RHEA:18849
+xref: RHEA:53208
+xref: RHEA:56108
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: skos:exactMatch EC:1.14.14.90
property_value: skos:exactMatch RHEA:18849
+property_value: skos:narrowMatch RHEA:53208
+property_value: skos:narrowMatch RHEA:56108
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28183" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -209782,9 +212795,6 @@
namespace: molecular_function
def: "OBSOLETE. 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]
comment: This term was obsoleted because it represents a specific susbstrate of sterol 12-alpha-hydroxylase activity ; GO:0008397.
-xref: Reactome:R-HSA-192157 "CYP8B1 12-hydroxylates 4CHOL7aOLONE"
-xref: Reactome:R-HSA-193709 "CYP8B1 12-hydroxylates 4CHOL7a,24(S)DIOL"
-xref: Reactome:R-HSA-193845 "CYP8B1 12-hydroxylates 4CHOL7a,27DONE"
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
is_obsolete: true
@@ -209794,7 +212804,7 @@
id: GO:0033779
name: obsolete 5-beta-cholestane-3-alpha,7-alpha-diol 12-alpha-hydroxylase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: 5beta-cholestane-3alpha,7alpha-diol + H+ + NADPH + O2 = 5beta-cholestane-3alpha,7alpha,12alpha-triol + H2O + NADP+." [GOC:curator]
+def: "OBSOLETE. Catalysis of the reaction: 5beta-cholestane-3alpha,7alpha-diol + H+ + NADPH + O2 = 5beta-cholestane-3alpha,7alpha,12alpha-triol + H2O + NADP+." [GOC:curators]
comment: This term was obsoleted because it represents a specific susbstrate of sterol 12-alpha-hydroxylase activity ; GO:0008397.
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
@@ -210022,10 +213032,18 @@
synonym: "bile-acid 7alpha-dehydroxylase activity" RELATED []
synonym: "cholate 7alpha-dehydroxylase activity" RELATED []
xref: EC:1.1.1.395
+xref: RHEA:52584
+xref: RHEA:52588
+xref: RHEA:52592
+xref: RHEA:52596
xref: RHEA:55380
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.395
property_value: skos:exactMatch RHEA:55380
+property_value: skos:narrowMatch RHEA:52584
+property_value: skos:narrowMatch RHEA:52588
+property_value: skos:narrowMatch RHEA:52592
+property_value: skos:narrowMatch RHEA:52596
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22749" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -210106,10 +213124,14 @@
xref: KEGG_REACTION:R07229
xref: MetaCyc:RXN0-2101
xref: RHEA:14029
+xref: RHEA:51636
+xref: RHEA:80603
xref: UM-BBD_reactionID:r0828
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.97.1.9
property_value: skos:exactMatch RHEA:14029
+property_value: skos:narrowMatch RHEA:51636
+property_value: skos:narrowMatch RHEA:80603
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -210125,6 +213147,7 @@
synonym: "type III iodothyronine deiodinase activity" NARROW [EC:1.21.99.3]
xref: EC:1.21.99.3
xref: MetaCyc:1.97.1.11-RXN
+xref: Reactome:R-HSA-350869 "Thyroxine is deiodinated to reverse triiodothyronine (RT3)"
xref: RHEA:18897
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
property_value: skos:exactMatch EC:1.21.99.3
@@ -210171,7 +213194,7 @@
id: GO:0033801
name: vitexin 2''-O-rhamnoside 7-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + vitexin 2''-O-beta-L-rhamnoside = S-adenosyl-L-homocysteine + 7-O-methylvitexin 2''-O-beta-L-rhamnoside." [EC:2.1.1.153]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + vitexin 2''-O-beta-L-rhamnoside = S-adenosyl-L-homocysteine + 7-O-methylvitexin 2''-O-beta-L-rhamnoside." [RHEA:11432]
synonym: "S-adenosyl-L-methionine:vitexin-2''-O-beta-L-rhamnoside 7-O-methyltransferase activity" RELATED [EC:2.1.1.153]
xref: EC:2.1.1.153
xref: MetaCyc:RXN-4981
@@ -210865,10 +213888,12 @@
xref: EC:2.4.1.244
xref: MetaCyc:2.4.1.244-RXN
xref: RHEA:20493
+xref: RHEA:86247
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.244
property_value: skos:exactMatch MetaCyc:2.4.1.244-RXN
property_value: skos:exactMatch RHEA:20493
+property_value: skos:narrowMatch RHEA:86247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18752" xsd:anyURI
[Term]
@@ -211009,14 +214034,15 @@
[Term]
id: GO:0033852
-name: thyroid-hormone transaminase activity
+name: thyroid-hormone:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + 3,5,3'-triiodo-L-thyronine = 3,5,3'-triiodothyropyruvate + L-glutamate." [EC:2.6.1.26, RHEA:19133]
+def: "Catalysis of the reaction: 3,3',5-triiodo-L-thyronine + 2-oxoglutarate = 3,5,3'-triiodothyropyruvate + L-glutamate." [RHEA:19133]
synonym: "3,5-dinitrotyrosine aminotransferase activity" RELATED [EC:2.6.1.26]
synonym: "3,5-dinitrotyrosine transaminase activity" RELATED [EC:2.6.1.26]
synonym: "L-3,5,3'-triiodothyronine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.26]
synonym: "thyroid hormone aminotransferase activity" RELATED [EC:2.6.1.26]
synonym: "thyroid-hormone aminotransferase activity" RELATED [EC:2.6.1.26]
+synonym: "thyroid-hormone transaminase activity" BROAD []
xref: EC:2.6.1.26
xref: KEGG_REACTION:R03952
xref: MetaCyc:THYROID-HORMONE-AMINOTRANSFERASE-RXN
@@ -211025,12 +214051,14 @@
property_value: skos:exactMatch EC:2.6.1.26
property_value: skos:exactMatch RHEA:19133
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0033853
-name: aspartate-prephenate aminotransferase activity
+name: L-aspartate:prephenate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-arogenate + oxaloacetate = prephenate + L-aspartate." [RHEA:20445]
+synonym: "aspartate-prephenate aminotransferase activity" EXACT []
synonym: "L-arogenate:oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.78]
synonym: "L-aspartate:prephenate aminotransferase activity" RELATED [EC:2.6.1.78]
synonym: "PAT" RELATED [EC:2.6.1.78]
@@ -211039,16 +214067,18 @@
xref: EC:2.6.1.78
xref: MetaCyc:PREPHENATE-ASP-TRANSAMINE-RXN
xref: RHEA:20445
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.78
property_value: skos:exactMatch RHEA:20445
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0033854
-name: glutamate-prephenate aminotransferase activity
+name: L-glutamate:prephenate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-arogenate = L-glutamate + prephenate." [EC:2.6.1.79, RHEA:22880]
+def: "Catalysis of the reaction: 2-oxoglutarate + L-arogenate = L-glutamate + prephenate." [RHEA:22880]
+synonym: "glutamate-prephenate aminotransferase activity" EXACT []
synonym: "L-arogenate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.79]
synonym: "L-glutamate:prephenate aminotransferase activity" RELATED [EC:2.6.1.79]
synonym: "PAT" RELATED [EC:2.6.1.79]
@@ -211057,20 +214087,22 @@
xref: KEGG_REACTION:R07276
xref: MetaCyc:PREPHENATE-TRANSAMINE-RXN
xref: RHEA:22880
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.79
property_value: skos:exactMatch RHEA:22880
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0033855
-name: nicotianamine aminotransferase activity
+name: nicotianamine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + nicotianamine = 3''-deamino-3''-oxonicotianamine + L-glutamate." [EC:2.6.1.80, RHEA:22104]
+def: "Catalysis of the reaction: nicotianamine + 2-oxoglutarate = 3''-deamino-3''-oxonicotianamine + L-glutamate." [RHEA:22104]
synonym: "NAAT" RELATED [EC:2.6.1.80]
synonym: "NAAT-I" RELATED [EC:2.6.1.80]
synonym: "NAAT-II" RELATED [EC:2.6.1.80]
synonym: "NAAT-III" RELATED [EC:2.6.1.80]
+synonym: "nicotianamine aminotransferase activity" EXACT []
synonym: "nicotianamine transaminase activity" RELATED [EC:2.6.1.80]
synonym: "nicotianamine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.80]
xref: EC:2.6.1.80
@@ -211081,6 +214113,7 @@
property_value: skos:exactMatch EC:2.6.1.80
property_value: skos:exactMatch RHEA:22104
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0033856
@@ -212034,6 +215067,8 @@
xref: Reactome:R-HSA-548890 "Removal of the third glucose by glucosidase II and release from the chaperone"
xref: Reactome:R-HSA-9683663 "N-glycan trimming of Spike"
xref: Reactome:R-HSA-9694364 "N-glycan glucose trimming of Spike"
+xref: Reactome:R-HSA-9932352 "Glucosidase II removes glucose residue from Glu2Man9GlucNAc2-CDH1"
+xref: Reactome:R-HSA-9932913 "Glucosidase II removes glucose residue from Glu1Man9GlucNAc2-CDH1"
is_a: GO:0090599 ! alpha-glucosidase activity
property_value: skos:exactMatch EC:3.2.1.84
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -212051,9 +215086,11 @@
xref: EC:3.2.1.85
xref: MetaCyc:6-PHOSPHO-BETA-GALACTOSIDASE-RXN
xref: RHEA:24568
+xref: RHEA:42404
is_a: GO:0015925 ! galactosidase activity
property_value: skos:exactMatch EC:3.2.1.85
property_value: skos:exactMatch RHEA:24568
+property_value: skos:narrowMatch RHEA:42404
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -214092,7 +217129,6 @@
synonym: "negative regulation by symbiont of plant hypersensitive response" NARROW [GOC:pamgo_curators]
synonym: "suppression by symbiont of host defense-related programmed cell death" EXACT []
synonym: "suppression of HR" NARROW [GOC:pamgo_curators]
-xref: Reactome:R-HSA-9636569 "Suppression of autophagy"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29278" xsd:anyURI
is_obsolete: true
replaced_by: GO:0052041
@@ -214166,10 +217202,14 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)." [RHEA:22508]
xref: RHEA:22508
+xref: RHEA:67728
+xref: RHEA:86319
is_a: GO:0016779 ! nucleotidyltransferase activity
is_a: GO:0140097 ! catalytic activity, acting on DNA
relationship: part_of GO:0071897 ! DNA biosynthetic process
property_value: skos:exactMatch RHEA:22508
+property_value: skos:narrowMatch RHEA:67728
+property_value: skos:narrowMatch RHEA:86319
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28442" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30036" xsd:anyURI
@@ -215792,7 +218832,7 @@
id: GO:0034203
name: glycolipid translocation
namespace: biological_process
-def: "The translocation, or flipping, of glycolipid molecules from one monolayer of a membrane bilayer to the opposite monolayer." [GOC:go_curators, PMID:11807558]
+def: "The translocation, or flipping, of glycolipid molecules from one monolayer of a membrane bilayer to the opposite monolayer." [GOC:curators, PMID:11807558]
is_a: GO:0034204 ! lipid translocation
is_a: GO:0046836 ! glycolipid transport
@@ -216143,7 +219183,7 @@
def: "Binding to a glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes." [GOC:vw]
comment: Note that this term should be used to annotate gene products that interact non-covalently with GPI anchors, and not proteins that have GPI anchors covalently attached.
synonym: "glycosylphosphatidylinositol binding" EXACT []
-is_a: GO:0035091 ! phosphatidylinositol binding
+is_a: GO:0005543 ! phospholipid binding
is_a: GO:0051861 ! glycolipid binding
[Term]
@@ -216169,7 +219209,7 @@
name: macrophage fusion
namespace: biological_process
def: "The binding and fusion of a macrophage to one or more other cells to form a multinucleated cell." [GOC:sl]
-is_a: GO:0000768 ! syncytium formation by plasma membrane fusion
+is_a: GO:0000768 ! syncytium formation by cell-cell fusion
[Term]
id: GO:0034239
@@ -216208,12 +219248,11 @@
name: negative regulation of syncytium formation by plasma membrane fusion
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mah]
-is_a: GO:0051093 ! negative regulation of developmental process
is_a: GO:0051129 ! negative regulation of cellular component organization
is_a: GO:0060142 ! regulation of syncytium formation by plasma membrane fusion
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0000768 ! syncytium formation by plasma membrane fusion
-relationship: negatively_regulates GO:0000768 ! syncytium formation by plasma membrane fusion
+intersection_of: negatively_regulates GO:0000768 ! syncytium formation by cell-cell fusion
+relationship: negatively_regulates GO:0000768 ! syncytium formation by cell-cell fusion
[Term]
id: GO:0034243
@@ -216519,30 +219558,28 @@
[Term]
id: GO:0034268
-name: discadenine biosynthetic process
+name: obsolete discadenine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of discadenine, (2S)-2-amino-4-{6-[(3-methylbut-2-en-1-yl)amino]-3H-purin-3-yl}butanoic acid." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of discadenine, (2S)-2-amino-4-{6-[(3-methylbut-2-en-1-yl)amino]-3H-purin-3-yl}butanoic acid." [GOC:mah]
+comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
synonym: "discadenine anabolism" EXACT []
synonym: "discadenine biosynthesis" EXACT []
synonym: "discadenine formation" EXACT []
synonym: "discadenine synthesis" EXACT []
-is_a: GO:0009691 ! cytokinin biosynthetic process
-is_a: GO:0072522 ! purine-containing compound biosynthetic process
-is_a: GO:0170034 ! L-amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034269
-name: discadenine catabolic process
+name: obsolete discadenine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of discadenine, (2S)-2-amino-4-{6-[(3-methylbut-2-en-1-yl)amino]-3H-purin-3-yl}butanoic acid." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of discadenine, (2S)-2-amino-4-{6-[(3-methylbut-2-en-1-yl)amino]-3H-purin-3-yl}butanoic acid." [GOC:mah]
+comment: This term was obsoleted because there is no evidence that a specific pathway for discadenine degradation exists.
synonym: "discadenine breakdown" EXACT []
synonym: "discadenine catabolism" EXACT []
synonym: "discadenine degradation" EXACT []
-is_a: GO:0009823 ! cytokinin catabolic process
-is_a: GO:0072523 ! purine-containing compound catabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034270
@@ -217445,24 +220482,29 @@
synonym: "NAD biosynthetic process via the salvage pathway" EXACT []
synonym: "NAD salvage" EXACT []
synonym: "NAD salvage pathway" EXACT []
+xref: MetaCyc:NAD-BIOSYNTHESIS-II
xref: MetaCyc:NAD-BIOSYNTHESIS-III
xref: MetaCyc:PWY-5381
xref: MetaCyc:PWY-7761
xref: MetaCyc:PWY-8511
+xref: MetaCyc:PWY3O-4106
xref: MetaCyc:PWY3O-4107
xref: MetaCyc:PYRIDNUCSAL-PWY
is_a: GO:0009435 ! NAD+ biosynthetic process
is_a: GO:0019365 ! pyridine nucleotide salvage
is_a: GO:0032261 ! purine nucleotide salvage
+property_value: skos:narrowMatch MetaCyc:NAD-BIOSYNTHESIS-II
property_value: skos:narrowMatch MetaCyc:NAD-BIOSYNTHESIS-III
property_value: skos:narrowMatch MetaCyc:PWY-5381
property_value: skos:narrowMatch MetaCyc:PWY-7761
property_value: skos:narrowMatch MetaCyc:PWY-8511
+property_value: skos:narrowMatch MetaCyc:PWY3O-4106
property_value: skos:narrowMatch MetaCyc:PWY3O-4107
property_value: skos:narrowMatch MetaCyc:PYRIDNUCSAL-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21577" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29050" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29666" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0034356
@@ -217472,8 +220514,6 @@
comment: This term was obsoleted because it is the unique child class of NAD biosynthetic process via the salvage pathway ; GO:0034355.
synonym: "nicotinamide riboside salvage pathway" EXACT []
synonym: "NR salvage pathway" EXACT []
-xref: MetaCyc:PWY3O-4106
-xref: Reactome:R-HSA-197264 "Nicotinamide salvaging"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29050" xsd:anyURI
is_obsolete: true
replaced_by: GO:0034355
@@ -217491,8 +220531,8 @@
name: plasma lipoprotein particle
namespace: cellular_component
def: "A spherical particle with a hydrophobic core of triglycerides and/or cholesterol esters, surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Plasma lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood or lymph." [GOC:BHF, GOC:expert_pt, GOC:rl]
+is_a: GO:0140392 ! extracellular protein-containing complex
is_a: GO:1990777 ! lipoprotein particle
-relationship: part_of GO:0005615 ! extracellular space
[Term]
id: GO:0034359
@@ -217786,6 +220826,7 @@
synonym: "gamma-aminobutyric acid-alpha-ketoglutaric acid aminotransferase activity" RELATED [EC:2.6.1.19]
xref: EC:2.6.1.19
xref: MetaCyc:GABATRANSAM-RXN
+xref: Reactome:R-HSA-916855 "PXLP-K357-ABAT dimer:2Fe-2S transforms GABA to SUCCSA"
xref: RHEA:23352
is_a: GO:0008483 ! transaminase activity
property_value: skos:exactMatch EC:2.6.1.19
@@ -218782,9 +221823,15 @@
xref: MetaCyc:PHOSPHOLIPASE-C-RXN
xref: Reactome:R-HSA-9680388 "CSF1R-associated PLCG2 hydrolyzes phosphatidylcholine"
xref: RHEA:10604
+xref: RHEA:45304
+xref: RHEA:78939
+xref: RHEA:78947
is_a: GO:0004629 ! C-type glycerophospholipase activity
property_value: skos:exactMatch EC:3.1.4.3
property_value: skos:exactMatch RHEA:10604
+property_value: skos:narrowMatch RHEA:45304
+property_value: skos:narrowMatch RHEA:78939
+property_value: skos:narrowMatch RHEA:78947
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30949" xsd:anyURI
@@ -218806,6 +221853,7 @@
synonym: "chondroitin 2-O-sulfotransferase activity" EXACT []
synonym: "chondroitin 2-O-sulphotransferase activity" EXACT []
xref: MetaCyc:RXN-11560
+xref: Reactome:R-HSA-9941305 "UST transfers sulfate to (2-)GlcA-GalNAc-6-sulfate"
is_a: GO:0034481 ! chondroitin sulfotransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28380" xsd:anyURI
@@ -218838,10 +221886,14 @@
xref: MetaCyc:RXN-10036
xref: Reactome:R-HSA-1675949 "PI(3,4,5)P3 is dephosphorylated to PI(3,4)P2 by INPP5[2] at the plasma membrane"
xref: RHEA:25528
+xref: RHEA:43548
+xref: RHEA:43556
is_a: GO:0034594 ! phosphatidylinositol trisphosphate phosphatase activity
is_a: GO:0034595 ! phosphatidylinositol phosphate 5-phosphatase activity
property_value: skos:exactMatch EC:3.1.3.86
property_value: skos:exactMatch RHEA:25528
+property_value: skos:narrowMatch RHEA:43548
+property_value: skos:narrowMatch RHEA:43556
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25279" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -219379,31 +222431,37 @@
[Term]
id: GO:0034547
-name: N-cyclopropylmelamine deaminase activity
+name: obsolete N-cyclopropylmelamine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyromazine + H2O = N-cyclopropylammeline + NH3." [UM-BBD_reactionID:r0825]
+def: "OBSOLETE. Catalysis of the reaction: cyromazine + H2O = N-cyclopropylammeline + NH3." [UM-BBD_reactionID:r0825]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: MetaCyc:RXN-8018
xref: UM-BBD_reactionID:r0825
-is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034548
-name: N-cyclopropylammeline deaminase activity
+name: obsolete N-cyclopropylammeline deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-cyclopropylammeline + H2O = N-cyclopropylammelide + NH3." [UM-BBD_reactionID:r0826]
+def: "OBSOLETE. Catalysis of the reaction: N-cyclopropylammeline + H2O = N-cyclopropylammelide + NH3." [UM-BBD_reactionID:r0826]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: MetaCyc:RXN-8019
xref: UM-BBD_reactionID:r0826
-is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034549
-name: N-cyclopropylammelide alkylamino hydrolase activity
+name: obsolete N-cyclopropylammelide alkylamino hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-cyclopropylammelide + H2O = cyclopropylamine + cyanuric acid." [UM-BBD_reactionID:r0827]
+def: "OBSOLETE. Catalysis of the reaction: N-cyclopropylammelide + H2O = cyclopropylamine + cyanuric acid." [UM-BBD_reactionID:r0827]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: KEGG_REACTION:R06972
xref: MetaCyc:RXN-8020
xref: UM-BBD_reactionID:r0827
-is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034550
@@ -219472,13 +222530,13 @@
[Term]
id: GO:0034557
-name: 2-hydroxylaminobenzoate reductase activity
+name: obsolete 2-hydroxylaminobenzoate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxylaminobenzoate + NAD(P)H = anthranilate + NAD(P)+ + H2O." [MetaCyc:RXN-8848]
+def: "OBSOLETE. Catalysis of the reaction: 2-hydroxylaminobenzoate + NAD(P)H = anthranilate + NAD(P)+ + H2O." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "o-hydroxylaminobenzoate nitroreductase activity" RELATED [UM-BBD_reactionID:r0850]
-xref: MetaCyc:RXN-8848
-xref: UM-BBD_reactionID:r0850
-is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034558
@@ -219985,8 +223043,6 @@
def: "OBSOLETE. Catalysis of the exonucleolytic cleavage of oligoribonucleotides to yield ribonucleoside 5'-phosphates." [GOC:mah]
comment: This term was obsoleted because it corresponds to an assay.
synonym: "RNA oligonucleotidase activity" EXACT []
-xref: Reactome:R-HSA-9009950 "PDE12 cleaves 2'-5' oligoadenylates"
-xref: Reactome:R-HSA-9615042 "Viral 2',5'-PDE cleaves 2'-5' oligoadenylates"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24408" xsd:anyURI
is_obsolete: true
@@ -220038,6 +223094,7 @@
synonym: "H4biopterin binding" EXACT []
synonym: "sapropterin binding" EXACT []
xref: Reactome:R-HSA-1497784 "The cofactor BH4 is required for electron transfer in the eNOS catalytic cycle"
+xref: Reactome:R-HSA-1497796 "BH2 binding can lead to eNOS uncoupling"
is_a: GO:0005488 ! binding
[Term]
@@ -220411,18 +223468,21 @@
name: nucleobase-containing compound biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah]
+subset: gocheck_do_not_annotate
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid anabolism" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid formation" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0009058 ! biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
[Term]
id: GO:0034655
name: nucleobase-containing compound catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah]
+subset: gocheck_do_not_annotate
subset: goslim_chembl
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb]
@@ -220430,6 +223490,7 @@
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT []
is_a: GO:0006139 ! nucleobase-containing compound metabolic process
is_a: GO:0009056 ! catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
[Term]
id: GO:0034656
@@ -220570,7 +223631,7 @@
id: GO:0034670
name: chemotaxis to arachidonate
namespace: biological_process
-def: "The directed movement of a motile cell or organism in response to the presence of arachidonic acid." [GOC:go_curators, PMID:18202452]
+def: "The directed movement of a motile cell or organism in response to the presence of arachidonic acid." [GOC:curators, PMID:18202452]
synonym: "chemotaxis to arachidonic acid" EXACT []
is_a: GO:0006935 ! chemotaxis
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI
@@ -221082,10 +224143,12 @@
name: piecemeal microautophagy of the nucleus
namespace: biological_process
def: "Degradation of a cell nucleus by microautophagy." [GOC:autophagy, GOC:jp, PMID:18701704]
+synonym: "micronucleophagy" BROAD [PMID:18701704]
synonym: "PMN" EXACT []
is_a: GO:0016237 ! microautophagy
is_a: GO:0044804 ! nucleophagy
relationship: has_part GO:1905690 ! nucleus disassembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31715" xsd:anyURI
[Term]
id: GO:0034728
@@ -221172,8 +224235,28 @@
xref: MetaCyc:STEROL-O-ACYLTRANSFERASE-RXN
xref: Reactome:R-HSA-8876696 "SOAT1,2 transfer acyl group to CHOL forming CHEST"
xref: RHEA:17729
+xref: RHEA:41436
+xref: RHEA:42792
+xref: RHEA:42796
+xref: RHEA:42812
+xref: RHEA:42816
+xref: RHEA:46612
+xref: RHEA:46620
+xref: RHEA:64320
+xref: RHEA:64324
+xref: RHEA:64328
is_a: GO:0004772 ! sterol O-acyltransferase activity
property_value: skos:exactMatch RHEA:17729
+property_value: skos:narrowMatch RHEA:41436
+property_value: skos:narrowMatch RHEA:42792
+property_value: skos:narrowMatch RHEA:42796
+property_value: skos:narrowMatch RHEA:42812
+property_value: skos:narrowMatch RHEA:42816
+property_value: skos:narrowMatch RHEA:46612
+property_value: skos:narrowMatch RHEA:46620
+property_value: skos:narrowMatch RHEA:64320
+property_value: skos:narrowMatch RHEA:64324
+property_value: skos:narrowMatch RHEA:64328
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -221300,7 +224383,7 @@
def: "A protein complex that acts as an aryl hydrocarbon (Ah) receptor. Cytosolic and nuclear Ah receptor complexes have different subunit composition, but both contain the ligand-binding subunit AhR." [GOC:mah, PMID:7598497]
synonym: "AhR complex" EXACT []
synonym: "AHRC" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
@@ -222091,13 +225174,12 @@
[Term]
id: GO:0034823
-name: citronellyl-CoA ligase activity
+name: obsolete citronellyl-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: citronellate + CoASH + ATP = citronellyl-CoA + AMP + PPi." [UM-BBD_reactionID:r1157]
-xref: KEGG_REACTION:R08088
-xref: UM-BBD_reactionID:r1157
-is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
+def: "OBSOLETE. Catalysis of the reaction: citronellate + CoASH + ATP = citronellyl-CoA + AMP + PPi." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034824
@@ -222571,11 +225653,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O." [RHEA:47148]
xref: EC:1.17.5.2
+xref: RHEA:27902
xref: RHEA:47148
xref: UM-BBD_reactionID:r1321
is_a: GO:0033695 ! oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.17.5.2
property_value: skos:exactMatch RHEA:47148
+property_value: skos:narrowMatch RHEA:27902
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -222916,12 +226000,12 @@
[Term]
id: GO:0034912
-name: phthalate 3,4-cis-dihydrodiol dehydrogenase activity
+name: obsolete phthalate 3,4-cis-dihydrodiol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phthalate 3,4-cis-dihydrodiol + NAD+ = 3,4-dihydroxyphthalate + NADH + H+." [UM-BBD_reactionID:r1445]
-xref: MetaCyc:RXN5F9-56
-xref: UM-BBD_reactionID:r1445
-is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: phthalate 3,4-cis-dihydrodiol + NAD+ = 3,4-dihydroxyphthalate + NADH + H+." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0034914
@@ -224199,7 +227283,7 @@
id: GO:0035050
name: embryonic heart tube development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field." [GOC:curators]
is_a: GO:0035295 ! tube development
is_a: GO:0060429 ! epithelium development
relationship: part_of GO:0007507 ! heart development
@@ -224494,9 +227578,10 @@
id: GO:0035091
name: phosphatidylinositol binding
namespace: molecular_function
-def: "Binding to an inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, ISBN:0198506732, PMID:11395417]
+def: "Binding to an inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [PMID:11395417]
synonym: "phosphoinositide binding" EXACT []
-is_a: GO:0005543 ! phospholipid binding
+is_a: GO:0043168 ! anion binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0035092
@@ -224891,7 +227976,7 @@
name: forelimb morphogenesis
namespace: biological_process
alt_id: GO:0035140
-def: "The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." [GOC:go_curators]
+def: "The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." [GOC:curators]
synonym: "arm morphogenesis" NARROW [GOC:bf, GOC:cjm]
is_a: GO:0035108 ! limb morphogenesis
@@ -224899,7 +227984,7 @@
id: GO:0035137
name: hindlimb morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the hindlimb are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the hindlimb are generated and organized." [GOC:curators]
is_a: GO:0035108 ! limb morphogenesis
[Term]
@@ -226015,9 +229100,13 @@
id: GO:0035248
name: alpha-1,4-N-acetylgalactosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an N-acetyl-beta-D-galactosaminyl derivative + UDP-N-acetyl-alpha-D-galactosamine = an N-acetyl-alpha-D-galactosaminyl-(1->4)-N-acetyl-beta-D-galactosaminyl derivative + UDP + H+." [PMID:15130086]
+def: "Catalysis of the reaction: an N-acetyl-beta-D-galactosaminyl derivative + UDP-N-acetyl-alpha-D-galactosamine = an N-acetyl-alpha-D-galactosaminyl-(1->4)-N-acetyl-beta-D-galactosaminyl derivative + UDP + H+." [PMID:15130086, RHEA:86251]
synonym: "alpha-1,4-GalNAc transferase activity" EXACT []
+xref: RHEA:86251
+xref: RHEA:86255
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
+property_value: skos:exactMatch RHEA:86251
+property_value: skos:narrowMatch RHEA:86255
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31147" xsd:anyURI
[Term]
@@ -226051,9 +229140,8 @@
name: UDP-xylosyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a xylosyl group from UDP-xylose to an acceptor molecule." [PMID:30127001]
-xref: Reactome:R-HSA-5617138 "B4GAT1:GYLTL1B transfers Xyl from UDP-Xyl to GlcA-Xyl-GlcA"
xref: Reactome:R-HSA-6785668 "Defective LARGE does not transfer Xyl from UDP-Xyl to GlcA"
-xref: Reactome:R-HSA-9638090 "B4GAT1:LARGE transfers Xyl from UDP-Xyl to GlcA-Xyl-GlcA"
+xref: Reactome:R-HSA-9638090 "LARGE1,2 elongates matriglycan chain with Xyl"
is_a: GO:0008194 ! UDP-glycosyltransferase activity
is_a: GO:0042285 ! xylosyltransferase activity
@@ -227284,6 +230372,7 @@
namespace: molecular_function
def: "Binding to a selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation." [GOC:imk, PMID:10760958]
synonym: "SECIS binding" EXACT []
+xref: Reactome:R-HSA-2408529 "Sec-tRNA(Sec):EEFSEC:GTP binds to 80S Ribosome"
is_a: GO:0003729 ! mRNA binding
created_by: bf
creation_date: 2010-03-11T10:42:28Z
@@ -227410,12 +230499,14 @@
[Term]
id: GO:0035380
-name: very long-chain-3-hydroxyacyl-CoA dehydrogenase activity
+name: very long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD(P)+ = 3-oxoacyl-CoA + NAD(P)H + H+, where the acyl group is a very long-chain fatty acid residue. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons." [GOC:pde]
+def: "Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD(P)+ = 3-oxoacyl-CoA + NAD(P)H + H+, where the acyl group is a very long-chain fatty acid residue. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons." [RHEA:78927]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+synonym: "very long-chain-3-hydroxyacyl-CoA dehydrogenase activity" BROAD []
synonym: "very-long-chain-3-hydroxyacyl-CoA dehydrogenase activity" EXACT []
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+xref: RHEA:78927
+is_a: GO:0003857 ! (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
created_by: bf
creation_date: 2010-03-18T11:23:05Z
@@ -228027,6 +231118,7 @@
def: "The process in which a phosphate is transported across a membrane." [GOC:vw]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "phosphate ion membrane transport" EXACT []
+xref: Reactome:R-HSA-427652 "Sodium-coupled phosphate cotransporters"
is_a: GO:0006817 ! phosphate ion transport
is_a: GO:0055085 ! transmembrane transport
created_by: bf
@@ -228806,9 +231898,11 @@
synonym: "carnosine biosynthesis" EXACT []
synonym: "carnosine formation" EXACT []
synonym: "carnosine synthesis" EXACT []
+xref: MetaCyc:PWY66-420
is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0035498 ! carnosine metabolic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
created_by: bf
creation_date: 2010-04-29T01:20:56Z
@@ -228858,7 +231952,7 @@
id: GO:0035504
name: obsolete regulation of myosin light chain kinase activity
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22455" xsd:anyURI
is_obsolete: true
@@ -228869,7 +231963,7 @@
id: GO:0035505
name: obsolete positive regulation of myosin light chain kinase activity
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22455" xsd:anyURI
is_obsolete: true
@@ -228880,7 +231974,7 @@
id: GO:0035506
name: obsolete negative regulation of myosin light chain kinase activity
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of myosin light chain kinase activity." [GOC:bf, GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28482" xsd:anyURI
is_obsolete: true
@@ -228891,7 +231985,7 @@
id: GO:0035507
name: obsolete regulation of myosin-light-chain-phosphatase activity
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:curators]
comment: The reason for obsoletion is that this term represents a single-step process (regulation of MF).
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28499" xsd:anyURI
is_obsolete: true
@@ -228902,7 +231996,7 @@
id: GO:0035508
name: obsolete positive regulation of myosin-light-chain-phosphatase activity
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:curators]
comment: The reason for obsoletion is that this term represents a single-step process (regulation of MF).
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28499" xsd:anyURI
is_obsolete: true
@@ -228913,7 +232007,7 @@
id: GO:0035509
name: obsolete negative regulation of myosin-light-chain-phosphatase activity
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of myosin-light-chain-phosphatase activity." [GOC:bf, GOC:curators]
comment: The reason for obsoletion is that this term represents a single-step process (regulation of MF).
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28499" xsd:anyURI
is_obsolete: true
@@ -229010,10 +232104,18 @@
xref: Reactome:R-HSA-112118 "Oxidative demethylation of 1-meA damaged DNA by ALKBH2"
xref: Reactome:R-HSA-112123 "Oxidative demethylation of 1-meA damaged DNA By ALKBH3"
xref: RHEA:30299
+xref: RHEA:70435
+xref: RHEA:70439
+xref: RHEA:70443
+xref: RHEA:70447
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0035514 ! DNA demethylase activity
property_value: skos:exactMatch EC:1.14.11.33
property_value: skos:exactMatch RHEA:30299
+property_value: skos:narrowMatch RHEA:70435
+property_value: skos:narrowMatch RHEA:70439
+property_value: skos:narrowMatch RHEA:70443
+property_value: skos:narrowMatch RHEA:70447
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21159" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: bf
@@ -229690,9 +232792,13 @@
synonym: "histone H4K20me demethylase activity" EXACT []
xref: Reactome:R-HSA-2172678 "PHF8 demethylates histone H4K20me1"
xref: RHEA:67804
+xref: RHEA:85907
+xref: RHEA:85911
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0141058 ! histone H4 demethylase activity
property_value: skos:narrowMatch RHEA:67804
+property_value: skos:narrowMatch RHEA:85907
+property_value: skos:narrowMatch RHEA:85911
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21089" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29636" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30578" xsd:anyURI
@@ -230448,7 +233554,7 @@
id: GO:0035636
name: obsolete multi-organism signaling
namespace: biological_process
-def: "OBSOLETE. The transfer of information between living organisms." [GOC:go_curators]
+def: "OBSOLETE. The transfer of information between living organisms." [GOC:curators]
comment: This term was obsoleted because it was a grouping term but had no subclasses.
synonym: "multi-organism signalling" EXACT [GOC:bf]
synonym: "pheromone signaling" NARROW [GOC:bf]
@@ -230462,7 +233568,7 @@
id: GO:0035637
name: obsolete multicellular organismal signaling
namespace: biological_process
-def: "OBSOLETE. The transfer of information occurring at the level of a multicellular organism." [GOC:go_curators]
+def: "OBSOLETE. The transfer of information occurring at the level of a multicellular organism." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "multicellular organismal signalling" EXACT [GOC:bf]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24029" xsd:anyURI
@@ -230859,6 +233965,7 @@
def: "The process in which an oligopeptide is transported across a membrane. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages." [GOC:vw, ISBN:0198506732]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "oligopeptide membrane transport" EXACT []
+xref: Reactome:R-HSA-9959399 "SLC-mediated transport of oligopeptides"
is_a: GO:0006857 ! oligopeptide transport
is_a: GO:0055085 ! transmembrane transport
created_by: bf
@@ -231065,7 +234172,7 @@
name: macrophage migration inhibitory factor receptor complex
namespace: cellular_component
def: "A protein complex that binds macrophage migration inhibitory factor. Comprises CD74 and CD44 cell surface proteins." [GOC:BHF, PMID:12782713, PMID:17045821]
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bf
creation_date: 2011-02-25T11:33:15Z
@@ -231421,6 +234528,7 @@
def: "A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:vw]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "sodium ion membrane transport" EXACT []
+xref: Reactome:R-HSA-425986 "Sodium/Proton exchangers"
is_a: GO:0006814 ! sodium ion transport
is_a: GO:0098655 ! monoatomic cation transmembrane transport
created_by: bf
@@ -231696,11 +234804,14 @@
[Term]
id: GO:0035751
-name: regulation of lysosomal lumen pH
+name: obsolete regulation of lysosomal lumen pH
namespace: biological_process
-def: "Any process that modulates the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion." [GOC:rph]
-is_a: GO:0051453 ! regulation of intracellular pH
-relationship: part_of GO:0007040 ! lysosome organization
+def: "OBSOLETE. Any process that modulates the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion." [GOC:rph]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+consider: GO:0007042
+consider: GO:0035752
created_by: bf
creation_date: 2011-03-23T10:23:41Z
@@ -231708,9 +234819,8 @@
id: GO:0035752
name: lysosomal lumen pH elevation
namespace: biological_process
-def: "Any process that increases the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion." [GOC:bf, GOC:rph]
+def: "Any process that increases the pH of the lysosomal lumen, corresponding to a decrease in hydrogen ion concentration." [GOC:bf, GOC:rph]
synonym: "lysosome pH elevation" EXACT [GOC:bf, GOC:rph]
-is_a: GO:0035751 ! regulation of lysosomal lumen pH
is_a: GO:0051454 ! intracellular pH elevation
created_by: bf
creation_date: 2011-03-23T10:24:24Z
@@ -231902,7 +235012,7 @@
id: GO:0035770
name: ribonucleoprotein granule
namespace: cellular_component
-def: "A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions." [GOC:go_curators, GOC:sp, PMID:16520386, PMID:20368989, PMID:21436445]
+def: "A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions." [GOC:curators, GOC:sp, PMID:16520386, PMID:20368989, PMID:21436445]
synonym: "mRNP granule" EXACT []
synonym: "RNA granule" NARROW []
synonym: "RNP granule" EXACT []
@@ -232336,6 +235446,7 @@
synonym: "vitelline membrane" NARROW [PMID:16944418, PMID:17163408]
synonym: "zona pellucida" NARROW [PMID:16944418, PMID:17163408]
is_a: GO:0140047 ! specialized extracellular matrix
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: bf
creation_date: 2011-04-19T02:07:23Z
@@ -233509,18 +236620,21 @@
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lack of contact with other members of the same species." [GOC:bf, PMID:20203532]
synonym: "response to social isolation" EXACT [PMID:20203532]
-is_a: GO:0006950 ! response to stress
+is_a: GO:0033555 ! multicellular organismal response to stress
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31407" xsd:anyURI
created_by: bf
creation_date: 2011-06-22T09:39:57Z
[Term]
id: GO:0035901
-name: cellular response to isolation stress
+name: obsolete cellular response to isolation stress
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lack of contact with other members of the same species." [GOC:bf, PMID:20203532]
+def: "OBSOLETE. Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lack of contact with other members of the same species." [GOC:bf, PMID:20203532]
+comment: This term was obsoleted because it represents the molecular activities involved in response to isolation stress ; GO:0035900.
synonym: "cellular response to social isolation" EXACT [PMID:20203532]
-is_a: GO:0033554 ! cellular response to stress
-is_a: GO:0035900 ! response to isolation stress
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31407" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0035900
created_by: bf
creation_date: 2011-06-22T09:43:34Z
@@ -233816,6 +236930,7 @@
def: "The process in which a rRNA, ribosomal ribonucleic acid, is transported from the cytosol into the mitochondrial matrix." [GOC:ans, PMID:20691904]
synonym: "cytoplasmic RNA import into mitochondrion" NARROW [GOC:ans]
synonym: "nuclear-encoded RNA import into mitochondrion" NARROW [GOC:bf]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0050658 ! RNA transport
is_a: GO:0055085 ! transmembrane transport
created_by: bf
@@ -234737,6 +237852,8 @@
xref: MetaCyc:PWY-2201
is_a: GO:0006730 ! one-carbon metabolic process
is_a: GO:0046653 ! tetrahydrofolate metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-2201
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: bf
creation_date: 2011-09-02T01:35:49Z
@@ -234760,8 +237877,12 @@
synonym: "'de novo' pyridoxal 5'-phosphate formation" EXACT [GOC:bf]
synonym: "'de novo' pyridoxal 5'-phosphate synthesis" EXACT [GOC:bf]
synonym: "'de novo' pyridoxal phosphate biosynthetic process" BROAD [GOC:bf]
+xref: MetaCyc:PWY-6466
xref: MetaCyc:PYRIDOXSYN-PWY
-is_a: GO:0042823 ! pyridoxal phosphate biosynthetic process
+is_a: GO:0042823 ! pyridoxal 5'-phosphate biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-6466
+property_value: skos:narrowMatch MetaCyc:PYRIDOXSYN-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: bf
creation_date: 2011-09-06T02:04:53Z
@@ -234853,11 +237974,15 @@
synonym: "protein glutamine N-methylase activity" EXACT []
synonym: "protein glutamine N-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-6800138 "N6AMT1:TRMT112 transfers CH3 group from AdoMet to ETF1 dimer"
+xref: RHEA:45020
+xref: RHEA:50904
xref: RHEA:57452
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch RHEA:57452
+property_value: skos:narrowMatch RHEA:45020
+property_value: skos:narrowMatch RHEA:50904
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29860" xsd:anyURI
created_by: bf
creation_date: 2011-10-03T02:27:05Z
@@ -235421,6 +238546,7 @@
synonym: "peptidyl-succinyllysine desuccinylase activity" EXACT []
synonym: "succinyl lysine desuccinylase activity" BROAD [GOC:bf]
synonym: "succinyllysine desuccinylase activity" BROAD []
+xref: Reactome:R-HSA-9955518 "SIRT5 desuccinylates CPS1"
xref: RHEA:47668
is_a: GO:0141218 ! NAD-dependent protein lysine deacylase activity
relationship: part_of GO:0036049 ! peptidyl-lysine desuccinylation
@@ -235711,7 +238837,7 @@
id: GO:0036081
name: extracellular ammonia-gated monoatomic ion channel activity
namespace: molecular_function
-def: "Enables the transmembrane transfer of an ion by a channel that opens when extracellular ammonia (NH3) has been bound by the channel complex or one of its constituent parts." [GOC:sart, PMID:19135896]
+def: "Enables the transmembrane transfer of an ion by a channel that opens when extracellular ammonia (NH4+) has been bound by the channel complex or one of its constituent parts." [GOC:sart, PMID:19135896]
synonym: "extracellular ammonia-gated ion channel activity" BROAD []
synonym: "ionotropic ammonia receptor activity" RELATED [PMID:19135896]
is_a: GO:0005230 ! extracellular ligand-gated monoatomic ion channel activity
@@ -235793,12 +238919,14 @@
id: GO:0036088
name: D-serine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-serine, the D-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid." [GOC:imk]
+def: "The chemical reactions and pathways resulting in the breakdown of D-serine." [GOC:curators]
synonym: "D-serine breakdown" EXACT [GOC:bf]
synonym: "D-serine catabolism" EXACT [GOC:bf]
synonym: "D-serine degradation" EXACT [GOC:bf]
+xref: MetaCyc:PWY0-1535
is_a: GO:0019478 ! D-amino acid catabolic process
-is_a: GO:0070178 ! D-serine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
created_by: bf
creation_date: 2012-01-06T10:58:51Z
@@ -236459,11 +239587,15 @@
xref: MetaCyc:RXN-22839
xref: Reactome:R-HSA-9630967 "RIOX2Fe2+ hydroxylates a histidine residue of RPL27A"
xref: Reactome:R-HSA-9630993 "RIOX1:Fe2+ hydroxylates a histidine residue of RPL8"
+xref: RHEA:54024
xref: RHEA:54256
+xref: RHEA:54264
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:1.14.11.79
property_value: skos:exactMatch RHEA:54256
+property_value: skos:narrowMatch RHEA:54024
+property_value: skos:narrowMatch RHEA:54264
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27537" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: bf
@@ -236480,11 +239612,15 @@
xref: EC:1.14.11.30
xref: MetaCyc:RXN-11321
xref: RHEA:54260
+xref: RHEA:54268
+xref: RHEA:54272
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:54260
property_value: skos:narrowMatch EC:1.14.11.30
property_value: skos:narrowMatch MetaCyc:RXN-11321
+property_value: skos:narrowMatch RHEA:54268
+property_value: skos:narrowMatch RHEA:54272
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23829" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: bf
@@ -236782,7 +239918,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: 3-methoxy-4-hydroxy-5-decaprenylbenzoic acid -> 2-methoxy-6-decaprenylphenol + CO2." [GOC:mw, PMID:620805, PMID:7028108]
comment: The reason for obsoletion is that this term is equivalent to 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity.
-xref: Reactome:R-HSA-2162195 "COQ4 decarboxylates MHDB"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29459" xsd:anyURI
is_obsolete: true
replaced_by: GO:0120539
@@ -237807,6 +240942,7 @@
namespace: biological_process
def: "The directed movement of cadmium ions into the vacuole." [GOC:al]
synonym: "vacuolar cadmium import" RELATED [GOC:bf]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0070574 ! cadmium ion transmembrane transport
created_by: bf
@@ -238842,9 +241978,17 @@
xref: KEGG_REACTION:R09704
xref: MetaCyc:RXN-9781
xref: RHEA:46624
+xref: RHEA:83951
+xref: RHEA:83991
+xref: RHEA:84227
+xref: RHEA:84231
is_a: GO:0016854 ! racemase and epimerase activity
property_value: skos:exactMatch EC:5.1.99.5
property_value: skos:exactMatch RHEA:46624
+property_value: skos:narrowMatch RHEA:83951
+property_value: skos:narrowMatch RHEA:83991
+property_value: skos:narrowMatch RHEA:84227
+property_value: skos:narrowMatch RHEA:84231
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: bf
creation_date: 2012-09-19T10:47:56Z
@@ -239302,7 +242446,7 @@
id: GO:0036381
name: pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH3, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate." [EC:4.3.3.6, GOC:rs]
+def: "Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH4+, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH4+ = pyridoxal 5'-phosphate + 4 H2O + phosphate." [EC:4.3.3.6, GOC:rs]
synonym: "PdxST activity" RELATED [EC:4.3.3.6]
synonym: "pyridoxal 5'-phosphate synthase (glutamine hydrolyzing) activity" RELATED [EC:4.3.3.6]
xref: EC:4.3.3.6
@@ -239471,8 +242615,9 @@
id: GO:0036393
name: thiocyanate peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: thiocyanate (SCN-) + hydrogen peroxide (H2O2) = hypothiocyanite (OSCN-) + 2 H2O. Catalyzes the hydrogen peroxide oxidation of thiocyanate." [GOC:pm, PMID:12626341]
+def: "Catalysis of the reaction: thiocyanate + H2O2 + H+ = hypothiocyanous acid + H2O." [GOC:pm, PMID:12626341, RHEA:69416]
synonym: "lactoperoxidase activity" BROAD [PMID:12626341, Wikipedia:Lactoperoxidase]
+xref: RHEA:69416
is_a: GO:0004601 ! peroxidase activity
relationship: part_of GO:0018969 ! thiocyanate metabolic process
created_by: bf
@@ -239524,10 +242669,14 @@
xref: EC:1.17.5.3
xref: KEGG_REACTION:R09494
xref: MetaCyc:FORMATEDEHYDROG-RXN
+xref: RHEA:29063
+xref: RHEA:29071
xref: RHEA:48592
is_a: GO:0033695 ! oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.17.5.3
property_value: skos:exactMatch RHEA:48592
+property_value: skos:narrowMatch RHEA:29063
+property_value: skos:narrowMatch RHEA:29071
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: bf
@@ -239911,12 +243060,12 @@
[Term]
id: GO:0036426
-name: ditrans, polycis-undecaprenyl-phosphate mannosyltransferase activity
+name: obsolete ditrans, polycis-undecaprenyl-phosphate mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ditrans,octacis-undecaprenyl phosphate + GDP-alpha-D-mannose = D-mannosyl undecaprenyl phosphate+ GDP." [GOC:curators]
-xref: KEGG_REACTION:R07257
-xref: MetaCyc:2.4.1.54-RXN
-is_a: GO:0047267 ! undecaprenyl-phosphate mannosyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: ditrans,octacis-undecaprenyl phosphate + GDP-alpha-D-mannose = D-mannosyl undecaprenyl phosphate+ GDP." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
created_by: bf
creation_date: 2013-09-16T13:21:01Z
@@ -240149,6 +243298,7 @@
synonym: "mitochondrial calcium ion import" BROAD [GOC:vw]
synonym: "mitochondrial calcium uptake" EXACT []
is_a: GO:0006851 ! mitochondrial calcium ion transmembrane transport
+is_a: GO:0010496 ! intercellular transport
created_by: bf
creation_date: 2013-10-28T09:32:39Z
@@ -240262,6 +243412,7 @@
def: "Catalysis of the transfer of a iron-sulfur cluster from one compound (donor) to another (acceptor)." [GOC:bhm]
synonym: "Fe-S transferase activity" EXACT [GOC:bf]
xref: Reactome:R-HSA-2564828 "CIA Targeting Complex transfers 4Fe-4S cluster to apoproteins"
+xref: Reactome:R-HSA-8878815 "Formation of 4Fe-4S cluster on ISCA1:ISCA2"
is_a: GO:0016782 ! transferase activity, transferring sulphur-containing groups
created_by: bf
creation_date: 2013-11-14T11:17:37Z
@@ -241585,11 +244736,13 @@
synonym: "receptor activity involved in receptor-mediated endocytosis" NARROW [GOC:bf]
synonym: "transport receptor activity" BROAD [GOC:signaling]
xref: Reactome:R-HSA-203716 "eNOS:Caveolin-1 complex binds to Nostrin"
+xref: Reactome:R-HSA-2160915 "Receptor-mediated uptake of HA"
xref: Reactome:R-HSA-3000103 "CUBN:AMN binds CBLIF:RCbl"
xref: Reactome:R-HSA-3000112 "CD320-mediated TCN2:RCbl uptake and delivery to lysosome"
xref: Reactome:R-HSA-3000122 "CD320 binds extracellular TCN2:RCbl"
xref: Reactome:R-HSA-3000137 "CUBN:AMN-mediated CBLIF:RCbl uptake and delivery to lysosome"
xref: Reactome:R-HSA-350168 "LRP2-mediated uptake of extracellular CUBN:GC:25(OH)D"
+xref: Reactome:R-HSA-350186 "CUBN binds GC:25(OH)D"
xref: Reactome:R-HSA-9759202 "LRP2-mediated TCN2:RCbl uptake and delivery to lysosome"
xref: Reactome:R-HSA-9759209 "LRP2 binds extracellular TCN2:RCbl"
is_a: GO:0003674 ! molecular_function
@@ -241997,7 +245150,7 @@
synonym: "nitric oxide-cGMP-mediated signaling pathway" EXACT []
synonym: "nitric oxide-cGMP-mediated signalling pathway" EXACT [GOC:mah]
synonym: "NO-cGMP signaling pathway" EXACT [PMID:22019632]
-is_a: GO:0007263 ! nitric oxide mediated signal transduction
+is_a: GO:0141124 ! intracellular signaling cassette
created_by: bf
creation_date: 2012-01-10T05:32:39Z
@@ -242573,7 +245726,7 @@
def: "A protein complex containing at least a type II activin receptor, a type I activin receptor, and a coreceptor (EGF-CFC protein) such as Cripto or Cryptic. Nodal receptor complexes are capable of binding a nodal protein and transducing the signal into the cell." [GOC:bf, GOC:signaling, PMID:11024047, PMID:15062104]
comment: Nodal signals through activin receptors but (unlike activin) also requires EGF-CFC coreceptors (such as Cripto or Cryptic in mammals) to signal. This term is intended for receptor/co-receptor components and not a nodal-receptor complex.
synonym: "ActRIIB.ALK4.EGF-CFC complex" NARROW [GOC:bf]
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bf
creation_date: 2012-02-17T11:12:21Z
@@ -246888,7 +250041,7 @@
id: GO:0040013
name: negative regulation of locomotion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism." [GOC:curators]
synonym: "down regulation of locomotion" EXACT []
synonym: "down-regulation of locomotion" EXACT []
synonym: "downregulation of locomotion" EXACT []
@@ -246938,7 +250091,7 @@
id: GO:0040017
name: positive regulation of locomotion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." [GOC:curators]
synonym: "activation of locomotion" NARROW []
synonym: "stimulation of locomotion" NARROW []
synonym: "up regulation of locomotion" EXACT []
@@ -246954,7 +250107,7 @@
id: GO:0040018
name: positive regulation of multicellular organism growth
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size." [GOC:curators, GOC:dph, GOC:tb]
synonym: "positive regulation of body growth" EXACT [GOC:dph, GOC:tb]
synonym: "positive regulation of body size" EXACT [GOC:dph, GOC:tb]
is_a: GO:0040014 ! regulation of multicellular organism growth
@@ -246968,7 +250121,7 @@
id: GO:0040019
name: positive regulation of embryonic development
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of embryonic development." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of embryonic development." [GOC:curators]
synonym: "activation of embryonic development" NARROW []
synonym: "stimulation of embryonic development" NARROW []
synonym: "up regulation of embryonic development" EXACT []
@@ -247146,7 +250299,7 @@
id: GO:0040036
name: regulation of fibroblast growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "regulation of FGF receptor signaling pathway" EXACT []
synonym: "regulation of FGF receptor signalling pathway" EXACT []
synonym: "regulation of FGFR signaling pathway" EXACT []
@@ -247160,7 +250313,7 @@
id: GO:0040037
name: negative regulation of fibroblast growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "down regulation of fibroblast growth factor receptor signaling pathway" EXACT []
synonym: "down-regulation of fibroblast growth factor receptor signaling pathway" EXACT []
synonym: "downregulation of fibroblast growth factor receptor signaling pathway" EXACT []
@@ -247211,6 +250364,7 @@
synonym: "translocation of peptides or proteins into other organism involved in symbiotic interaction" BROAD []
synonym: "transport of peptides or proteins into host" EXACT []
synonym: "transport of peptides or proteins into other organism during symbiotic interaction" BROAD []
+xref: Reactome:R-HSA-9760173 "Secretion of toxins"
is_a: GO:0044417 ! translocation of molecules into host
[Term]
@@ -247449,7 +250603,6 @@
namespace: molecular_function
def: "Binds to and stops, prevents or reduces an ATP hydrolysis activity." [GOC:jl]
synonym: "adenosinetriphosphatase inhibitor" EXACT []
-is_a: GO:0060590 ! ATPase regulator activity
is_a: GO:0140678 ! molecular function inhibitor activity
relationship: negatively_regulates GO:0140657 ! ATP-dependent activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20955" xsd:anyURI
@@ -247619,7 +250772,7 @@
id: GO:0042053
name: regulation of dopamine metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:curators]
synonym: "regulation of dopamine metabolism" EXACT []
is_a: GO:0042069 ! regulation of catecholamine metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -247648,7 +250801,7 @@
id: GO:0042056
name: chemoattractant activity
namespace: molecular_function
-def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal." [GOC:go_curators, ISBN:0198506732]
+def: "Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal." [GOC:curators, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_pir
synonym: "attractant" BROAD []
@@ -247673,7 +250826,7 @@
id: GO:0042058
name: regulation of epidermal growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "regulation of EGF receptor signaling pathway" EXACT []
synonym: "regulation of EGF receptor signalling pathway" EXACT []
synonym: "regulation of EGFR signaling pathway" EXACT []
@@ -247686,7 +250839,7 @@
id: GO:0042059
name: negative regulation of epidermal growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "down regulation of epidermal growth factor receptor signaling pathway" EXACT []
synonym: "down-regulation of epidermal growth factor receptor signaling pathway" EXACT []
synonym: "downregulation of epidermal growth factor receptor signaling pathway" EXACT []
@@ -247767,7 +250920,7 @@
id: GO:0042068
name: obsolete regulation of pteridine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "regulation of pteridine metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30570" xsd:anyURI
@@ -247777,7 +250930,7 @@
id: GO:0042069
name: regulation of catecholamine metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines." [GOC:curators]
synonym: "regulation of catecholamine metabolism" EXACT []
is_a: GO:0033238 ! regulation of amine metabolic process
is_a: GO:0080090 ! regulation of primary metabolic process
@@ -247919,7 +251072,7 @@
id: GO:0042081
name: obsolete GSI anchor metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving glycosylsphingolipidinositol (GSI) anchors, which attach membrane proteins to the lipid bilayer of the cell membrane." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving glycosylsphingolipidinositol (GSI) anchors, which attach membrane proteins to the lipid bilayer of the cell membrane." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "GPI/GSI anchor metabolic process" BROAD []
synonym: "GPI/GSI anchor metabolism" BROAD []
@@ -247931,7 +251084,7 @@
id: GO:0042082
name: obsolete GSI anchor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a glycosylsphingolipidinositol (GSI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The sphingolipid group is linked, via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via a ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GSI anchors have variants on this canonical linkage." [GOC:go_curators, GOC:jsg]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a glycosylsphingolipidinositol (GSI) anchor that attaches some membrane proteins to the lipid bilayer of the cell membrane. The sphingolipid group is linked, via the C-6 hydroxyl residue of inositol to a carbohydrate chain which is itself linked to the protein via a ethanolamine phosphate group, its amino group forming an amide linkage with the C-terminal carboxyl of the protein. Some GSI anchors have variants on this canonical linkage." [GOC:curators, GOC:jsg]
comment: This term was obsoleted because it represents a molecular function.
synonym: "GPI/GSI anchor biosynthesis" BROAD []
synonym: "GPI/GSI anchor biosynthetic process" BROAD []
@@ -248281,12 +251434,18 @@
def: "The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances." [GOC:das, GOC:mah, PMID:10542156, PMID:8122899]
synonym: "assimilatory nitrate reduction" NARROW []
xref: MetaCyc:PWY-381
+xref: MetaCyc:PWY-5675
+xref: MetaCyc:PWY490-3
is_a: GO:0042126 ! nitrate metabolic process
is_a: GO:0071941 ! nitrogen cycle metabolic process
relationship: has_part GO:0015112 ! nitrate transmembrane transporter activity
relationship: has_part GO:0098809 ! nitrite reductase activity
+property_value: skos:narrowMatch MetaCyc:PWY-381
+property_value: skos:narrowMatch MetaCyc:PWY-5675
+property_value: skos:narrowMatch MetaCyc:PWY490-3
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27216" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30537" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0042129
@@ -248492,6 +251651,7 @@
namespace: biological_process
def: "The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport." [GOC:jl, PMID:10873832, PMID:16936697]
synonym: "retrograde (endosome to Golgi) transport" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016197 ! endosomal transport
is_a: GO:0016482 ! cytosolic transport
@@ -248607,12 +251767,13 @@
[Term]
id: GO:0042162
-name: telomeric DNA binding
+name: telomeric repeat DNA binding
namespace: molecular_function
-def: "Binding to a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end." [GOC:jl, SO:0000624]
-synonym: "telomere binding" EXACT []
+def: "Any molecular function by which a gene product interacts selectively and non-covalently with a telomeric DNA repeat sequence." [GOC:vw, SO:0000624]
+synonym: "telomere binding" BROAD []
synonym: "telomeric repeat binding" EXACT []
is_a: GO:0043565 ! sequence-specific DNA binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31610" xsd:anyURI
[Term]
id: GO:0042163
@@ -248683,14 +251844,14 @@
id: GO:0042169
name: SH2 domain binding
namespace: molecular_function
-def: "Binding to a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class." [GOC:go_curators, Pfam:PF00017]
+def: "Binding to a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class." [GOC:curators, Pfam:PF00017]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0042170
name: plastid membrane
namespace: cellular_component
-def: "Either of the lipid bilayers that surround a plastid and form the plastid envelope." [GOC:mah]
+def: "Any lipid bilayer that surrounds a plastid or is part of the plastid envelope. Primary plastids (in plants, green algae, red algae, and glaucophytes) are surrounded by two membranes; complex plastids derived from secondary endosymbiosis are surrounded by three or four membranes." [GOC:mah, PMID:20124341]
is_a: GO:0031090 ! organelle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: part_of GO:0009536 ! plastid
@@ -248718,7 +251879,7 @@
id: GO:0042174
name: negative regulation of sporulation resulting in formation of a cellular spore
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation." [GOC:curators]
synonym: "down regulation of sporulation" EXACT []
synonym: "down-regulation of sporulation" EXACT []
synonym: "downregulation of sporulation" EXACT []
@@ -248750,7 +251911,7 @@
namespace: biological_process
alt_id: GO:1903362
alt_id: GO:2000598
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators, GOC:jl]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:curators, GOC:jl]
synonym: "regulation of cellular protein breakdown" EXACT [GOC:TermGenie]
synonym: "regulation of cellular protein catabolic process" EXACT []
synonym: "regulation of cellular protein catabolism" EXACT [GOC:TermGenie]
@@ -248864,7 +252025,7 @@
id: GO:0042181
name: ketone biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:curators]
synonym: "ketone anabolism" EXACT []
synonym: "ketone biosynthesis" EXACT []
synonym: "ketone formation" EXACT []
@@ -248876,7 +252037,7 @@
id: GO:0042182
name: ketone catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:curators]
synonym: "ketone breakdown" EXACT []
synonym: "ketone catabolism" EXACT []
synonym: "ketone degradation" EXACT []
@@ -248900,7 +252061,7 @@
id: GO:0042184
name: xylene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of xylene, a mixture of three colorless, aromatic hydrocarbon liquids, ortho-, meta- and para-xylene." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of xylene, a mixture of three colorless, aromatic hydrocarbon liquids, ortho-, meta- and para-xylene." [GOC:curators]
synonym: "xylene breakdown" EXACT []
synonym: "xylene catabolism" EXACT []
synonym: "xylene degradation" EXACT []
@@ -248912,7 +252073,7 @@
id: GO:0042185
name: m-xylene catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of m-xylene, 1,3-dimethylbenzene, a colorless, liquid aromatic hydrocarbon." [GOC:go_curators, GOC:jl]
+def: "The chemical reactions and pathways resulting in the breakdown of m-xylene, 1,3-dimethylbenzene, a colorless, liquid aromatic hydrocarbon." [GOC:curators, GOC:jl]
synonym: "m-xylene breakdown" EXACT []
synonym: "m-xylene catabolism" EXACT []
synonym: "m-xylene degradation" EXACT []
@@ -249029,7 +252190,7 @@
id: GO:0042194
name: quinate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of quinate, the anion of quinic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of quinate, the anion of quinic acid." [GOC:curators]
synonym: "quinate anabolism" EXACT []
synonym: "quinate biosynthesis" EXACT []
synonym: "quinate formation" EXACT []
@@ -249307,26 +252468,27 @@
id: GO:0042217
name: 1-aminocyclopropane-1-carboxylate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 1-aminocyclopropane-1-carboxylate, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of 1-aminocyclopropane-1-carboxylate, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [UM-BBD_pathwayID:acp]
synonym: "1-aminocyclopropane-1-carboxylate breakdown" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate catabolism" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate degradation" EXACT []
-is_a: GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
+xref: UM-BBD_pathwayID:acp
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
id: GO:0042218
-name: 1-aminocyclopropane-1-carboxylate biosynthetic process
+name: obsolete 1-aminocyclopropane-1-carboxylate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 1-aminocyclopropane-1-carboxylate, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 1-aminocyclopropane-1-carboxylate, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants." [GOC:curators]
+comment: This term was obsoleted because it represents an intermediate in ethylene biosynthesis.
synonym: "1-aminocyclopropane-1-carboxylate anabolism" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate biosynthesis" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate formation" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate synthesis" EXACT []
-is_a: GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
-is_a: GO:1901607 ! alpha-amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+consider: GO:0009693
[Term]
id: GO:0042219
@@ -249895,6 +253057,7 @@
def: "Catalysis of the transfer of ISG15 from one protein to another via the reaction X-ISG15 + Y = Y-ISG15 + X, where both X-ISG15 and Y-ISG15 are covalent linkages." [GOC:mah, PMID:12826404]
synonym: "ISG15 conjugating enzyme activity" NARROW []
xref: Reactome:R-HSA-5653754 "UBE2L6:TRIM25 ISGylates monoUb:K164-PCNA"
+xref: Reactome:R-HSA-9927247 "ISGylation of DDX58 (RIG-I)"
is_a: GO:0019787 ! ubiquitin-like protein transferase activity
[Term]
@@ -249966,7 +253129,7 @@
id: GO:0042304
name: regulation of fatty acid biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils." [GOC:go_curators, GOC:jl]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils." [GOC:curators, GOC:jl]
synonym: "regulation of fatty acid anabolism" EXACT []
synonym: "regulation of fatty acid biosynthesis" EXACT []
synonym: "regulation of fatty acid formation" EXACT []
@@ -250155,7 +253318,7 @@
id: GO:0042321
name: negative regulation of circadian sleep/wake cycle, sleep
namespace: biological_process
-def: "Any process that stops, prevents or reduces the duration or quality of sleep, a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals." [GOC:go_curators, GOC:jl, ISBN:0192800981]
+def: "Any process that stops, prevents or reduces the duration or quality of sleep, a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals." [GOC:curators, GOC:jl, ISBN:0192800981]
synonym: "down regulation of circadian sleep/wake cycle, sleep" EXACT []
synonym: "down-regulation of circadian sleep/wake cycle, sleep" EXACT []
synonym: "downregulation of circadian sleep/wake cycle, sleep" EXACT []
@@ -250172,7 +253335,7 @@
id: GO:0042322
name: negative regulation of circadian sleep/wake cycle, REM sleep
namespace: biological_process
-def: "Any process that stops, prevents or reduces the duration or quality of rapid eye movement (REM) sleep." [GOC:go_curators, GOC:jl]
+def: "Any process that stops, prevents or reduces the duration or quality of rapid eye movement (REM) sleep." [GOC:curators, GOC:jl]
synonym: "down regulation of circadian sleep/wake cycle, REM sleep" EXACT []
synonym: "down-regulation of circadian sleep/wake cycle, REM sleep" EXACT []
synonym: "downregulation of circadian sleep/wake cycle, REM sleep" EXACT []
@@ -250536,8 +253699,15 @@
synonym: "L-fucose breakdown" EXACT []
synonym: "L-fucose catabolism" EXACT []
synonym: "L-fucose degradation" EXACT []
-is_a: GO:0019317 ! fucose catabolic process
+xref: MetaCyc:FUCCAT-PWY
+xref: MetaCyc:PWY-8318
+xref: MetaCyc:PWY-8444
+is_a: GO:0019320 ! hexose catabolic process
is_a: GO:0042354 ! L-fucose metabolic process
+property_value: skos:narrowMatch MetaCyc:FUCCAT-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-8318
+property_value: skos:narrowMatch MetaCyc:PWY-8444
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0042356
@@ -250618,7 +253788,7 @@
synonym: "tocopherol metabolic process" EXACT []
synonym: "tocopherol metabolism" EXACT []
synonym: "vitamin E metabolism" EXACT []
-xref: Reactome:R-HSA-8877627 "Vitamin E"
+xref: Reactome:R-HSA-8877627 "Vitamin E transport"
is_a: GO:0008152 ! metabolic process
[Term]
@@ -250647,6 +253817,7 @@
synonym: "fat-soluble vitamin biosynthesis" EXACT []
synonym: "fat-soluble vitamin formation" EXACT []
synonym: "fat-soluble vitamin synthesis" EXACT []
+xref: Reactome:R-HSA-6806667 "Metabolism of fat-soluble vitamins"
is_a: GO:0009110 ! vitamin biosynthetic process
[Term]
@@ -250668,6 +253839,7 @@
synonym: "water-soluble vitamin biosynthesis" EXACT []
synonym: "water-soluble vitamin formation" EXACT []
synonym: "water-soluble vitamin synthesis" EXACT []
+xref: Reactome:R-HSA-196849 "Metabolism of water-soluble vitamins and cofactors"
is_a: GO:0009110 ! vitamin biosynthetic process
[Term]
@@ -250684,7 +253856,7 @@
id: GO:0042366
name: cobalamin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:curators]
synonym: "cobalamin breakdown" EXACT []
synonym: "cobalamin catabolism" EXACT []
synonym: "cobalamin degradation" EXACT []
@@ -251086,7 +254258,7 @@
id: GO:0042402
name: biogenic amine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:go_curators, GOC:jl, ISBN:0198506732]
+def: "The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." [GOC:curators, GOC:jl, ISBN:0198506732]
synonym: "biogenic amine breakdown" EXACT []
synonym: "biogenic amine catabolism" EXACT []
synonym: "biogenic amine degradation" EXACT []
@@ -251190,7 +254362,6 @@
xref: MetaCyc:6-CARBOXYHEXANOATE--COA-LIGASE-RXN
xref: RHEA:14781
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.14
property_value: skos:exactMatch RHEA:14781
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -251204,8 +254375,15 @@
synonym: "taurine biosynthesis" EXACT []
synonym: "taurine formation" EXACT []
synonym: "taurine synthesis" EXACT []
+xref: MetaCyc:PWY-5331
+xref: MetaCyc:PWY-7850
+xref: MetaCyc:PWY-8359
is_a: GO:0019530 ! taurine metabolic process
is_a: GO:0046305 ! alkanesulfonate biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-5331
+property_value: skos:narrowMatch MetaCyc:PWY-7850
+property_value: skos:narrowMatch MetaCyc:PWY-8359
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
[Term]
id: GO:0042413
@@ -251385,6 +254563,7 @@
xref: MetaCyc:CHOLINE-BETAINE-ANA-PWY
xref: MetaCyc:P542-PWY
xref: MetaCyc:PWY-3721
+xref: MetaCyc:PWY-7167
xref: MetaCyc:PWY-7494
xref: Reactome:R-HSA-6798163 "Choline catabolism"
is_a: GO:0019695 ! choline metabolic process
@@ -251392,9 +254571,11 @@
property_value: skos:narrowMatch MetaCyc:CHOLINE-BETAINE-ANA-PWY
property_value: skos:narrowMatch MetaCyc:P542-PWY
property_value: skos:narrowMatch MetaCyc:PWY-3721
+property_value: skos:narrowMatch MetaCyc:PWY-7167
property_value: skos:narrowMatch MetaCyc:PWY-7494
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30537" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0042427
@@ -251405,11 +254586,16 @@
synonym: "serotonin biosynthesis" EXACT []
synonym: "serotonin formation" EXACT []
synonym: "serotonin synthesis" EXACT []
+xref: MetaCyc:PWY-6030
+xref: MetaCyc:PWY-8475
xref: Wikipedia:Serotonin
is_a: GO:0042428 ! serotonin metabolic process
is_a: GO:0042435 ! indole-containing compound biosynthetic process
is_a: GO:0046189 ! phenol-containing compound biosynthetic process
is_a: GO:1901162 ! primary amino compound biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-6030
+property_value: skos:narrowMatch MetaCyc:PWY-8475
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31658" xsd:anyURI
[Term]
id: GO:0042428
@@ -251651,22 +254837,25 @@
[Term]
id: GO:0042450
-name: L-arginine biosynthetic process via ornithine
+name: obsolete L-arginine biosynthetic process via ornithine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine." [GOC:jl]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "arginine anabolism via ornithine" EXACT []
synonym: "arginine biosynthesis, acetylated pathway" EXACT []
synonym: "arginine formation via ornithine" EXACT []
synonym: "arginine synthesis via ornithine" EXACT []
synonym: "classical arginine biosynthesis pathway" EXACT []
-is_a: GO:0006526 ! L-arginine biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29602" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006526
[Term]
id: GO:0042451
name: purine nucleoside biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of any purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of any purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside)." [GOC:curators]
synonym: "purine nucleoside anabolism" EXACT []
synonym: "purine nucleoside biosynthesis" EXACT []
synonym: "purine nucleoside formation" EXACT []
@@ -251684,6 +254873,7 @@
synonym: "deoxyguanosine biosynthesis" EXACT []
synonym: "deoxyguanosine formation" EXACT []
synonym: "deoxyguanosine synthesis" EXACT []
+is_a: GO:0046120 ! 2'-deoxyribonucleoside biosynthetic process
is_a: GO:0046123 ! purine deoxyribonucleoside biosynthetic process
[Term]
@@ -251736,7 +254926,7 @@
id: GO:0042458
name: obsolete nopaline catabolic process to proline
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of nopaline into other compounds, including proline." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of nopaline into other compounds, including proline." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "nopaline breakdown to proline" EXACT []
synonym: "nopaline degradation to proline" EXACT []
@@ -251747,7 +254937,7 @@
id: GO:0042459
name: obsolete octopine catabolic process to proline
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of octopine into other compounds, including proline." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of octopine into other compounds, including proline." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "octopine breakdown to proline" EXACT []
synonym: "octopine degradation to proline" EXACT []
@@ -251759,7 +254949,7 @@
name: photoreceptor cell development
namespace: biological_process
alt_id: GO:0046531
-def: "Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light." [GOC:go_curators]
+def: "Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light." [GOC:curators]
synonym: "photoreceptor morphogenesis" EXACT []
is_a: GO:0048666 ! neuron development
relationship: part_of GO:0046530 ! photoreceptor cell differentiation
@@ -252448,14 +255638,14 @@
id: GO:0042549
name: photosystem II stabilization
namespace: biological_process
-def: "The stabilization of the photosystem II protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis." [GOC:go_curators]
+def: "The stabilization of the photosystem II protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis." [GOC:curators]
is_a: GO:0042548 ! regulation of photosynthesis, light reaction
[Term]
id: GO:0042550
name: photosystem I stabilization
namespace: biological_process
-def: "The stabilization of the photosystem I protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis." [GOC:go_curators]
+def: "The stabilization of the photosystem I protein complex, resulting from the phosphorylation of its structural protein subunits, in a cell actively involved in photosynthesis." [GOC:curators]
is_a: GO:0042548 ! regulation of photosynthesis, light reaction
[Term]
@@ -252636,7 +255826,7 @@
synonym: "antibody" EXACT [GOC:add]
xref: Wikipedia:Antibody
is_a: GO:0019814 ! immunoglobulin complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0042572
@@ -252692,7 +255882,7 @@
id: GO:0042576
name: obsolete aspartyl aminopeptidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the release of an N-terminal aspartate or glutamate from a peptide, with a preference for aspartate." [GOC:curator]
+def: "OBSOLETE. Catalysis of the release of an N-terminal aspartate or glutamate from a peptide, with a preference for aspartate." [GOC:curators]
comment: This term was made obsolete because it represents a gene product.
synonym: "aspartyl aminopeptidase activity" EXACT []
is_obsolete: true
@@ -252852,14 +256042,14 @@
id: GO:0042593
name: glucose homeostasis
namespace: biological_process
-def: "Any process involved in the maintenance of an internal steady state of glucose within an organism or cell." [GOC:go_curators]
+def: "Any process involved in the maintenance of an internal steady state of glucose within an organism or cell." [GOC:curators]
is_a: GO:0033500 ! carbohydrate homeostasis
[Term]
id: GO:0042594
name: response to starvation
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment." [GOC:curators]
subset: goslim_yeast
is_a: GO:0006950 ! response to stress
is_a: GO:0031667 ! response to nutrient levels
@@ -252868,7 +256058,7 @@
id: GO:0042595
name: behavioral response to starvation
namespace: biological_process
-def: "Any process that results in a change in the behavior of an organism as a result of deprivation of nourishment." [GOC:go_curators]
+def: "Any process that results in a change in the behavior of an organism as a result of deprivation of nourishment." [GOC:curators]
synonym: "behavioural response to starvation" EXACT []
is_a: GO:0042594 ! response to starvation
@@ -252877,7 +256067,7 @@
name: fear response
namespace: biological_process
alt_id: GO:0001663
-def: "The response of an organism to a perceived external threat." [GOC:go_curators]
+def: "The response of an organism to a perceived external threat." [GOC:curators]
synonym: "physiological fear response" EXACT []
is_a: GO:0033555 ! multicellular organismal response to stress
@@ -252886,13 +256076,15 @@
name: periplasmic space
namespace: cellular_component
alt_id: GO:0005620
-def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:go_curators, GOC:md]
+def: "The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria)." [GOC:curators, GOC:md]
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "periplasm" EXACT []
is_a: GO:0110165 ! cellular anatomical structure
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0042598
@@ -253160,10 +256352,12 @@
synonym: "P-P-bond-hydrolysis-driven transmembrane transporter activity" BROAD []
synonym: "P-P-bond-hydrolysis-driven transporter" BROAD []
xref: EC:7.2.2.-
+xref: Reactome:R-HSA-1454916 "The ABCC family mediates organic anion transport"
xref: Reactome:R-HSA-1467457 "ABCA8,B1,B5 transport xenobiotics from cytosol to extracellular region"
xref: Reactome:R-HSA-2161506 "abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate"
xref: Reactome:R-HSA-2161538 "abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate"
xref: Reactome:R-HSA-390393 "Peroxisomal uptake of very long-chain fatty acyl CoA"
+xref: Reactome:R-HSA-5690340 "Defective ABCC6 does not transport organic anion from cytosol to extracellular region"
xref: Reactome:R-HSA-9033499 "PEX1:PEX6:PEX26:ZFAND6 dissociates Ub:PEX5L and PEX7 from PEX14:PEX13:PEX2:PEX10:PEX12 and translocates PEX5L and PEX7 from the peroxisomal membrane to the cytosol"
xref: Reactome:R-HSA-9033505 "PEX1:PEX6:PEX26:ZFAND6:Ub:PEX5S,L:PEX14:PEX13:PEX2:PEX10:PEX12 dissociates yielding cytosolic Ub:PEX5S,L and membrane PEX14:PEX13:PEX2:PEX10:PEX12"
xref: Reactome:R-HSA-9659680 "ABCB1 transports xenobiotics out of the cell"
@@ -253228,7 +256422,7 @@
id: GO:0042631
name: cellular response to water deprivation
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of water." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of water." [GOC:curators]
synonym: "cellular response to drought" EXACT []
is_a: GO:0009414 ! response to water deprivation
is_a: GO:0033554 ! cellular response to stress
@@ -253240,7 +256434,7 @@
namespace: biological_process
alt_id: GO:2000188
alt_id: GO:2000189
-def: "Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell." [GOC:go_curators]
+def: "Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell." [GOC:curators]
synonym: "positive regulation of cholesterol homeostasis" RELATED []
synonym: "regulation of cholesterol homeostasis" RELATED []
is_a: GO:0055092 ! sterol homeostasis
@@ -253249,14 +256443,14 @@
id: GO:0042633
name: hair cycle
namespace: biological_process
-def: "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:go_curators, PMID:12230507]
+def: "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:curators, PMID:12230507]
is_a: GO:0042303 ! molting cycle
[Term]
id: GO:0042634
name: regulation of hair cycle
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:go_curators, PMID:12230507]
+def: "Any process that modulates the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:curators, PMID:12230507]
is_a: GO:0051239 ! regulation of multicellular organismal process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042633 ! hair cycle
@@ -253266,7 +256460,7 @@
id: GO:0042635
name: positive regulation of hair cycle
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:go_curators, PMID:12230507]
+def: "Any process that activates or increases the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:curators, PMID:12230507]
synonym: "activation of hair cycle" NARROW []
synonym: "stimulation of hair cycle" NARROW []
synonym: "up regulation of hair cycle" EXACT []
@@ -253282,7 +256476,7 @@
id: GO:0042636
name: negative regulation of hair cycle
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:go_curators, PMID:12230507]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." [GOC:curators, PMID:12230507]
synonym: "down regulation of hair cycle" EXACT []
synonym: "down-regulation of hair cycle" EXACT []
synonym: "downregulation of hair cycle" EXACT []
@@ -253340,7 +256534,7 @@
id: GO:0042641
name: actomyosin
namespace: cellular_component
-def: "Any complex of actin, myosin, and accessory proteins." [GOC:go_curators]
+def: "Any complex of actin, myosin, and accessory proteins." [GOC:curators]
synonym: "actomyosin complex" EXACT []
synonym: "actomyosin structure" EXACT []
is_a: GO:0110165 ! cellular anatomical structure
@@ -253350,7 +256544,7 @@
id: GO:0042642
name: actomyosin, myosin complex part
namespace: cellular_component
-def: "The myosin part of any complex of actin, myosin, and accessory proteins." [GOC:go_curators]
+def: "The myosin part of any complex of actin, myosin, and accessory proteins." [GOC:curators]
is_a: GO:0016459 ! myosin complex
intersection_of: GO:0016459 ! myosin complex
intersection_of: part_of GO:0042641 ! actomyosin
@@ -253360,7 +256554,7 @@
id: GO:0042643
name: obsolete actomyosin, actin portion
namespace: cellular_component
-def: "OBSOLETE. The actin part of any complex of actin, myosin, and accessory proteins." [GOC:go_curators]
+def: "OBSOLETE. The actin part of any complex of actin, myosin, and accessory proteins." [GOC:curators]
comment: This term was obsoleted because it corresponds to a gene product, actin.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19570" xsd:anyURI
is_obsolete: true
@@ -253516,7 +256710,7 @@
id: GO:0042659
name: regulation of cell fate specification
namespace: biological_process
-def: "Any process that mediates the adoption of a specific fate by a cell." [GOC:go_curators]
+def: "Any process that mediates the adoption of a specific fate by a cell." [GOC:curators]
is_a: GO:0010453 ! regulation of cell fate commitment
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0001708 ! cell fate specification
@@ -253526,7 +256720,7 @@
id: GO:0042660
name: positive regulation of cell fate specification
namespace: biological_process
-def: "Any process that activates or enables a cell to adopt a specific fate." [GOC:go_curators]
+def: "Any process that activates or enables a cell to adopt a specific fate." [GOC:curators]
synonym: "activation of cell fate specification" NARROW []
synonym: "stimulation of cell fate specification" NARROW []
synonym: "up regulation of cell fate specification" EXACT []
@@ -253542,7 +256736,7 @@
id: GO:0042661
name: regulation of mesodermal cell fate specification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mesoderm cell fate specification." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of mesoderm cell fate specification." [GOC:curators]
is_a: GO:0042659 ! regulation of cell fate specification
is_a: GO:1905770 ! regulation of mesodermal cell differentiation
is_a: GO:2000027 ! regulation of animal organ morphogenesis
@@ -253554,7 +256748,7 @@
id: GO:0042662
name: negative regulation of mesodermal cell fate specification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification." [GOC:curators]
synonym: "down regulation of mesodermal cell fate specification" EXACT []
synonym: "down-regulation of mesodermal cell fate specification" EXACT []
synonym: "downregulation of mesodermal cell fate specification" EXACT []
@@ -253571,7 +256765,7 @@
id: GO:0042663
name: regulation of endodermal cell fate specification
namespace: biological_process
-def: "Any process that mediates the specification of a cell into an endoderm cell." [GOC:go_curators]
+def: "Any process that mediates the specification of a cell into an endoderm cell." [GOC:curators]
synonym: "regulation of endoderm cell fate specification" EXACT []
is_a: GO:0042659 ! regulation of cell fate specification
is_a: GO:1903224 ! regulation of endodermal cell differentiation
@@ -253583,7 +256777,7 @@
id: GO:0042664
name: negative regulation of endodermal cell fate specification
namespace: biological_process
-def: "Any process that restricts, stops or prevents a cell from specifying into an endoderm cell." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from specifying into an endoderm cell." [GOC:curators]
synonym: "down regulation of endodermal cell fate specification" EXACT []
synonym: "down-regulation of endodermal cell fate specification" EXACT []
synonym: "downregulation of endodermal cell fate specification" EXACT []
@@ -253602,7 +256796,7 @@
id: GO:0042665
name: regulation of ectodermal cell fate specification
namespace: biological_process
-def: "Any process that mediates the specification of a cell into an ectoderm cell." [GOC:go_curators]
+def: "Any process that mediates the specification of a cell into an ectoderm cell." [GOC:curators]
synonym: "regulation of ectoderm cell fate specification" EXACT []
is_a: GO:0042659 ! regulation of cell fate specification
intersection_of: GO:0065007 ! biological regulation
@@ -253613,7 +256807,7 @@
id: GO:0042666
name: negative regulation of ectodermal cell fate specification
namespace: biological_process
-def: "Any process that restricts, stops or prevents a cell from specifying into an ectoderm cell." [GOC:go_curators]
+def: "Any process that restricts, stops or prevents a cell from specifying into an ectoderm cell." [GOC:curators]
synonym: "down regulation of ectodermal cell fate specification" EXACT []
synonym: "down-regulation of ectodermal cell fate specification" EXACT []
synonym: "downregulation of ectodermal cell fate specification" EXACT []
@@ -253631,7 +256825,7 @@
id: GO:0042667
name: auditory receptor cell fate specification
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into an auditory hair cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into an auditory hair cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:curators]
synonym: "auditory hair cell fate specification" EXACT []
is_a: GO:0048665 ! neuron fate specification
relationship: part_of GO:0009912 ! auditory receptor cell fate commitment
@@ -253640,7 +256834,7 @@
id: GO:0042668
name: auditory receptor cell fate determination
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into an auditory hair cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into an auditory hair cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
synonym: "auditory hair cell fate determination" EXACT []
is_a: GO:0048664 ! neuron fate determination
relationship: part_of GO:0009912 ! auditory receptor cell fate commitment
@@ -253649,7 +256843,7 @@
id: GO:0042669
name: regulation of inner ear auditory receptor cell fate specification
namespace: biological_process
-def: "Any process that mediates the specification of a cell into an auditory hair cell." [GOC:go_curators]
+def: "Any process that mediates the specification of a cell into an auditory hair cell." [GOC:curators]
synonym: "regulation of auditory hair cell fate specification" EXACT []
is_a: GO:0042659 ! regulation of cell fate specification
is_a: GO:0045607 ! regulation of inner ear auditory receptor cell differentiation
@@ -253661,14 +256855,14 @@
id: GO:0042670
name: retinal cone cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell." [GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell." [GOC:curators]
is_a: GO:0060219 ! camera-type eye photoreceptor cell differentiation
[Term]
id: GO:0042671
name: retinal cone cell fate determination
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into a retinal cone cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into a retinal cone cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:curators]
is_a: GO:0043703 ! photoreceptor cell fate determination
relationship: part_of GO:0046551 ! retinal cone cell fate commitment
@@ -253676,7 +256870,7 @@
id: GO:0042672
name: retinal cone cell fate specification
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into a retinal cone cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into a retinal cone cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:curators]
is_a: GO:0043704 ! photoreceptor cell fate specification
relationship: part_of GO:0046551 ! retinal cone cell fate commitment
@@ -253684,7 +256878,7 @@
id: GO:0042673
name: regulation of retinal cone cell fate specification
namespace: biological_process
-def: "Any process that mediates the specification of a cell into a retinal cone cell." [GOC:go_curators]
+def: "Any process that mediates the specification of a cell into a retinal cone cell." [GOC:curators]
is_a: GO:0042659 ! regulation of cell fate specification
is_a: GO:0060222 ! regulation of retinal cone cell fate commitment
intersection_of: GO:0065007 ! biological regulation
@@ -253759,7 +256953,7 @@
id: GO:0042684
name: cardioblast cell fate commitment
namespace: biological_process
-def: "The process in which a cell becomes committed to becoming a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "The process in which a cell becomes committed to becoming a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
is_a: GO:0060911 ! cardiac cell fate commitment
relationship: part_of GO:0010002 ! cardioblast differentiation
@@ -253767,7 +256961,7 @@
id: GO:0042685
name: cardioblast cell fate specification
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into a cardioblast cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into a cardioblast cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
is_a: GO:0060912 ! cardiac cell fate specification
relationship: part_of GO:0042684 ! cardioblast cell fate commitment
@@ -253775,7 +256969,7 @@
id: GO:0042686
name: regulation of cardioblast cell fate specification
namespace: biological_process
-def: "Any process that mediates the specification of a cell into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:go_curators]
+def: "Any process that mediates the specification of a cell into a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." [GOC:curators]
is_a: GO:0051890 ! regulation of cardioblast differentiation
is_a: GO:2000043 ! regulation of cardiac cell fate specification
intersection_of: GO:0065007 ! biological regulation
@@ -253793,7 +256987,7 @@
id: GO:0042689
name: regulation of crystal cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of crystal cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of crystal cell differentiation." [GOC:curators]
is_a: GO:0045610 ! regulation of hemocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042688 ! crystal cell differentiation
@@ -253803,7 +256997,7 @@
id: GO:0042690
name: negative regulation of crystal cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of crystal cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of crystal cell differentiation." [GOC:curators]
synonym: "down regulation of crystal cell differentiation" EXACT []
synonym: "down-regulation of crystal cell differentiation" EXACT []
synonym: "downregulation of crystal cell differentiation" EXACT []
@@ -253818,7 +257012,7 @@
id: GO:0042691
name: positive regulation of crystal cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of crystal cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of crystal cell differentiation." [GOC:curators]
synonym: "activation of crystal cell differentiation" NARROW []
synonym: "stimulation of crystal cell differentiation" NARROW []
synonym: "up regulation of crystal cell differentiation" EXACT []
@@ -253834,7 +257028,7 @@
id: GO:0042692
name: muscle cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." [CL:0000187, GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." [CL:0000187, GOC:curators]
synonym: "myogenesis" RELATED []
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0061061 ! muscle structure development
@@ -253843,7 +257037,7 @@
id: GO:0042693
name: muscle cell fate commitment
namespace: biological_process
-def: "The process in which the cellular identity of muscle cells is acquired and determined." [CL:0000187, GOC:go_curators]
+def: "The process in which the cellular identity of muscle cells is acquired and determined." [CL:0000187, GOC:curators]
is_a: GO:0045165 ! cell fate commitment
relationship: part_of GO:0042692 ! muscle cell differentiation
@@ -253851,7 +257045,7 @@
id: GO:0042694
name: muscle cell fate specification
namespace: biological_process
-def: "The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [CL:0000187, GOC:go_curators]
+def: "The process in which a cell becomes capable of differentiating autonomously into a muscle cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [CL:0000187, GOC:curators]
is_a: GO:0001708 ! cell fate specification
relationship: part_of GO:0042693 ! muscle cell fate commitment
@@ -253954,7 +257148,7 @@
id: GO:0042705
name: ocellus photoreceptor cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of a photoreceptor cell found in the ocellus." [GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires specialized features of a photoreceptor cell found in the ocellus." [GOC:curators]
is_a: GO:0046530 ! photoreceptor cell differentiation
[Term]
@@ -253998,6 +257192,7 @@
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_pir
+xref: Reactome:R-HSA-9931953 "Biofilm formation"
is_a: GO:0098630 ! aggregation of unicellular organisms
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17727" xsd:anyURI
@@ -254013,7 +257208,7 @@
id: GO:0042712
name: paternal behavior
namespace: biological_process
-def: "Male behaviors associated with the care and rearing offspring." [GOC:go_curators]
+def: "Male behaviors associated with the care and rearing offspring." [GOC:curators]
synonym: "paternal behaviour" EXACT []
is_a: GO:0060746 ! parental behavior
@@ -254450,7 +257645,7 @@
id: GO:0042753
name: positive regulation of circadian rhythm
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior." [GOC:curators]
synonym: "activation of circadian rhythm" NARROW []
synonym: "stimulation of circadian rhythm" NARROW []
synonym: "up regulation of circadian rhythm" EXACT []
@@ -254466,7 +257661,7 @@
id: GO:0042754
name: negative regulation of circadian rhythm
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior." [GOC:curators]
synonym: "down regulation of circadian rhythm" EXACT []
synonym: "down-regulation of circadian rhythm" EXACT []
synonym: "downregulation of circadian rhythm" EXACT []
@@ -254558,15 +257753,19 @@
synonym: "very-long-chain fatty acid formation" EXACT []
synonym: "very-long-chain fatty acid synthesis" EXACT []
xref: MetaCyc:PWY-5080
+xref: MetaCyc:PWY-7036
is_a: GO:0000038 ! very long-chain fatty acid metabolic process
is_a: GO:0006633 ! fatty acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:PWY-5080
+property_value: skos:narrowMatch MetaCyc:PWY-7036
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0042762
name: regulation of sulfur metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur." [GOC:curators]
synonym: "regulation of sulfur metabolism" EXACT []
synonym: "regulation of sulphur metabolic process" EXACT []
synonym: "regulation of sulphur metabolism" EXACT []
@@ -254587,7 +257786,7 @@
id: GO:0042764
name: ascospore-type prospore
namespace: cellular_component
-def: "An immature spore undergoing development. The spore usually consists of nucleic acid, prospore membrane(s) that encase the nucleic acid, and ultimately a cell wall that covers the membrane(s). This type of spore is observed in ascospore-forming fungi." [GOC:go_curators]
+def: "An immature spore undergoing development. The spore usually consists of nucleic acid, prospore membrane(s) that encase the nucleic acid, and ultimately a cell wall that covers the membrane(s). This type of spore is observed in ascospore-forming fungi." [GOC:curators]
is_a: GO:0042763 ! intracellular immature spore
[Term]
@@ -254664,7 +257863,7 @@
id: GO:0042769
name: obsolete DNA damage response, detection of DNA damage
namespace: biological_process
-def: "OBSOLETE. The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal." [GOC:go_curators]
+def: "OBSOLETE. The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal." [GOC:curators]
comment: This term has been obsoleted because it represents a molecular function.
synonym: "detection of DNA damage during DNA damage response" EXACT []
synonym: "DNA damage response, perception of DNA damage" RELATED []
@@ -254679,7 +257878,7 @@
name: signal transduction in response to DNA damage
namespace: biological_process
alt_id: GO:0006975
-def: "A cascade of processes induced by the detection of DNA damage within a cell." [GOC:go_curators]
+def: "A cascade of processes induced by the detection of DNA damage within a cell." [GOC:curators]
synonym: "DNA damage induced protein phosphorylation" NARROW []
synonym: "DNA damage response, signal transduction" EXACT []
synonym: "response to DNA damage stimulus by intracellular signaling cascade" EXACT [GOC:dph, GOC:tb]
@@ -254691,7 +257890,7 @@
id: GO:0042771
name: intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
namespace: biological_process
-def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered." [GOC:curators, GOC:mtg_apoptosis]
synonym: "DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis" RELATED []
is_a: GO:0008630 ! intrinsic apoptotic signaling pathway in response to DNA damage
is_a: GO:0072332 ! intrinsic apoptotic signaling pathway by p53 class mediator
@@ -254700,7 +257899,7 @@
id: GO:0042772
name: DNA damage response, signal transduction resulting in transcription
namespace: biological_process
-def: "A cascade of processes initiated in response to the detection of DNA damage, and resulting in the induction of transcription." [GOC:go_curators]
+def: "A cascade of processes initiated in response to the detection of DNA damage, and resulting in the induction of transcription." [GOC:curators]
is_a: GO:0042770 ! signal transduction in response to DNA damage
[Term]
@@ -254762,14 +257961,14 @@
id: GO:0042778
name: tRNA end turnover
namespace: biological_process
-def: "The process in which the 3'-terminal CCA of a tRNA is removed and restored. This often happens to uncharged tRNA." [GOC:go_curators]
+def: "The process in which the 3'-terminal CCA of a tRNA is removed and restored. This often happens to uncharged tRNA." [GOC:curators]
is_a: GO:0006399 ! tRNA metabolic process
[Term]
id: GO:0042779
name: obsolete tRNA 3'-trailer cleavage
namespace: biological_process
-def: "OBSOLETE. Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both." [GOC:go_curators]
+def: "OBSOLETE. Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both." [GOC:curators]
comment: The reason for obsoletion is that the term represents a molecular function.
synonym: "removal of tRNA 3'-trailer sequence" EXACT []
synonym: "tRNA 3'-end cleavage" EXACT []
@@ -254781,7 +257980,7 @@
id: GO:0042780
name: tRNA 3'-end processing
namespace: biological_process
-def: "The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA." [GOC:go_curators]
+def: "The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA." [GOC:curators]
synonym: "tRNA 3' processing" EXACT []
is_a: GO:0008033 ! tRNA processing
is_a: GO:0031123 ! RNA 3'-end processing
@@ -255044,13 +258243,14 @@
synonym: "histone methyltransferase activity (H3-K4 specific)" EXACT []
synonym: "histone-H3K4 methyltransferase activity" EXACT []
xref: Reactome:R-HSA-1214188 "PRDM9 trimethylates histone H3"
-xref: Reactome:R-HSA-3364026 "SET1 complex trimethylates H3K4 at the MYC gene"
+xref: Reactome:R-HSA-3364026 "MLL2 complex trimethylates H3K4 at the MYC gene"
xref: Reactome:R-HSA-8865498 "KMT2A trimethylates nucleosomes at the SPI1 gene locus producing H3K4Me3 mark"
xref: Reactome:R-HSA-8936481 "Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter"
xref: Reactome:R-HSA-8936621 "Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter"
xref: Reactome:R-HSA-8937016 "Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter"
xref: Reactome:R-HSA-8937050 "Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter"
-xref: Reactome:R-HSA-9843121 "KMT2D,(KMT2C) complex monomethylates nucleosomes at PPARG:RXRA-bound enhancers"
+xref: Reactome:R-HSA-9843121 "MLL4-ASCOM, (MLL3-ASCOM) complex monomethylates nucleosomes at PPARG:RXRA-bound enhancers"
+xref: Reactome:R-HSA-9909628 "Trimethylation of CD274 gene chromatin by MLL1/3 complex"
is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
is_a: GO:0140938 ! histone H3 methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24866" xsd:anyURI
@@ -255180,7 +258380,7 @@
id: GO:0042813
name: Wnt receptor activity
namespace: molecular_function
-def: "Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:go_curators]
+def: "Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity." [GOC:curators]
subset: goslim_chembl
synonym: "frizzled receptor activity" RELATED []
synonym: "frizzled-2 receptor activity" RELATED []
@@ -255278,7 +258478,7 @@
[Term]
id: GO:0042822
-name: pyridoxal phosphate metabolic process
+name: pyridoxal 5'-phosphate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6." [GOC:jl]
synonym: "active vitamin B6 metabolic process" EXACT []
@@ -255291,7 +258491,7 @@
[Term]
id: GO:0042823
-name: pyridoxal phosphate biosynthetic process
+name: pyridoxal 5'-phosphate biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6." [GOC:jl]
synonym: "active vitamin B6 biosynthesis" EXACT []
@@ -255302,7 +258502,7 @@
synonym: "pyridoxal phosphate synthesis" EXACT []
xref: MetaCyc:PWY0-845
is_a: GO:0042819 ! vitamin B6 biosynthetic process
-is_a: GO:0042822 ! pyridoxal phosphate metabolic process
+is_a: GO:0042822 ! pyridoxal 5'-phosphate metabolic process
is_a: GO:0046184 ! aldehyde biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
@@ -255367,7 +258567,7 @@
id: GO:0042834
name: peptidoglycan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls." [GOC:go_curators, PMID:14698226]
+def: "Interacting selectively and non-covalently, in a non-covalent manner, with peptidoglycan, any of a class of glycoconjugates found in bacterial cell walls." [GOC:curators, PMID:14698226]
is_a: GO:0005539 ! glycosaminoglycan binding
[Term]
@@ -255413,9 +258613,14 @@
synonym: "D-glucarate degradation" EXACT []
synonym: "saccharate catabolic process" EXACT []
synonym: "saccharate catabolism" EXACT []
+xref: MetaCyc:GLUCARDEG-PWY
+xref: MetaCyc:PWY-6499
is_a: GO:0016052 ! carbohydrate catabolic process
-is_a: GO:0019394 ! glucarate catabolic process
+is_a: GO:0019579 ! aldaric acid catabolic process
is_a: GO:0042836 ! D-glucarate metabolic process
+property_value: skos:narrowMatch MetaCyc:GLUCARDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6499
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0042839
@@ -255478,8 +258683,21 @@
synonym: "D-xylose breakdown" EXACT []
synonym: "D-xylose catabolism" EXACT []
synonym: "D-xylose degradation" EXACT []
+xref: MetaCyc:PWY-5516
+xref: MetaCyc:PWY-6760
+xref: MetaCyc:PWY-7294
+xref: MetaCyc:PWY-8020
+xref: MetaCyc:PWY-8330
+xref: MetaCyc:XYLCAT-PWY
is_a: GO:0019323 ! pentose catabolic process
is_a: GO:0042732 ! D-xylose metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5516
+property_value: skos:narrowMatch MetaCyc:PWY-6760
+property_value: skos:narrowMatch MetaCyc:PWY-7294
+property_value: skos:narrowMatch MetaCyc:PWY-8020
+property_value: skos:narrowMatch MetaCyc:PWY-8330
+property_value: skos:narrowMatch MetaCyc:XYLCAT-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0042844
@@ -255566,48 +258784,55 @@
[Term]
id: GO:0042851
-name: L-alanine metabolic process
+name: obsolete L-alanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid." [GOC:jl, GOC:jsg, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways involving L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid." [GOC:jl, GOC:jsg, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "L-alanine metabolism" EXACT []
-is_a: GO:0006522 ! alanine metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+xref: Reactome:R-HSA-8964540 "Alanine metabolism"
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0042852
+consider: GO:0042853
[Term]
id: GO:0042852
name: L-alanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid." [GOC:jl, GOC:jsg, GOC:mah, MetaCyc:PWY0-1061]
+def: "The chemical reactions and pathways resulting in the formation of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid." [GOC:jl, GOC:jsg, GOC:mah]
synonym: "L-alanine anabolism" EXACT []
synonym: "L-alanine biosynthesis" EXACT []
synonym: "L-alanine formation" EXACT []
synonym: "L-alanine synthesis" EXACT []
-xref: MetaCyc:PWY0-1061
+xref: MetaCyc:ALANINE-SYN2-PWY
+xref: MetaCyc:ALANINE-VALINESYN-PWY
+xref: MetaCyc:PWY0-1021
is_a: GO:0006523 ! alanine biosynthetic process
is_a: GO:0009079 ! pyruvate family amino acid biosynthetic process
-is_a: GO:0042851 ! L-alanine metabolic process
-property_value: skos:exactMatch MetaCyc:PWY0-1061
+property_value: skos:narrowMatch MetaCyc:ALANINE-SYN2-PWY
+property_value: skos:narrowMatch MetaCyc:ALANINE-VALINESYN-PWY
+property_value: skos:narrowMatch MetaCyc:PWY0-1021
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29444" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
[Term]
id: GO:0042853
name: L-alanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid." [GOC:jl, GOC:jsg, GOC:mah]
+def: "The chemical reactions and pathways resulting in the breakdown of L-alanine." [GOC:curators]
synonym: "L-alanine breakdown" EXACT []
synonym: "L-alanine catabolism" EXACT []
synonym: "L-alanine degradation" EXACT []
xref: MetaCyc:ALACAT2-PWY
xref: MetaCyc:ALADEG-PWY
xref: MetaCyc:ALANINE-DEG3-PWY
-is_a: GO:0042851 ! L-alanine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:ALACAT2-PWY
property_value: skos:narrowMatch MetaCyc:ALADEG-PWY
property_value: skos:narrowMatch MetaCyc:ALANINE-DEG3-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
[Term]
id: GO:0042854
@@ -255784,11 +259009,12 @@
id: GO:0042866
name: pyruvate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate." [GOC:curators]
synonym: "pyruvate anabolism" EXACT []
synonym: "pyruvate biosynthesis" EXACT []
synonym: "pyruvate formation" EXACT []
synonym: "pyruvate synthesis" EXACT []
+xref: Reactome:R-HSA-70268 "Pyruvate metabolism"
is_a: GO:0006090 ! pyruvate metabolic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
@@ -255796,7 +259022,7 @@
id: GO:0042867
name: pyruvate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pyruvate, 2-oxopropanoate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of pyruvate, 2-oxopropanoate." [GOC:curators]
synonym: "pyruvate breakdown" EXACT []
synonym: "pyruvate catabolism" EXACT []
synonym: "pyruvate degradation" EXACT []
@@ -255815,7 +259041,7 @@
id: GO:0042869
name: aldarate transmembrane transport
namespace: biological_process
-def: "The process in which aldarate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators]
+def: "The process in which aldarate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:curators]
synonym: "aldarate transport" RELATED []
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -255859,7 +259085,7 @@
id: GO:0042876
name: aldarate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of aldarate from one side of a membrane to the other." [GOC:go_curators, PMID:15034926]
+def: "Enables the transfer of aldarate from one side of a membrane to the other." [GOC:curators, PMID:15034926]
is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:0042869 ! aldarate transmembrane transport
@@ -255891,13 +259117,16 @@
[Term]
id: GO:0042881
-name: D-galactonate transmembrane transporter activity
+name: D-galactonate:proton symporter activity
namespace: molecular_function
-def: "Enables the transfer of D-galactonate, the D-enantiomer of galactonate, from one side of a membrane to the other." [GOC:jl, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
-is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: D-galactonate(out) + H+(out) = D-galactonate(in) + H+(in)." [RHEA:29835]
+synonym: "D-galactonate transmembrane transporter activity" BROAD []
+xref: RHEA:29835
+is_a: GO:0005351 ! carbohydrate:proton symporter activity
+is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
is_a: GO:0042879 ! aldonate transmembrane transporter activity
relationship: part_of GO:0042875 ! D-galactonate transmembrane transport
+property_value: skos:exactMatch RHEA:29835
[Term]
id: GO:0042882
@@ -256135,7 +259364,7 @@
name: xenobiotic transport
namespace: biological_process
alt_id: GO:0015893
-def: "The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
+def: "The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:curators, GOC:krc]
subset: goslim_pir
synonym: "drug transport" RELATED []
is_a: GO:0006810 ! transport
@@ -256159,7 +259388,7 @@
alt_id: GO:0015559
alt_id: GO:0015564
alt_id: GO:0090484
-def: "Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
+def: "Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:curators, GOC:krc]
subset: goslim_metagenomics
synonym: "drug transmembrane transporter activity" RELATED []
synonym: "drug transporter activity" RELATED []
@@ -256169,6 +259398,15 @@
synonym: "xenobiotic transporter activity" RELATED []
xref: Reactome:R-HSA-5625574 "Defective SLC22A18 does not exchange extracellular organic cations for cytosolic H+"
xref: Reactome:R-HSA-597628 "SLC22A18 exchanges extracellular organic cations for cytosolic H+"
+xref: Reactome:R-HSA-9911512 "AcrA:AcrB:TolC transports antibiotics from the cytosol to the periplasm"
+xref: Reactome:R-HSA-9911517 "MdfA transports tetracyclines from the cytosol to the periplasmic space"
+xref: Reactome:R-HSA-9913106 "TetB exports tetracyclines"
+xref: Reactome:R-HSA-9913128 "TetA exports tetracyclines"
+xref: Reactome:R-HSA-9913437 "Pef exports fluoroquinolones"
+xref: Reactome:R-HSA-9913672 "OqxA exports fluoroquinolones"
+xref: Reactome:R-HSA-9914089 "MdtE:MdtF:TolC exports beta-lactams to the periplasm"
+xref: Reactome:R-HSA-9931163 "Gdx dimer exports cationic aromatics to periplasm"
+xref: Reactome:R-HSA-9931565 "EmrE dimer exports xenobiotics to periplasm"
is_a: GO:0022857 ! transmembrane transporter activity
relationship: part_of GO:0042908 ! xenobiotic transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19460" xsd:anyURI
@@ -256234,7 +259472,7 @@
id: GO:0042920
name: 3-hydroxyphenylpropionic acid transmembrane transport
namespace: biological_process
-def: "The directed movement of 3-hydroxyphenylpropionic acid across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators, PMID:9098055]
+def: "The directed movement of 3-hydroxyphenylpropionic acid across a lipid bilayer, from one side of a membrane to the other." [GOC:curators, PMID:9098055]
synonym: "3-(3-hydroxyphenyl)propionic acid transport" EXACT []
synonym: "3-hydroxyphenylpropionic acid transport" BROAD []
synonym: "m-hydroxyphenylpropionic acid transport" EXACT []
@@ -256331,6 +259569,8 @@
def: "Enables the directed movement of the siderochrome enterochelin, a cyclic trimer of 2, 3 dihydroxybenzoylserine from one side of a membrane to the other." [GOC:jl]
synonym: "enterobactin transporter activity" RELATED []
synonym: "enterochelin transporter activity" EXACT []
+xref: Reactome:R-HSA-9911595 "EntS transports enterobactin from cytosol to periplasmic space"
+xref: Reactome:R-HSA-9911600 "Efflux pump complexes transport enterobactin from periplasmic space to extracellular region"
is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
relationship: part_of GO:0042930 ! enterobactin transport
@@ -256609,7 +259849,7 @@
id: GO:0042964
name: obsolete thioredoxin reduction
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the reduction of thioredoxin, a small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the reduction of thioredoxin, a small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
synonym: "thioredoxin anabolism" EXACT []
synonym: "thioredoxin biosynthesis" EXACT []
@@ -256622,7 +259862,7 @@
id: GO:0042965
name: obsolete glutaredoxin biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a small disulfide-containing redox protein that serves as a glutathione-disulfide oxidoreductase." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a small disulfide-containing redox protein that serves as a glutathione-disulfide oxidoreductase." [GOC:curators]
comment: This term was made obsolete because it refers to the biosynthesis of a protein.
synonym: "glutaredoxin anabolism" EXACT []
synonym: "glutaredoxin biosynthesis" EXACT []
@@ -256634,7 +259874,7 @@
id: GO:0042966
name: biotin carboxyl carrier protein biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of the biotin carboxyl carrier protein, a subunit of acetyl-coenzyme A carboxylase." [GOC:go_curators, PMID:8102363]
+def: "The chemical reactions and pathways resulting in the formation of the biotin carboxyl carrier protein, a subunit of acetyl-coenzyme A carboxylase." [GOC:curators, PMID:8102363]
synonym: "BCCP biosynthesis" EXACT []
synonym: "BCCP biosynthetic process" EXACT []
synonym: "biotin carboxyl carrier protein anabolism" EXACT []
@@ -256647,7 +259887,7 @@
id: GO:0042967
name: obsolete acyl-carrier-protein biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acyl-carrier protein." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acyl-carrier protein." [GOC:curators]
comment: The reason for obsoletion is that acyl-carrier-protein is synthesized by the ribosome like any other protein.
synonym: "ACP biosynthesis" EXACT []
synonym: "ACP biosynthetic process" EXACT []
@@ -256674,7 +259914,7 @@
id: GO:0042969
name: obsolete lactone transport
namespace: biological_process
-def: "OBSOLETE. The directed movement of lactone from one side of a membrane to the other. A lactone is a cyclic ester of a hydroxy carboxylic acid, containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:go_curators]
+def: "OBSOLETE. The directed movement of lactone from one side of a membrane to the other. A lactone is a cyclic ester of a hydroxy carboxylic acid, containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:curators]
comment: This term aws obsoleted because there is no evidence for a specific pathway to transport lactone.
is_obsolete: true
@@ -256682,7 +259922,7 @@
id: GO:0042970
name: L-homoserine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of homoserine from one side of a membrane to the other. Homoserine is alpha-amino-gamma-hydroxybutyric acid, an intermediate in the biosynthesis of cystathionine, threonine and methionine." [GOC:go_curators, ISBN:0198506732]
+def: "Enables the transfer of homoserine from one side of a membrane to the other. Homoserine is alpha-amino-gamma-hydroxybutyric acid, an intermediate in the biosynthesis of cystathionine, threonine and methionine." [GOC:curators, ISBN:0198506732]
synonym: "homoserine transmembrane transporter activity" BROAD []
synonym: "homoserine transporter activity" BROAD []
is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
@@ -256694,7 +259934,7 @@
id: GO:0042971
name: obsolete lactone transmembrane transporter activity
namespace: molecular_function
-def: "OBSOLETE. Enables the transfer of lactone from one side of a membrane to the other. A lactone is a cyclic ester of a hydroxy carboxylic acid, containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:go_curators]
+def: "OBSOLETE. Enables the transfer of lactone from one side of a membrane to the other. A lactone is a cyclic ester of a hydroxy carboxylic acid, containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring." [GOC:curators]
comment: This term was obsoleted because there is no evidence for a specific lactone transporter.
is_obsolete: true
@@ -256791,6 +260031,7 @@
namespace: molecular_function
def: "Binds to and increases ornithine decarboxylase activity." [GOC:jl]
synonym: "L-ornithine carboxy-lyase activator activity" NARROW []
+xref: Reactome:R-HSA-9955574 "ODC dimerizes"
is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0042979 ! ornithine decarboxylase regulator activity
relationship: positively_regulates GO:0004586 ! ornithine decarboxylase activity
@@ -256833,7 +260074,7 @@
id: GO:0042982
name: amyloid precursor protein metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators]
+def: "The chemical reactions and pathways involving amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:curators]
synonym: "amyloid precursor protein metabolism" EXACT []
synonym: "APP metabolic process" EXACT []
synonym: "APP metabolism" EXACT []
@@ -256843,7 +260084,7 @@
id: GO:0042983
name: amyloid precursor protein biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:curators]
synonym: "amyloid precursor protein anabolism" EXACT []
synonym: "amyloid precursor protein biosynthesis" EXACT []
synonym: "amyloid precursor protein formation" EXACT []
@@ -256857,7 +260098,7 @@
id: GO:0042984
name: regulation of amyloid precursor protein biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:curators]
synonym: "regulation of amyloid precursor protein anabolism" EXACT []
synonym: "regulation of amyloid precursor protein biosynthesis" EXACT []
synonym: "regulation of amyloid precursor protein formation" EXACT []
@@ -256873,7 +260114,7 @@
id: GO:0042985
name: negative regulation of amyloid precursor protein biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:curators]
synonym: "down regulation of amyloid precursor protein biosynthetic process" EXACT []
synonym: "down-regulation of amyloid precursor protein biosynthetic process" EXACT []
synonym: "downregulation of amyloid precursor protein biosynthetic process" EXACT []
@@ -256894,7 +260135,7 @@
id: GO:0042986
name: positive regulation of amyloid precursor protein biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta." [GOC:curators]
synonym: "activation of amyloid precursor protein biosynthetic process" NARROW []
synonym: "positive regulation of amyloid precursor protein anabolism" EXACT []
synonym: "positive regulation of amyloid precursor protein biosynthesis" EXACT []
@@ -256916,7 +260157,7 @@
id: GO:0042987
name: amyloid precursor protein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of amyloid precursor protein (APP), the precursor of amyloid-beta, a glycoprotein associated with Alzheimer's disease." [GOC:curators]
synonym: "amyloid precursor protein breakdown" EXACT []
synonym: "amyloid precursor protein catabolism" EXACT []
synonym: "amyloid precursor protein degradation" EXACT []
@@ -256936,7 +260177,7 @@
id: GO:0042989
name: obsolete sequestering of actin monomers
namespace: biological_process
-def: "OBSOLETE. The selective interaction of actin monomers with specific molecules that inhibit their polymerization by preventing their access to other monomers." [GOC:go_curators]
+def: "OBSOLETE. The selective interaction of actin monomers with specific molecules that inhibit their polymerization by preventing their access to other monomers." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function, not biological process
synonym: "actin monomer retention" EXACT []
synonym: "actin monomer sequestering" EXACT []
@@ -257215,7 +260456,7 @@
namespace: biological_process
alt_id: GO:0001747
alt_id: GO:0031075
-def: "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:go_curators, GOC:mtg_sensu]
+def: "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." [GOC:curators, GOC:mtg_sensu]
is_a: GO:0001654 ! eye development
[Term]
@@ -257234,8 +260475,8 @@
namespace: biological_process
def: "Any process that modulates the binding and fusion of a sperm to the oocyte plasma membrane." [GOC:jl, PMID:11483596]
synonym: "regulation of sperm-oocyte fusion" NARROW []
+is_a: GO:0050794 ! regulation of cellular process
is_a: GO:0051239 ! regulation of multicellular organismal process
-is_a: GO:1903729 ! regulation of plasma membrane organization
is_a: GO:2000241 ! regulation of reproductive process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0007342 ! fusion of sperm to egg plasma membrane involved in single fertilization
@@ -257253,7 +260494,7 @@
synonym: "inhibition of sperm-oocyte fusion" NARROW []
synonym: "negative regulation of sperm-oocyte fusion" NARROW []
is_a: GO:0043012 ! regulation of fusion of sperm to egg plasma membrane
-is_a: GO:0051129 ! negative regulation of cellular component organization
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:2000242 ! negative regulation of reproductive process
intersection_of: GO:0065007 ! biological regulation
@@ -257291,7 +260532,7 @@
id: GO:0043021
name: ribonucleoprotein complex binding
namespace: molecular_function
-def: "Binding to a complex of RNA and protein." [GOC:bf, GOC:go_curators, GOC:vk]
+def: "Binding to a complex of RNA and protein." [GOC:bf, GOC:curators, GOC:vk]
subset: goslim_pir
synonym: "protein-RNA complex binding" EXACT [GOC:bf, GOC:vk]
synonym: "ribonucleoprotein binding" EXACT [GOC:bf, GOC:vk]
@@ -257303,7 +260544,7 @@
name: ribosome binding
namespace: molecular_function
alt_id: GO:0030376
-def: "Binding to a ribosome." [GOC:go_curators]
+def: "Binding to a ribosome." [GOC:curators]
synonym: "ribosome receptor activity" NARROW []
is_a: GO:0043021 ! ribonucleoprotein complex binding
@@ -257311,21 +260552,21 @@
id: GO:0043023
name: ribosomal large subunit binding
namespace: molecular_function
-def: "Binding to a large ribosomal subunit." [GOC:go_curators]
+def: "Binding to a large ribosomal subunit." [GOC:curators]
is_a: GO:0043022 ! ribosome binding
[Term]
id: GO:0043024
name: ribosomal small subunit binding
namespace: molecular_function
-def: "Binding to a small ribosomal subunit." [GOC:go_curators]
+def: "Binding to a small ribosomal subunit." [GOC:curators]
is_a: GO:0043022 ! ribosome binding
[Term]
id: GO:0043025
name: neuronal cell body
namespace: cellular_component
-def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:go_curators]
+def: "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." [GOC:curators]
comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
subset: goslim_pir
synonym: "neuron cell body" EXACT []
@@ -257507,7 +260748,7 @@
id: GO:0043045
name: epigenetic programming of gene expression
namespace: biological_process
-def: "A epigenetic process that happens during embryonic development that modulates gene expression potential at later stages of development of the organism, including the adult. Epigenetic regulation takes place via chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine DNA methylation." [GOC:go_curators, PMID:12138111, PMID:22868271]
+def: "A epigenetic process that happens during embryonic development that modulates gene expression potential at later stages of development of the organism, including the adult. Epigenetic regulation takes place via chromatin remodeling either by modifying higher order chromatin fiber structure, nucleosomal histones, or cytosine DNA methylation." [GOC:curators, PMID:12138111, PMID:22868271]
synonym: "de novo DNA methylation" RELATED []
synonym: "DNA methylation involved in embryo development" RELATED []
synonym: "epigenetic regulation of embryonic gene expression" RELATED []
@@ -257519,7 +260760,7 @@
id: GO:0043046
name: obsolete DNA methylation involved in gamete generation
namespace: biological_process
-def: "OBSOLETE. The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete." [GOC:go_curators, PMID:12138111]
+def: "OBSOLETE. The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete." [GOC:curators, PMID:12138111]
comment: This term was obsoleted because it represent the same process as genomic imprinting ; GO:0071514 .
synonym: "de novo DNA methylation" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25313" xsd:anyURI
@@ -257532,7 +260773,7 @@
namespace: molecular_function
def: "Binding to single-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
synonym: "telomeric ssDNA binding" EXACT [GOC:mah]
-is_a: GO:0042162 ! telomeric DNA binding
+is_a: GO:0042162 ! telomeric repeat DNA binding
is_a: GO:0098847 ! sequence-specific single stranded DNA binding
[Term]
@@ -257545,6 +260786,7 @@
synonym: "dolichyl monophosphate formation" EXACT []
synonym: "dolichyl monophosphate synthesis" EXACT []
xref: MetaCyc:PWY-6129
+xref: Reactome:R-HSA-446199 "Synthesis of dolichyl-phosphate"
is_a: GO:0008654 ! phospholipid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30675" xsd:anyURI
@@ -257552,7 +260794,7 @@
id: GO:0043049
name: otic placode formation
namespace: biological_process
-def: "The initial developmental process that will lead to the formation of the vertebrate inner ear. The otic placode forms as a thickening of the head ectoderm adjacent to the developing hindbrain." [GOC:go_curators, PMID:12668634]
+def: "The initial developmental process that will lead to the formation of the vertebrate inner ear. The otic placode forms as a thickening of the head ectoderm adjacent to the developing hindbrain." [GOC:curators, PMID:12668634]
is_a: GO:0060788 ! ectodermal placode formation
relationship: part_of GO:0030916 ! otic vesicle formation
@@ -257617,21 +260859,21 @@
id: GO:0043056
name: forward locomotion
namespace: biological_process
-def: "Anterior movement of an organism, following the direction of the head of the animal." [GOC:go_curators]
+def: "Anterior movement of an organism, following the direction of the head of the animal." [GOC:curators]
is_a: GO:0033058 ! directional locomotion
[Term]
id: GO:0043057
name: backward locomotion
namespace: biological_process
-def: "Posterior movement of an organism, e.g. following the direction of the tail of an animal." [GOC:go_curators]
+def: "Posterior movement of an organism, e.g. following the direction of the tail of an animal." [GOC:curators]
is_a: GO:0033058 ! directional locomotion
[Term]
id: GO:0043058
name: regulation of backward locomotion
namespace: biological_process
-def: "Any process that modulates the speed, mechanical force, or rhythm of the posterior movement of an organism." [GOC:go_curators]
+def: "Any process that modulates the speed, mechanical force, or rhythm of the posterior movement of an organism." [GOC:curators]
is_a: GO:0040012 ! regulation of locomotion
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0043057 ! backward locomotion
@@ -257641,7 +260883,7 @@
id: GO:0043059
name: regulation of forward locomotion
namespace: biological_process
-def: "Any process that modulates the speed, mechanical force, or rhythm of the anterior movement of an organism." [GOC:go_curators]
+def: "Any process that modulates the speed, mechanical force, or rhythm of the anterior movement of an organism." [GOC:curators]
is_a: GO:0040012 ! regulation of locomotion
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0043056 ! forward locomotion
@@ -257797,7 +261039,7 @@
id: GO:0043073
name: germ cell nucleus
namespace: cellular_component
-def: "The nucleus of a germ cell, a reproductive cell in multicellular organisms." [CL:0000586, GOC:go_curators]
+def: "The nucleus of a germ cell, a reproductive cell in multicellular organisms." [CL:0000586, GOC:curators]
synonym: "germ-cell nucleus" EXACT []
is_a: GO:0005634 ! nucleus
@@ -257861,7 +261103,9 @@
def: "The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released." [GOC:jl, PMID:30784960]
subset: goslim_synapse
xref: NIF_Subcellular:sao243541954
-is_a: GO:0005576 ! extracellular region
+is_a: GO:0110165 ! cellular anatomical structure
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0043084
@@ -257994,7 +261238,7 @@
name: purine nucleobase salvage
namespace: biological_process
def: "Any process that generates purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, from derivatives of them without de novo synthesis." [GOC:jl]
-synonym: "purine base salvage" EXACT [GOC:go_curators]
+synonym: "purine base salvage" EXACT [GOC:curators]
is_a: GO:0009113 ! purine nucleobase biosynthetic process
is_a: GO:0043101 ! purine-containing compound salvage
@@ -258030,7 +261274,7 @@
name: pyrimidine nucleobase salvage
namespace: biological_process
def: "Any process that generates pyrimidine nucleobases, 1,3-diazine organic nitrogenous bases, from derivatives of them without de novo synthesis." [GOC:jl]
-synonym: "pyrimidine base salvage" EXACT [GOC:go_curators]
+synonym: "pyrimidine base salvage" EXACT [GOC:curators]
is_a: GO:0008655 ! pyrimidine-containing compound salvage
is_a: GO:0019856 ! pyrimidine nucleobase biosynthetic process
@@ -258094,7 +261338,7 @@
id: GO:0043107
name: type IV pilus-dependent motility
namespace: biological_process
-def: "Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility." [GOC:go_curators, PMID:12704238]
+def: "Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility." [GOC:curators, PMID:12704238]
synonym: "social gliding motility" NARROW []
synonym: "TFP-dependent motility" EXACT []
synonym: "TFP-dependent movement" EXACT []
@@ -258107,7 +261351,7 @@
id: GO:0043108
name: pilus retraction
namespace: biological_process
-def: "The process of withdrawing a pilus back into a cell." [GOC:go_curators, PMID:17355871]
+def: "The process of withdrawing a pilus back into a cell." [GOC:curators, PMID:17355871]
is_a: GO:0043711 ! pilus organization
[Term]
@@ -258348,7 +261592,6 @@
name: ubiquitin binding
namespace: molecular_function
def: "Binding to ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation." [GOC:ecd]
-xref: Reactome:R-HSA-1169404 "Transfer of ISG15 from E1 to E2 (UBCH8)"
xref: Reactome:R-HSA-205008 "Polyubiquitinated NRIF binds to p62 (Sequestosome)"
xref: Reactome:R-HSA-983152 "Transfer of ubiquitin from E1 to E2"
is_a: GO:0032182 ! ubiquitin-like protein binding
@@ -258413,7 +261656,7 @@
synonym: "glycerol-1-phosphatase activity" BROAD [EC:3.1.3.21]
synonym: "glycerol-3-phosphatase activity" BROAD []
xref: MetaCyc:RXN-14965
-xref: Reactome:R-HSA-8955794 "PGP:Mg2+ dimer hydrolyses 3PG to glycerol"
+xref: Reactome:R-HSA-8955794 "PGP:Mg2+ dimer hydrolyses G3P to glycerol"
xref: RHEA:66372
is_a: GO:0016791 ! phosphatase activity
property_value: skos:broadMatch EC:3.1.3.21
@@ -258468,6 +261711,7 @@
synonym: "DNA helicase IV activity" NARROW []
xref: EC:5.6.2.3
xref: Reactome:R-HSA-6782131 "ERCC2-facilitated RNA Pol II backtracking in TC-NER"
+xref: Reactome:R-HSA-9914438 "TWNK (PEO1) unwinds double-stranded mitochondrial DNA at the replication fork"
is_a: GO:0003678 ! DNA helicase activity
property_value: skos:exactMatch EC:5.6.2.3
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23533" xsd:anyURI
@@ -258493,7 +261737,7 @@
id: GO:0043144
name: sno(s)RNA processing
namespace: biological_process
-def: "Any process involved in the conversion of a primary snoRNA family RNA transcript into a mature snoRNA (eukaryota) or sRNA (archaea)." [GOC:go_curators, GOC:krc, PMID:12773397]
+def: "Any process involved in the conversion of a primary snoRNA family RNA transcript into a mature snoRNA (eukaryota) or sRNA (archaea)." [GOC:curators, GOC:krc, PMID:12773397]
subset: goslim_yeast
is_a: GO:0006396 ! RNA processing
is_a: GO:0016074 ! sno(s)RNA metabolic process
@@ -258503,7 +261747,7 @@
id: GO:0043145
name: sno(s)RNA 3'-end cleavage
namespace: biological_process
-def: "The endonucleolytic cleavage of snoRNA 3' ends, which is required for mature snoRNAs to be functional." [GOC:go_curators, PMID:12773397]
+def: "The endonucleolytic cleavage of snoRNA 3' ends, which is required for mature snoRNAs to be functional." [GOC:curators, PMID:12773397]
synonym: "sno(s)RNA 3' end cleavage" EXACT []
synonym: "snoRNA 3'-end cleavage" NARROW []
synonym: "sRNA 3'-end cleavage" NARROW []
@@ -258514,7 +261758,7 @@
id: GO:0043149
name: stress fiber assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a stress fiber. A stress fiber is a contractile actin filament bundle that consists of short actin filaments with alternating polarity." [GOC:go_curators, GOC:mah, PMID:16651381]
+def: "The aggregation, arrangement and bonding together of a set of components to form a stress fiber. A stress fiber is a contractile actin filament bundle that consists of short actin filaments with alternating polarity." [GOC:curators, GOC:mah, PMID:16651381]
synonym: "actin cable assembly" RELATED [GOC:mah]
synonym: "actin cable formation" RELATED [GOC:mah]
synonym: "stress fibre biosynthesis" RELATED []
@@ -258526,7 +261770,7 @@
id: GO:0043150
name: DNA synthesis involved in double-strand break repair via homologous recombination
namespace: biological_process
-def: "The synthesis of DNA that contributes to the process of double-strand break repair via homologous recombination." [GOC:go_curators]
+def: "The synthesis of DNA that contributes to the process of double-strand break repair via homologous recombination." [GOC:curators]
synonym: "DNA synthesis during double-strand break repair via homologous recombination" RELATED [GOC:dph, GOC:tb]
is_a: GO:0000731 ! DNA synthesis involved in DNA repair
intersection_of: GO:0071897 ! DNA biosynthetic process
@@ -258537,7 +261781,7 @@
id: GO:0043151
name: obsolete DNA synthesis involved in double-strand break repair via single-strand annealing
namespace: biological_process
-def: "OBSOLETE. The synthesis of DNA that contributes to the process of double-strand break repair via single-strand annealing." [GOC:go_curators]
+def: "OBSOLETE. The synthesis of DNA that contributes to the process of double-strand break repair via single-strand annealing." [GOC:curators]
comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
synonym: "DNA synthesis during double-strand break repair via single-strand annealing" RELATED [GOC:dph, GOC:tb]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31306" xsd:anyURI
@@ -258573,7 +261817,6 @@
synonym: "inhibition of caspase activity" NARROW []
synonym: "negative regulation of caspase activation" EXACT []
synonym: "negative regulation of caspase activity" BROAD []
-xref: Reactome:R-HSA-5218900 "CASP8 activity is inhibited"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
@@ -258631,7 +261874,7 @@
id: GO:0043160
name: acrosomal lumen
namespace: cellular_component
-def: "The volume enclosed within the acrosome membrane." [GOC:go_curators]
+def: "The volume enclosed within the acrosome membrane." [GOC:curators]
is_a: GO:0034774 ! secretory granule lumen
is_a: GO:0043202 ! lysosomal lumen
relationship: part_of GO:0001669 ! acrosomal vesicle
@@ -258640,7 +261883,7 @@
id: GO:0043161
name: proteasome-mediated ubiquitin-dependent protein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome." [GOC:curators]
synonym: "proteasomal pathway" EXACT []
synonym: "proteasomal processing" RELATED []
synonym: "proteasomal ubiquitin-dependent protein breakdown" EXACT []
@@ -258817,14 +262060,14 @@
id: GO:0043179
name: rhythmic excitation
namespace: biological_process
-def: "Any process involved in the generation of rhythmic, synchronous excitatory synaptic inputs in a neural circuit." [GOC:go_curators, ISBN:0195088433]
+def: "Any process involved in the generation of rhythmic, synchronous excitatory synaptic inputs in a neural circuit." [GOC:curators, ISBN:0195088433]
is_a: GO:0060024 ! rhythmic synaptic transmission
[Term]
id: GO:0043180
name: rhythmic inhibition
namespace: biological_process
-def: "Any process involved in the generation of rhythmic, synchronous inhibitory synaptic inputs in a neural circuit." [GOC:go_curators]
+def: "Any process involved in the generation of rhythmic, synchronous inhibitory synaptic inputs in a neural circuit." [GOC:curators]
is_a: GO:0060024 ! rhythmic synaptic transmission
[Term]
@@ -259056,7 +262299,7 @@
id: GO:0043207
name: response to external biotic stimulus
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things." [GOC:curators]
is_a: GO:0009605 ! response to external stimulus
is_a: GO:0009607 ! response to biotic stimulus
@@ -259247,8 +262490,6 @@
synonym: "anion-transporting ATPase activity" EXACT []
synonym: "ATP-dependent anion transmembrane transporter activity" EXACT []
synonym: "ATPase-coupled anion transmembrane transporter activity" EXACT []
-xref: Reactome:R-HSA-1454916 "The ABCC family mediates organic anion transport"
-xref: Reactome:R-HSA-5690340 "Defective ABCC6 does not transport organic anion from cytosol to extracellular region"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
replaced_by: GO:0042626
@@ -259257,7 +262498,7 @@
id: GO:0043226
name: organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." [GOC:curators]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_pir
@@ -259271,7 +262512,7 @@
id: GO:0043227
name: membrane-bounded organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "membrane-enclosed organelle" EXACT []
xref: NIF_Subcellular:sao414196390
@@ -259285,7 +262526,7 @@
id: GO:0043228
name: membraneless organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_mouse
synonym: "biological condensate" RELATED []
@@ -259302,7 +262543,7 @@
id: GO:0043229
name: intracellular organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_pir
is_a: GO:0043226 ! organelle
@@ -259326,7 +262567,7 @@
id: GO:0043231
name: intracellular membrane-bounded organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "intracellular membrane-enclosed organelle" EXACT []
@@ -259339,7 +262580,7 @@
id: GO:0043232
name: intracellular membraneless organelle
namespace: cellular_component
-def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
+def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "intracellular non-membrane-bounded organelle" EXACT []
@@ -259363,11 +262604,13 @@
[Term]
id: GO:0043235
-name: receptor complex
+name: signaling receptor complex
namespace: cellular_component
-def: "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:go_curators]
+def: "Any protein complex that binds a signaling molecule such as a hormone, neurotransmitter, molecular pattern recognition receptor (PAMPs and DAMPS), or an intracellular messenger to initiate a change in cell function." [GOC:curators]
subset: goslim_pir
+synonym: "receptor complex" BROAD []
is_a: GO:0032991 ! protein-containing complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31605" xsd:anyURI
[Term]
id: GO:0043236
@@ -259385,7 +262628,7 @@
id: GO:0043237
name: laminin-1 binding
namespace: molecular_function
-def: "Binding to laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1." [GOC:go_curators]
+def: "Binding to laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1." [GOC:curators]
synonym: "laminin-111 binding" EXACT [GOC:dph, PMID:15979864]
is_a: GO:0043236 ! laminin binding
@@ -259472,7 +262715,7 @@
id: GO:0043248
name: proteasome assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a mature, active proteasome complex." [GOC:go_curators, PMID:10872471]
+def: "The aggregation, arrangement and bonding together of a mature, active proteasome complex." [GOC:curators, PMID:10872471]
synonym: "26S proteasome assembly" NARROW []
synonym: "proteasome complex assembly" EXACT []
synonym: "proteasome maturation" EXACT []
@@ -259493,7 +262736,7 @@
id: GO:0043250
name: obsolete sodium-dependent organic anion transmembrane transporter activity
namespace: molecular_function
-def: "OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other, in a sodium dependent manner." [GOC:go_curators]
+def: "OBSOLETE. Enables the transfer of organic anions from one side of a membrane to the other, in a sodium dependent manner." [GOC:curators]
comment: The reason for obsoletion is that this term was an unnecessary and confusing grouping term.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
is_obsolete: true
@@ -259503,15 +262746,15 @@
id: GO:0043251
name: sodium-dependent organic anion transport
namespace: biological_process
-def: "The directed, sodium-dependent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+def: "The directed, sodium-dependent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
is_a: GO:0015711 ! organic anion transport
[Term]
id: GO:0043252
name: sodium-independent organic anion transport
namespace: biological_process
-def: "The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
-xref: Reactome:R-HSA-879518 "Transport of organic anions"
+def: "The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
+xref: Reactome:R-HSA-879518 "Organic anion transport by SLCO transporters"
is_a: GO:0015711 ! organic anion transport
[Term]
@@ -259558,10 +262801,10 @@
def: "A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes." [PMID:15979864, PMID:21421915, PMID:23263632]
subset: goslim_pir
synonym: "laminin complex" BROAD []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0140144 ! non-collagenous component of basement membrane
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140349 ! laminin network
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30807" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31490" xsd:anyURI
[Term]
id: GO:0043257
@@ -259895,7 +263138,6 @@
comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "regulation of caspase activation" NARROW []
synonym: "regulation of caspase activity" BROAD []
-xref: Reactome:R-HSA-205025 "NADE modulates death signalling"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
@@ -259903,7 +263145,7 @@
id: GO:0043282
name: chordate pharyngeal muscle development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the pharyngeal muscle over time, from its formation to the mature structure. A pharyngeal muscle is any muscle that forms part of the pharynx." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the pharyngeal muscle over time, from its formation to the mature structure. A pharyngeal muscle is any muscle that forms part of the pharynx." [GOC:curators]
is_a: GO:0007517 ! muscle organ development
relationship: part_of GO:0160093 ! chordate pharynx development
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18285" xsd:anyURI
@@ -259979,7 +263221,7 @@
id: GO:0043292
name: contractile muscle fiber
namespace: cellular_component
-def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:go_curators, ISBN:0815316194]
+def: "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." [GOC:curators, ISBN:0815316194]
synonym: "contractile fibre" EXACT []
is_a: GO:0043232 ! intracellular membraneless organelle
is_a: GO:0099512 ! supramolecular fiber
@@ -260020,7 +263262,7 @@
id: GO:0043296
name: apical junction complex
namespace: cellular_component
-def: "A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability." [GOC:go_curators, GOC:kmv, PMID:12525486, PMID:15196556]
+def: "A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability." [GOC:curators, GOC:kmv, PMID:12525486, PMID:15196556]
synonym: "apical cell junction complex" EXACT [GOC:mah]
synonym: "apical junction" EXACT []
is_a: GO:0005911 ! cell-cell junction
@@ -260029,7 +263271,7 @@
id: GO:0043297
name: apical junction assembly
namespace: biological_process
-def: "The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents." [GOC:go_curators, PMID:10854689, PMID:14729475, PMID:15196556]
+def: "The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents." [GOC:curators, PMID:10854689, PMID:14729475, PMID:15196556]
synonym: "apical junction complex assembly" EXACT [GOC:mah]
is_a: GO:0007043 ! cell-cell junction assembly
@@ -260448,14 +263690,14 @@
id: GO:0043325
name: phosphatidylinositol-3,4-bisphosphate binding
namespace: molecular_function
-def: "Binding to phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions." [GOC:bf, GOC:go_curators]
+def: "Binding to phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions." [GOC:bf, GOC:curators]
is_a: GO:1902936 ! phosphatidylinositol bisphosphate binding
[Term]
id: GO:0043326
name: chemotaxis to folate
namespace: biological_process
-def: "The directed movement of a motile cell or organism in response to the presence of folate." [GOC:go_curators]
+def: "The directed movement of a motile cell or organism in response to the presence of folate." [GOC:curators]
is_a: GO:0006935 ! chemotaxis
is_a: GO:0051593 ! response to folic acid
@@ -260463,7 +263705,7 @@
id: GO:0043327
name: chemotaxis to cAMP
namespace: biological_process
-def: "The directed movement of a motile cell or organism in response to the presence of 3',5'-cAMP." [GOC:go_curators]
+def: "The directed movement of a motile cell or organism in response to the presence of 3',5'-cAMP." [GOC:curators]
synonym: "chemotaxis to 3',5' cAMP" EXACT []
synonym: "chemotaxis to 3',5'-cAMP" EXACT []
synonym: "chemotaxis to adenosine 3',5'-cyclophosphate" EXACT []
@@ -260513,7 +263755,7 @@
id: GO:0043330
name: response to exogenous dsRNA
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus." [GOC:curators]
comment: Note that the presence of exogenous double-stranded RNA is usually indicative of a viral infection. Consider also annotating to 'response to virus ; GO:0009615'.
synonym: "response to exogenous double-stranded RNA" EXACT []
synonym: "response to viral dsRNA" NARROW []
@@ -260618,7 +263860,7 @@
id: GO:0043353
name: enucleate erythrocyte differentiation
namespace: biological_process
-def: "The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus." [GOC:go_curators]
+def: "The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus." [GOC:curators]
synonym: "enucleate RBC differentiation" EXACT [CL:0000232]
synonym: "enucleate red blood cell differentiation" EXACT [CL:0000232]
is_a: GO:0030218 ! erythrocyte differentiation
@@ -260627,7 +263869,7 @@
id: GO:0043354
name: enucleate erythrocyte maturation
namespace: biological_process
-def: "A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus." [GOC:go_curators]
+def: "A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus." [GOC:curators]
synonym: "enucleate RBC maturation" EXACT [CL:0000232]
synonym: "enucleate red blood cell maturation" EXACT [CL:0000232]
is_a: GO:0043249 ! erythrocyte maturation
@@ -260659,9 +263901,11 @@
def: "Catalyzes the activation of an enzyme by generating an organic free radical on a glycine residue via a homolytic cleavage of S-adenosyl-L-methionine (SAM)." [GOC:jl, PMID:24486374]
subset: goslim_pir
synonym: "catalysis of free radical formation" BROAD []
+xref: RHEA:19225
xref: RHEA:61976
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch RHEA:61976
+property_value: skos:narrowMatch RHEA:19225
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14190" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30701" xsd:anyURI
@@ -261070,7 +264314,7 @@
id: GO:0043393
name: regulation of protein binding
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of protein binding." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of protein binding." [GOC:curators]
subset: gocheck_do_not_annotate
is_a: GO:0051098 ! regulation of binding
intersection_of: GO:0065007 ! biological regulation
@@ -261097,7 +264341,7 @@
id: GO:0043396
name: corticotropin-releasing hormone secretion
namespace: biological_process
-def: "The regulated release of corticotropin-releasing hormone (CRH), a polypeptide hormone involved in the stress response. CRH is produced by the hypothalamus and stimulates corticotropic cells of the anterior lobe of the pituitary to produce corticotropic hormone (CTH) and other biologically active substances e.g. 2-endorphin, release of CRH is affected by serum levels of cortisol, by stress and by the sleep/wake cycle." [GOC:go_curators, PMID:11027914]
+def: "The regulated release of corticotropin-releasing hormone (CRH), a polypeptide hormone involved in the stress response. CRH is produced by the hypothalamus and stimulates corticotropic cells of the anterior lobe of the pituitary to produce corticotropic hormone (CTH) and other biologically active substances e.g. 2-endorphin, release of CRH is affected by serum levels of cortisol, by stress and by the sleep/wake cycle." [GOC:curators, PMID:11027914]
synonym: "corticotropin-releasing factor secretion" EXACT []
synonym: "CRF secretion" EXACT []
synonym: "CRH secretion" EXACT []
@@ -261107,7 +264351,7 @@
id: GO:0043397
name: regulation of corticotropin-releasing hormone secretion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of corticotropin-releasing hormone secretion." [GOC:go_curators, PMID:11027914]
+def: "Any process that modulates the frequency, rate or extent of corticotropin-releasing hormone secretion." [GOC:curators, PMID:11027914]
synonym: "regulation of corticotropin-releasing factor secretion" EXACT []
synonym: "regulation of CRF secretion" EXACT []
synonym: "regulation of CRH secretion" EXACT []
@@ -261120,7 +264364,7 @@
id: GO:0043398
name: HLH domain binding
namespace: molecular_function
-def: "Binding to a Helix Loop Helix domain, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization." [GOC:go_curators, Prosite:PDOC0038]
+def: "Binding to a Helix Loop Helix domain, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization." [GOC:curators, Prosite:PDOC0038]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -261189,7 +264433,7 @@
id: GO:0043405
name: regulation of MAP kinase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of MAP kinase activity." [GOC:curators, GOC:dph]
subset: gocheck_obsoletion_candidate
synonym: "Regulation of MAPK activity" EXACT [GOC:dph]
synonym: "regulation of mitogen activated protein kinase activity" EXACT []
@@ -261203,7 +264447,7 @@
id: GO:0043406
name: positive regulation of MAP kinase activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of MAP kinase activity." [GOC:curators, GOC:dph]
subset: gocheck_obsoletion_candidate
synonym: "positive regulation of mitogen activated protein kinase activity" EXACT []
synonym: "positive regulation of mitogen-activated protein kinase activity" EXACT []
@@ -261222,7 +264466,7 @@
id: GO:0043407
name: negative regulation of MAP kinase activity
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity." [GOC:dph, GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity." [GOC:curators, GOC:dph]
subset: gocheck_obsoletion_candidate
synonym: "down regulation of MAPK activity" EXACT []
synonym: "down-regulation of MAPK activity" EXACT []
@@ -261241,7 +264485,7 @@
id: GO:0043408
name: regulation of MAPK cascade
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade." [GOC:curators]
synonym: "regulation of MAP kinase cascade" EXACT [GOC:signaling]
synonym: "regulation of MAP kinase kinase kinase cascade" EXACT []
synonym: "regulation of MAPKKK cascade" EXACT [GOC:signaling]
@@ -261258,7 +264502,7 @@
id: GO:0043409
name: negative regulation of MAPK cascade
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade." [GOC:curators]
synonym: "down regulation of MAPK cascade" EXACT [GOC:signaling]
synonym: "down regulation of MAPKKK cascade" EXACT []
synonym: "down-regulation of MAPK cascade" EXACT [GOC:signaling]
@@ -261284,7 +264528,7 @@
id: GO:0043410
name: positive regulation of MAPK cascade
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade." [GOC:curators]
synonym: "activation of MAPK cascade" NARROW [GOC:signaling]
synonym: "activation of MAPKKK cascade" NARROW []
synonym: "positive regulation of MAP kinase cascade" EXACT [GOC:signaling]
@@ -261310,7 +264554,7 @@
id: GO:0043411
name: obsolete myopalladin binding
namespace: molecular_function
-def: "OBSOLETE. Binding to myopalladin, a myofibrillar protein with titin-like Ig domains." [GOC:go_curators]
+def: "OBSOLETE. Binding to myopalladin, a myofibrillar protein with titin-like Ig domains." [GOC:curators]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "myopalladin binding" EXACT []
is_obsolete: true
@@ -261320,7 +264564,7 @@
id: GO:0043412
name: macromolecule modification
namespace: biological_process
-def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators]
+def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:curators]
subset: gocheck_obsoletion_candidate
subset: goslim_pir
is_a: GO:0043170 ! macromolecule metabolic process
@@ -261340,7 +264584,7 @@
id: GO:0043414
name: macromolecule methylation
namespace: biological_process
-def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule." [GOC:go_curators]
+def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0032259 ! methylation
is_a: GO:0043412 ! macromolecule modification
@@ -261417,21 +264661,21 @@
[Term]
id: GO:0043420
-name: anthranilate metabolic process
+name: obsolete anthranilate metabolic process
namespace: biological_process
alt_id: GO:0018869
-def: "The chemical reactions and pathways involving anthranilate (2-aminobenzoate)." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving anthranilate (2-aminobenzoate)." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "2-aminobenzoate metabolic process" EXACT []
synonym: "2-aminobenzoate metabolism" EXACT []
+synonym: "anthranilate catabolic process" BROAD []
synonym: "anthranilate metabolism" EXACT []
synonym: "anthranilic acid metabolic process" NARROW []
synonym: "anthranilic acid metabolism" NARROW []
synonym: "ortho-aminobenzoic acid metabolic process" NARROW []
synonym: "ortho-aminobenzoic acid metabolism" NARROW []
-xref: UM-BBD_pathwayID:abz2
-is_a: GO:0009072 ! aromatic amino acid metabolic process
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0042537 ! benzene-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0043421
@@ -261451,10 +264695,20 @@
synonym: "ortho-aminobenzoic acid catabolic process" NARROW []
synonym: "ortho-aminobenzoic acid catabolism" NARROW []
xref: MetaCyc:2AMINOBENZDEG-PWY
+xref: MetaCyc:PWY-6077
+xref: MetaCyc:PWY-6079
+xref: MetaCyc:PWY-6504
+xref: UM-BBD_pathwayID:abz
+xref: UM-BBD_pathwayID:abz2
is_a: GO:0009074 ! aromatic amino acid family catabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0043420 ! anthranilate metabolic process
+is_a: GO:0042537 ! benzene-containing compound metabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:2AMINOBENZDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6077
+property_value: skos:narrowMatch MetaCyc:PWY-6079
+property_value: skos:narrowMatch MetaCyc:PWY-6504
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0043422
@@ -261910,19 +265164,24 @@
[Term]
id: GO:0043464
-name: malolactic fermentation
+name: L-malate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving the enzymatic conversion of L-malate to L-lactate and carbon dioxide." [PMID:10427020, PMID:8808948]
-comment: Despite the name, this is not an ATP-generating fermentation process. See MetaCyc:PWY-7685.
+def: "The chemical reactions and pathways resulting in the breakdown of L-malate." [PMID:10427020, PMID:8808948]
+comment: Despite the synonym 'malolactic fermentation', this is not an ATP-generating fermentation process. See MetaCyc:PWY-7685.
synonym: "L-malate fermentation" BROAD []
synonym: "malate fermentation" BROAD []
synonym: "malo-lactate fermentation" EXACT []
synonym: "malolactate fermentation" EXACT []
+synonym: "malolactic fermentation" EXACT []
xref: MetaCyc:PWY-7685
+xref: MetaCyc:PWY-7686
xref: Wikipedia:Malolactic_fermentation
is_a: GO:0006108 ! malate metabolic process
-relationship: has_part GO:0043883 ! malolactic enzyme activity
+is_a: GO:0043649 ! dicarboxylic acid catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-7685
+property_value: skos:narrowMatch MetaCyc:PWY-7686
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0043465
@@ -261940,7 +265199,7 @@
namespace: biological_process
def: "OBSOLETE. The anaerobic conversion of pyrimidine nucleobases, yielding energy in the form of ATP." [GOC:jl]
comment: The reason for obsoletion is that this term is not clearly defined.
-synonym: "pyrimidine base fermentation" EXACT [GOC:go_curators]
+synonym: "pyrimidine base fermentation" EXACT [GOC:curators]
synonym: "pyrimidine fermentation" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
is_obsolete: true
@@ -261959,14 +265218,16 @@
[Term]
id: GO:0043468
-name: regulation of fucose catabolic process
+name: regulation of L-fucose catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of fucose." [GOC:mlg]
+def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of L-fucose." [GOC:mlg]
+synonym: "regulation of fucose catabolic process" RELATED []
is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0019317 ! fucose catabolic process
-relationship: regulates GO:0019317 ! fucose catabolic process
+intersection_of: regulates GO:0042355 ! L-fucose catabolic process
+relationship: regulates GO:0042355 ! L-fucose catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31652" xsd:anyURI
[Term]
id: GO:0043469
@@ -262129,6 +265390,7 @@
name: endosome to pigment granule transport
namespace: biological_process
def: "The directed movement of substances from endosomes to pigment granules." [GOC:jl]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
relationship: part_of GO:0048757 ! pigment granule maturation
@@ -262170,7 +265432,7 @@
id: GO:0043489
name: RNA stabilization
namespace: biological_process
-def: "Prevention of degradation of RNA molecules." [GOC:go_curators]
+def: "Prevention of degradation of RNA molecules." [GOC:curators]
is_a: GO:0043487 ! regulation of RNA stability
is_a: GO:1902369 ! negative regulation of RNA catabolic process
@@ -262186,7 +265448,7 @@
xref: Reactome:R-HSA-9856872 "Malate-aspartate shuttle"
xref: Wikipedia:Malate-aspartate_shuttle
is_a: GO:0019674 ! NAD+ metabolic process
-relationship: has_part GO:0004069 ! L-aspartate:2-oxoglutarate aminotransferase activity
+relationship: has_part GO:0004069 ! L-aspartate:2-oxoglutarate transaminase activity
relationship: has_part GO:0030060 ! L-malate dehydrogenase (NAD+) activity
relationship: has_part GO:1990542 ! mitochondrial transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28982" xsd:anyURI
@@ -262244,11 +265506,13 @@
id: GO:0043495
name: protein-membrane adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a protein or a protein complex with a membrane, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:go_curators]
+def: "The binding activity of a molecule that brings together a protein or a protein complex with a membrane, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:curators]
synonym: "anchoring" RELATED []
synonym: "protein membrane adaptor" EXACT []
synonym: "protein membrane adaptor activity" EXACT []
synonym: "protein membrane anchor" RELATED []
+xref: Reactome:R-HSA-5333678 "CPNEs bind PL"
+xref: Reactome:R-HSA-6809764 "SBF1 binds MTMR2"
is_a: GO:0030674 ! protein-macromolecule adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19090" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24964" xsd:anyURI
@@ -262321,7 +265585,7 @@
id: GO:0043502
name: regulation of muscle adaptation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of muscle adaptation." [GOC:go_curators, GOC:mtg_muscle]
+def: "Any process that modulates the frequency, rate or extent of muscle adaptation." [GOC:curators, GOC:mtg_muscle]
synonym: "regulation of muscle plasticity" RELATED []
is_a: GO:0048583 ! regulation of response to stimulus
is_a: GO:0090257 ! regulation of muscle system process
@@ -262355,7 +265619,7 @@
id: GO:0043505
name: CENP-A containing nucleosome
namespace: cellular_component
-def: "A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3)." [GOC:go_curators, PMID:15175412, PMID:16183641]
+def: "A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3)." [GOC:curators, PMID:15175412, PMID:16183641]
synonym: "CenH3 containing nucleosome" EXACT []
synonym: "CENP-S-T-W-X" EXACT [GOC:vw, PMID:22304917]
synonym: "centromere specific nucleosome" RELATED []
@@ -262417,7 +265681,7 @@
name: activin A complex
namespace: cellular_component
alt_id: GO:0048181
-def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A)." [GOC:go_curators]
+def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta-A subunits (sometimes known as activin beta-A or activin/inhibin beta-A)." [GOC:curators]
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and an inhibin alpha subunit. See also the cellular component term 'inhibin complex ; GO:0043511'.
is_a: GO:0048180 ! activin complex
@@ -262426,7 +265690,7 @@
name: activin B complex
namespace: cellular_component
alt_id: GO:0048182
-def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta-B subunits (sometimes known as activin beta-B or activin/inhibin beta-B)." [GOC:go_curators]
+def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta-B subunits (sometimes known as activin beta-B or activin/inhibin beta-B)." [GOC:curators]
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'.
is_a: GO:0048180 ! activin complex
@@ -262437,8 +265701,7 @@
def: "Heterodimeric hormone composed of an inhibin alpha subunit complexed with either an inhibin beta-A subunit, to form inhibin A, or an inhibin beta-B subunit, to form inhibin B." [GOC:jl]
comment: Note that the actions of the inhibin complex are the opposite of those of the activin complex, which is a dimer of an inhibin beta-A and/or inhibin beta-B subunit. See also the cellular component term 'activin complex ; GO:0048180'.
subset: goslim_pir
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0043512
@@ -262467,8 +265730,7 @@
synonym: "IL12B" NARROW [GOC:add]
synonym: "p35" NARROW [GOC:add]
synonym: "p40" NARROW [GOC:add]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0043515
@@ -262573,7 +265835,7 @@
id: GO:0043523
name: regulation of neuron apoptotic process
namespace: biological_process
-def: "Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons." [GOC:curators, GOC:mtg_apoptosis]
synonym: "regulation of apoptosis of neuronal cells" EXACT []
synonym: "regulation of apoptosis of neurons" EXACT []
synonym: "regulation of neuron apoptosis" NARROW []
@@ -262590,7 +265852,7 @@
id: GO:0043524
name: negative regulation of neuron apoptotic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons." [GOC:curators, GOC:mtg_apoptosis]
synonym: "down regulation of neuron apoptosis" EXACT []
synonym: "down-regulation of neuron apoptosis" EXACT []
synonym: "downregulation of neuron apoptosis" EXACT []
@@ -262608,7 +265870,7 @@
id: GO:0043525
name: positive regulation of neuron apoptotic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process." [GOC:curators, GOC:mtg_apoptosis]
synonym: "activation of neuron apoptosis" NARROW []
synonym: "positive regulation of neuron apoptosis" NARROW []
synonym: "positive regulation of programmed cell death, neurons" EXACT []
@@ -262690,7 +265952,7 @@
id: GO:0043533
name: inositol 1,3,4,5 tetrakisphosphate binding
namespace: molecular_function
-def: "Binding to inositol 1,3,4,5 tetrakisphosphate." [GOC:go_curators]
+def: "Binding to inositol 1,3,4,5 tetrakisphosphate." [GOC:curators]
synonym: "InsP4 binding" EXACT []
synonym: "IP4 binding" EXACT []
is_a: GO:0043168 ! anion binding
@@ -262707,7 +265969,7 @@
id: GO:0043535
name: regulation of blood vessel endothelial cell migration
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:curators]
is_a: GO:0010594 ! regulation of endothelial cell migration
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0043534 ! blood vessel endothelial cell migration
@@ -262717,7 +265979,7 @@
id: GO:0043536
name: positive regulation of blood vessel endothelial cell migration
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:curators]
synonym: "activation of blood vessel endothelial cell migration" NARROW []
synonym: "stimulation of blood vessel endothelial cell migration" NARROW []
synonym: "up regulation of blood vessel endothelial cell migration" EXACT []
@@ -262733,7 +265995,7 @@
id: GO:0043537
name: negative regulation of blood vessel endothelial cell migration
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels." [GOC:curators]
synonym: "down regulation of blood vessel endothelial cell migration" EXACT []
synonym: "down-regulation of blood vessel endothelial cell migration" EXACT []
synonym: "downregulation of blood vessel endothelial cell migration" EXACT []
@@ -262748,7 +266010,7 @@
id: GO:0043538
name: obsolete regulation of actin phosphorylation
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the transfer of one or more phosphate groups to an actin molecule." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the transfer of one or more phosphate groups to an actin molecule." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28482" xsd:anyURI
@@ -262758,7 +266020,7 @@
id: GO:0043539
name: protein serine/threonine kinase activator activity
namespace: molecular_function
-def: "Binds to and increases the activity of a protein serine/threonine kinase." [GOC:go_curators]
+def: "Binds to and increases the activity of a protein serine/threonine kinase." [GOC:curators]
synonym: "protein ser/thr kinase activator activity" EXACT []
is_a: GO:0030295 ! protein kinase activator activity
relationship: positively_regulates GO:0004674 ! protein serine/threonine kinase activity
@@ -262791,7 +266053,7 @@
id: GO:0043542
name: endothelial cell migration
namespace: biological_process
-def: "The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:go_curators]
+def: "The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:curators]
is_a: GO:0016477 ! cell migration
[Term]
@@ -262800,7 +266062,6 @@
namespace: biological_process
def: "The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid." [GOC:jl]
subset: gocheck_obsoletion_candidate
-subset: goslim_yeast
synonym: "protein amino acid acylation" EXACT [GOC:bf]
is_a: GO:0036211 ! protein modification process
@@ -262808,7 +266069,7 @@
id: GO:0043544
name: lipoamide binding
namespace: molecular_function
-def: "Binding to lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:go_curators]
+def: "Binding to lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:curators]
is_a: GO:1901681 ! sulfur compound binding
[Term]
@@ -263331,7 +266592,7 @@
name: endospore external encapsulating structure
namespace: cellular_component
alt_id: GO:0055030
-def: "The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer." [GOC:go_curators, PMID:15035041]
+def: "The structures that lie outside the inner membrane and surround the entire endospore; consists of a peptidoglycan-containing inner layer (the endospore cortex) surrounded by a multilayered proteinaceous coat. An exosporium may be present as an extreme outer layer." [GOC:curators, PMID:15035041]
subset: goslim_pir
synonym: "endospore wall" EXACT [GOC:mah]
synonym: "peptidoglycan-based spore wall" EXACT [GOC:mtg_sensu]
@@ -263347,7 +266608,7 @@
synonym: "exospore" RELATED []
synonym: "perispore" RELATED []
is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0043591 ! endospore external encapsulating structure
+relationship: part_of GO:0005618 ! cell wall
[Term]
id: GO:0043593
@@ -263585,7 +266846,7 @@
id: GO:0043615
name: astrocyte cell migration
namespace: biological_process
-def: "The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord." [CL:0000127, GOC:go_curators]
+def: "The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord." [CL:0000127, GOC:curators]
synonym: "astrocyte migration" EXACT []
synonym: "astrocytic glial cell migration" EXACT []
is_a: GO:0008347 ! glial cell migration
@@ -263986,11 +267247,13 @@
[Term]
id: GO:0043655
-name: host extracellular space
+name: host extracellular region
namespace: cellular_component
-def: "The space within a host but external to the plasma membrane of host cells, e.g. within host bloodstream." [GOC:cc]
+def: "The space within a host but external to the plasma membrane of host cells, e.g. host bloodstream." [GOC:cc]
synonym: "extracellular space of host" EXACT []
+synonym: "host extracellular space" EXACT []
is_a: GO:0018995 ! host cellular component
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31545" xsd:anyURI
[Term]
id: GO:0043656
@@ -264229,10 +267492,6 @@
synonym: "Cu2+-exporting ATPase activity" RELATED [EC:7.2.2.9]
xref: EC:7.2.2.9
xref: MetaCyc:TRANS-RXN-178
-xref: Reactome:R-HSA-3697838 "ATP7A transfers Cu from ATOX1 to SOD3"
-xref: Reactome:R-HSA-6803545 "ATP7A transports cytosolic Cu2+ to phagosomal lumen"
-xref: Reactome:R-HSA-936802 "ATP7A transports cytosolic Cu2+ to extracellular region"
-xref: Reactome:R-HSA-936895 "ATP7B transports cytosolic Cu2+ to Golgi lumen"
xref: RHEA:10376
is_a: GO:0005375 ! copper ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
@@ -264717,10 +267976,12 @@
[Term]
id: GO:0043730
-name: 5-ureido-4-imidazole carboxylate hydrolase activity
+name: obsolete 5-ureido-4-imidazole carboxylate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-ureido-4-imidazole carboxylate + H2O = 5-amino-4-imidazole carboxylate + NH3 + CO2." [GOC:jl]
-is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
+def: "OBSOLETE. Catalysis of the reaction: 5-ureido-4-imidazole carboxylate + H2O = 5-amino-4-imidazole carboxylate + NH3 + CO2." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0043731
@@ -265011,12 +268272,16 @@
xref: EC:2.3.1.168
xref: MetaCyc:2.3.1.168-RXN
xref: RHEA:18865
+xref: RHEA:84647
+xref: RHEA:84651
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:broadMatch EC:1.2.1.25
property_value: skos:broadMatch MetaCyc:1.2.1.25-RXN
property_value: skos:exactMatch EC:2.3.1.168
property_value: skos:exactMatch MetaCyc:2.3.1.168-RXN
property_value: skos:narrowMatch RHEA:18865
+property_value: skos:narrowMatch RHEA:84647
+property_value: skos:narrowMatch RHEA:84651
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17835" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29951" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30031" xsd:anyURI
@@ -265088,7 +268353,7 @@
xref: EC:6.2.1.13
xref: MetaCyc:ACETATE--COA-LIGASE-ADP-FORMING-RXN
xref: RHEA:15081
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.13
property_value: skos:exactMatch RHEA:15081
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -265111,12 +268376,16 @@
[Term]
id: GO:0043760
-name: acetyldiaminopimelate aminotransferase activity
+name: obsolete acetyldiaminopimelate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-acetyl-L-2,6-diaminoheptanedioate + 2-oxoglutarate = N-acetyl-2-L-amino-6-oxoheptanedioate + L-glutamate." [PMID:1906065]
+def: "OBSOLETE. Catalysis of the reaction: N-acetyl-L-2,6-diaminoheptanedioate + 2-oxoglutarate = N-acetyl-2-L-amino-6-oxoheptanedioate + L-glutamate." [PMID:1906065]
+comment: This term was obsoleted because there is no evidence that this reaction exists. This was an alternative succinyldiaminopimelate aminotransferase substrate tested in PMID:1906065.
+synonym: "acetyldiaminopimelate aminotransferase activity" BROAD []
synonym: "N-acetyl-diaminopimelate aminotransferase activity" EXACT []
synonym: "N-acetyl-L,L-diaminopimelate aminotransferase activity" EXACT []
-is_a: GO:0008483 ! transaminase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+is_obsolete: true
+consider: GO:0009016
[Term]
id: GO:0043761
@@ -265558,7 +268827,7 @@
id: GO:0043799
name: glycine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reactions: (1) glycine + H2O + O2 = glyoxylate + NH3 + hydrogen peroxide; (2) D-alanine + H2O + O2 = pyruvate + NH3 + hydrogen peroxide; (3) sarcosine + H2O + O2 = glyoxylate + methylamine + hydrogen peroxide; (4) N-ethylglycine + H2O + O2 = glyoxylate + ethylamine + hydrogen peroxide." [EC:1.4.3.19]
+def: "Catalysis of the reactions: (1) glycine + H2O + O2 = glyoxylate + NH4+ + H2O2; (2) D-alanine + H2O + O2 = pyruvate + NH4+ + H2O2; (3) sarcosine + H2O + O2 = glyoxylate + methylamine + H2O2; (4) N-ethylglycine + H2O + O2 = glyoxylate + ethylamine + H2O2." [EC:1.4.3.19]
synonym: "glycine:oxygen oxidoreductase (deaminating)" EXACT []
xref: EC:1.4.3.19
xref: MetaCyc:1.4.3.19-RXN
@@ -265750,10 +269019,12 @@
def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate." [PMID:10224048, RHEA:55652]
synonym: "phosphatidylinositol 4-phosphate phosphatase activity" EXACT []
xref: MetaCyc:RXN-10961
+xref: RHEA:45836
xref: RHEA:55652
is_a: GO:0034596 ! phosphatidylinositol phosphate 4-phosphatase activity
is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
property_value: skos:exactMatch RHEA:55652
+property_value: skos:narrowMatch RHEA:45836
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24252" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30293" xsd:anyURI
@@ -265948,9 +269219,9 @@
[Term]
id: GO:0043825
-name: succinylornithine transaminase activity
+name: succinylornithine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + N(2)-succinyl-L-ornithine = N-succinyl-L-glutamate 5-semialdehyde + L-glutamate." [EC:2.6.1.81, RHEA:16953]
+def: "Catalysis of the reaction: N(2)-succinyl-L-ornithine + 2-oxoglutarate = N-succinyl-L-glutamate 5-semialdehyde + L-glutamate." [RHEA:16953]
synonym: "2-N-succinyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity" RELATED [EC:2.6.1.81]
synonym: "AstC" RELATED []
synonym: "N(2)-succinylornithine 5-aminotransferase activity" RELATED [EC:2.6.1.81]
@@ -265960,6 +269231,7 @@
synonym: "succinyl ornithine transaminase activity" EXACT []
synonym: "succinyl-ornithine transaminase activity" RELATED [EC:2.6.1.81]
synonym: "succinylornithine aminotransferase activity" BROAD [EC:2.6.1.81]
+synonym: "succinylornithine transaminase activity" EXACT []
xref: EC:2.6.1.81
xref: KEGG_REACTION:R04217
xref: MetaCyc:SUCCORNTRANSAM-RXN
@@ -265968,6 +269240,7 @@
property_value: skos:exactMatch EC:2.6.1.81
property_value: skos:exactMatch RHEA:16953
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0043826
@@ -266018,7 +269291,7 @@
id: GO:0043829
name: tRNA-specific adenosine-37 deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine-37 + H2O = inosine-37 + NH3, in a tRNA-Ala molecule." [PMID:8915538, PMID:9707437, RHEA:50968]
+def: "Catalysis of the reaction: adenosine-37 + H2O = inosine-37 + NH4+, in a tRNA-Ala molecule." [PMID:8915538, PMID:9707437, RHEA:50968]
synonym: "TAD1" RELATED []
synonym: "tRNA(Ala)-A37 deaminase activity" EXACT []
synonym: "tRNA-specific adenosine deaminase 1" EXACT []
@@ -266314,7 +269587,7 @@
id: GO:0043852
name: monomethylamine methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: monomethylamine + a monomethylamine corrinoid protein = a methylated monomethylamine corrinoid protein + NH3." [PMID:9195968]
+def: "Catalysis of the reaction: Co(I)-[methylamine-specific corrinoid protein] + methylamine + H+ = methyl-Co(III)-[methylamine-specific corrinoid protein] + NH4+." [PMID:9195968, RHEA:26059]
comment: This function is the first step in the pathway of methanogenesis from monomethylamine.
synonym: "MMAMT" RELATED []
synonym: "monomethylamine:corrinoid methyltransferase activity" EXACT []
@@ -266644,7 +269917,7 @@
id: GO:0043877
name: galactosamine-6-phosphate isomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galactosamine 6-phosphate + H2O = D-tagatose 6-phosphate + NH3." [PMID:10931310]
+def: "Catalysis of the reaction: D-galactosamine 6-phosphate + H2O = D-tagatose 6-phosphate + NH4+." [PMID:10931310]
comment: This function is part of the pathway of N-acetyl-galactosamine and galactosamine utilization.
synonym: "AgaI" RELATED []
synonym: "galactosamine-6-phosphate deaminase activity" EXACT []
@@ -266749,7 +270022,7 @@
id: GO:0043884
name: CO-methylating acetyl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + corrinoid protein = CO + methylcorrinoid protein + CoA." [EC:2.3.1.169, PMID:1748656]
+def: "Catalysis of the reaction: Co(I)-[corrinoid Fe-S protein] + acetyl-CoA + H+ = methyl-Co(III)-[corrinoid Fe-S protein] + CO + CoA." [PMID:1748656, RHEA:45212]
synonym: "acetyl-CoA synthase activity" BROAD []
synonym: "acetyl-CoA:corrinoid protein O-acetyltransferase activity" EXACT []
synonym: "ACS" RELATED [EC:2.3.1.169]
@@ -266930,11 +270203,15 @@
id: GO:0043894
name: acetyl-CoA synthetase acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the acetylation of residue Lys609 of the enzyme acetyl-CoA synthetase, using acetyl-CoA as substrate." [PMID:15236963]
-synonym: "Pat" RELATED []
-synonym: "Pat enzyme" EXACT []
+def: "Catalysis of the acetylation of a lysine of the enzyme acetyl-CoA ligase, using acetyl-CoA as substrate. In Bacillus subtilis, this is Lys609, but it may correspond to another position in orthologs. This acetylation results in inhibition of acetyl-CoA synthetase." [PMID:15236963, PMID:39019872, PMID:40089509]
+synonym: "acetate CoA ligase acetyltransferase activity" EXACT []
+synonym: "acetate-CoA ligase acetyltransferase activity" EXACT []
+synonym: "acetyl CoA synthetase acetyltransferase activity" EXACT []
+synonym: "Pat enzyme" BROAD []
synonym: "protein acetyltransferase activity" BROAD []
-is_a: GO:0016407 ! acetyltransferase activity
+is_a: GO:0055104 ! ligase inhibitor activity
+is_a: GO:0061733 ! protein-lysine-acetyltransferase activity
+relationship: negatively_regulates GO:0003987 ! acetyl-CoA synthetase activity
[Term]
id: GO:0043895
@@ -267139,11 +270416,15 @@
[Term]
id: GO:0043911
-name: D-lysine transaminase activity
+name: D-lysine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-lysine + 2-oxoglutarate = L-glutamate + 6-amino-2-oxohexanoate." [GOC:jl, PMID:17259313]
+def: "Catalysis of the reaction: D-lysine + 2-oxoglutarate = 6-amino-2-oxohexanoate + L-glutamate." [PMID:17259313, RHEA:37587]
synonym: "D-lysine aminotransferase activity" EXACT []
-is_a: GO:0008483 ! transaminase activity
+synonym: "D-lysine transaminase activity" BROAD []
+xref: RHEA:37587
+is_a: GO:0140385 ! amino acid transaminase activity
+property_value: skos:exactMatch RHEA:37587
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0043912
@@ -267168,21 +270449,27 @@
[Term]
id: GO:0043914
-name: NADPH:sulfur oxidoreductase activity
+name: NAD(P)H sulfur oxidoreductase (CoA-dependent) activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADPH + H+ + sulfur = hydrogen sulfide + NADP+." [GOC:jl, PMID:17449625]
+def: "Catalysis of the reaction: hydrogen sulfide + NAD(P)+ = sulfur + NAD(P)H." [EC:1.8.1.18, PMID:17449625]
synonym: "CoA-dependent NAD(P)H sulfur oxidoreductase activity" EXACT []
synonym: "coenzyme A-dependent NAD(P)H sulfur oxidoreductase activity" EXACT []
synonym: "NAD(P)H elemental sulfur oxidoreductase activity" EXACT []
synonym: "NAD(P)H sulfur oxidoreductase activity" EXACT []
synonym: "NAD(P)H sulphur oxidoreductase activity" EXACT []
synonym: "NAD(P)H:sulfur oxidoreductase activity" EXACT []
+synonym: "NADPH:sulfur oxidoreductase activity" NARROW []
synonym: "NADPH:sulphur oxidoreductase activity" EXACT []
synonym: "NSR" EXACT []
xref: EC:1.8.1.18
-is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
+xref: RHEA:36595
+xref: RHEA:36599
+is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
property_value: skos:exactMatch EC:1.8.1.18
+property_value: skos:narrowMatch RHEA:36595
+property_value: skos:narrowMatch RHEA:36599
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
[Term]
id: GO:0043915
@@ -267648,7 +270935,6 @@
xref: EC:6.2.1.36
xref: RHEA:26534
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.36
property_value: skos:exactMatch RHEA:26534
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -267728,10 +271014,12 @@
[Term]
id: GO:0043960
-name: L-erythro-3-methylmalyl-CoA dehydratase activity
+name: obsolete L-erythro-3-methylmalyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-erythro-3-methylmalyl-CoA = mesaconyl-CoA + H2O." [GOC:jl]
-is_a: GO:0016836 ! hydro-lyase activity
+def: "OBSOLETE. Catalysis of the reaction: L-erythro-3-methylmalyl-CoA = mesaconyl-CoA + H2O." [GOC:jl]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0043961
@@ -268249,6 +271537,8 @@
synonym: "regulation by symbiont of host system process" NARROW []
xref: Reactome:R-HSA-9635644 "Inhibition of membrane repair"
xref: Reactome:R-HSA-9636667 "Manipulation of host energy metabolism"
+xref: Reactome:R-HSA-9833110 "RSV-host interactions"
+xref: Reactome:R-HSA-9918481 "Dengue Virus-Host Interactions"
is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0051701 ! biological process involved in interaction with host
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18719" xsd:anyURI
@@ -268654,7 +271944,7 @@
id: GO:0044038
name: cell wall macromolecule biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of a macromolecule destined to form part of a cell wall." [GOC:curators]
synonym: "cell wall macromolecule anabolism" EXACT [GOC:mah]
synonym: "cell wall macromolecule biosynthesis" EXACT [GOC:mah]
synonym: "cell wall macromolecule biosynthetic process at cellular level" EXACT [GOC:mah]
@@ -270092,6 +273382,7 @@
name: protein folding chaperone
namespace: molecular_function
def: "Binding to a protein or a protein-containing complex to assist the protein folding process." [GOC:mtg_cambridge_2009]
+comment: Note that a protein folding chaperone binds an unfolded protein to fold it. Do not confuse with unfolded protein holdase activity, which binds an unfolded protein and keeps it unfolded to deliver it to its final destination.
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
@@ -270105,6 +273396,7 @@
is_a: GO:0003674 ! molecular_function
relationship: has_part GO:0051082 ! unfolded protein binding
relationship: part_of GO:0006457 ! protein folding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30552" xsd:anyURI
created_by: jl
creation_date: 2009-09-25T11:33:48Z
@@ -270628,11 +273920,10 @@
id: GO:0044237
name: obsolete cellular metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:curators]
comment: The reason for obsoletion is that this term is now redundant with GO:0008152, metabolic process
synonym: "cellular metabolism" EXACT []
synonym: "intermediary metabolism" RELATED [GOC:mah]
-xref: Reactome:R-HSA-1428517 "Aerobic respiration and respiratory electron transport"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008152
@@ -270641,13 +273932,14 @@
id: GO:0044238
name: primary metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators]
+def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_euk_cellular_processes_ribbon
subset: goslim_pir
subset: goslim_plant_ribbon
subset: goslim_prokaryote_ribbon
synonym: "primary metabolism" EXACT []
+xref: Reactome:R-HSA-71291 "Metabolism of amino acids and derivatives"
xref: Wikipedia:Primary_metabolite
is_a: GO:0008152 ! metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI
@@ -270668,7 +273960,7 @@
id: GO:0044241
name: lipid digestion
namespace: biological_process
-def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism." [GOC:go_curators]
+def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism." [GOC:curators]
xref: Reactome:R-HSA-192456 "Digestion of dietary lipid"
is_a: GO:0007586 ! digestion
@@ -270690,7 +273982,7 @@
id: GO:0044245
name: polysaccharide digestion
namespace: biological_process
-def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism." [GOC:go_curators]
+def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism." [GOC:curators]
xref: Reactome:R-HSA-189085 "Digestion of dietary carbohydrate"
is_a: GO:0007586 ! digestion
@@ -270775,7 +274067,7 @@
id: GO:0044256
name: protein digestion
namespace: biological_process
-def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested proteins into components that may be easily absorbed and directed into metabolism." [GOC:go_curators]
+def: "The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested proteins into components that may be easily absorbed and directed into metabolism." [GOC:curators]
is_a: GO:0007586 ! digestion
[Term]
@@ -270953,11 +274245,13 @@
namespace: biological_process
def: "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
+subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_flybase_ribbon
subset: goslim_metagenomics
synonym: "small molecule metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: jl
creation_date: 2010-01-26T12:05:20Z
@@ -270967,9 +274261,11 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:vw]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
+subset: gocheck_do_not_annotate
synonym: "small molecule catabolism" EXACT []
is_a: GO:0009056 ! catabolic process
is_a: GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: jl
creation_date: 2010-01-26T12:06:10Z
@@ -270979,11 +274275,13 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:vw]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
+subset: gocheck_do_not_annotate
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "small molecule biosynthesis" EXACT []
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: jl
creation_date: 2010-01-26T12:06:49Z
@@ -271122,7 +274420,7 @@
id: GO:0044297
name: cell body
namespace: cellular_component
-def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GOC:go_curators]
+def: "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." [GOC:curators]
comment: Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
synonym: "cell soma" EXACT []
xref: FBbt:00005107
@@ -272284,6 +275582,7 @@
synonym: "symbiotic interaction between organisms" RELATED []
synonym: "symbiotic interaction between species" RELATED []
synonym: "symbiotic process" RELATED []
+xref: Reactome:R-HSA-9839923 "Dengue Virus Infection"
is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14807" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
@@ -272309,6 +275608,7 @@
synonym: "adhesion to other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "adhesion to other organism involved in symbiotic interaction" EXACT []
synonym: "host adhesion" NARROW []
+xref: Reactome:R-HSA-9638630 "Attachment of bacteria to epithelial cells"
is_a: GO:0051701 ! biological process involved in interaction with host
[Term]
@@ -273817,9 +277117,19 @@
synonym: "very long chain fatty-acyl-CoA oxidase activity" EXACT []
synonym: "very-long-chain acyl-CoA oxidase activity" EXACT []
synonym: "VLC fatty-acyl-CoA oxidase activity" EXACT []
+xref: RHEA:39119
+xref: RHEA:39135
+xref: RHEA:40319
+xref: RHEA:78631
xref: RHEA:78847
+xref: RHEA:83047
is_a: GO:0003997 ! acyl-CoA oxidase activity
property_value: skos:exactMatch RHEA:78847
+property_value: skos:narrowMatch RHEA:39119
+property_value: skos:narrowMatch RHEA:39135
+property_value: skos:narrowMatch RHEA:40319
+property_value: skos:narrowMatch RHEA:78631
+property_value: skos:narrowMatch RHEA:83047
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24703" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28733" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -273876,7 +277186,7 @@
id: GO:0044540
name: L-cystine L-cysteine-lyase (deaminating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cystine + H2O = pyruvate + NH3 + thiocysteine. Thiocysteine is also known as cysteine persulfide." [RHEA:24927]
+def: "Catalysis of the reaction: L-cystine + H2O = S-sulfanyl-L-cysteine + pyruvate + NH4+." [RHEA:24927]
xref: EC:4.4.1.35
xref: KEGG_REACTION:R02408
xref: RHEA:24927
@@ -274250,6 +277560,7 @@
def: "A bacterial cell envelope-associated multiprotein system, which binds and degrades starch." [GOC:mengo_curators, GOC:tt, PMID:19553672]
synonym: "Sus complex" EXACT []
is_a: GO:0098796 ! membrane protein complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0009279 ! cell outer membrane
created_by: jl
creation_date: 2012-04-18T02:46:24Z
@@ -274504,9 +277815,15 @@
name: 17-beta-hydroxysteroid dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: a 17-beta-hydroxysteroid + NAD+ = a 17-oxosteroid + NADH + H+." [PMID:17074428, RHEA:81599]
+xref: RHEA:41992
+xref: RHEA:42124
+xref: RHEA:46220
xref: RHEA:81599
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch RHEA:81599
+property_value: skos:narrowMatch RHEA:41992
+property_value: skos:narrowMatch RHEA:42124
+property_value: skos:narrowMatch RHEA:46220
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21791" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29321" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -275206,7 +278523,7 @@
id: GO:0044655
name: phagosome reneutralization
namespace: biological_process
-def: "Any process that increases the pH of the phagosome, measured by the concentration of the hydrogen ion, as part of the process of phagosome maturation." [GOC:rjd, PMID:22008230]
+def: "Any process that increases the pH of the phagosome, corresponding to a decrease in hydrogen ion concentration, as part of the process of phagosome maturation." [GOC:rjd, PMID:22008230]
synonym: "phagosomal reneutralization" EXACT []
synonym: "phagosome pH elevation" EXACT []
is_a: GO:0051454 ! intracellular pH elevation
@@ -276059,6 +279376,7 @@
name: protein transmembrane import into intracellular organelle
namespace: biological_process
def: "The directed movement of proteins into an intracellular organelle, across a membrane." [GOC:jl]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0033365 ! protein localization to organelle
is_a: GO:0065002 ! intracellular protein transmembrane transport
is_a: GO:0072594 ! establishment of protein localization to organelle
@@ -276567,6 +279885,7 @@
name: trans-Golgi network to recycling endosome transport
namespace: biological_process
def: "The directed movement of substances, in membrane-bounded vesicles, from the trans-Golgi network to the recycling endosomes." [GOC:lb, PMID:18779367]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016197 ! endosomal transport
created_by: jl
creation_date: 2013-08-27T16:04:00Z
@@ -276701,35 +280020,30 @@
[Term]
id: GO:0044813
-name: pyruvate fermentation via PFOR
+name: pyruvate fermentation to butanoate
namespace: biological_process
-def: "The anaerobic chemical reactions and pathways resulting in the breakdown of pyruvate via pyruvate:ferredoxin oxidoreductase (PFOR) activity. This pathway is found in strict anaerobes such as Clostridia species." [GOC:mengo_curators, PMID:20395274, PMID:20692761]
+def: "The anaerobic chemical reactions and pathways resulting in the breakdown of pyruvate into butanoate. This pathway is found in strict anaerobes such as Clostridia species." [GOC:mengo_curators, PMID:20395274, PMID:20692761]
synonym: "glycolytic fermentation via PFOR pathway" RELATED []
+synonym: "pyruvate fermentation via PFOR" EXACT []
xref: MetaCyc:CENTFERM-PWY
+is_a: GO:0019605 ! butyrate metabolic process
is_a: GO:0019660 ! pyruvate fermentation
-intersection_of: GO:0019660 ! pyruvate fermentation
-intersection_of: has_part GO:0019164 ! pyruvate synthase activity
-relationship: has_part GO:0019164 ! pyruvate synthase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24644" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
created_by: jl
creation_date: 2013-09-18T16:04:00Z
[Term]
id: GO:0044814
-name: pyruvate fermentation via PFL
+name: obsolete pyruvate fermentation via PFL
namespace: biological_process
-def: "The anaerobic metabolic process in which pyruvate is converted to acetyl-CoA and formate by the action of pyruvate formate lyase (PFL), typically occurring in facultative anaerobic bacteria during mixed-acid fermentation." [PMID:19752030, PMID:2248795]
-synonym: "glycolytic fermentation via PFL pathway" RELATED []
-xref: MetaCyc:PWY-5480
-xref: MetaCyc:PWY-5485
-is_a: GO:0019660 ! pyruvate fermentation
-intersection_of: GO:0019660 ! pyruvate fermentation
-intersection_of: has_part GO:0008861 ! formate C-acetyltransferase activity
-relationship: has_part GO:0008861 ! formate C-acetyltransferase activity
-property_value: skos:narrowMatch MetaCyc:PWY-5480
-property_value: skos:narrowMatch MetaCyc:PWY-5485
+def: "OBSOLETE. The anaerobic metabolic process in which pyruvate is converted to acetyl-CoA and formate by the action of pyruvate formate lyase (PFL), typically occurring in facultative anaerobic bacteria during mixed-acid fermentation." [PMID:19752030, PMID:2248795]
+comment: The reason for obsoletion is that this term represents a single enzymatic step (the conversion of pyruvate to acetyl-CoA and formate by pyruvate formate lyase) which is a molecular function, not a biological process.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29511" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31679" xsd:anyURI
+is_obsolete: true
+consider: GO:0008861
created_by: jl
creation_date: 2013-09-18T16:56:02Z
@@ -277099,6 +280413,7 @@
synonym: "iron acquisition" BROAD []
synonym: "iron acquisition by symbiont from host" EXACT []
synonym: "iron acquisition by symbiont from host heme" NARROW []
+xref: Reactome:R-HSA-9638482 "Metal ion assimilation from the host"
is_a: GO:0044002 ! acquisition of nutrients from host
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17896" xsd:anyURI
created_by: jl
@@ -277652,7 +280967,7 @@
id: GO:0045019
name: negative regulation of nitric oxide biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:curators]
synonym: "down regulation of nitric oxide biosynthetic process" EXACT []
synonym: "down-regulation of nitric oxide biosynthetic process" EXACT []
synonym: "downregulation of nitric oxide biosynthetic process" EXACT []
@@ -277728,14 +281043,16 @@
[Term]
id: GO:0045026
-name: plasma membrane fusion
+name: obsolete plasma membrane fusion
namespace: biological_process
alt_id: GO:0006947
-def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle]
+def: "OBSOLETE. The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle]
+comment: This term is represented by another term.
synonym: "cell fusion" BROAD []
synonym: "cell-cell fusion" BROAD []
-is_a: GO:0007009 ! plasma membrane organization
-is_a: GO:0061025 ! membrane fusion
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31270" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0140253
[Term]
id: GO:0045027
@@ -277892,6 +281209,7 @@
synonym: "protein import into mitochondrial intermembrane space, nonconservative" NARROW [GOC:mcc]
synonym: "protein transport into mitochondrial IMS" EXACT []
synonym: "protein transport into mitochondrial intermembrane space" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0070585 ! protein localization to mitochondrion
is_a: GO:0071806 ! protein transmembrane transport
is_a: GO:0072594 ! establishment of protein localization to organelle
@@ -278125,6 +281443,7 @@
def: "The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma." [CL:0000545, GOC:ebc]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "T-helper 1 cell development" RELATED [GOC:add]
+xref: Reactome:R-HSA-9942503 "Differentiation of naive CD+ T cells to T helper 1 cells (Th1 cells)"
is_a: GO:0002287 ! alpha-beta T cell activation involved in immune response
is_a: GO:0002292 ! T cell differentiation involved in immune response
is_a: GO:0042093 ! T-helper cell differentiation
@@ -278222,7 +281541,7 @@
id: GO:0045071
name: negative regulation of viral genome replication
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication." [GOC:curators]
synonym: "down regulation of viral genome replication" EXACT []
synonym: "down-regulation of viral genome replication" EXACT []
synonym: "downregulation of viral genome replication" EXACT []
@@ -278281,7 +281600,7 @@
id: GO:0045091
name: regulation of single stranded viral RNA replication via double stranded DNA intermediate
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate." [GOC:curators]
synonym: "regulation of retroviral genome replication" EXACT [GOC:bf, GOC:jl]
is_a: GO:0045069 ! regulation of viral genome replication
is_a: GO:2001141 ! regulation of RNA biosynthetic process
@@ -278479,7 +281798,7 @@
id: GO:0045112
name: integrin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of integrins, a large family of transmembrane proteins that act as receptors for cell-adhesion molecules." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of integrins, a large family of transmembrane proteins that act as receptors for cell-adhesion molecules." [GOC:curators, ISBN:0198506732]
synonym: "integrin anabolism" EXACT []
synonym: "integrin biosynthesis" EXACT []
synonym: "integrin formation" EXACT []
@@ -278491,7 +281810,7 @@
id: GO:0045113
name: regulation of integrin biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:curators]
synonym: "regulation of integrin anabolism" EXACT []
synonym: "regulation of integrin biosynthesis" EXACT []
synonym: "regulation of integrin formation" EXACT []
@@ -278505,7 +281824,7 @@
id: GO:0045114
name: beta 2 integrin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of beta 2 integrins, a subfamily of integrins which contain the beta 2 subunit." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of beta 2 integrins, a subfamily of integrins which contain the beta 2 subunit." [GOC:curators]
synonym: "beta 2 integrin anabolism" EXACT []
synonym: "beta 2 integrin biosynthesis" EXACT []
synonym: "beta 2 integrin formation" EXACT []
@@ -278516,7 +281835,7 @@
id: GO:0045115
name: regulation of beta 2 integrin biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:curators]
synonym: "regulation of beta 2 integrin anabolism" EXACT []
synonym: "regulation of beta 2 integrin biosynthesis" EXACT []
synonym: "regulation of beta 2 integrin formation" EXACT []
@@ -278540,7 +281859,7 @@
id: GO:0045117
name: azole transmembrane transport
namespace: biological_process
-def: "The directed movement of azoles, heterocyclic compounds found in many biologically important substances, across a lipid bilayer, across a membrane." [GOC:go_curators, ISBN:3527307206, Wikipedia:Azole]
+def: "The directed movement of azoles, heterocyclic compounds found in many biologically important substances, across a lipid bilayer, across a membrane." [GOC:curators, ISBN:3527307206, Wikipedia:Azole]
synonym: "azole transport" RELATED []
is_a: GO:0055085 ! transmembrane transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -278627,6 +281946,7 @@
name: bioactive lipid receptor activity
namespace: molecular_function
def: "Combining with a bioactive lipid and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. A bioactive lipid is a lipid for which changes in lipid levels result in functional consequences in a variety of cellular processes." [GOC:bf, GOC:mah, PMID:12215548, PMID:18216770]
+xref: Reactome:R-HSA-400434 "FFAR1 binds fatty acids"
is_a: GO:0004930 ! G protein-coupled receptor activity
[Term]
@@ -278692,7 +282012,7 @@
synonym: "keratan sulphotransferase activity" EXACT []
xref: EC:2.8.2.21
xref: MetaCyc:KERATAN-SULFOTRANSFERASE-RXN
-xref: Reactome:R-HSA-2046175 "Further sulfation on galactose residues produces KSPG"
+xref: Reactome:R-HSA-2046175 "CHST1 transfers sulfate to Gal on keratan chain"
is_a: GO:0050698 ! proteoglycan sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.21
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28380" xsd:anyURI
@@ -278802,7 +282122,7 @@
id: GO:0045139
name: obsolete copper sensitivity/resistance
namespace: biological_process
-def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
+def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:curators]
comment: This term was made obsolete because 'sensitivity/resistance' implies a phenotype rather than a biological process.
synonym: "copper sensitivity/resistance" EXACT []
is_obsolete: true
@@ -278892,7 +282212,7 @@
id: GO:0045147
name: obsolete regulation of initiation of acetate catabolic process by acetate
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "regulation of initiation of acetate breakdown by acetate" EXACT []
synonym: "regulation of initiation of acetate degradation by acetate" EXACT []
@@ -279085,7 +282405,7 @@
id: GO:0045168
name: cell-cell signaling involved in cell fate commitment
namespace: biological_process
-def: "Signaling at long or short range between cells that results in the commitment of a cell to a certain fate." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Signaling at long or short range between cells that results in the commitment of a cell to a certain fate." [GOC:curators, GOC:dph, GOC:tb]
synonym: "cell fate commitment, cell-cell signaling" EXACT []
synonym: "cell fate commitment, cell-cell signalling" EXACT []
synonym: "cell-cell signaling during in cell fate commitment" EXACT []
@@ -279132,7 +282452,7 @@
id: GO:0045173
name: O-sialoglycoprotein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of O-sialoglycoproteins, glycoproteins which contain sialic acid as one of their carbohydrates. They are often found on or in the cell or tissue membranes and participate in a variety of biological activities." [GOC:go_curators, PMID:8824323]
+def: "The chemical reactions and pathways resulting in the breakdown of O-sialoglycoproteins, glycoproteins which contain sialic acid as one of their carbohydrates. They are often found on or in the cell or tissue membranes and participate in a variety of biological activities." [GOC:curators, PMID:8824323]
synonym: "O-sialoglycoprotein breakdown" EXACT []
synonym: "O-sialoglycoprotein catabolism" EXACT []
synonym: "O-sialoglycoprotein degradation" EXACT []
@@ -279301,7 +282621,7 @@
id: GO:0045188
name: regulation of circadian sleep/wake cycle, non-REM sleep
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of non-rapid eye movement sleep." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of non-rapid eye movement sleep." [GOC:curators]
synonym: "regulation of non-REM sleep" EXACT []
is_a: GO:0045187 ! regulation of circadian sleep/wake cycle, sleep
intersection_of: GO:0065007 ! biological regulation
@@ -279354,7 +282674,7 @@
id: GO:0045192
name: obsolete low-density lipoprotein catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of low-density lipoproteins, also known as beta lipoproteins, one of the classes of lipoproteins found in the bloodstream of animals, acting as a carrier for cholesterol and fats." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of low-density lipoproteins, also known as beta lipoproteins, one of the classes of lipoproteins found in the bloodstream of animals, acting as a carrier for cholesterol and fats." [GOC:curators, ISBN:0198506732]
comment: This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds.
synonym: "LDL catabolic process" EXACT []
synonym: "LDL catabolism" EXACT []
@@ -279368,7 +282688,7 @@
id: GO:0045193
name: obsolete acetylated low-density lipoprotein catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of acetylated low-density lipoproteins." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of acetylated low-density lipoproteins." [GOC:curators]
comment: This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds.
synonym: "Ac-LDL catabolic process" EXACT []
synonym: "Ac-LDL catabolism" EXACT []
@@ -279382,7 +282702,7 @@
id: GO:0045194
name: obsolete oxidized low-density lipoprotein catabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of oxidized low-density lipoproteins." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of oxidized low-density lipoproteins." [GOC:curators]
comment: This term was made obsolete because low-density lipoprotein is a macromolecular complex, not a single class of molecule; its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds.
synonym: "Ox-LDL catabolic process" EXACT []
synonym: "Ox-LDL catabolism" EXACT []
@@ -279482,7 +282802,7 @@
id: GO:0045203
name: obsolete integral component of cell outer membrane
namespace: cellular_component
-def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:dos, GOC:go_curators, GOC:mtg_sensu]
+def: "OBSOLETE. The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:curators, GOC:dos, GOC:mtg_sensu]
comment: This term was obsoleted because it represents protein topology, not a cellular component.
synonym: "integral to cell outer membrane" NARROW []
synonym: "integral to external membrane" RELATED []
@@ -279605,7 +282925,7 @@
id: GO:0045213
name: obsolete neurotransmitter receptor metabolic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways involving neurotransmitter receptors." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving neurotransmitter receptors." [GOC:curators]
comment: The reason for obsoletion is that 'neurotransmitter' is unnecessary grouping in the metabolism branch of the ontology, and it creates true path violations.
synonym: "neurotransmitter receptor metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25736" xsd:anyURI
@@ -279654,7 +282974,7 @@
id: GO:0045219
name: obsolete regulation of FasL production
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "regulation of FasL anabolism" EXACT []
synonym: "regulation of FasL biosynthesis" EXACT []
@@ -279668,7 +282988,7 @@
id: GO:0045220
name: obsolete positive regulation of FasL production
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "activation of FasL biosynthetic process" NARROW []
synonym: "positive regulation of FasL anabolism" EXACT []
@@ -279688,7 +283008,7 @@
id: GO:0045221
name: obsolete negative regulation of FasL production
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "down regulation of FasL biosynthetic process" EXACT []
synonym: "down-regulation of FasL biosynthetic process" EXACT []
@@ -279707,7 +283027,7 @@
id: GO:0045222
name: obsolete CD4 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions." [GOC:curators, ISBN:0198506732]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "CD4 anabolism" EXACT []
synonym: "CD4 biosynthesis" EXACT []
@@ -279721,7 +283041,7 @@
id: GO:0045223
name: obsolete regulation of CD4 production
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "regulation of CD4 anabolism" EXACT []
synonym: "regulation of CD4 biosynthesis" EXACT []
@@ -279736,7 +283056,7 @@
id: GO:0045224
name: obsolete positive regulation of CD4 production
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "activation of CD4 biosynthetic process" NARROW []
synonym: "positive regulation of CD4 anabolism" EXACT []
@@ -279756,7 +283076,7 @@
id: GO:0045225
name: obsolete negative regulation of CD4 production
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." [GOC:curators]
comment: The reason for obsoletion is that this term represents a gene product.
synonym: "down regulation of CD4 biosynthetic process" EXACT []
synonym: "down-regulation of CD4 biosynthetic process" EXACT []
@@ -279775,7 +283095,7 @@
id: GO:0045226
name: obsolete extracellular polysaccharide biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures." [GOC:ai, GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures." [GOC:ai, GOC:curators]
comment: The reason for obsoletion is that this term is now redundant with GO:0000271, polysaccharide biosynthetic process
synonym: "extracellular polysaccharide anabolism" EXACT []
synonym: "extracellular polysaccharide biosynthesis" EXACT []
@@ -279789,7 +283109,7 @@
id: GO:0045227
name: capsule polysaccharide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of polysaccharides that make up the capsule, a protective structure surrounding some species of bacteria and fungi." [GOC:curators]
synonym: "capsular polysaccharide biosynthesis" EXACT []
synonym: "capsular polysaccharide biosynthetic process" EXACT []
synonym: "capsule polysaccharide anabolism" EXACT []
@@ -279803,7 +283123,7 @@
id: GO:0045228
name: slime layer polysaccharide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of polysaccharides in the slime layer, a diffused layer of polysaccharide exterior to the bacterial cell wall." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of polysaccharides in the slime layer, a diffused layer of polysaccharide exterior to the bacterial cell wall." [GOC:curators]
synonym: "slime layer polysaccharide anabolism" EXACT []
synonym: "slime layer polysaccharide biosynthesis" EXACT []
synonym: "slime layer polysaccharide formation" EXACT []
@@ -280311,6 +283631,7 @@
is_a: GO:0070069 ! cytochrome complex
is_a: GO:0098803 ! respiratory chain complex
is_a: GO:1902495 ! transmembrane transporter complex
+is_a: GO:1990204 ! oxidoreductase complex
[Term]
id: GO:0045276
@@ -280342,6 +283663,7 @@
is_a: GO:0070069 ! cytochrome complex
is_a: GO:0098803 ! respiratory chain complex
is_a: GO:1902495 ! transmembrane transporter complex
+is_a: GO:1990204 ! oxidoreductase complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27727" xsd:anyURI
[Term]
@@ -280551,15 +283873,16 @@
[Term]
id: GO:0045303
-name: diaminobutyrate-2-oxoglutarate transaminase activity
+name: L-2,4-diaminobutyrate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-2,4-diaminobutyrate = L-aspartate 4-semialdehyde + L-glutamate." [EC:2.6.1.76, RHEA:11160]
+def: "Catalysis of the reaction: L-2,4-diaminobutanoate + 2-oxoglutarate = L-aspartate 4-semialdehyde + L-glutamate." [RHEA:11160]
synonym: "2,4-diaminobutyrate 4-aminotransferase activity" RELATED [EC:2.6.1.76]
synonym: "DAB aminotransferase activity" RELATED [EC:2.6.1.76]
synonym: "DABA aminotransferase activity" RELATED [EC:2.6.1.76]
synonym: "diaminibutyric acid aminotransferase activity" RELATED [EC:2.6.1.76]
synonym: "diaminobutyrate transaminase activity" RELATED [EC:2.6.1.76]
synonym: "diaminobutyrate--2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.76]
+synonym: "diaminobutyrate-2-oxoglutarate transaminase activity" EXACT []
synonym: "EctB" RELATED [EC:2.6.1.76]
synonym: "L-2,4-diaminobutanoate:2-oxoglutarate 4-aminotransferase activity" RELATED [EC:2.6.1.76]
synonym: "L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase activity" RELATED [EC:2.6.1.76]
@@ -280572,6 +283895,7 @@
property_value: skos:exactMatch EC:2.6.1.76
property_value: skos:exactMatch RHEA:11160
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0045304
@@ -280619,7 +283943,7 @@
id: GO:0045309
name: protein phosphorylated amino acid binding
namespace: molecular_function
-def: "Binding to a phosphorylated amino acid residue within a protein." [GOC:go_curators]
+def: "Binding to a phosphorylated amino acid residue within a protein." [GOC:curators]
synonym: "phosphoprotein amino acid binding" RELATED []
is_a: GO:0051219 ! phosphoprotein binding
@@ -280627,7 +283951,7 @@
id: GO:0045310
name: obsolete phosphoserine/phosphothreonine binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively with a phosphorylated serine or threonine residue within a protein." [GOC:go_curators]
+def: "OBSOLETE. Interacting selectively with a phosphorylated serine or threonine residue within a protein." [GOC:curators]
comment: This term was made obsolete because it represents two functions.
synonym: "phosphoserine/phosphothreonine binding" EXACT []
is_obsolete: true
@@ -280646,13 +283970,15 @@
id: GO:0045312
name: nor-spermidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of nor-spermidine, a compound related to spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of nor-spermidine, a compound related to spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:curators]
synonym: "nor-spermidine anabolism" EXACT []
synonym: "nor-spermidine biosynthesis" EXACT []
synonym: "nor-spermidine formation" EXACT []
synonym: "nor-spermidine synthesis" EXACT []
+xref: MetaCyc:PWY-6562
is_a: GO:0006596 ! polyamine biosynthetic process
is_a: GO:0046204 ! nor-spermidine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0045313
@@ -280770,6 +284096,7 @@
namespace: biological_process
def: "The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport." [PMID:11872141]
is_a: GO:0007034 ! vacuolar transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016192 ! vesicle-mediated transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29318" xsd:anyURI
@@ -280884,7 +284211,7 @@
id: GO:0045334
name: clathrin-coated endocytic vesicle
namespace: cellular_component
-def: "A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance." [GOC:go_curators]
+def: "A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance." [GOC:curators]
xref: NIF_Subcellular:sao1243595998
is_a: GO:0030136 ! clathrin-coated vesicle
is_a: GO:0030139 ! endocytic vesicle
@@ -280893,7 +284220,7 @@
id: GO:0045335
name: phagocytic vesicle
namespace: cellular_component
-def: "A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis." [GOC:go_curators, ISBN:0198506732]
+def: "A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis." [GOC:curators, ISBN:0198506732]
synonym: "phagosome" EXACT []
xref: Wikipedia:Phagosome
is_a: GO:0030139 ! endocytic vesicle
@@ -280902,7 +284229,7 @@
id: GO:0045336
name: clathrin-coated phagocytic vesicle
namespace: cellular_component
-def: "A clathrin-coated, membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis." [GOC:go_curators, ISBN:0198506732]
+def: "A clathrin-coated, membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis." [GOC:curators, ISBN:0198506732]
synonym: "clathrin-coated phagosome" EXACT []
is_a: GO:0045334 ! clathrin-coated endocytic vesicle
is_a: GO:0045335 ! phagocytic vesicle
@@ -280925,7 +284252,7 @@
id: GO:0045338
name: farnesyl diphosphate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving farnesyl diphosphate, an intermediate in carotenoid, sesquiterpene, squalene and sterol biosynthesis, as well as a substrate in protein farnesylation." [GOC:go_curators]
+def: "The chemical reactions and pathways involving farnesyl diphosphate, an intermediate in carotenoid, sesquiterpene, squalene and sterol biosynthesis, as well as a substrate in protein farnesylation." [GOC:curators]
synonym: "farnesyl diphosphate metabolism" EXACT []
is_a: GO:0006644 ! phospholipid metabolic process
is_a: GO:0006721 ! terpenoid metabolic process
@@ -280934,7 +284261,7 @@
id: GO:0045339
name: farnesyl diphosphate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of farnesyl diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of farnesyl diphosphate." [GOC:curators]
synonym: "farnesyl diphosphate breakdown" EXACT []
synonym: "farnesyl diphosphate catabolism" EXACT []
synonym: "farnesyl diphosphate degradation" EXACT []
@@ -280946,7 +284273,7 @@
id: GO:0045340
name: mercury ion binding
namespace: molecular_function
-def: "Binding to a mercury ion (Hg2+)." [GOC:go_curators]
+def: "Binding to a mercury ion (Hg2+)." [GOC:curators]
synonym: "Hg ion binding" EXACT []
synonym: "mercury binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -280955,7 +284282,7 @@
id: GO:0045341
name: MHC class I biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of major histocompatibility protein class I." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of major histocompatibility protein class I." [GOC:curators]
synonym: "major histocompatibility complex class I biosynthesis" EXACT []
synonym: "major histocompatibility complex class I biosynthetic process" EXACT []
synonym: "MHC class I anabolism" EXACT []
@@ -280968,7 +284295,7 @@
id: GO:0045342
name: MHC class II biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of major histocompatibility protein class II." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of major histocompatibility protein class II." [GOC:curators]
synonym: "major histocompatibility complex class II biosynthesis" EXACT []
synonym: "major histocompatibility complex class II biosynthetic process" EXACT []
synonym: "MHC class II anabolism" EXACT []
@@ -280981,7 +284308,7 @@
id: GO:0045343
name: regulation of MHC class I biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:curators]
synonym: "regulation of major histocompatibility complex class I biosynthesis" EXACT []
synonym: "regulation of major histocompatibility complex class I biosynthetic process" EXACT []
synonym: "regulation of MHC class I anabolism" EXACT []
@@ -280997,7 +284324,7 @@
id: GO:0045344
name: negative regulation of MHC class I biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:curators]
synonym: "down regulation of MHC class I biosynthetic process" EXACT []
synonym: "down-regulation of MHC class I biosynthetic process" EXACT []
synonym: "downregulation of MHC class I biosynthetic process" EXACT []
@@ -281018,7 +284345,7 @@
id: GO:0045345
name: positive regulation of MHC class I biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class I." [GOC:curators]
synonym: "activation of MHC class I biosynthetic process" NARROW []
synonym: "positive regulation of major histocompatibility complex class I biosynthesis" EXACT []
synonym: "positive regulation of major histocompatibility complex class I biosynthetic process" EXACT []
@@ -281040,7 +284367,7 @@
id: GO:0045346
name: regulation of MHC class II biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:curators]
synonym: "regulation of major histocompatibility complex class II biosynthesis" EXACT []
synonym: "regulation of major histocompatibility complex class II biosynthetic process" EXACT []
synonym: "regulation of MHC class II anabolism" EXACT []
@@ -281056,7 +284383,7 @@
id: GO:0045347
name: negative regulation of MHC class II biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:curators]
synonym: "down regulation of MHC class II biosynthetic process" EXACT []
synonym: "down-regulation of MHC class II biosynthetic process" EXACT []
synonym: "downregulation of MHC class II biosynthetic process" EXACT []
@@ -281077,7 +284404,7 @@
id: GO:0045348
name: positive regulation of MHC class II biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II." [GOC:curators]
synonym: "activation of MHC class II biosynthetic process" NARROW []
synonym: "positive regulation of major histocompatibility complex class II biosynthesis" EXACT []
synonym: "positive regulation of major histocompatibility complex class II biosynthetic process" EXACT []
@@ -281124,7 +284451,7 @@
id: GO:0045428
name: regulation of nitric oxide biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:curators]
synonym: "regulation of nitric oxide anabolism" EXACT []
synonym: "regulation of nitric oxide biosynthesis" EXACT []
synonym: "regulation of nitric oxide formation" EXACT []
@@ -281139,7 +284466,7 @@
id: GO:0045429
name: positive regulation of nitric oxide biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." [GOC:curators]
synonym: "activation of nitric oxide biosynthetic process" NARROW []
synonym: "positive regulation of nitric oxide anabolism" EXACT []
synonym: "positive regulation of nitric oxide biosynthesis" EXACT []
@@ -281179,10 +284506,16 @@
synonym: "FLS activity" RELATED [EC:1.14.20.6]
xref: EC:1.14.20.6
xref: RHEA:21088
+xref: RHEA:61132
+xref: RHEA:61136
+xref: RHEA:61140
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
relationship: part_of GO:0051555 ! flavonol biosynthetic process
property_value: skos:exactMatch EC:1.14.20.6
property_value: skos:exactMatch RHEA:21088
+property_value: skos:narrowMatch RHEA:61132
+property_value: skos:narrowMatch RHEA:61136
+property_value: skos:narrowMatch RHEA:61140
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -281299,7 +284632,7 @@
id: GO:0045443
name: juvenile hormone secretion
namespace: biological_process
-def: "The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:go_curators, ISBN:0198547684]
+def: "The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:curators, ISBN:0198547684]
is_a: GO:0046865 ! terpenoid transport
is_a: GO:0060986 ! endocrine hormone secretion
is_a: GO:0140353 ! lipid export from cell
@@ -281308,7 +284641,7 @@
id: GO:0045444
name: fat cell differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [CL:0000136, GOC:go_curators]
+def: "The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." [CL:0000136, GOC:curators]
synonym: "adipocyte cell differentiation" EXACT []
synonym: "adipocyte differentiation" EXACT []
synonym: "adipogenesis" RELATED []
@@ -281319,7 +284652,7 @@
id: GO:0045445
name: myoblast differentiation
namespace: biological_process
-def: "The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers." [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
+def: "The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers." [CL:0000056, GOC:curators, GOC:mtg_muscle]
synonym: "myoblast cell differentiation" EXACT []
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0061061 ! muscle structure development
@@ -281328,7 +284661,7 @@
id: GO:0045446
name: endothelial cell differentiation
namespace: biological_process
-def: "The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." [CL:0000115, GOC:go_curators]
+def: "The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." [CL:0000115, GOC:curators]
is_a: GO:0030855 ! epithelial cell differentiation
relationship: part_of GO:0003158 ! endothelium development
@@ -281336,7 +284669,7 @@
id: GO:0045448
name: mitotic cell cycle, embryonic
namespace: biological_process
-def: "The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo." [GOC:go_curators]
+def: "The eukaryotic cell cycle in which a cell is duplicated without changing ploidy, occurring in the embryo." [GOC:curators]
is_a: GO:0000278 ! mitotic cell cycle
relationship: part_of GO:0009790 ! embryo development
@@ -281344,7 +284677,7 @@
id: GO:0045450
name: bicoid mRNA localization
namespace: biological_process
-def: "Any process in which bicoid mRNA is transported to and maintained within the oocyte as part of the specification of the anterior/posterior axis." [GOC:go_curators]
+def: "Any process in which bicoid mRNA is transported to and maintained within the oocyte as part of the specification of the anterior/posterior axis." [GOC:curators]
synonym: "bicoid mRNA localisation" EXACT [GOC:mah]
synonym: "establishment and maintenance of bicoid mRNA localization" EXACT []
is_a: GO:0060811 ! intracellular mRNA localization involved in anterior/posterior axis specification
@@ -281354,7 +284687,7 @@
id: GO:0045451
name: pole plasm oskar mRNA localization
namespace: biological_process
-def: "Any process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:go_curators]
+def: "Any process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:curators]
synonym: "establishment and maintenance of oskar mRNA localization in pole plasm" EXACT []
synonym: "establishment and maintenance of pole plasm oskar mRNA localization" EXACT []
synonym: "oocyte pole plasm oskar mRNA localization" EXACT []
@@ -281404,7 +284737,7 @@
id: GO:0045456
name: ecdysteroid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." [GOC:curators]
synonym: "ecdysteroid anabolism" EXACT []
synonym: "ecdysteroid biosynthesis" EXACT []
synonym: "ecdysteroid formation" EXACT []
@@ -281418,14 +284751,14 @@
id: GO:0045457
name: ecdysteroid secretion
namespace: biological_process
-def: "The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." [GOC:go_curators]
+def: "The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." [GOC:curators]
is_a: GO:0035929 ! steroid hormone secretion
[Term]
id: GO:0045458
name: recombination within rDNA repeats
namespace: biological_process
-def: "Genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:go_curators, ISBN:0198506732]
+def: "Genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:curators, ISBN:0198506732]
comment: Note that this term was reinstated from obsolete.
synonym: "recombination within ribosomal DNA repeats" EXACT []
is_a: GO:0006310 ! DNA recombination
@@ -281542,21 +284875,21 @@
name: response to ethanol
namespace: biological_process
alt_id: GO:0017036
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus." [GOC:curators]
is_a: GO:0097305 ! response to alcohol
[Term]
id: GO:0045472
name: response to ether
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ether stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ether stimulus." [GOC:curators]
is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:0045473
name: obsolete response to ethanol (sensu Insecta)
namespace: biological_process
-def: "OBSOLETE. A change in state or activity of an insect (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus." [GOC:go_curators, GOC:jid]
+def: "OBSOLETE. A change in state or activity of an insect (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus." [GOC:curators, GOC:jid]
comment: This term was made obsolete because there is no clear difference between the sensu Insecta term and the generic term.
synonym: "response to ethanol (sensu Insecta)" EXACT []
is_obsolete: true
@@ -281566,7 +284899,7 @@
id: GO:0045474
name: obsolete response to ether (sensu Insecta)
namespace: biological_process
-def: "OBSOLETE. A change in state or activity of an insect (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ether stimulus." [GOC:go_curators, GOC:jid]
+def: "OBSOLETE. A change in state or activity of an insect (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ether stimulus." [GOC:curators, GOC:jid]
comment: This term was made obsolete because there is no clear difference between the sensu Insecta term and the generic term.
synonym: "response to ether (sensu Insecta)" EXACT []
is_obsolete: true
@@ -281576,7 +284909,7 @@
id: GO:0045475
name: locomotor rhythm
namespace: biological_process
-def: "The rhythm of the locomotor activity of an organism during its 24 hour activity cycle." [GOC:go_curators]
+def: "The rhythm of the locomotor activity of an organism during its 24 hour activity cycle." [GOC:curators]
synonym: "circadian locomotor activity rhythm" NARROW []
is_a: GO:0007626 ! locomotory behavior
is_a: GO:0048512 ! circadian behavior
@@ -281612,7 +284945,7 @@
id: GO:0045478
name: fusome organization
namespace: biological_process
-def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells." [GOC:dph, GOC:go_curators, GOC:jl, GOC:mah]
+def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fusome, a large intracellular spectrin-rich structure found in insect germline cells and mammalian hematopoietic cells." [GOC:curators, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_pir
synonym: "fusome organisation" EXACT []
synonym: "fusome organization and biogenesis" RELATED [GOC:mah]
@@ -281632,7 +284965,7 @@
id: GO:0045480
name: galactose oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-galactose + O2 = D-galacto-hexodialdose + hydrogen peroxide." [EC:1.1.3.9]
+def: "Catalysis of the reaction: D-galactose + O2 = D-galacto-hexodialdose + H2O2." [RHEA:24160]
synonym: "beta-galactose oxidase activity" RELATED [EC:1.1.3.9]
synonym: "D-galactose oxidase activity" RELATED [EC:1.1.3.9]
synonym: "D-galactose:oxygen 6-oxidoreductase activity" RELATED [EC:1.1.3.9]
@@ -281696,9 +285029,10 @@
[Term]
id: GO:0045484
-name: L-lysine 6-transaminase activity
+name: L-lysine:2-oxoglutarate 6-transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine." [EC:2.6.1.36, RHEA:21200]
+def: "Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine." [RHEA:21200]
+synonym: "L-lysine 6-transaminase activity" EXACT []
synonym: "L-lysine aminotransferase activity" RELATED [EC:2.6.1.36]
synonym: "L-lysine transaminase activity" RELATED [EC:2.6.1.36]
synonym: "L-lysine-alpha-ketoglutarate 6-aminotransferase activity" RELATED [EC:2.6.1.36]
@@ -281712,10 +285046,11 @@
xref: KEGG_REACTION:R00457
xref: MetaCyc:L-LYSINE-AMINOTRANSFERASE-RXN
xref: RHEA:21200
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.36
property_value: skos:exactMatch RHEA:21200
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0045485
@@ -281743,17 +285078,21 @@
xref: EC:1.14.11.9
xref: MetaCyc:1.14.11.9-RXN
xref: RHEA:18621
+xref: RHEA:61084
+xref: RHEA:61088
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
property_value: skos:exactMatch EC:1.14.11.9
property_value: skos:exactMatch MetaCyc:1.14.11.9-RXN
property_value: skos:exactMatch RHEA:18621
+property_value: skos:narrowMatch RHEA:61084
+property_value: skos:narrowMatch RHEA:61088
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
[Term]
id: GO:0045487
name: gibberellin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of gibberellin. Gibberellins are a class of highly modified terpenes that function as plant growth regulators." [GOC:curators]
synonym: "gibberellic acid breakdown" NARROW []
synonym: "gibberellic acid catabolic process" NARROW []
synonym: "gibberellic acid catabolism" NARROW []
@@ -281775,7 +285114,7 @@
id: GO:0045489
name: pectin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues." [GOC:go_curators, PMID:11931668]
+def: "The chemical reactions and pathways resulting in the formation of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues." [GOC:curators, PMID:11931668]
synonym: "pectin anabolism" EXACT []
synonym: "pectin biosynthesis" EXACT []
synonym: "pectin formation" EXACT []
@@ -281787,7 +285126,7 @@
id: GO:0045490
name: pectin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues." [GOC:go_curators, PMID:11931668]
+def: "The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues." [GOC:curators, PMID:11931668]
synonym: "pectin breakdown" EXACT []
synonym: "pectin catabolism" EXACT []
synonym: "pectin degradation" EXACT []
@@ -281798,7 +285137,7 @@
id: GO:0045491
name: xylan metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:go_curators, PMID:11931668]
+def: "The chemical reactions and pathways involving xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:curators, PMID:11931668]
synonym: "xylan metabolism" EXACT []
is_a: GO:0005976 ! polysaccharide metabolic process
@@ -281806,7 +285145,7 @@
id: GO:0045492
name: xylan biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:go_curators, PMID:11931668]
+def: "The chemical reactions and pathways resulting in the formation of xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:curators, PMID:11931668]
synonym: "xylan anabolism" EXACT []
synonym: "xylan biosynthesis" EXACT []
synonym: "xylan formation" EXACT []
@@ -281818,7 +285157,7 @@
id: GO:0045493
name: xylan catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:go_curators, PMID:11931668]
+def: "The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone." [GOC:curators, PMID:11931668]
synonym: "xylan breakdown" EXACT []
synonym: "xylan catabolism" EXACT []
synonym: "xylan degradation" EXACT []
@@ -281888,7 +285227,7 @@
id: GO:0045501
name: regulation of sevenless signaling pathway
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the sevenless signaling pathway." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the sevenless signaling pathway." [GOC:curators]
synonym: "regulation of sev signaling pathway" EXACT []
synonym: "regulation of sevenless signalling pathway" EXACT []
is_a: GO:0009966 ! regulation of signal transduction
@@ -281963,7 +285302,7 @@
id: GO:0045510
name: interleukin-24 binding
namespace: molecular_function
-def: "Binding to interleukin-24." [GOC:go_curators]
+def: "Binding to interleukin-24." [GOC:curators]
synonym: "IL-24 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -281971,7 +285310,7 @@
id: GO:0045511
name: interleukin-25 binding
namespace: molecular_function
-def: "Binding to interleukin-25." [GOC:go_curators]
+def: "Binding to interleukin-25." [GOC:curators]
synonym: "IL-25 binding" EXACT []
is_a: GO:0019975 ! interleukin-17 binding
@@ -281979,7 +285318,7 @@
id: GO:0045512
name: interleukin-26 binding
namespace: molecular_function
-def: "Binding to interleukin-26." [GOC:go_curators]
+def: "Binding to interleukin-26." [GOC:curators]
synonym: "IL-26 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -281987,7 +285326,7 @@
id: GO:0045513
name: interleukin-27 binding
namespace: molecular_function
-def: "Binding to interleukin-27." [GOC:go_curators]
+def: "Binding to interleukin-27." [GOC:curators]
synonym: "IL-27 binding" EXACT []
is_a: GO:0019975 ! interleukin-17 binding
@@ -281995,7 +285334,7 @@
id: GO:0045514
name: interleukin-16 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-16 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-16 receptor." [GOC:curators]
synonym: "IL-16" NARROW []
synonym: "interleukin-16 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282004,7 +285343,7 @@
id: GO:0045515
name: interleukin-18 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-18 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-18 receptor." [GOC:curators]
synonym: "IL-18" NARROW []
synonym: "interleukin-18 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282013,7 +285352,7 @@
id: GO:0045516
name: interleukin-19 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-19 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-19 receptor." [GOC:curators]
synonym: "IL-19" NARROW []
synonym: "interleukin-19 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282022,7 +285361,7 @@
id: GO:0045517
name: interleukin-20 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-20 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-20 receptor." [GOC:curators]
synonym: "IL-20" NARROW []
synonym: "interleukin-20 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282031,7 +285370,7 @@
id: GO:0045518
name: interleukin-22 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-22 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-22 receptor." [GOC:curators]
synonym: "IL-22" NARROW []
synonym: "interleukin-22 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282040,7 +285379,7 @@
id: GO:0045519
name: interleukin-23 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-23 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-23 receptor." [GOC:curators]
synonym: "IL-23" NARROW []
synonym: "interleukin-23 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282049,7 +285388,7 @@
id: GO:0045520
name: interleukin-24 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-24 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-24 receptor." [GOC:curators]
synonym: "IL-24" NARROW []
synonym: "interleukin-24 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282058,7 +285397,7 @@
id: GO:0045521
name: interleukin-25 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-25 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-25 receptor." [GOC:curators]
synonym: "IL-25" NARROW []
synonym: "interleukin-25 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282067,7 +285406,7 @@
id: GO:0045522
name: interleukin-26 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-26 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-26 receptor." [GOC:curators]
synonym: "IL-26" NARROW []
synonym: "interleukin-26 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282076,7 +285415,7 @@
id: GO:0045523
name: interleukin-27 receptor binding
namespace: molecular_function
-def: "Binding to an interleukin-27 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-27 receptor." [GOC:curators]
synonym: "IL-27" NARROW []
synonym: "interleukin-27 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -282085,7 +285424,7 @@
id: GO:0045540
name: regulation of cholesterol biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:curators]
synonym: "regulation of cholesterol anabolism" EXACT []
synonym: "regulation of cholesterol biosynthesis" EXACT []
synonym: "regulation of cholesterol formation" EXACT []
@@ -282102,7 +285441,7 @@
id: GO:0045541
name: negative regulation of cholesterol biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:curators]
synonym: "down regulation of cholesterol biosynthetic process" EXACT []
synonym: "down-regulation of cholesterol biosynthetic process" EXACT []
synonym: "downregulation of cholesterol biosynthetic process" EXACT []
@@ -282123,7 +285462,7 @@
id: GO:0045542
name: positive regulation of cholesterol biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol." [GOC:curators]
synonym: "activation of cholesterol biosynthetic process" NARROW []
synonym: "positive regulation of cholesterol anabolism" EXACT []
synonym: "positive regulation of cholesterol biosynthesis" EXACT []
@@ -282181,7 +285520,7 @@
id: GO:0045545
name: syndecan binding
namespace: molecular_function
-def: "Binding to syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells." [GOC:go_curators, PMID:9355727]
+def: "Binding to syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells." [GOC:curators, PMID:9355727]
is_a: GO:0043394 ! proteoglycan binding
[Term]
@@ -282281,10 +285620,12 @@
synonym: "NADPH-dihydromyricetin reductase activity" RELATED [EC:1.1.1.219]
xref: EC:1.1.1.219
xref: MetaCyc:RXN-17678
+xref: RHEA:23016
xref: RHEA:54444
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.219
property_value: skos:exactMatch RHEA:54444
+property_value: skos:narrowMatch RHEA:23016
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30173" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -282292,7 +285633,7 @@
id: GO:0045557
name: obsolete TRAIL receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "TRAIL receptor anabolism" EXACT []
synonym: "TRAIL receptor biosynthesis" EXACT []
@@ -282305,7 +285646,7 @@
id: GO:0045558
name: obsolete TRAIL receptor 1 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of TRAIL-R1 (TNF-related apoptosis inducing ligand receptor 1), which engages a caspase-dependent apoptotic pathway." [GOC:go_curators, PMID:9311998]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of TRAIL-R1 (TNF-related apoptosis inducing ligand receptor 1), which engages a caspase-dependent apoptotic pathway." [GOC:curators, PMID:9311998]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "TRAIL receptor 1 anabolism" EXACT []
synonym: "TRAIL receptor 1 biosynthesis" EXACT []
@@ -282319,7 +285660,7 @@
id: GO:0045559
name: obsolete TRAIL receptor 2 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of TRAIL-R2 (TNF-related apoptosis inducing ligand receptor 2), which engages a caspase-dependent apoptotic pathway and mediates apoptosis via the intracellular adaptor molecule FADD/MORT1." [GOC:go_curators, PMID:9311998]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of TRAIL-R2 (TNF-related apoptosis inducing ligand receptor 2), which engages a caspase-dependent apoptotic pathway and mediates apoptosis via the intracellular adaptor molecule FADD/MORT1." [GOC:curators, PMID:9311998]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "TRAIL receptor 2 anabolism" EXACT []
synonym: "TRAIL receptor 2 biosynthesis" EXACT []
@@ -282333,7 +285674,7 @@
id: GO:0045560
name: obsolete regulation of TRAIL receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "regulation of TRAIL receptor anabolism" EXACT []
synonym: "regulation of TRAIL receptor biosynthesis" EXACT []
@@ -282346,7 +285687,7 @@
id: GO:0045561
name: obsolete regulation of TRAIL receptor 1 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "regulation of TRAIL receptor 1 anabolism" EXACT []
synonym: "regulation of TRAIL receptor 1 biosynthesis" EXACT []
@@ -282359,7 +285700,7 @@
id: GO:0045562
name: obsolete regulation of TRAIL receptor 2 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "regulation of TRAIL receptor 2 anabolism" EXACT []
synonym: "regulation of TRAIL receptor 2 biosynthesis" EXACT []
@@ -282372,7 +285713,7 @@
id: GO:0045563
name: obsolete negative regulation of TRAIL receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "down regulation of TRAIL receptor biosynthetic process" EXACT []
synonym: "down-regulation of TRAIL receptor biosynthetic process" EXACT []
@@ -282389,7 +285730,7 @@
id: GO:0045564
name: obsolete positive regulation of TRAIL receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the TRAIL (TNF-related apoptosis inducing ligand) receptor." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "activation of TRAIL receptor biosynthetic process" NARROW []
synonym: "positive regulation of TRAIL receptor anabolism" EXACT []
@@ -282407,7 +285748,7 @@
id: GO:0045565
name: obsolete negative regulation of TRAIL receptor 1 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "down regulation of TRAIL receptor 1 biosynthetic process" EXACT []
synonym: "down-regulation of TRAIL receptor 1 biosynthetic process" EXACT []
@@ -282424,7 +285765,7 @@
id: GO:0045566
name: obsolete positive regulation of TRAIL receptor 1 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 1." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "activation of TRAIL receptor 1 biosynthetic process" NARROW []
synonym: "positive regulation of TRAIL receptor 1 anabolism" EXACT []
@@ -282442,7 +285783,7 @@
id: GO:0045567
name: obsolete negative regulation of TRAIL receptor 2 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "down regulation of TRAIL receptor 2 biosynthetic process" EXACT []
synonym: "down-regulation of TRAIL receptor 2 biosynthetic process" EXACT []
@@ -282459,7 +285800,7 @@
id: GO:0045568
name: obsolete positive regulation of TRAIL receptor 2 biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of TRAIL (TNF-related apoptosis inducing ligand) receptor 2." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "activation of TRAIL receptor 2 biosynthetic process" NARROW []
synonym: "positive regulation of TRAIL receptor 2 anabolism" EXACT []
@@ -282477,7 +285818,7 @@
id: GO:0045569
name: TRAIL binding
namespace: molecular_function
-def: "Binding to TRAIL (TNF-related apoptosis inducing ligand), a member of the tumor necrosis factor ligand family that rapidly induces apoptosis in a variety of transformed cell lines." [GOC:go_curators, PMID:9082980]
+def: "Binding to TRAIL (TNF-related apoptosis inducing ligand), a member of the tumor necrosis factor ligand family that rapidly induces apoptosis in a variety of transformed cell lines." [GOC:curators, PMID:9082980]
subset: goslim_chembl
synonym: "Apo-2L binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -282486,7 +285827,7 @@
id: GO:0045570
name: regulation of imaginal disc growth
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the growth of the imaginal disc." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the growth of the imaginal disc." [GOC:curators]
is_a: GO:0048638 ! regulation of developmental growth
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0007446 ! imaginal disc growth
@@ -282496,7 +285837,7 @@
id: GO:0045571
name: negative regulation of imaginal disc growth
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of imaginal disc growth." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of imaginal disc growth." [GOC:curators]
synonym: "down regulation of imaginal disc growth" EXACT []
synonym: "down-regulation of imaginal disc growth" EXACT []
synonym: "downregulation of imaginal disc growth" EXACT []
@@ -282511,7 +285852,7 @@
id: GO:0045572
name: positive regulation of imaginal disc growth
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of imaginal disc growth." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of imaginal disc growth." [GOC:curators]
synonym: "activation of imaginal disc growth" NARROW []
synonym: "stimulation of imaginal disc growth" NARROW []
synonym: "up regulation of imaginal disc growth" EXACT []
@@ -282527,7 +285868,7 @@
id: GO:0045574
name: sterigmatocystin catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sterigmatocystin, a carcinogenic mycotoxin produced in high yields by strains of the common molds." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of sterigmatocystin, a carcinogenic mycotoxin produced in high yields by strains of the common molds." [GOC:curators]
synonym: "sterigmatocystin breakdown" EXACT []
synonym: "sterigmatocystin catabolism" EXACT []
synonym: "sterigmatocystin degradation" EXACT []
@@ -282553,7 +285894,7 @@
id: GO:0045577
name: regulation of B cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of B cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of B cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of B cell development" RELATED [GOC:add]
synonym: "regulation of B lymphocyte differentiation" EXACT []
@@ -282569,7 +285910,7 @@
id: GO:0045578
name: negative regulation of B cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of B cell differentiation" EXACT []
synonym: "down-regulation of B cell differentiation" EXACT []
@@ -282590,7 +285931,7 @@
id: GO:0045579
name: positive regulation of B cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of B cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of B cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of B cell differentiation" NARROW []
synonym: "positive regulation of B cell development" RELATED [GOC:add]
@@ -282612,7 +285953,7 @@
id: GO:0045580
name: regulation of T cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of T cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of T cell development" RELATED [GOC:add]
synonym: "regulation of T lymphocyte differentiation" EXACT []
@@ -282628,7 +285969,7 @@
id: GO:0045581
name: negative regulation of T cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of T cell differentiation" EXACT []
synonym: "down-regulation of T cell differentiation" EXACT []
@@ -282649,7 +285990,7 @@
id: GO:0045582
name: positive regulation of T cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of T cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of T cell differentiation" NARROW []
synonym: "positive regulation of T cell development" RELATED [GOC:add]
@@ -282671,7 +286012,7 @@
id: GO:0045583
name: regulation of cytotoxic T cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of cytotoxic T cell development" RELATED [GOC:add]
synonym: "regulation of cytotoxic T lymphocyte differentiation" EXACT []
@@ -282686,7 +286027,7 @@
id: GO:0045584
name: negative regulation of cytotoxic T cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of cytotoxic T cell differentiation" EXACT []
synonym: "down-regulation of cytotoxic T cell differentiation" EXACT []
@@ -282706,7 +286047,7 @@
id: GO:0045585
name: positive regulation of cytotoxic T cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cytotoxic T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of cytotoxic T cell differentiation" NARROW []
synonym: "positive regulation of cytotoxic T cell development" RELATED [GOC:add]
@@ -282727,7 +286068,7 @@
id: GO:0045586
name: regulation of gamma-delta T cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of gamma-delta T cell development" RELATED [GOC:add]
synonym: "regulation of gamma-delta T lymphocyte differentiation" EXACT []
@@ -282743,7 +286084,7 @@
id: GO:0045587
name: negative regulation of gamma-delta T cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of gamma-delta T cell differentiation" EXACT []
synonym: "down-regulation of gamma-delta T cell differentiation" EXACT []
@@ -282764,7 +286105,7 @@
id: GO:0045588
name: positive regulation of gamma-delta T cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of gamma-delta T cell differentiation" NARROW []
synonym: "positive regulation of gamma-delta T cell development" RELATED [GOC:add]
@@ -282851,7 +286192,7 @@
id: GO:0045592
name: regulation of cumulus cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:curators]
synonym: "regulation of ovarian cumulus cell differentiation" EXACT []
is_a: GO:0030856 ! regulation of epithelial cell differentiation
is_a: GO:2000387 ! regulation of antral ovarian follicle growth
@@ -282863,7 +286204,7 @@
id: GO:0045593
name: negative regulation of cumulus cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:curators]
synonym: "down regulation of cumulus cell differentiation" EXACT []
synonym: "down-regulation of cumulus cell differentiation" EXACT []
synonym: "downregulation of cumulus cell differentiation" EXACT []
@@ -282880,7 +286221,7 @@
id: GO:0045594
name: positive regulation of cumulus cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of ovarian cumulus cell differentiation." [GOC:curators]
synonym: "activation of cumulus cell differentiation" NARROW []
synonym: "positive regulation of ovarian cumulus cell differentiation" EXACT []
synonym: "stimulation of cumulus cell differentiation" NARROW []
@@ -282898,7 +286239,7 @@
id: GO:0045595
name: regulation of cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." [GOC:curators]
is_a: GO:0050793 ! regulation of developmental process
is_a: GO:0050794 ! regulation of cellular process
intersection_of: GO:0065007 ! biological regulation
@@ -282909,7 +286250,7 @@
id: GO:0045596
name: negative regulation of cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." [GOC:curators]
synonym: "down regulation of cell differentiation" EXACT []
synonym: "down-regulation of cell differentiation" EXACT []
synonym: "downregulation of cell differentiation" EXACT []
@@ -282925,7 +286266,7 @@
id: GO:0045597
name: positive regulation of cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cell differentiation." [GOC:curators]
synonym: "activation of cell differentiation" NARROW []
synonym: "stimulation of cell differentiation" NARROW []
synonym: "up regulation of cell differentiation" EXACT []
@@ -282942,7 +286283,7 @@
id: GO:0045598
name: regulation of fat cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of adipocyte differentiation." [GOC:curators]
synonym: "regulation of adipocyte cell differentiation" EXACT []
synonym: "regulation of adipocyte differentiation" EXACT []
is_a: GO:0045595 ! regulation of cell differentiation
@@ -282954,7 +286295,7 @@
id: GO:0045599
name: negative regulation of fat cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation." [GOC:curators]
synonym: "down regulation of fat cell differentiation" EXACT []
synonym: "down-regulation of fat cell differentiation" EXACT []
synonym: "downregulation of fat cell differentiation" EXACT []
@@ -282971,7 +286312,7 @@
id: GO:0045600
name: positive regulation of fat cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of adipocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of adipocyte differentiation." [GOC:curators]
synonym: "activation of fat cell differentiation" NARROW []
synonym: "positive regulation of adipocyte cell differentiation" EXACT []
synonym: "positive regulation of adipocyte differentiation" EXACT []
@@ -282989,7 +286330,7 @@
id: GO:0045601
name: regulation of endothelial cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of endothelial cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of endothelial cell differentiation." [GOC:curators]
is_a: GO:0030856 ! regulation of epithelial cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0045446 ! endothelial cell differentiation
@@ -282999,7 +286340,7 @@
id: GO:0045602
name: negative regulation of endothelial cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation." [GOC:curators]
synonym: "down regulation of endothelial cell differentiation" EXACT []
synonym: "down-regulation of endothelial cell differentiation" EXACT []
synonym: "downregulation of endothelial cell differentiation" EXACT []
@@ -283014,7 +286355,7 @@
id: GO:0045603
name: positive regulation of endothelial cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation." [GOC:curators]
synonym: "activation of endothelial cell differentiation" NARROW []
synonym: "stimulation of endothelial cell differentiation" NARROW []
synonym: "up regulation of endothelial cell differentiation" EXACT []
@@ -283030,7 +286371,7 @@
id: GO:0045604
name: regulation of epidermal cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of epidermal cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of epidermal cell differentiation." [GOC:curators]
synonym: "regulation of hypodermal cell differentiation" RELATED [GOC:kmv, GOC:rk]
is_a: GO:0030856 ! regulation of epithelial cell differentiation
is_a: GO:0045682 ! regulation of epidermis development
@@ -283042,7 +286383,7 @@
id: GO:0045605
name: negative regulation of epidermal cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation." [GOC:curators]
synonym: "down regulation of epidermal cell differentiation" EXACT []
synonym: "down-regulation of epidermal cell differentiation" EXACT []
synonym: "downregulation of epidermal cell differentiation" EXACT []
@@ -283059,7 +286400,7 @@
id: GO:0045606
name: positive regulation of epidermal cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation." [GOC:curators]
synonym: "activation of epidermal cell differentiation" NARROW []
synonym: "positive regulation of hypodermal cell differentiation" RELATED [GOC:kmv, GOC:rk]
synonym: "stimulation of epidermal cell differentiation" NARROW []
@@ -283077,7 +286418,7 @@
id: GO:0045607
name: regulation of inner ear auditory receptor cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of auditory hair cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of auditory hair cell differentiation." [GOC:curators]
synonym: "regulation of auditory hair cell differentiation" EXACT []
synonym: "regulation of auditory receptor cell differentiation" RELATED []
is_a: GO:0045604 ! regulation of epidermal cell differentiation
@@ -283090,7 +286431,7 @@
id: GO:0045608
name: negative regulation of inner ear auditory receptor cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of auditory hair cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of auditory hair cell differentiation." [GOC:curators]
synonym: "down regulation of auditory receptor cell differentiation" EXACT []
synonym: "down-regulation of auditory receptor cell differentiation" EXACT []
synonym: "downregulation of auditory receptor cell differentiation" EXACT []
@@ -283108,7 +286449,7 @@
id: GO:0045609
name: positive regulation of inner ear auditory receptor cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of auditory hair cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of auditory hair cell differentiation." [GOC:curators]
synonym: "activation of auditory receptor cell differentiation" NARROW []
synonym: "positive regulation of auditory hair cell differentiation" EXACT []
synonym: "positive regulation of auditory receptor cell differentiation" RELATED []
@@ -283127,7 +286468,7 @@
id: GO:0045610
name: regulation of hemocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of hemocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of hemocyte differentiation." [GOC:curators]
synonym: "regulation of arthropod blood cell differentiation" EXACT []
is_a: GO:0002682 ! regulation of immune system process
is_a: GO:0045595 ! regulation of cell differentiation
@@ -283140,7 +286481,7 @@
id: GO:0045611
name: negative regulation of hemocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of hemocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of hemocyte differentiation." [GOC:curators]
synonym: "down regulation of hemocyte differentiation" EXACT []
synonym: "down-regulation of hemocyte differentiation" EXACT []
synonym: "downregulation of hemocyte differentiation" EXACT []
@@ -283157,7 +286498,7 @@
id: GO:0045612
name: positive regulation of hemocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of hemocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of hemocyte differentiation." [GOC:curators]
synonym: "activation of hemocyte differentiation" NARROW []
synonym: "positive regulation of arthropod blood cell differentiation" EXACT []
synonym: "stimulation of hemocyte differentiation" NARROW []
@@ -283175,7 +286516,7 @@
id: GO:0045613
name: regulation of plasmatocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of plasmatocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of plasmatocyte differentiation." [GOC:curators]
is_a: GO:0045610 ! regulation of hemocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042387 ! plasmatocyte differentiation
@@ -283185,7 +286526,7 @@
id: GO:0045614
name: negative regulation of plasmatocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of plasmatocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of plasmatocyte differentiation." [GOC:curators]
synonym: "down regulation of plasmatocyte differentiation" EXACT []
synonym: "down-regulation of plasmatocyte differentiation" EXACT []
synonym: "downregulation of plasmatocyte differentiation" EXACT []
@@ -283200,7 +286541,7 @@
id: GO:0045615
name: positive regulation of plasmatocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of plasmatocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of plasmatocyte differentiation." [GOC:curators]
synonym: "activation of plasmatocyte differentiation" NARROW []
synonym: "stimulation of plasmatocyte differentiation" NARROW []
synonym: "up regulation of plasmatocyte differentiation" EXACT []
@@ -283216,7 +286557,7 @@
id: GO:0045616
name: regulation of keratinocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of keratinocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of keratinocyte differentiation." [GOC:curators]
xref: Reactome:R-HSA-8939242 "RUNX1 regulates transcription of genes involved in differentiation of keratinocytes"
is_a: GO:0045604 ! regulation of epidermal cell differentiation
intersection_of: GO:0065007 ! biological regulation
@@ -283227,7 +286568,7 @@
id: GO:0045617
name: negative regulation of keratinocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte differentiation." [GOC:curators]
synonym: "down regulation of keratinocyte differentiation" EXACT []
synonym: "down-regulation of keratinocyte differentiation" EXACT []
synonym: "downregulation of keratinocyte differentiation" EXACT []
@@ -283243,7 +286584,7 @@
id: GO:0045618
name: positive regulation of keratinocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation." [GOC:curators]
synonym: "activation of keratinocyte differentiation" NARROW []
synonym: "stimulation of keratinocyte differentiation" NARROW []
synonym: "up regulation of keratinocyte differentiation" EXACT []
@@ -283260,7 +286601,7 @@
id: GO:0045619
name: regulation of lymphocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of lymphocyte differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of lymphocyte development" RELATED [GOC:add]
is_a: GO:0051249 ! regulation of lymphocyte activation
@@ -283273,7 +286614,7 @@
id: GO:0045620
name: negative regulation of lymphocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of lymphocyte differentiation" EXACT []
synonym: "down-regulation of lymphocyte differentiation" EXACT []
@@ -283291,7 +286632,7 @@
id: GO:0045621
name: positive regulation of lymphocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of lymphocyte differentiation" NARROW []
synonym: "positive regulation of lymphocyte development" RELATED [GOC:add]
@@ -283310,7 +286651,7 @@
id: GO:0045622
name: regulation of T-helper cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of T-helper cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of T-helper cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of T-helper cell development" RELATED [GOC:add]
is_a: GO:0043370 ! regulation of CD4-positive, alpha-beta T cell differentiation
@@ -283323,7 +286664,7 @@
id: GO:0045623
name: negative regulation of T-helper cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of T-helper cell differentiation" EXACT []
synonym: "down-regulation of T-helper cell differentiation" EXACT []
@@ -283341,7 +286682,7 @@
id: GO:0045624
name: positive regulation of T-helper cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of T-helper cell differentiation" NARROW []
synonym: "positive regulation of T-helper cell development" RELATED [GOC:add]
@@ -283360,7 +286701,7 @@
id: GO:0045625
name: regulation of T-helper 1 cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of T-helper 1 cell development" RELATED [GOC:add]
is_a: GO:0002697 ! regulation of immune effector process
@@ -283374,7 +286715,7 @@
id: GO:0045626
name: negative regulation of T-helper 1 cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of T-helper 1 cell differentiation" EXACT []
synonym: "down-regulation of T-helper 1 cell differentiation" EXACT []
@@ -283393,7 +286734,7 @@
id: GO:0045627
name: positive regulation of T-helper 1 cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of T-helper 1 cell differentiation" NARROW []
synonym: "positive regulation of T-helper 1 cell development" RELATED [GOC:add]
@@ -283412,7 +286753,7 @@
id: GO:0045628
name: regulation of T-helper 2 cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "regulation of T-helper 2 cell development" RELATED [GOC:add]
is_a: GO:0002697 ! regulation of immune effector process
@@ -283426,7 +286767,7 @@
id: GO:0045629
name: negative regulation of T-helper 2 cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "down regulation of T-helper 2 cell differentiation" EXACT []
synonym: "down-regulation of T-helper 2 cell differentiation" EXACT []
@@ -283445,7 +286786,7 @@
id: GO:0045630
name: positive regulation of T-helper 2 cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation." [GOC:curators]
comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'.
synonym: "activation of T-helper 2 cell differentiation" NARROW []
synonym: "positive regulation of T-helper 2 cell development" RELATED [GOC:add]
@@ -283465,7 +286806,7 @@
id: GO:0045631
name: regulation of mechanoreceptor differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mechanoreceptor differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of mechanoreceptor differentiation." [GOC:curators]
is_a: GO:0045664 ! regulation of neuron differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042490 ! mechanoreceptor differentiation
@@ -283475,7 +286816,7 @@
id: GO:0045632
name: negative regulation of mechanoreceptor differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mechanoreceptor differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of mechanoreceptor differentiation." [GOC:curators]
synonym: "down regulation of mechanoreceptor differentiation" EXACT []
synonym: "down-regulation of mechanoreceptor differentiation" EXACT []
synonym: "downregulation of mechanoreceptor differentiation" EXACT []
@@ -283490,7 +286831,7 @@
id: GO:0045633
name: positive regulation of mechanoreceptor differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of mechanoreceptor differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of mechanoreceptor differentiation." [GOC:curators]
synonym: "activation of mechanoreceptor differentiation" NARROW []
synonym: "stimulation of mechanoreceptor differentiation" NARROW []
synonym: "up regulation of mechanoreceptor differentiation" EXACT []
@@ -283506,7 +286847,7 @@
id: GO:0045634
name: regulation of melanocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of melanocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of melanocyte differentiation." [GOC:curators]
synonym: "regulation of melanophore differentiation" EXACT []
is_a: GO:0050932 ! regulation of pigment cell differentiation
intersection_of: GO:0065007 ! biological regulation
@@ -283517,7 +286858,7 @@
id: GO:0045635
name: negative regulation of melanocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of melanocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of melanocyte differentiation." [GOC:curators]
synonym: "down regulation of melanocyte differentiation" EXACT []
synonym: "down-regulation of melanocyte differentiation" EXACT []
synonym: "downregulation of melanocyte differentiation" EXACT []
@@ -283533,7 +286874,7 @@
id: GO:0045636
name: positive regulation of melanocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of melanocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of melanocyte differentiation." [GOC:curators]
synonym: "activation of melanocyte differentiation" NARROW []
synonym: "positive regulation of melanophore differentiation" EXACT []
synonym: "stimulation of melanocyte differentiation" NARROW []
@@ -283550,7 +286891,7 @@
id: GO:0045637
name: regulation of myeloid cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of myeloid cell differentiation." [GOC:curators]
xref: Reactome:R-HSA-8939246 "RUNX1 regulates transcription of genes involved in differentiation of myeloid cells"
is_a: GO:1903706 ! regulation of hemopoiesis
intersection_of: GO:0065007 ! biological regulation
@@ -283561,7 +286902,7 @@
id: GO:0045638
name: negative regulation of myeloid cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation." [GOC:curators]
synonym: "down regulation of myeloid cell differentiation" EXACT []
synonym: "down-regulation of myeloid cell differentiation" EXACT []
synonym: "downregulation of myeloid cell differentiation" EXACT []
@@ -283576,7 +286917,7 @@
id: GO:0045639
name: positive regulation of myeloid cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation." [GOC:curators]
synonym: "activation of myeloid cell differentiation" NARROW []
synonym: "stimulation of myeloid cell differentiation" NARROW []
synonym: "up regulation of myeloid cell differentiation" EXACT []
@@ -283592,7 +286933,7 @@
id: GO:0045640
name: regulation of basophil differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of basophil differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of basophil differentiation." [GOC:curators]
is_a: GO:0030852 ! regulation of granulocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030221 ! basophil differentiation
@@ -283602,7 +286943,7 @@
id: GO:0045641
name: negative regulation of basophil differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation." [GOC:curators]
synonym: "down regulation of basophil differentiation" EXACT []
synonym: "down-regulation of basophil differentiation" EXACT []
synonym: "downregulation of basophil differentiation" EXACT []
@@ -283617,7 +286958,7 @@
id: GO:0045642
name: positive regulation of basophil differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of basophil differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of basophil differentiation." [GOC:curators]
synonym: "activation of basophil differentiation" NARROW []
synonym: "stimulation of basophil differentiation" NARROW []
synonym: "up regulation of basophil differentiation" EXACT []
@@ -283633,7 +286974,7 @@
id: GO:0045643
name: regulation of eosinophil differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of eosinophil differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of eosinophil differentiation." [GOC:curators]
is_a: GO:0030852 ! regulation of granulocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030222 ! eosinophil differentiation
@@ -283643,7 +286984,7 @@
id: GO:0045644
name: negative regulation of eosinophil differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of eosinophil differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of eosinophil differentiation." [GOC:curators]
synonym: "down regulation of eosinophil differentiation" EXACT []
synonym: "down-regulation of eosinophil differentiation" EXACT []
synonym: "downregulation of eosinophil differentiation" EXACT []
@@ -283658,7 +286999,7 @@
id: GO:0045645
name: positive regulation of eosinophil differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of eosinophil differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of eosinophil differentiation." [GOC:curators]
synonym: "activation of eosinophil differentiation" NARROW []
synonym: "stimulation of eosinophil differentiation" NARROW []
synonym: "up regulation of eosinophil differentiation" EXACT []
@@ -283674,7 +287015,7 @@
id: GO:0045646
name: regulation of erythrocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of erythrocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of erythrocyte differentiation." [GOC:curators]
synonym: "regulation of RBC differentiation" EXACT [CL:0000232]
synonym: "regulation of red blood cell differentiation" EXACT [CL:0000232]
is_a: GO:0045637 ! regulation of myeloid cell differentiation
@@ -283686,7 +287027,7 @@
id: GO:0045647
name: negative regulation of erythrocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation." [GOC:curators]
synonym: "down regulation of erythrocyte differentiation" EXACT []
synonym: "down-regulation of erythrocyte differentiation" EXACT []
synonym: "downregulation of erythrocyte differentiation" EXACT []
@@ -283703,7 +287044,7 @@
id: GO:0045648
name: positive regulation of erythrocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation." [GOC:curators]
synonym: "activation of erythrocyte differentiation" NARROW []
synonym: "positive regulation of RBC differentiation" EXACT [CL:0000232]
synonym: "positive regulation of red blood cell differentiation" EXACT [CL:0000232]
@@ -283721,7 +287062,7 @@
id: GO:0045649
name: regulation of macrophage differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of macrophage differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of macrophage differentiation." [GOC:curators]
is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030225 ! macrophage differentiation
@@ -283731,7 +287072,7 @@
id: GO:0045650
name: negative regulation of macrophage differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation." [GOC:curators]
synonym: "down regulation of macrophage differentiation" EXACT []
synonym: "down-regulation of macrophage differentiation" EXACT []
synonym: "downregulation of macrophage differentiation" EXACT []
@@ -283746,7 +287087,7 @@
id: GO:0045651
name: positive regulation of macrophage differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of macrophage differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of macrophage differentiation." [GOC:curators]
synonym: "activation of macrophage differentiation" NARROW []
synonym: "stimulation of macrophage differentiation" NARROW []
synonym: "up regulation of macrophage differentiation" EXACT []
@@ -283762,7 +287103,7 @@
id: GO:0045652
name: regulation of megakaryocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of megakaryocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of megakaryocyte differentiation." [GOC:curators]
xref: Reactome:R-HSA-8936459 "RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function"
is_a: GO:0045637 ! regulation of myeloid cell differentiation
intersection_of: GO:0065007 ! biological regulation
@@ -283773,7 +287114,7 @@
id: GO:0045653
name: negative regulation of megakaryocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation." [GOC:curators]
synonym: "down regulation of megakaryocyte differentiation" EXACT []
synonym: "down-regulation of megakaryocyte differentiation" EXACT []
synonym: "downregulation of megakaryocyte differentiation" EXACT []
@@ -283788,7 +287129,7 @@
id: GO:0045654
name: positive regulation of megakaryocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation." [GOC:curators]
synonym: "activation of megakaryocyte differentiation" NARROW []
synonym: "stimulation of megakaryocyte differentiation" NARROW []
synonym: "up regulation of megakaryocyte differentiation" EXACT []
@@ -283804,7 +287145,7 @@
id: GO:0045655
name: regulation of monocyte differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of monocyte differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of monocyte differentiation." [GOC:curators]
is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030224 ! monocyte differentiation
@@ -283814,7 +287155,7 @@
id: GO:0045656
name: negative regulation of monocyte differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation." [GOC:curators]
synonym: "down regulation of monocyte differentiation" EXACT []
synonym: "down-regulation of monocyte differentiation" EXACT []
synonym: "downregulation of monocyte differentiation" EXACT []
@@ -283829,7 +287170,7 @@
id: GO:0045657
name: positive regulation of monocyte differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of monocyte differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of monocyte differentiation." [GOC:curators]
synonym: "activation of monocyte differentiation" NARROW []
synonym: "stimulation of monocyte differentiation" NARROW []
synonym: "up regulation of monocyte differentiation" EXACT []
@@ -283845,7 +287186,7 @@
id: GO:0045658
name: regulation of neutrophil differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of neutrophil differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of neutrophil differentiation." [GOC:curators]
is_a: GO:0030852 ! regulation of granulocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030223 ! neutrophil differentiation
@@ -283855,7 +287196,7 @@
id: GO:0045659
name: negative regulation of neutrophil differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation." [GOC:curators]
synonym: "down regulation of neutrophil differentiation" EXACT []
synonym: "down-regulation of neutrophil differentiation" EXACT []
synonym: "downregulation of neutrophil differentiation" EXACT []
@@ -283870,7 +287211,7 @@
id: GO:0045660
name: positive regulation of neutrophil differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of neutrophil differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of neutrophil differentiation." [GOC:curators]
synonym: "activation of neutrophil differentiation" NARROW []
synonym: "stimulation of neutrophil differentiation" NARROW []
synonym: "up regulation of neutrophil differentiation" EXACT []
@@ -283886,7 +287227,7 @@
id: GO:0045661
name: regulation of myoblast differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
+def: "Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:curators, GOC:mtg_muscle]
is_a: GO:0045595 ! regulation of cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0045445 ! myoblast differentiation
@@ -283896,7 +287237,7 @@
id: GO:0045662
name: negative regulation of myoblast differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:curators, GOC:mtg_muscle]
synonym: "down regulation of myoblast differentiation" EXACT []
synonym: "down-regulation of myoblast differentiation" EXACT []
synonym: "downregulation of myoblast differentiation" EXACT []
@@ -283911,7 +287252,7 @@
id: GO:0045663
name: positive regulation of myoblast differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:go_curators, GOC:mtg_muscle]
+def: "Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." [CL:0000056, GOC:curators, GOC:mtg_muscle]
synonym: "activation of myoblast differentiation" NARROW []
synonym: "stimulation of myoblast differentiation" NARROW []
synonym: "up regulation of myoblast differentiation" EXACT []
@@ -283927,7 +287268,7 @@
id: GO:0045664
name: regulation of neuron differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of neuron differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of neuron differentiation." [GOC:curators]
is_a: GO:0045595 ! regulation of cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030182 ! neuron differentiation
@@ -283937,7 +287278,7 @@
id: GO:0045665
name: negative regulation of neuron differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation." [GOC:curators]
synonym: "down regulation of neuron differentiation" EXACT []
synonym: "down-regulation of neuron differentiation" EXACT []
synonym: "downregulation of neuron differentiation" EXACT []
@@ -283952,7 +287293,7 @@
id: GO:0045666
name: positive regulation of neuron differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of neuron differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of neuron differentiation." [GOC:curators]
synonym: "activation of neuron differentiation" NARROW []
synonym: "stimulation of neuron differentiation" NARROW []
synonym: "up regulation of neuron differentiation" EXACT []
@@ -283968,7 +287309,7 @@
id: GO:0045667
name: regulation of osteoblast differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of osteoblast differentiation." [GOC:curators]
is_a: GO:0045595 ! regulation of cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0001649 ! osteoblast differentiation
@@ -283978,7 +287319,7 @@
id: GO:0045668
name: negative regulation of osteoblast differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation." [GOC:curators]
synonym: "down regulation of osteoblast differentiation" EXACT []
synonym: "down-regulation of osteoblast differentiation" EXACT []
synonym: "downregulation of osteoblast differentiation" EXACT []
@@ -283993,7 +287334,7 @@
id: GO:0045669
name: positive regulation of osteoblast differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of osteoblast differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of osteoblast differentiation." [GOC:curators]
synonym: "activation of osteoblast differentiation" NARROW []
synonym: "stimulation of osteoblast differentiation" NARROW []
synonym: "up regulation of osteoblast differentiation" EXACT []
@@ -284009,7 +287350,7 @@
id: GO:0045670
name: regulation of osteoclast differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of osteoclast differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of osteoclast differentiation." [GOC:curators]
is_a: GO:0002761 ! regulation of myeloid leukocyte differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0030316 ! osteoclast differentiation
@@ -284019,7 +287360,7 @@
id: GO:0045671
name: negative regulation of osteoclast differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation." [GOC:curators]
synonym: "down regulation of osteoclast differentiation" EXACT []
synonym: "down-regulation of osteoclast differentiation" EXACT []
synonym: "downregulation of osteoclast differentiation" EXACT []
@@ -284034,7 +287375,7 @@
id: GO:0045672
name: positive regulation of osteoclast differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of osteoclast differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of osteoclast differentiation." [GOC:curators]
synonym: "activation of osteoclast differentiation" NARROW []
synonym: "stimulation of osteoclast differentiation" NARROW []
synonym: "up regulation of osteoclast differentiation" EXACT []
@@ -284050,7 +287391,7 @@
id: GO:0045676
name: regulation of R7 cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of R7 differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of R7 differentiation." [GOC:curators]
is_a: GO:0110116 ! regulation of compound eye photoreceptor cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0045466 ! R7 cell differentiation
@@ -284060,7 +287401,7 @@
id: GO:0045677
name: negative regulation of R7 cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of R7cell differentiation." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of R7cell differentiation." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of R7 differentiation" EXACT []
synonym: "down-regulation of R7 differentiation" EXACT []
synonym: "downregulation of R7 differentiation" EXACT []
@@ -284076,7 +287417,7 @@
id: GO:0045678
name: positive regulation of R7 cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of R7 cell differentiation." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of R7 cell differentiation." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of R7 differentiation" NARROW []
synonym: "positive regulation of R7 differentiation" EXACT [GOC:dph, GOC:tb]
synonym: "stimulation of R7 differentiation" NARROW []
@@ -284093,7 +287434,7 @@
id: GO:0045679
name: regulation of R8 cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of R8 differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of R8 differentiation." [GOC:curators]
is_a: GO:0110116 ! regulation of compound eye photoreceptor cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0045465 ! R8 cell differentiation
@@ -284103,7 +287444,7 @@
id: GO:0045680
name: negative regulation of R8 cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of R8 cell differentiation." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of R8 cell differentiation." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of R8 differentiation" EXACT []
synonym: "down-regulation of R8 differentiation" EXACT []
synonym: "downregulation of R8 differentiation" EXACT []
@@ -284119,7 +287460,7 @@
id: GO:0045681
name: positive regulation of R8 cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of R8 cell differentiation." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of R8 cell differentiation." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of R8 differentiation" NARROW []
synonym: "positive regulation of R8 differentiation" EXACT [GOC:dph, GOC:tb]
synonym: "stimulation of R8 differentiation" NARROW []
@@ -284136,7 +287477,7 @@
id: GO:0045682
name: regulation of epidermis development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of epidermis development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of epidermis development." [GOC:curators]
synonym: "regulation of epidermal development" EXACT []
synonym: "regulation of hypodermis development" RELATED [GOC:kmv, GOC:rk]
is_a: GO:0050793 ! regulation of developmental process
@@ -284148,7 +287489,7 @@
id: GO:0045683
name: negative regulation of epidermis development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development." [GOC:curators]
synonym: "down regulation of epidermis development" EXACT []
synonym: "down-regulation of epidermis development" EXACT []
synonym: "downregulation of epidermis development" EXACT []
@@ -284165,7 +287506,7 @@
id: GO:0045684
name: positive regulation of epidermis development
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of epidermis development." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of epidermis development." [GOC:curators]
synonym: "activation of epidermis development" NARROW []
synonym: "positive regulation of epidermal development" EXACT []
synonym: "positive regulation of hypodermis development" RELATED [GOC:kmv, GOC:rk]
@@ -284183,7 +287524,7 @@
id: GO:0045685
name: regulation of glial cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of glia cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of glia cell differentiation." [GOC:curators]
synonym: "regulation of glia cell differentiation" EXACT []
synonym: "regulation of neuroglia differentiation" EXACT []
is_a: GO:0045595 ! regulation of cell differentiation
@@ -284195,7 +287536,7 @@
id: GO:0045686
name: negative regulation of glial cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation." [GOC:curators]
synonym: "down regulation of glial cell differentiation" EXACT []
synonym: "down-regulation of glial cell differentiation" EXACT []
synonym: "downregulation of glial cell differentiation" EXACT []
@@ -284212,7 +287553,7 @@
id: GO:0045687
name: positive regulation of glial cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of glia cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of glia cell differentiation." [GOC:curators]
synonym: "activation of glial cell differentiation" NARROW []
synonym: "positive regulation of glia cell differentiation" EXACT []
synonym: "positive regulation of neuroglia differentiation" EXACT []
@@ -284230,7 +287571,7 @@
id: GO:0045688
name: regulation of antipodal cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of antipodal cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that modulates the frequency, rate or extent of antipodal cell differentiation." [GOC:curators, GOC:mtg_plant]
is_a: GO:0045595 ! regulation of cell differentiation
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009557 ! antipodal cell differentiation
@@ -284240,7 +287581,7 @@
id: GO:0045689
name: negative regulation of antipodal cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of antipodal cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of antipodal cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "down regulation of antipodal cell differentiation" EXACT []
synonym: "down-regulation of antipodal cell differentiation" EXACT []
synonym: "downregulation of antipodal cell differentiation" EXACT []
@@ -284255,7 +287596,7 @@
id: GO:0045690
name: positive regulation of antipodal cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of antipodal cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that activates or increases the frequency, rate or extent of antipodal cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "activation of antipodal cell differentiation" NARROW []
synonym: "stimulation of antipodal cell differentiation" NARROW []
synonym: "up regulation of antipodal cell differentiation" EXACT []
@@ -284272,7 +287613,7 @@
id: GO:0045691
name: regulation of embryo sac central cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of female gametophyte central cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that modulates the frequency, rate or extent of female gametophyte central cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "regulation of female gametophyte central cell differentiation" EXACT []
is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:2000026 ! regulation of multicellular organismal development
@@ -284284,7 +287625,7 @@
id: GO:0045692
name: negative regulation of embryo sac central cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryo sac central cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryo sac central cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "down regulation of female gametophyte central cell differentiation" EXACT []
synonym: "down-regulation of female gametophyte central cell differentiation" EXACT []
synonym: "downregulation of female gametophyte central cell differentiation" EXACT []
@@ -284301,7 +287642,7 @@
id: GO:0045693
name: positive regulation of embryo sac central cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of embryo sac central cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that activates or increases the frequency, rate or extent of embryo sac central cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "activation of female gametophyte central cell differentiation" NARROW []
synonym: "positive regulation of female gametophyte central cell differentiation" EXACT []
synonym: "stimulation of female gametophyte central cell differentiation" NARROW []
@@ -284319,7 +287660,7 @@
id: GO:0045694
name: regulation of embryo sac egg cell differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that modulates the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "regulation of female gametophyte egg cell differentiation" EXACT []
is_a: GO:0045595 ! regulation of cell differentiation
is_a: GO:2000241 ! regulation of reproductive process
@@ -284331,7 +287672,7 @@
id: GO:0045695
name: negative regulation of embryo sac egg cell differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "down regulation of female gametophyte egg cell differentiation" EXACT []
synonym: "down-regulation of female gametophyte egg cell differentiation" EXACT []
synonym: "downregulation of female gametophyte egg cell differentiation" EXACT []
@@ -284349,7 +287690,7 @@
id: GO:0045696
name: positive regulation of embryo sac egg cell differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:go_curators, GOC:mtg_plant]
+def: "Any process that activates or increases the frequency, rate or extent of embryo sac egg cell differentiation." [GOC:curators, GOC:mtg_plant]
synonym: "activation of female gametophyte egg cell differentiation" NARROW []
synonym: "positive regulation of female gametophyte egg cell differentiation" EXACT []
synonym: "stimulation of female gametophyte egg cell differentiation" NARROW []
@@ -284368,7 +287709,7 @@
id: GO:0045697
name: regulation of synergid differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of synergid cell differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of synergid cell differentiation." [GOC:curators]
synonym: "regulation of synergid cell differentiation" EXACT []
is_a: GO:0045595 ! regulation of cell differentiation
intersection_of: GO:0065007 ! biological regulation
@@ -284379,7 +287720,7 @@
id: GO:0045698
name: negative regulation of synergid differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of synergid cell differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of synergid cell differentiation." [GOC:curators]
synonym: "down regulation of synergid differentiation" EXACT []
synonym: "down-regulation of synergid differentiation" EXACT []
synonym: "downregulation of synergid differentiation" EXACT []
@@ -284396,7 +287737,7 @@
id: GO:0045699
name: positive regulation of synergid differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of synergid cell differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of synergid cell differentiation." [GOC:curators]
synonym: "activation of synergid differentiation" NARROW []
synonym: "positive regulation of synergid cell differentiation" EXACT []
synonym: "stimulation of synergid differentiation" NARROW []
@@ -284414,7 +287755,7 @@
id: GO:0045700
name: regulation of spermatid nuclear differentiation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation." [GOC:curators]
is_a: GO:0051239 ! regulation of multicellular organismal process
is_a: GO:1903353 ! regulation of nucleus organization
intersection_of: GO:0065007 ! biological regulation
@@ -284425,7 +287766,7 @@
id: GO:0045701
name: negative regulation of spermatid nuclear differentiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation." [GOC:curators]
synonym: "down regulation of spermatid nuclear differentiation" EXACT []
synonym: "down-regulation of spermatid nuclear differentiation" EXACT []
synonym: "downregulation of spermatid nuclear differentiation" EXACT []
@@ -284443,7 +287784,7 @@
id: GO:0045702
name: positive regulation of spermatid nuclear differentiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation." [GOC:curators]
synonym: "activation of spermatid nuclear differentiation" NARROW []
synonym: "stimulation of spermatid nuclear differentiation" NARROW []
synonym: "up regulation of spermatid nuclear differentiation" EXACT []
@@ -284468,7 +287809,7 @@
id: GO:0045704
name: regulation of salivary gland boundary specification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of salivary gland determination." [GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of salivary gland determination." [GOC:curators, GOC:tb]
synonym: "regulation of salivary gland determination" EXACT [GOC:tb]
is_a: GO:0050793 ! regulation of developmental process
is_a: GO:0051239 ! regulation of multicellular organismal process
@@ -284480,7 +287821,7 @@
id: GO:0045705
name: negative regulation of salivary gland boundary specification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination." [GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination." [GOC:curators, GOC:tb]
synonym: "down regulation of salivary gland determination" EXACT []
synonym: "down-regulation of salivary gland determination" EXACT []
synonym: "downregulation of salivary gland determination" EXACT []
@@ -284497,7 +287838,7 @@
id: GO:0045706
name: positive regulation of salivary gland boundary specification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination." [GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination." [GOC:curators, GOC:tb]
synonym: "activation of salivary gland determination" NARROW []
synonym: "positive regulation of salivary gland determination" EXACT [GOC:tb]
synonym: "stimulation of salivary gland determination" NARROW []
@@ -284515,7 +287856,7 @@
id: GO:0045707
name: regulation of adult salivary gland boundary specification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:curators, GOC:tb]
synonym: "regulation of adult salivary gland determination" EXACT [GOC:tb]
is_a: GO:0045704 ! regulation of salivary gland boundary specification
intersection_of: GO:0065007 ! biological regulation
@@ -284526,7 +287867,7 @@
id: GO:0045708
name: regulation of larval salivary gland boundary specification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:curators, GOC:tb]
synonym: "regulation of larval salivary gland determination" EXACT [GOC:tb]
is_a: GO:0045704 ! regulation of salivary gland boundary specification
intersection_of: GO:0065007 ! biological regulation
@@ -284537,7 +287878,7 @@
id: GO:0045709
name: negative regulation of adult salivary gland boundary specification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:curators, GOC:tb]
synonym: "down regulation of adult salivary gland determination" EXACT []
synonym: "down-regulation of adult salivary gland determination" EXACT []
synonym: "downregulation of adult salivary gland determination" EXACT []
@@ -284553,7 +287894,7 @@
id: GO:0045710
name: negative regulation of larval salivary gland boundary specification
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:curators, GOC:tb]
synonym: "down regulation of larval salivary gland determination" EXACT []
synonym: "down-regulation of larval salivary gland determination" EXACT []
synonym: "downregulation of larval salivary gland determination" EXACT []
@@ -284569,7 +287910,7 @@
id: GO:0045711
name: positive regulation of adult salivary gland boundary specification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination in an adult organism." [GOC:curators, GOC:tb]
synonym: "activation of adult salivary gland determination" NARROW []
synonym: "positive regulation of adult salivary gland determination" EXACT [GOC:tb]
synonym: "stimulation of adult salivary gland determination" NARROW []
@@ -284586,7 +287927,7 @@
id: GO:0045712
name: positive regulation of larval salivary gland boundary specification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of salivary gland determination in a larval organism." [GOC:curators, GOC:tb]
synonym: "activation of larval salivary gland determination" NARROW []
synonym: "positive regulation of larval salivary gland determination" EXACT [GOC:tb]
synonym: "stimulation of larval salivary gland determination" NARROW []
@@ -284603,7 +287944,7 @@
id: GO:0045713
name: obsolete low-density lipoprotein particle receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of low-density lipoprotein receptors, cell surface proteins that mediate the endocytosis of low-density lipoprotein particles by cells." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of low-density lipoprotein receptors, cell surface proteins that mediate the endocytosis of low-density lipoprotein particles by cells." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "LDLr biosynthesis" EXACT []
synonym: "LDLr biosynthetic process" EXACT []
@@ -284619,7 +287960,7 @@
id: GO:0045714
name: obsolete regulation of low-density lipoprotein particle receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein particle receptors." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein particle receptors." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "regulation of LDLr biosynthesis" EXACT []
synonym: "regulation of LDLr biosynthetic process" EXACT []
@@ -284635,7 +287976,7 @@
id: GO:0045715
name: obsolete negative regulation of low-density lipoprotein particle receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein particle receptors." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein particle receptors." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "down regulation of low-density lipoprotein receptor biosynthetic process" EXACT []
synonym: "down-regulation of low-density lipoprotein receptor biosynthetic process" EXACT []
@@ -284653,7 +287994,7 @@
id: GO:0045716
name: obsolete positive regulation of low-density lipoprotein particle receptor biosynthetic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein receptors." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein receptors." [GOC:curators]
comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "activation of low-density lipoprotein receptor biosynthetic process" NARROW []
synonym: "positive regulation of low-density lipoprotein receptor anabolism" EXACT []
@@ -284672,7 +288013,7 @@
id: GO:0045717
name: negative regulation of fatty acid biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids." [GOC:curators]
synonym: "down regulation of fatty acid biosynthetic process" EXACT []
synonym: "down-regulation of fatty acid biosynthetic process" EXACT []
synonym: "downregulation of fatty acid biosynthetic process" EXACT []
@@ -284692,7 +288033,7 @@
id: GO:0045718
name: obsolete negative regulation of flagellum assembly
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a flagellum." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a flagellum." [GOC:curators]
comment: This term was made obsolete because microtubule-based flagellum (GO:0009434) and motile cilium (GO:0031514), as referenced by this term, were determined to be equivalent and merged. When a merge for this term was considered, it was noticed that both eukaryotic and prokaryotic proteins are annotated to it because its meaning had been ambiguous so obsoletion was considered safest.
synonym: "down regulation of flagellum assembly" EXACT []
synonym: "down-regulation of flagellum assembly" EXACT []
@@ -284708,7 +288049,7 @@
id: GO:0045719
name: negative regulation of glycogen biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:curators]
synonym: "down regulation of glycogen biosynthetic process" EXACT []
synonym: "down-regulation of glycogen biosynthetic process" EXACT []
synonym: "downregulation of glycogen biosynthetic process" EXACT []
@@ -284728,7 +288069,7 @@
id: GO:0045720
name: negative regulation of integrin biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:curators]
synonym: "down regulation of integrin biosynthetic process" EXACT []
synonym: "down-regulation of integrin biosynthetic process" EXACT []
synonym: "downregulation of integrin biosynthetic process" EXACT []
@@ -284748,7 +288089,7 @@
id: GO:0045721
name: negative regulation of gluconeogenesis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis." [GOC:curators]
synonym: "down regulation of gluconeogenesis" EXACT []
synonym: "down-regulation of gluconeogenesis" EXACT []
synonym: "downregulation of gluconeogenesis" EXACT []
@@ -284765,7 +288106,7 @@
id: GO:0045722
name: positive regulation of gluconeogenesis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of gluconeogenesis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of gluconeogenesis." [GOC:curators]
synonym: "activation of gluconeogenesis" NARROW []
synonym: "stimulation of gluconeogenesis" NARROW []
synonym: "up regulation of gluconeogenesis" EXACT []
@@ -284782,7 +288123,7 @@
id: GO:0045723
name: positive regulation of fatty acid biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids." [GOC:curators]
synonym: "activation of fatty acid biosynthetic process" NARROW []
synonym: "positive regulation of fatty acid anabolism" EXACT []
synonym: "positive regulation of fatty acid biosynthesis" EXACT []
@@ -284803,7 +288144,7 @@
id: GO:0045724
name: positive regulation of cilium assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the formation of a cilium." [GOC:cilia, GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the formation of a cilium." [GOC:cilia, GOC:curators]
synonym: "activation of cilium assembly" NARROW []
synonym: "positive regulation of flagellum assembly" BROAD []
synonym: "positive regulation of flagellum biogenesis" RELATED [GOC:mah]
@@ -284822,7 +288163,7 @@
id: GO:0045725
name: positive regulation of glycogen biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." [GOC:curators]
synonym: "activation of glycogen biosynthetic process" NARROW []
synonym: "positive regulation of glycogen anabolism" EXACT []
synonym: "positive regulation of glycogen biosynthesis" EXACT []
@@ -284843,7 +288184,7 @@
id: GO:0045726
name: positive regulation of integrin biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of integrins." [GOC:curators]
synonym: "activation of integrin biosynthetic process" NARROW []
synonym: "positive regulation of integrin anabolism" EXACT []
synonym: "positive regulation of integrin biosynthesis" EXACT []
@@ -284865,7 +288206,7 @@
name: positive regulation of translation
namespace: biological_process
alt_id: GO:0045946
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of protein biosynthetic process" NARROW []
synonym: "positive regulation of protein anabolism" EXACT []
synonym: "positive regulation of protein biosynthesis" EXACT []
@@ -284920,7 +288261,7 @@
namespace: biological_process
alt_id: GO:1903364
alt_id: GO:2000600
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." [GOC:curators]
synonym: "activation of cellular protein breakdown" NARROW [GOC:TermGenie]
synonym: "activation of cellular protein catabolic process" NARROW [GOC:TermGenie]
synonym: "activation of cellular protein catabolism" NARROW [GOC:TermGenie]
@@ -284967,7 +288308,7 @@
name: acetate catabolic process
namespace: biological_process
alt_id: GO:0019663
-def: "The chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid." [GOC:curators]
synonym: "acetate breakdown" EXACT []
synonym: "acetate catabolism" EXACT []
synonym: "acetate degradation" EXACT []
@@ -284979,7 +288320,7 @@
id: GO:0045734
name: regulation of acetate catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate, the anion of acetic acid." [GOC:curators]
synonym: "regulation of acetate breakdown" EXACT []
synonym: "regulation of acetate catabolism" EXACT []
synonym: "regulation of acetate degradation" EXACT []
@@ -285008,7 +288349,7 @@
id: GO:0045736
name: negative regulation of cyclin-dependent protein serine/threonine kinase activity
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity." [GOC:go_curators, GOC:pr]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity." [GOC:curators, GOC:pr]
subset: gocheck_obsoletion_candidate
is_a: GO:0000079 ! regulation of cyclin-dependent protein serine/threonine kinase activity
is_a: GO:0045786 ! negative regulation of cell cycle
@@ -285022,7 +288363,7 @@
id: GO:0045737
name: positive regulation of cyclin-dependent protein serine/threonine kinase activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of CDK activity." [GOC:go_curators, GOC:pr]
+def: "Any process that activates or increases the frequency, rate or extent of CDK activity." [GOC:curators, GOC:pr]
subset: gocheck_obsoletion_candidate
synonym: "activation of cyclin-dependent protein kinase activity" BROAD []
synonym: "positive regulation of CDK activity" BROAD []
@@ -285043,7 +288384,7 @@
id: GO:0045738
name: negative regulation of DNA repair
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA repair." [GOC:curators]
synonym: "down regulation of DNA repair" EXACT []
synonym: "down-regulation of DNA repair" EXACT []
synonym: "downregulation of DNA repair" EXACT []
@@ -285059,7 +288400,7 @@
id: GO:0045739
name: positive regulation of DNA repair
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA repair." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of DNA repair." [GOC:curators]
synonym: "activation of DNA repair" NARROW []
synonym: "stimulation of DNA repair" NARROW []
synonym: "up regulation of DNA repair" EXACT []
@@ -285076,7 +288417,7 @@
id: GO:0045740
name: positive regulation of DNA replication
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA replication." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of DNA replication." [GOC:curators]
synonym: "activation of DNA replication" NARROW []
synonym: "stimulation of DNA replication" NARROW []
synonym: "up regulation of DNA replication" EXACT []
@@ -285093,7 +288434,7 @@
id: GO:0045741
name: obsolete positive regulation of epidermal growth factor-activated receptor activity
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function. Consider molecular function regulator activity ; GO:0098772 or a child.
synonym: "activation of epidermal growth factor receptor activity" NARROW []
synonym: "positive regulation of EGF receptor activity" EXACT []
@@ -285112,7 +288453,7 @@
id: GO:0045742
name: positive regulation of epidermal growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "activation of epidermal growth factor receptor signaling pathway" NARROW []
synonym: "positive regulation of EGF receptor signaling pathway" EXACT []
synonym: "positive regulation of EGF receptor signalling pathway" EXACT []
@@ -285132,7 +288473,7 @@
id: GO:0045743
name: positive regulation of fibroblast growth factor receptor signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity." [GOC:curators]
synonym: "activation of fibroblast growth factor receptor signaling pathway" NARROW []
synonym: "positive regulation of FGF receptor signaling pathway" EXACT []
synonym: "positive regulation of FGF receptor signalling pathway" EXACT []
@@ -285151,7 +288492,7 @@
id: GO:0045744
name: negative regulation of G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway." [GOC:curators]
synonym: "down regulation of G-protein coupled receptor protein signaling pathway" EXACT []
synonym: "down-regulation of G-protein coupled receptor protein signaling pathway" EXACT []
synonym: "downregulation of G-protein coupled receptor protein signaling pathway" EXACT []
@@ -285173,7 +288514,7 @@
id: GO:0045745
name: positive regulation of G protein-coupled receptor signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of G protein-coupled receptor signaling pathway activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of G protein-coupled receptor signaling pathway activity." [GOC:curators]
synonym: "activation of G-protein coupled receptor protein signaling pathway" NARROW []
synonym: "positive regulation of G protein coupled receptor protein signaling pathway" EXACT []
synonym: "positive regulation of G protein coupled receptor protein signalling pathway" EXACT []
@@ -285197,7 +288538,7 @@
id: GO:0045746
name: negative regulation of Notch signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway." [GOC:curators]
synonym: "down regulation of Notch signaling pathway" EXACT []
synonym: "down-regulation of Notch signaling pathway" EXACT []
synonym: "downregulation of Notch signaling pathway" EXACT []
@@ -285216,7 +288557,7 @@
id: GO:0045747
name: positive regulation of Notch signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway." [GOC:curators]
synonym: "activation of Notch signaling pathway" NARROW []
synonym: "positive regulation of N signaling pathway" EXACT []
synonym: "positive regulation of N signalling pathway" EXACT []
@@ -285235,7 +288576,7 @@
id: GO:0045748
name: positive regulation of R8 cell spacing in compound eye
namespace: biological_process
-def: "Any process that activates or enforces the correct R8 cell spacing in a compound eye." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or enforces the correct R8 cell spacing in a compound eye." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of R8 spacing" NARROW []
synonym: "positive regulation of R8 spacing" EXACT [GOC:dph, GOC:tb]
synonym: "stimulation of R8 spacing" NARROW []
@@ -285248,7 +288589,7 @@
id: GO:0045749
name: obsolete negative regulation of S phase of mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of S phase of mitotic cell cycle activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of S phase of mitotic cell cycle activity." [GOC:curators]
comment: This term was made obsolete as part of the cell cycle overhaul. This is because it was decided that cell cycle phases are intervals and so cannot be regulated, rather it is the transitions between the phases that are regulated.
synonym: "down regulation of S phase of mitotic cell cycle" EXACT []
synonym: "down-regulation of S phase of mitotic cell cycle" EXACT []
@@ -285262,7 +288603,7 @@
id: GO:0045750
name: obsolete positive regulation of S phase of mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of S phase of mitotic cell cycle activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of S phase of mitotic cell cycle activity." [GOC:curators]
comment: This term was made obsolete as part of the cell cycle overhaul. This is because it was decided that cell cycle phases are intervals and so cannot be regulated, rather it is the transitions between the phases that are regulated.
synonym: "activation of S phase of mitotic cell cycle" NARROW []
synonym: "positive regulation of S phase of mitotic cell cycle" EXACT []
@@ -285277,7 +288618,7 @@
id: GO:0045751
name: negative regulation of Toll signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Tl signaling pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the Tl signaling pathway." [GOC:curators]
synonym: "down regulation of Toll signaling pathway" EXACT []
synonym: "down-regulation of Toll signaling pathway" EXACT []
synonym: "downregulation of Toll signaling pathway" EXACT []
@@ -285294,7 +288635,7 @@
id: GO:0045752
name: positive regulation of Toll signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the Tl signaling pathway." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the Tl signaling pathway." [GOC:curators]
synonym: "activation of Toll signaling pathway" NARROW []
synonym: "positive regulation of Tl signaling pathway" EXACT []
synonym: "positive regulation of Tl signalling pathway" EXACT []
@@ -285312,7 +288653,7 @@
id: GO:0045753
name: negative regulation of acetate catabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:curators]
synonym: "down regulation of acetate catabolic process" EXACT []
synonym: "down-regulation of acetate catabolic process" EXACT []
synonym: "downregulation of acetate catabolic process" EXACT []
@@ -285331,7 +288672,7 @@
id: GO:0045754
name: positive regulation of acetate catabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:curators]
synonym: "activation of acetate catabolic process" NARROW []
synonym: "positive regulation of acetate breakdown" EXACT []
synonym: "positive regulation of acetate catabolism" EXACT []
@@ -285351,7 +288692,7 @@
id: GO:0045755
name: obsolete negative regulation of initiation of acetate catabolic process by acetate
namespace: biological_process
-def: "OBSOLETE. Any process that stops or prevents the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops or prevents the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "down regulation of initiation of acetate catabolic process by acetate" EXACT []
synonym: "down-regulation of initiation of acetate catabolic process by acetate" EXACT []
@@ -285366,7 +288707,7 @@
id: GO:0045756
name: obsolete positive regulation of initiation of acetate catabolic process by acetate
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the activation, by acetate, of the chemical reactions and pathways resulting in the breakdown of acetate." [GOC:curators]
comment: The reason for obsoletion is that this term represents a molecular function.
synonym: "activation of initiation of acetate catabolic process by acetate" NARROW []
synonym: "positive regulation of initiation of acetate breakdown by acetate" EXACT []
@@ -285382,7 +288723,7 @@
id: GO:0045757
name: obsolete negative regulation of actin polymerization and/or depolymerization
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of actin polymerization and/or depolymerization." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of actin polymerization and/or depolymerization." [GOC:curators]
comment: This term was made obsolete because it has been split.
synonym: "negative regulation of actin polymerization and/or depolymerization" EXACT []
is_obsolete: true
@@ -285393,7 +288734,7 @@
id: GO:0045758
name: obsolete positive regulation of actin polymerization and/or depolymerization
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of actin polymerization and/or depolymerization." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of actin polymerization and/or depolymerization." [GOC:curators]
comment: This term was made obsolete because it has been split.
synonym: "positive regulation of actin polymerization and/or depolymerization" EXACT []
is_obsolete: true
@@ -285404,7 +288745,7 @@
id: GO:0045759
name: negative regulation of action potential
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:curators]
synonym: "down regulation of action potential" EXACT []
synonym: "down-regulation of action potential" EXACT []
synonym: "downregulation of action potential" EXACT []
@@ -285419,7 +288760,7 @@
id: GO:0045760
name: positive regulation of action potential
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:curators]
synonym: "activation of action potential" NARROW []
synonym: "stimulation of action potential" NARROW []
synonym: "up regulation of action potential" EXACT []
@@ -285435,7 +288776,7 @@
id: GO:0045761
name: regulation of adenylate cyclase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of adenylate cyclase activity." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of adenylate cyclase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "adenylate cyclase regulator" RELATED []
synonym: "regulation of adenylyl cyclase activity" EXACT []
@@ -285448,7 +288789,7 @@
id: GO:0045762
name: positive regulation of adenylate cyclase activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of adenylate cyclase activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of adenylate cyclase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "adenylate cyclase activator" RELATED []
synonym: "positive regulation of adenylyl cyclase activity" EXACT []
@@ -285467,7 +288808,7 @@
id: GO:0045763
name: negative regulation of amino acid metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:curators]
synonym: "down regulation of amino acid metabolic process" EXACT []
synonym: "down-regulation of amino acid metabolic process" EXACT []
synonym: "downregulation of amino acid metabolic process" EXACT []
@@ -285484,7 +288825,7 @@
id: GO:0045764
name: positive regulation of amino acid metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid." [GOC:curators]
synonym: "activation of amino acid metabolic process" NARROW []
synonym: "positive regulation of amino acid metabolism" EXACT []
synonym: "positive regulation of cellular amino acid metabolic process" EXACT []
@@ -285502,7 +288843,7 @@
id: GO:0045765
name: regulation of angiogenesis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of angiogenesis." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of angiogenesis." [GOC:curators]
is_a: GO:0022603 ! regulation of anatomical structure morphogenesis
is_a: GO:1901342 ! regulation of vasculature development
intersection_of: GO:0065007 ! biological regulation
@@ -285513,7 +288854,7 @@
id: GO:0045766
name: positive regulation of angiogenesis
namespace: biological_process
-def: "Any process that activates or increases angiogenesis." [GOC:go_curators]
+def: "Any process that activates or increases angiogenesis." [GOC:curators]
synonym: "activation of angiogenesis" NARROW []
synonym: "stimulation of angiogenesis" NARROW []
synonym: "up regulation of angiogenesis" EXACT []
@@ -285529,7 +288870,7 @@
id: GO:0045767
name: obsolete regulation of anti-apoptosis
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of anti-apoptosis." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of anti-apoptosis." [GOC:curators, GOC:mtg_apoptosis]
comment: This term was made obsolete because it was ill-defined.
synonym: "regulation of anti-apoptosis" EXACT []
is_obsolete: true
@@ -285538,7 +288879,7 @@
id: GO:0045768
name: obsolete positive regulation of anti-apoptosis
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of anti-apoptosis." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of anti-apoptosis." [GOC:curators, GOC:mtg_apoptosis]
comment: This term was made obsolete because it was ill-defined.
synonym: "activation of anti-apoptosis" NARROW []
synonym: "positive regulation of anti-apoptosis" EXACT []
@@ -285552,7 +288893,7 @@
id: GO:0045769
name: negative regulation of asymmetric cell division
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division." [GOC:curators]
synonym: "down regulation of asymmetric cell division" EXACT []
synonym: "down-regulation of asymmetric cell division" EXACT []
synonym: "downregulation of asymmetric cell division" EXACT []
@@ -285567,7 +288908,7 @@
id: GO:0045770
name: positive regulation of asymmetric cell division
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of asymmetric cell division." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of asymmetric cell division." [GOC:curators]
synonym: "activation of asymmetric cell division" NARROW []
synonym: "stimulation of asymmetric cell division" NARROW []
synonym: "up regulation of asymmetric cell division" EXACT []
@@ -285583,7 +288924,7 @@
id: GO:0045771
name: negative regulation of autophagosome size
namespace: biological_process
-def: "Any process that reduces autophagosome size." [GOC:autophagy, GOC:go_curators]
+def: "Any process that reduces autophagosome size." [GOC:autophagy, GOC:curators]
synonym: "down regulation of autophagic vacuole size" EXACT []
synonym: "down-regulation of autophagic vacuole size" EXACT []
synonym: "downregulation of autophagic vacuole size" EXACT []
@@ -285595,7 +288936,7 @@
id: GO:0045772
name: positive regulation of autophagosome size
namespace: biological_process
-def: "Any process that increases autophagosome size." [GOC:autophagy, GOC:go_curators]
+def: "Any process that increases autophagosome size." [GOC:autophagy, GOC:curators]
synonym: "activation of autophagic vacuole size" NARROW []
synonym: "positive regulation of autophagic vacuole size" EXACT [GOC:autophagy]
synonym: "stimulation of autophagic vacuole size" NARROW []
@@ -285608,7 +288949,7 @@
id: GO:0045773
name: positive regulation of axon extension
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of axon extension." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of axon extension." [GOC:curators]
synonym: "activation of axon extension" NARROW []
synonym: "stimulation of axon extension" NARROW []
synonym: "up regulation of axon extension" EXACT []
@@ -285626,7 +288967,7 @@
id: GO:0045774
name: negative regulation of beta 2 integrin biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:curators]
synonym: "down regulation of beta 2 integrin biosynthetic process" EXACT []
synonym: "down-regulation of beta 2 integrin biosynthetic process" EXACT []
synonym: "downregulation of beta 2 integrin biosynthetic process" EXACT []
@@ -285645,7 +288986,7 @@
id: GO:0045775
name: positive regulation of beta 2 integrin biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of beta 2 integrins." [GOC:curators]
synonym: "activation of beta 2 integrin biosynthetic process" NARROW []
synonym: "positive regulation of beta 2 integrin anabolism" EXACT []
synonym: "positive regulation of beta 2 integrin biosynthesis" EXACT []
@@ -285665,7 +289006,7 @@
id: GO:0045776
name: negative regulation of blood pressure
namespace: biological_process
-def: "Any process in which the force of blood traveling through the circulatory system is decreased." [GOC:go_curators, GOC:mtg_cardio]
+def: "Any process in which the force of blood traveling through the circulatory system is decreased." [GOC:curators, GOC:mtg_cardio]
synonym: "down regulation of blood pressure" EXACT []
synonym: "down-regulation of blood pressure" EXACT []
synonym: "downregulation of blood pressure" EXACT []
@@ -285676,7 +289017,7 @@
id: GO:0045777
name: positive regulation of blood pressure
namespace: biological_process
-def: "Any process in which the force of blood traveling through the circulatory system is increased." [GOC:go_curators, GOC:mtg_cardio]
+def: "Any process in which the force of blood traveling through the circulatory system is increased." [GOC:curators, GOC:mtg_cardio]
synonym: "activation of blood pressure" NARROW []
synonym: "stimulation of blood pressure" NARROW []
synonym: "up regulation of blood pressure" EXACT []
@@ -285688,7 +289029,7 @@
id: GO:0045778
name: positive regulation of ossification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:curators]
synonym: "activation of ossification" NARROW []
synonym: "positive regulation of bone biosynthesis" EXACT []
synonym: "positive regulation of bone formation" EXACT []
@@ -285706,7 +289047,7 @@
id: GO:0045779
name: negative regulation of bone resorption
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption." [GOC:curators]
synonym: "down regulation of bone resorption" EXACT []
synonym: "down-regulation of bone resorption" EXACT []
synonym: "downregulation of bone resorption" EXACT []
@@ -285721,7 +289062,7 @@
id: GO:0045780
name: positive regulation of bone resorption
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of bone resorption." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of bone resorption." [GOC:curators]
synonym: "activation of bone resorption" NARROW []
synonym: "stimulation of bone resorption" NARROW []
synonym: "up regulation of bone resorption" EXACT []
@@ -285737,7 +289078,7 @@
id: GO:0045781
name: negative regulation of cell budding
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell budding." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell budding." [GOC:curators]
synonym: "down regulation of cell budding" EXACT []
synonym: "down-regulation of cell budding" EXACT []
synonym: "downregulation of cell budding" EXACT []
@@ -285754,7 +289095,7 @@
id: GO:0045782
name: positive regulation of cell budding
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cell budding." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cell budding." [GOC:curators]
synonym: "activation of cell budding" NARROW []
synonym: "positive regulation of budding" BROAD []
synonym: "stimulation of cell budding" NARROW []
@@ -285772,7 +289113,7 @@
id: GO:0045783
name: obsolete negative regulation of calcium in ER
namespace: biological_process
-def: "OBSOLETE. Any process that reduces the concentration of calcium in the ER." [GOC:go_curators]
+def: "OBSOLETE. Any process that reduces the concentration of calcium in the ER." [GOC:curators]
comment: This term was made obsolete because the term name is ambiguous and as a result, the term was incorrectly placed in the ontology (it was a descendant of 'protein transport').
synonym: "negative regulation of calcium in ER" EXACT []
is_obsolete: true
@@ -285783,7 +289124,7 @@
id: GO:0045784
name: obsolete positive regulation of calcium in ER
namespace: biological_process
-def: "OBSOLETE. Any process that increases the concentration of calcium in the ER." [GOC:go_curators]
+def: "OBSOLETE. Any process that increases the concentration of calcium in the ER." [GOC:curators]
comment: This term was made obsolete because the term name is ambiguous and as a result, the term was incorrectly placed in the ontology (it was a descendant of 'protein transport').
synonym: "positive regulation of calcium in ER" EXACT []
is_obsolete: true
@@ -285794,7 +289135,7 @@
id: GO:0045785
name: positive regulation of cell adhesion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cell adhesion." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cell adhesion." [GOC:curators]
synonym: "activation of cell adhesion" NARROW []
synonym: "stimulation of cell adhesion" NARROW []
synonym: "up regulation of cell adhesion" EXACT []
@@ -285810,7 +289151,7 @@
id: GO:0045786
name: negative regulation of cell cycle
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of progression through cell cycle" EXACT []
synonym: "down-regulation of progression through cell cycle" EXACT []
synonym: "downregulation of progression through cell cycle" EXACT []
@@ -285828,7 +289169,7 @@
id: GO:0045787
name: positive regulation of cell cycle
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of progression through the cell cycle." [GOC:go_curators]
+def: "Any process that activates or increases the rate or extent of progression through the cell cycle." [GOC:curators]
synonym: "activation of progression through cell cycle" NARROW []
synonym: "positive regulation of cell cycle progression" EXACT []
synonym: "positive regulation of progression through cell cycle" EXACT [GOC:dph, GOC:tb]
@@ -285847,7 +289188,7 @@
id: GO:0045792
name: negative regulation of cell size
namespace: biological_process
-def: "Any process that reduces cell size." [GOC:go_curators]
+def: "Any process that reduces cell size." [GOC:curators]
synonym: "down regulation of cell size" EXACT []
synonym: "down-regulation of cell size" EXACT []
synonym: "downregulation of cell size" EXACT []
@@ -285858,7 +289199,7 @@
id: GO:0045793
name: positive regulation of cell size
namespace: biological_process
-def: "Any process that increases cell size." [GOC:go_curators]
+def: "Any process that increases cell size." [GOC:curators]
synonym: "activation of cell size" NARROW []
synonym: "stimulation of cell size" NARROW []
synonym: "up regulation of cell size" EXACT []
@@ -285870,7 +289211,7 @@
id: GO:0045794
name: negative regulation of cell volume
namespace: biological_process
-def: "Any process that decreases cell volume." [GOC:go_curators]
+def: "Any process that decreases cell volume." [GOC:curators]
synonym: "cell regulatory volume decrease" RELATED [PMID:12388065]
synonym: "RVD" RELATED [PMID:12388065]
is_a: GO:0006884 ! cell volume homeostasis
@@ -285879,14 +289220,14 @@
id: GO:0045795
name: positive regulation of cell volume
namespace: biological_process
-def: "Any process that increases cell volume." [GOC:go_curators]
+def: "Any process that increases cell volume." [GOC:curators]
is_a: GO:0006884 ! cell volume homeostasis
[Term]
id: GO:0045796
name: negative regulation of intestinal cholesterol absorption
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine." [GOC:curators]
synonym: "down regulation of cholesterol absorption" EXACT []
synonym: "down-regulation of cholesterol absorption" EXACT []
synonym: "downregulation of cholesterol absorption" EXACT []
@@ -285901,7 +289242,7 @@
id: GO:0045797
name: positive regulation of intestinal cholesterol absorption
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of uptake of cholesterol into the blood by absorption from the intestine." [GOC:curators]
synonym: "activation of cholesterol absorption" NARROW []
synonym: "stimulation of cholesterol absorption" NARROW []
synonym: "up regulation of cholesterol absorption" EXACT []
@@ -285917,7 +289258,7 @@
id: GO:0045800
name: negative regulation of chitin-based cuticle tanning
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chitin-based cuticular tanning." [GOC:go_curators, GOC:jid, GOC:mtg_sensu]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chitin-based cuticular tanning." [GOC:curators, GOC:jid, GOC:mtg_sensu]
synonym: "down regulation of cuticle tanning" EXACT []
synonym: "down-regulation of cuticle tanning" EXACT []
synonym: "downregulation of cuticle tanning" EXACT []
@@ -285935,7 +289276,7 @@
id: GO:0045801
name: positive regulation of chitin-based cuticle tanning
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of chitin-based cuticular tanning." [GOC:go_curators, GOC:jid, GOC:mtg_sensu]
+def: "Any process that activates or increases the frequency, rate or extent of chitin-based cuticular tanning." [GOC:curators, GOC:jid, GOC:mtg_sensu]
synonym: "activation of cuticle tanning" NARROW []
synonym: "positive regulation of cuticle hardening" NARROW []
synonym: "positive regulation of cuticle tanning" EXACT []
@@ -285954,7 +289295,7 @@
id: GO:0045802
name: obsolete negative regulation of cytoskeleton
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:curators]
comment: This term was made obsolete because cytoskeleton is not a process, so the term made no sense.
synonym: "negative regulation of cytoskeleton" EXACT []
is_obsolete: true
@@ -285964,7 +289305,7 @@
id: GO:0045803
name: obsolete positive regulation of cytoskeleton
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the organization, biogenesis or maintenance of the cytoskeleton." [GOC:curators]
comment: This term was made obsolete because cytoskeleton is not a process, so the term made no sense.
synonym: "positive regulation of cytoskeleton" EXACT []
is_obsolete: true
@@ -285974,7 +289315,7 @@
id: GO:0045804
name: negative regulation of eclosion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of eclosion." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of eclosion." [GOC:curators]
synonym: "down regulation of eclosion" EXACT []
synonym: "down-regulation of eclosion" EXACT []
synonym: "downregulation of eclosion" EXACT []
@@ -285990,7 +289331,7 @@
id: GO:0045805
name: positive regulation of eclosion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of eclosion." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of eclosion." [GOC:curators]
synonym: "activation of eclosion" NARROW []
synonym: "stimulation of eclosion" NARROW []
synonym: "up regulation of eclosion" EXACT []
@@ -286006,7 +289347,7 @@
id: GO:0045806
name: negative regulation of endocytosis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis." [GOC:curators]
synonym: "down regulation of endocytosis" EXACT []
synonym: "down-regulation of endocytosis" EXACT []
synonym: "downregulation of endocytosis" EXACT []
@@ -286022,7 +289363,7 @@
id: GO:0045807
name: positive regulation of endocytosis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of endocytosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of endocytosis." [GOC:curators]
synonym: "activation of endocytosis" NARROW []
synonym: "stimulation of endocytosis" NARROW []
synonym: "up regulation of endocytosis" EXACT []
@@ -286039,7 +289380,7 @@
id: GO:0045808
name: negative regulation of establishment of competence for transformation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment of competence for transformation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment of competence for transformation." [GOC:curators]
synonym: "down regulation of establishment of competence for transformation" EXACT []
synonym: "down-regulation of establishment of competence for transformation" EXACT []
synonym: "downregulation of establishment of competence for transformation" EXACT []
@@ -286056,7 +289397,7 @@
id: GO:0045809
name: positive regulation of establishment of competence for transformation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of establishment of competence for transformation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of establishment of competence for transformation." [GOC:curators]
synonym: "activation of establishment of competence for transformation" NARROW []
synonym: "activator of the establishment of competence for transformation activity" RELATED []
synonym: "stimulation of establishment of competence for transformation" NARROW []
@@ -286074,7 +289415,7 @@
id: GO:0045812
name: negative regulation of Wnt signaling pathway, calcium modulating pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of frizzled-2 signaling pathway" EXACT []
synonym: "down-regulation of frizzled-2 signaling pathway" EXACT []
synonym: "downregulation of frizzled-2 signaling pathway" EXACT []
@@ -286093,7 +289434,7 @@
id: GO:0045813
name: positive regulation of Wnt signaling pathway, calcium modulating pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors leads to an increase in intracellular calcium and activation of protein kinase C (PKC)." [GOC:curators]
synonym: "activation of frizzled-2 signaling pathway" NARROW []
synonym: "positive regulation of frizzled-2 signaling pathway" EXACT []
synonym: "positive regulation of frizzled-2 signalling pathway" EXACT []
@@ -286157,7 +289498,7 @@
id: GO:0045818
name: negative regulation of glycogen catabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:curators]
synonym: "down regulation of glycogen catabolic process" EXACT []
synonym: "down-regulation of glycogen catabolic process" EXACT []
synonym: "downregulation of glycogen catabolic process" EXACT []
@@ -286178,7 +289519,7 @@
id: GO:0045819
name: positive regulation of glycogen catabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." [GOC:curators]
synonym: "activation of glycogen catabolic process" NARROW []
synonym: "positive regulation of glycogen breakdown" EXACT []
synonym: "positive regulation of glycogen catabolism" EXACT []
@@ -286200,7 +289541,7 @@
id: GO:0045820
name: negative regulation of glycolytic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis." [GOC:curators]
synonym: "down regulation of glycolysis" EXACT []
synonym: "down-regulation of glycolysis" EXACT []
synonym: "downregulation of glycolysis" EXACT []
@@ -286217,7 +289558,7 @@
id: GO:0045821
name: positive regulation of glycolytic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of glycolysis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of glycolysis." [GOC:curators]
synonym: "activation of glycolysis" NARROW []
synonym: "stimulation of glycolysis" NARROW []
synonym: "up regulation of glycolysis" EXACT []
@@ -286236,7 +289577,7 @@
id: GO:0045822
name: negative regulation of heart contraction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction." [GOC:curators]
synonym: "down regulation of heart contraction" EXACT []
synonym: "down-regulation of heart contraction" EXACT []
synonym: "downregulation of heart contraction" EXACT []
@@ -286252,7 +289593,7 @@
id: GO:0045823
name: positive regulation of heart contraction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of heart contraction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of heart contraction." [GOC:curators]
synonym: "activation of heart contraction" NARROW []
synonym: "positive regulation of cardiac contraction" EXACT []
synonym: "stimulation of heart contraction" NARROW []
@@ -286269,7 +289610,7 @@
id: GO:0045824
name: negative regulation of innate immune response
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response." [GOC:curators]
synonym: "down regulation of innate immune response" EXACT []
synonym: "down-regulation of innate immune response" EXACT []
synonym: "downregulation of innate immune response" EXACT []
@@ -286287,7 +289628,7 @@
id: GO:0045825
name: obsolete negative regulation of intermediate filament polymerization and/or depolymerization
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of intermediate filament polymerization and/or depolymerization." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of intermediate filament polymerization and/or depolymerization." [GOC:curators]
comment: This term was made obsolete because it has been split.
synonym: "negative regulation of intermediate filament polymerization and/or depolymerization" EXACT []
is_obsolete: true
@@ -286298,7 +289639,7 @@
id: GO:0045826
name: obsolete positive regulation of intermediate filament polymerization and/or depolymerization
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of intermediate filament polymerization and/or depolymerization." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of intermediate filament polymerization and/or depolymerization." [GOC:curators]
comment: This term was made obsolete because it has been split.
synonym: "positive regulation of intermediate filament polymerization and/or depolymerization" EXACT []
is_obsolete: true
@@ -286309,7 +289650,7 @@
id: GO:0045827
name: negative regulation of isoprenoid metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid." [GOC:curators]
synonym: "down regulation of isoprenoid metabolic process" EXACT []
synonym: "down-regulation of isoprenoid metabolic process" EXACT []
synonym: "downregulation of isoprenoid metabolic process" EXACT []
@@ -286325,7 +289666,7 @@
id: GO:0045828
name: obsolete positive regulation of isoprenoid metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving isoprenoid." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of isoprenoid metabolic process" NARROW []
synonym: "positive regulation of isoprenoid metabolism" EXACT []
@@ -286340,7 +289681,7 @@
id: GO:0045829
name: negative regulation of isotype switching
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching." [GOC:curators]
synonym: "down regulation of isotype switching" EXACT []
synonym: "down-regulation of isotype switching" EXACT []
synonym: "downregulation of isotype switching" EXACT []
@@ -286362,7 +289703,7 @@
id: GO:0045830
name: positive regulation of isotype switching
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of isotype switching." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of isotype switching." [GOC:curators]
synonym: "activation of isotype switching" NARROW []
synonym: "positive regulation of class switch recombination" EXACT []
synonym: "positive regulation of class switching" EXACT []
@@ -286385,7 +289726,7 @@
id: GO:0045831
name: obsolete negative regulation of light-activated channel activity
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of light-activated channel activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of light-activated channel activity." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of light-activated channel activity" EXACT []
synonym: "down-regulation of light-activated channel activity" EXACT []
@@ -286398,7 +289739,7 @@
id: GO:0045832
name: obsolete positive regulation of light-activated channel activity
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of light-activated channel activity." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of light-activated channel activity." [GOC:curators]
comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of light-activated channel activity" NARROW []
synonym: "stimulation of light-activated channel activity" NARROW []
@@ -286412,7 +289753,7 @@
id: GO:0045833
name: negative regulation of lipid metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:curators]
synonym: "down regulation of lipid metabolic process" EXACT []
synonym: "down-regulation of lipid metabolic process" EXACT []
synonym: "downregulation of lipid metabolic process" EXACT []
@@ -286428,7 +289769,7 @@
id: GO:0045834
name: positive regulation of lipid metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." [GOC:curators]
synonym: "activation of lipid metabolic process" NARROW []
synonym: "positive regulation of lipid metabolism" EXACT []
synonym: "stimulation of lipid metabolic process" NARROW []
@@ -286445,7 +289786,7 @@
id: GO:0045835
name: negative regulation of meiotic nuclear division
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis." [GOC:curators]
synonym: "down regulation of meiosis" EXACT []
synonym: "down-regulation of meiosis" EXACT []
synonym: "downregulation of meiosis" EXACT []
@@ -286463,7 +289804,7 @@
id: GO:0045836
name: positive regulation of meiotic nuclear division
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of meiosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of meiosis." [GOC:curators]
synonym: "activation of meiosis" NARROW []
synonym: "positive regulation of meiosis" EXACT []
synonym: "stimulation of meiosis" NARROW []
@@ -286482,7 +289823,7 @@
id: GO:0045837
name: negative regulation of membrane potential
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:curators]
synonym: "down regulation of membrane potential" EXACT []
synonym: "down-regulation of membrane potential" EXACT []
synonym: "downregulation of membrane potential" EXACT []
@@ -286494,7 +289835,7 @@
id: GO:0045838
name: positive regulation of membrane potential
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:curators]
synonym: "activation of membrane potential" NARROW []
synonym: "elevation of membrane potential" EXACT [GOC:rph]
synonym: "stimulation of membrane potential" NARROW []
@@ -286507,7 +289848,7 @@
id: GO:0045839
name: negative regulation of mitotic nuclear division
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of mitosis" EXACT []
synonym: "down-regulation of mitosis" EXACT []
synonym: "downregulation of mitosis" EXACT []
@@ -286525,7 +289866,7 @@
id: GO:0045840
name: positive regulation of mitotic nuclear division
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of mitosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of mitosis." [GOC:curators]
synonym: "activation of mitosis" NARROW []
synonym: "mitogenic activity" NARROW []
synonym: "positive regulation of mitosis" EXACT []
@@ -286544,7 +289885,7 @@
id: GO:0045841
name: negative regulation of mitotic metaphase/anaphase transition
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:curators]
synonym: "down regulation of mitotic metaphase/anaphase transition" EXACT []
synonym: "down-regulation of mitotic metaphase/anaphase transition" EXACT []
synonym: "downregulation of mitotic metaphase/anaphase transition" EXACT []
@@ -286562,7 +289903,7 @@
id: GO:0045842
name: positive regulation of mitotic metaphase/anaphase transition
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin." [GOC:curators]
synonym: "activation of mitotic metaphase/anaphase transition" NARROW []
synonym: "stimulation of mitotic metaphase/anaphase transition" NARROW []
synonym: "up regulation of mitotic metaphase/anaphase transition" EXACT []
@@ -286581,7 +289922,7 @@
id: GO:0045843
name: negative regulation of striated muscle tissue development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development." [GOC:curators]
synonym: "down regulation of striated muscle development" EXACT []
synonym: "down-regulation of striated muscle development" EXACT []
synonym: "downregulation of striated muscle development" EXACT []
@@ -286597,7 +289938,7 @@
id: GO:0045844
name: positive regulation of striated muscle tissue development
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of striated muscle development." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of striated muscle development." [GOC:curators]
synonym: "activation of striated muscle development" NARROW []
synonym: "stimulation of striated muscle development" NARROW []
synonym: "up regulation of striated muscle development" EXACT []
@@ -286614,7 +289955,7 @@
id: GO:0045847
name: negative regulation of nitrogen utilization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of nitrogen utilization." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of nitrogen utilization." [GOC:curators]
synonym: "down regulation of nitrogen utilization" EXACT []
synonym: "down-regulation of nitrogen utilization" EXACT []
synonym: "downregulation of nitrogen utilization" EXACT []
@@ -286629,7 +289970,7 @@
id: GO:0045848
name: positive regulation of nitrogen utilization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of nitrogen utilization." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of nitrogen utilization." [GOC:curators]
synonym: "activation of nitrogen utilization" NARROW []
synonym: "stimulation of nitrogen utilization" NARROW []
synonym: "up regulation of nitrogen utilization" EXACT []
@@ -286645,7 +289986,7 @@
id: GO:0045849
name: negative regulation of nurse cell apoptotic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of nurse cell apoptotic process." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of nurse cell apoptotic process." [GOC:curators, GOC:mtg_apoptosis]
synonym: "down regulation of nurse cell apoptosis" EXACT []
synonym: "down-regulation of nurse cell apoptosis" EXACT []
synonym: "downregulation of nurse cell apoptosis" EXACT []
@@ -286662,7 +290003,7 @@
id: GO:0045850
name: positive regulation of nurse cell apoptotic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of nurse cell apoptotic process." [GOC:go_curators, GOC:mtg_apoptosis]
+def: "Any process that activates or increases the frequency, rate or extent of nurse cell apoptotic process." [GOC:curators, GOC:mtg_apoptosis]
synonym: "activation of nurse cell apoptosis" NARROW []
synonym: "positive regulation of nurse cell apoptosis" NARROW []
synonym: "stimulation of nurse cell apoptosis" NARROW []
@@ -286680,7 +290021,7 @@
id: GO:0045851
name: pH reduction
namespace: biological_process
-def: "Any process that reduces the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion." [GOC:go_curators]
+def: "Any process that reduces the internal pH of an organism, part of an organism or a cell, corresponding to an increase in hydrogen ion concentration." [GOC:curators]
synonym: "acidification" EXACT []
is_a: GO:0006885 ! regulation of pH
@@ -286688,14 +290029,14 @@
id: GO:0045852
name: pH elevation
namespace: biological_process
-def: "Any process that increases the internal pH of an organism, part of an organism or a cell, measured by the concentration of the hydrogen ion." [GOC:go_curators]
+def: "Any process that increases the internal pH of an organism, part of an organism or a cell, corresponding to a decrease in hydrogen ion concentration." [GOC:curators]
is_a: GO:0006885 ! regulation of pH
[Term]
id: GO:0045853
name: negative regulation of bicoid mRNA localization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the process in which bicoid mRNA is transported to, or maintained in, a specific location." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the process in which bicoid mRNA is transported to, or maintained in, a specific location." [GOC:curators]
synonym: "down regulation of bicoid mRNA localization" EXACT []
synonym: "down-regulation of bicoid mRNA localization" EXACT []
synonym: "downregulation of bicoid mRNA localization" EXACT []
@@ -286711,7 +290052,7 @@
id: GO:0045854
name: positive regulation of bicoid mRNA localization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the process in which bicoid mRNA is transported to, or maintained in, a specific location." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the process in which bicoid mRNA is transported to, or maintained in, a specific location." [GOC:curators]
synonym: "activation of bicoid mRNA localization" NARROW []
synonym: "positive regulation of bicoid mRNA localisation" EXACT [GOC:mah]
synonym: "stimulation of bicoid mRNA localization" NARROW []
@@ -286729,7 +290070,7 @@
id: GO:0045855
name: negative regulation of pole plasm oskar mRNA localization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:curators]
synonym: "down regulation of pole plasm oskar mRNA localization" EXACT []
synonym: "down-regulation of pole plasm oskar mRNA localization" EXACT []
synonym: "downregulation of pole plasm oskar mRNA localization" EXACT []
@@ -286746,7 +290087,7 @@
id: GO:0045856
name: positive regulation of pole plasm oskar mRNA localization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm." [GOC:curators]
synonym: "activation of pole plasm oskar mRNA localization" NARROW []
synonym: "positive regulation of oocyte pole plasm oskar mRNA localization" EXACT []
synonym: "positive regulation of pole plasm oskar mRNA localisation" EXACT [GOC:mah]
@@ -286764,7 +290105,7 @@
id: GO:0045857
name: obsolete negative regulation of molecular function, epigenetic
namespace: biological_process
-def: "OBSOLETE. Any heritable epigenetic process that stops, prevents, or reduces the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any heritable epigenetic process that stops, prevents, or reduces the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:curators, GOC:dph, GOC:tb]
comment: This term was obsoleted because it is not an active process.
synonym: "down regulation of protein activity, epigenetic" EXACT []
synonym: "down-regulation of protein activity, epigenetic" EXACT []
@@ -286778,7 +290119,7 @@
id: GO:0045858
name: obsolete positive regulation of molecular function, epigenetic
namespace: biological_process
-def: "OBSOLETE. Any heritable epigenetic process that increases the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any heritable epigenetic process that increases the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:curators, GOC:dph, GOC:tb]
comment: This term was obsoleted because it is not an active process.
synonym: "activation of protein activity, epigenetic" NARROW []
synonym: "positive regulation of protein activity, epigenetic" EXACT [GOC:dph, GOC:tb]
@@ -286793,7 +290134,7 @@
id: GO:0045859
name: regulation of protein kinase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of protein kinase activity." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of protein kinase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
is_a: GO:0001932 ! regulation of protein phosphorylation
is_a: GO:0043549 ! regulation of kinase activity
@@ -286805,7 +290146,7 @@
id: GO:0045860
name: positive regulation of protein kinase activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of protein kinase activity." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of protein kinase activity." [GOC:curators]
subset: gocheck_obsoletion_candidate
synonym: "stimulation of protein kinase activity" NARROW []
synonym: "up regulation of protein kinase activity" EXACT []
@@ -286822,7 +290163,7 @@
id: GO:0045861
name: negative regulation of proteolysis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:curators]
synonym: "down regulation of proteolysis" EXACT []
synonym: "down-regulation of proteolysis" EXACT []
synonym: "downregulation of proteolysis" EXACT []
@@ -286838,7 +290179,7 @@
id: GO:0045862
name: positive regulation of proteolysis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." [GOC:curators]
synonym: "activation of proteolysis" NARROW []
synonym: "positive regulation of peptidolysis" EXACT []
synonym: "stimulation of proteolysis" NARROW []
@@ -286855,7 +290196,7 @@
id: GO:0045863
name: obsolete negative regulation of pteridine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "down regulation of pteridine metabolic process" EXACT []
synonym: "down-regulation of pteridine metabolic process" EXACT []
@@ -286869,7 +290210,7 @@
id: GO:0045864
name: obsolete positive regulation of pteridine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving pteridine." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of pteridine metabolic process" NARROW []
synonym: "positive regulation of pteridine metabolism" EXACT []
@@ -286884,7 +290225,7 @@
id: GO:0045865
name: obsolete regulation of recombination within rDNA repeats
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:curators, ISBN:0198506732]
comment: This term was made obsolete because it describes a substrate-specific process.
synonym: "regulation of recombination within rDNA repeats" EXACT []
is_obsolete: true
@@ -286894,7 +290235,7 @@
id: GO:0045866
name: obsolete positive regulation of recombination within rDNA repeats
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:go_curators, ISBN:0198506732]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:curators, ISBN:0198506732]
comment: This term was made obsolete because it describes a substrate-specific process.
synonym: "positive regulation of recombination within rDNA repeats" EXACT []
is_obsolete: true
@@ -286904,7 +290245,7 @@
id: GO:0045869
name: negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of single stranded viral RNA replication via double stranded DNA intermediate." [GOC:curators]
synonym: "down regulation of retroviral genome replication" EXACT []
synonym: "down-regulation of retroviral genome replication" EXACT []
synonym: "downregulation of retroviral genome replication" EXACT []
@@ -286922,7 +290263,7 @@
id: GO:0045870
name: positive regulation of single stranded viral RNA replication via double stranded DNA intermediate
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of retroviral genome replication." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of retroviral genome replication." [GOC:curators]
synonym: "activation of retroviral genome replication" NARROW []
synonym: "positive regulation of retroviral genome replication" EXACT [GOC:bf, GOC:jl]
synonym: "stimulation of retroviral genome replication" NARROW []
@@ -286940,7 +290281,7 @@
id: GO:0045871
name: obsolete negative regulation of rhodopsin gene expression
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of rhodopsin gene expression." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of rhodopsin gene expression." [GOC:curators, GOC:dph, GOC:tb]
comment: This term was obsoleted because it refers to a specific gene product. The gene product should be captured as an annotation extension using 'has input'.
synonym: "down regulation of rhodopsin gene activity" EXACT []
synonym: "down-regulation of rhodopsin gene activity" EXACT []
@@ -286954,7 +290295,7 @@
id: GO:0045872
name: obsolete positive regulation of rhodopsin gene expression
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of rhodopsin gene expression." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of rhodopsin gene expression." [GOC:curators, GOC:dph, GOC:tb]
comment: This term was obsoleted because it refers to a specific gene product. The gene product should be captured as an annotation extension using 'has input'.
synonym: "activation of rhodopsin gene activity" NARROW []
synonym: "positive regulation of rhodopsin gene activity" EXACT [GOC:dph, GOC:tb]
@@ -286969,7 +290310,7 @@
id: GO:0045873
name: negative regulation of sevenless signaling pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the sevenless signaling pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the sevenless signaling pathway." [GOC:curators]
synonym: "down regulation of sevenless signaling pathway" EXACT []
synonym: "down-regulation of sevenless signaling pathway" EXACT []
synonym: "downregulation of sevenless signaling pathway" EXACT []
@@ -286988,7 +290329,7 @@
id: GO:0045874
name: positive regulation of sevenless signaling pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the sevenless signaling pathway." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the sevenless signaling pathway." [GOC:curators]
synonym: "activation of sevenless signaling pathway" NARROW []
synonym: "positive regulation of sev signaling pathway" EXACT []
synonym: "positive regulation of sevenless signalling pathway" EXACT []
@@ -287006,7 +290347,7 @@
id: GO:0045875
name: negative regulation of sister chromatid cohesion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid cohesion." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid cohesion." [GOC:curators]
synonym: "down regulation of sister chromatid cohesion" EXACT []
synonym: "down-regulation of sister chromatid cohesion" EXACT []
synonym: "downregulation of sister chromatid cohesion" EXACT []
@@ -287022,7 +290363,7 @@
id: GO:0045876
name: positive regulation of sister chromatid cohesion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of sister chromatid cohesion." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of sister chromatid cohesion." [GOC:curators]
synonym: "activation of sister chromatid cohesion" NARROW []
synonym: "stimulation of sister chromatid cohesion" NARROW []
synonym: "up regulation of sister chromatid cohesion" EXACT []
@@ -287040,7 +290381,7 @@
name: negative regulation of smoothened signaling pathway
namespace: biological_process
alt_id: GO:0045877
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of smoothened signaling." [GOC:curators]
synonym: "down regulation of smoothened signaling pathway" EXACT []
synonym: "down-regulation of smoothened signaling pathway" EXACT []
synonym: "downregulation of smoothened signaling pathway" EXACT []
@@ -287062,7 +290403,7 @@
name: positive regulation of smoothened signaling pathway
namespace: biological_process
alt_id: GO:0045878
-def: "Any process that activates or increases the frequency, rate or extent of smoothened signaling." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of smoothened signaling." [GOC:curators]
synonym: "activation of smoothened signaling pathway" NARROW []
synonym: "positive regulation of hedgehog signaling pathway" EXACT [GOC:bf, GOC:ecd]
synonym: "positive regulation of hh signaling pathway" EXACT [GOC:bf, GOC:ecd]
@@ -287083,7 +290424,7 @@
id: GO:0045881
name: positive regulation of sporulation resulting in formation of a cellular spore
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of sporulation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of sporulation." [GOC:curators]
synonym: "activation of sporulation" NARROW []
synonym: "stimulation of sporulation" NARROW []
synonym: "up regulation of sporulation" EXACT []
@@ -287099,7 +290440,7 @@
id: GO:0045882
name: negative regulation of sulfur utilization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sulfur utilization." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of sulfur utilization." [GOC:curators]
synonym: "down regulation of sulfur utilization" EXACT []
synonym: "down-regulation of sulfur utilization" EXACT []
synonym: "downregulation of sulfur utilization" EXACT []
@@ -287115,7 +290456,7 @@
id: GO:0045883
name: positive regulation of sulfur utilization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of sulfur utilization." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of sulfur utilization." [GOC:curators]
synonym: "activation of sulfur utilization" NARROW []
synonym: "positive regulation of sulphur utilization" EXACT []
synonym: "stimulation of sulfur utilization" NARROW []
@@ -287132,7 +290473,7 @@
id: GO:0045884
name: obsolete regulation of survival gene product expression
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:dph, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:curators, GOC:dph, GOC:mtg_apoptosis, GOC:tb]
comment: This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
synonym: "regulation of survival gene product activity" BROAD [GOC:dph, GOC:tb]
synonym: "regulation of survival gene product expression" EXACT []
@@ -287143,7 +290484,7 @@
id: GO:0045885
name: obsolete positive regulation of survival gene product expression
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:dph, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of survival gene product expression; survival gene products are those that antagonize the apoptotic program. Regulation can be at the transcriptional, translational, or posttranslational level." [GOC:curators, GOC:dph, GOC:mtg_apoptosis, GOC:tb]
comment: This term was made obsolete because the meaning of the term is ambiguous: the same gene product may or may not have a role in apoptosis depending on the cell type, tissue type, condition, etc.
synonym: "activation of survival gene product activity" BROAD []
synonym: "positive regulation of survival gene product activity" BROAD [GOC:dph, GOC:tb]
@@ -287159,7 +290500,7 @@
id: GO:0045886
name: negative regulation of synaptic assembly at neuromuscular junction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic assembly at neuromuscular junction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic assembly at neuromuscular junction." [GOC:curators]
synonym: "down regulation of synaptic growth at neuromuscular junction" EXACT []
synonym: "down-regulation of synaptic growth at neuromuscular junction" EXACT []
synonym: "downregulation of synaptic growth at neuromuscular junction" EXACT []
@@ -287177,7 +290518,7 @@
id: GO:0045887
name: positive regulation of synaptic assembly at neuromuscular junction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of synaptic assembly at neuromuscular junction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of synaptic assembly at neuromuscular junction." [GOC:curators]
synonym: "activation of synaptic growth at neuromuscular junction" NARROW []
synonym: "positive regulation of synaptic growth at neuromuscular junction" RELATED []
synonym: "stimulation of synaptic growth at neuromuscular junction" NARROW []
@@ -287196,7 +290537,7 @@
id: GO:0045888
name: obsolete regulation of transcription of homeotic gene (Polycomb group)
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "regulation of transcription of homeotic gene (Polycomb group)" EXACT []
is_obsolete: true
@@ -287206,7 +290547,7 @@
id: GO:0045889
name: obsolete positive regulation of transcription of homeotic gene (Polycomb group)
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription of homeotic genes of the Polycomb group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "positive regulation of transcription of homeotic gene (Polycomb group)" EXACT []
is_obsolete: true
@@ -287216,7 +290557,7 @@
id: GO:0045890
name: obsolete regulation of transcription of homeotic gene (trithorax group)
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "regulation of transcription of homeotic gene (trithorax group)" EXACT []
is_obsolete: true
@@ -287226,7 +290567,7 @@
id: GO:0045891
name: obsolete negative regulation of transcription of homeotic gene (trithorax group)
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription of homeotic genes of the trithorax group." [GOC:curators]
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "negative regulation of transcription of homeotic gene (trithorax group)" EXACT []
is_obsolete: true
@@ -287239,7 +290580,7 @@
alt_id: GO:0016481
alt_id: GO:0032582
alt_id: GO:0061021
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
synonym: "down regulation of gene-specific transcription" RELATED []
synonym: "down regulation of transcription, DNA-dependent" EXACT []
synonym: "down-regulation of gene-specific transcription" RELATED []
@@ -287266,7 +290607,7 @@
alt_id: GO:0043193
alt_id: GO:0045941
alt_id: GO:0061020
-def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
synonym: "activation of gene-specific transcription" RELATED []
synonym: "activation of transcription, DNA-dependent" NARROW []
synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT []
@@ -287292,7 +290633,7 @@
id: GO:0045894
name: negative regulation of mating-type specific transcription, DNA-templated
namespace: biological_process
-def: "Any mating-type specific process that stops, prevents or reduces the rate of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any mating-type specific process that stops, prevents or reduces the rate of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
synonym: "down regulation of transcription, mating-type specific" EXACT []
synonym: "down-regulation of transcription, mating-type specific" EXACT []
synonym: "downregulation of transcription, mating-type specific" EXACT []
@@ -287305,7 +290646,7 @@
id: GO:0045895
name: positive regulation of mating-type specific transcription, DNA-templated
namespace: biological_process
-def: "Any mating-type specific process that activates or increases the rate of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+def: "Any mating-type specific process that activates or increases the rate of cellular DNA-templated transcription." [GOC:curators, GOC:txnOH]
synonym: "activation of transcription, mating-type specific" NARROW []
synonym: "positive regulation of mating-type specific transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "stimulation of transcription, mating-type specific" NARROW []
@@ -287319,7 +290660,7 @@
id: GO:0045896
name: obsolete regulation of transcription during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "mitotic regulation of transcription" EXACT []
synonym: "regulation of transcription, mitotic" EXACT [GOC:mah]
@@ -287332,7 +290673,7 @@
id: GO:0045897
name: obsolete positive regulation of transcription during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "activation of transcription during mitosis" NARROW [GOC:mah]
synonym: "mitotic activation of transcription" EXACT []
@@ -287350,7 +290691,7 @@
id: GO:0045898
name: regulation of RNA polymerase II transcription preinitiation complex assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:curators]
synonym: "regulation of RNA polymerase II transcriptional pre-initiation complex assembly" EXACT []
synonym: "regulation of RNA polymerase II transcriptional pre-initiation complex biosynthesis" EXACT []
synonym: "regulation of RNA polymerase II transcriptional preinitiation complex assembly" EXACT []
@@ -287365,7 +290706,7 @@
id: GO:0045899
name: positive regulation of RNA polymerase II transcription preinitiation complex assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly." [GOC:curators]
synonym: "activation of RNA polymerase II transcriptional preinitiation complex assembly" NARROW []
synonym: "positive regulation of RNA polymerase II transcriptional pre-initiation complex assembly" EXACT []
synonym: "positive regulation of RNA polymerase II transcriptional pre-initiation complex biosynthesis" EXACT []
@@ -287386,7 +290727,7 @@
id: GO:0045900
name: negative regulation of translational elongation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation." [GOC:curators]
synonym: "down regulation of translational elongation" EXACT []
synonym: "down-regulation of translational elongation" EXACT []
synonym: "downregulation of translational elongation" EXACT []
@@ -287401,7 +290742,7 @@
id: GO:0045901
name: positive regulation of translational elongation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of translational elongation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of translational elongation." [GOC:curators]
synonym: "activation of translational elongation" NARROW []
synonym: "stimulation of translational elongation" NARROW []
synonym: "up regulation of translational elongation" EXACT []
@@ -287442,7 +290783,7 @@
id: GO:0045904
name: negative regulation of translational termination
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination." [GOC:curators]
synonym: "down regulation of translational termination" EXACT []
synonym: "down-regulation of translational termination" EXACT []
synonym: "downregulation of translational termination" EXACT []
@@ -287458,7 +290799,7 @@
id: GO:0045905
name: positive regulation of translational termination
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of translational termination." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of translational termination." [GOC:curators]
synonym: "activation of translational termination" NARROW []
synonym: "stimulation of translational termination" NARROW []
synonym: "up regulation of translational termination" EXACT []
@@ -287475,7 +290816,7 @@
id: GO:0045906
name: negative regulation of vasoconstriction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of vasoconstriction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of vasoconstriction." [GOC:curators]
synonym: "down regulation of vasoconstriction" EXACT []
synonym: "down-regulation of vasoconstriction" EXACT []
synonym: "downregulation of vasoconstriction" EXACT []
@@ -287490,7 +290831,7 @@
id: GO:0045907
name: positive regulation of vasoconstriction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of vasoconstriction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of vasoconstriction." [GOC:curators]
synonym: "activation of vasoconstriction" NARROW []
synonym: "stimulation of vasoconstriction" NARROW []
synonym: "up regulation of vasoconstriction" EXACT []
@@ -287506,7 +290847,7 @@
id: GO:0045910
name: negative regulation of DNA recombination
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination." [GOC:curators]
synonym: "down regulation of DNA recombination" EXACT []
synonym: "down-regulation of DNA recombination" EXACT []
synonym: "downregulation of DNA recombination" EXACT []
@@ -287521,7 +290862,7 @@
id: GO:0045911
name: positive regulation of DNA recombination
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA recombination." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of DNA recombination." [GOC:curators]
synonym: "activation of DNA recombination" NARROW []
synonym: "stimulation of DNA recombination" NARROW []
synonym: "up regulation of DNA recombination" EXACT []
@@ -287537,7 +290878,7 @@
id: GO:0045912
name: negative regulation of carbohydrate metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." [GOC:curators]
synonym: "down regulation of carbohydrate metabolic process" EXACT []
synonym: "down-regulation of carbohydrate metabolic process" EXACT []
synonym: "downregulation of carbohydrate metabolic process" EXACT []
@@ -287553,7 +290894,7 @@
id: GO:0045913
name: positive regulation of carbohydrate metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." [GOC:curators]
synonym: "activation of carbohydrate metabolic process" NARROW []
synonym: "positive regulation of carbohydrate metabolism" EXACT []
synonym: "stimulation of carbohydrate metabolic process" NARROW []
@@ -287570,7 +290911,7 @@
id: GO:0045914
name: obsolete negative regulation of catecholamine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "down regulation of catecholamine metabolic process" EXACT []
synonym: "down-regulation of catecholamine metabolic process" EXACT []
@@ -287584,7 +290925,7 @@
id: GO:0045915
name: obsolete positive regulation of catecholamine metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of catecholamine metabolic process" NARROW []
synonym: "positive regulation of catecholamine metabolism" EXACT []
@@ -287599,7 +290940,7 @@
id: GO:0045916
name: negative regulation of complement activation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation." [GOC:curators]
synonym: "down regulation of complement activation" EXACT []
synonym: "down-regulation of complement activation" EXACT []
synonym: "downregulation of complement activation" EXACT []
@@ -287616,7 +290957,7 @@
id: GO:0045917
name: positive regulation of complement activation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of complement activation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of complement activation." [GOC:curators]
synonym: "activation of complement activation" NARROW []
synonym: "positive regulation of complement cascade" EXACT [GOC:add]
synonym: "stimulation of complement activation" NARROW []
@@ -287634,7 +290975,7 @@
id: GO:0045918
name: negative regulation of cytolysis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cytolysis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cytolysis." [GOC:curators]
synonym: "down regulation of cytolysis" EXACT []
synonym: "down-regulation of cytolysis" EXACT []
synonym: "downregulation of cytolysis" EXACT []
@@ -287649,7 +290990,7 @@
id: GO:0045919
name: positive regulation of cytolysis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cytolysis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of cytolysis." [GOC:curators]
synonym: "activation of cytolysis" NARROW []
synonym: "stimulation of cytolysis" NARROW []
synonym: "up regulation of cytolysis" EXACT []
@@ -287665,7 +291006,7 @@
id: GO:0045920
name: negative regulation of exocytosis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis." [GOC:curators]
synonym: "down regulation of exocytosis" EXACT []
synonym: "down-regulation of exocytosis" EXACT []
synonym: "downregulation of exocytosis" EXACT []
@@ -287680,7 +291021,7 @@
id: GO:0045921
name: positive regulation of exocytosis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of exocytosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of exocytosis." [GOC:curators]
synonym: "activation of exocytosis" NARROW []
synonym: "stimulation of exocytosis" NARROW []
synonym: "up regulation of exocytosis" EXACT []
@@ -287696,7 +291037,7 @@
id: GO:0045922
name: negative regulation of fatty acid metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:curators]
synonym: "down regulation of fatty acid metabolic process" EXACT []
synonym: "down-regulation of fatty acid metabolic process" EXACT []
synonym: "downregulation of fatty acid metabolic process" EXACT []
@@ -287713,7 +291054,7 @@
id: GO:0045923
name: positive regulation of fatty acid metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids." [GOC:curators]
synonym: "activation of fatty acid metabolic process" NARROW []
synonym: "positive regulation of fatty acid metabolism" EXACT []
synonym: "stimulation of fatty acid metabolic process" NARROW []
@@ -287732,7 +291073,7 @@
name: regulation of female receptivity
namespace: biological_process
alt_id: GO:0060181
-def: "Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of the willingness or readiness of a female to receive male advances." [GOC:curators, GOC:dph, GOC:tb]
synonym: "female receptivity" RELATED [GOC:dph, GOC:tb]
is_a: GO:0060180 ! female mating behavior
is_a: GO:0065008 ! regulation of biological quality
@@ -287741,7 +291082,7 @@
id: GO:0045925
name: positive regulation of female receptivity
namespace: biological_process
-def: "Any process that activates or increases the receptiveness of a female to male advances." [GOC:go_curators]
+def: "Any process that activates or increases the receptiveness of a female to male advances." [GOC:curators]
synonym: "activation of female receptivity" NARROW []
synonym: "stimulation of female receptivity" NARROW []
synonym: "up regulation of female receptivity" EXACT []
@@ -287753,7 +291094,7 @@
id: GO:0045926
name: negative regulation of growth
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators]
+def: "Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:curators]
synonym: "down regulation of growth" EXACT []
synonym: "down-regulation of growth" EXACT []
synonym: "downregulation of growth" EXACT []
@@ -287768,7 +291109,7 @@
id: GO:0045927
name: positive regulation of growth
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators]
+def: "Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:curators]
synonym: "activation of growth" NARROW []
synonym: "stimulation of growth" NARROW []
synonym: "up regulation of growth" EXACT []
@@ -287784,7 +291125,7 @@
id: GO:0045928
name: negative regulation of juvenile hormone metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:curators]
synonym: "down regulation of juvenile hormone metabolic process" EXACT []
synonym: "down-regulation of juvenile hormone metabolic process" EXACT []
synonym: "downregulation of juvenile hormone metabolic process" EXACT []
@@ -287800,7 +291141,7 @@
id: GO:0045929
name: obsolete positive regulation of juvenile hormone metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of juvenile hormone metabolic process" NARROW []
synonym: "positive regulation of juvenile hormone metabolism" EXACT []
@@ -287815,7 +291156,7 @@
id: GO:0045930
name: negative regulation of mitotic cell cycle
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of progression through mitotic cell cycle" EXACT []
synonym: "down-regulation of progression through mitotic cell cycle" EXACT []
synonym: "downregulation of progression through mitotic cell cycle" EXACT []
@@ -287833,7 +291174,7 @@
id: GO:0045931
name: positive regulation of mitotic cell cycle
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of progression through the mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the rate or extent of progression through the mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of progression through mitotic cell cycle" NARROW []
synonym: "positive regulation of mitotic cell cycle progression" EXACT []
synonym: "positive regulation of progression through mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
@@ -287851,7 +291192,7 @@
id: GO:0045932
name: negative regulation of muscle contraction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction." [GOC:curators]
synonym: "down regulation of muscle contraction" EXACT []
synonym: "down-regulation of muscle contraction" EXACT []
synonym: "downregulation of muscle contraction" EXACT []
@@ -287866,7 +291207,7 @@
id: GO:0045933
name: positive regulation of muscle contraction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of muscle contraction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of muscle contraction." [GOC:curators]
synonym: "activation of muscle contraction" NARROW []
synonym: "stimulation of muscle contraction" NARROW []
synonym: "up regulation of muscle contraction" EXACT []
@@ -287882,7 +291223,8 @@
id: GO:0045934
name: negative regulation of nucleobase-containing compound metabolic process
namespace: biological_process
-def: "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators]
+def: "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:curators]
+subset: gocheck_do_not_annotate
synonym: "down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
synonym: "down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
synonym: "downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT []
@@ -287894,12 +291236,13 @@
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process
relationship: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
[Term]
id: GO:0045935
name: obsolete positive regulation of nucleobase-containing compound metabolic process
namespace: biological_process
-def: "OBSOLETE. Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators]
+def: "OBSOLETE. Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW []
synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb]
@@ -287915,7 +291258,7 @@
id: GO:0045936
name: negative regulation of phosphate metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:curators]
synonym: "down regulation of phosphate metabolic process" EXACT []
synonym: "down-regulation of phosphate metabolic process" EXACT []
synonym: "downregulation of phosphate metabolic process" EXACT []
@@ -287930,7 +291273,7 @@
id: GO:0045937
name: positive regulation of phosphate metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates." [GOC:curators]
synonym: "activation of phosphate metabolic process" NARROW []
synonym: "positive regulation of phosphate metabolism" EXACT []
synonym: "stimulation of phosphate metabolic process" NARROW []
@@ -287946,7 +291289,7 @@
id: GO:0045938
name: positive regulation of circadian sleep/wake cycle, sleep
namespace: biological_process
-def: "Any process that activates or increases the duration or quality of sleep, a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals." [GOC:go_curators]
+def: "Any process that activates or increases the duration or quality of sleep, a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals." [GOC:curators]
synonym: "activation of circadian sleep/wake cycle, sleep" NARROW []
synonym: "positive regulation of sleep" EXACT []
synonym: "stimulation of circadian sleep/wake cycle, sleep" NARROW []
@@ -287964,7 +291307,7 @@
id: GO:0045939
name: negative regulation of steroid metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:curators]
synonym: "down regulation of steroid metabolic process" EXACT []
synonym: "down-regulation of steroid metabolic process" EXACT []
synonym: "downregulation of steroid metabolic process" EXACT []
@@ -287980,7 +291323,7 @@
id: GO:0045940
name: positive regulation of steroid metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids." [GOC:curators]
synonym: "activation of steroid metabolic process" NARROW []
synonym: "positive regulation of steroid metabolism" EXACT []
synonym: "stimulation of steroid metabolic process" NARROW []
@@ -287997,7 +291340,7 @@
id: GO:0045942
name: negative regulation of phosphorus utilization
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphorus utilization." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of phosphorus utilization." [GOC:curators]
synonym: "down regulation of phosphorus utilization" EXACT []
synonym: "down-regulation of phosphorus utilization" EXACT []
synonym: "downregulation of phosphorus utilization" EXACT []
@@ -288012,7 +291355,7 @@
id: GO:0045943
name: positive regulation of transcription by RNA polymerase I
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:go_curators, GOC:txnOH]
+def: "Any process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase I." [GOC:curators, GOC:txnOH]
synonym: "activation of transcription from RNA polymerase I promoter" NARROW []
synonym: "positive regulation of transcription from Pol I promoter" EXACT []
synonym: "positive regulation of transcription from RNA polymerase I promoter" EXACT []
@@ -288032,7 +291375,7 @@
namespace: biological_process
alt_id: GO:0010552
alt_id: GO:0045817
-def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH]
+def: "Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:curators, GOC:txnOH]
synonym: "activation of global transcription from RNA polymerase II promoter" RELATED []
synonym: "activation of transcription from RNA polymerase II promoter" EXACT []
synonym: "positive regulation of gene-specific transcription from RNA polymerase II promoter" RELATED []
@@ -288061,7 +291404,7 @@
id: GO:0045945
name: positive regulation of transcription by RNA polymerase III
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase III." [GOC:go_curators, GOC:txnOH]
+def: "Any process that activates or increases the frequency, rate or extent of transcription mediated by RNA polymerase III." [GOC:curators, GOC:txnOH]
synonym: "activation of transcription from RNA polymerase III promoter" NARROW []
synonym: "positive regulation of transcription from Pol III promoter" EXACT []
synonym: "positive regulation of transcription from RNA polymerase III promoter" EXACT []
@@ -288079,7 +291422,7 @@
id: GO:0045947
name: negative regulation of translational initiation
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation." [GOC:curators]
synonym: "down regulation of translational initiation" EXACT []
synonym: "down-regulation of translational initiation" EXACT []
synonym: "downregulation of translational initiation" EXACT []
@@ -288094,7 +291437,7 @@
id: GO:0045948
name: positive regulation of translational initiation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of translational initiation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of translational initiation." [GOC:curators]
synonym: "activation of translational initiation" NARROW []
synonym: "stimulation of translational initiation" NARROW []
synonym: "up regulation of translational initiation" EXACT []
@@ -288110,7 +291453,7 @@
id: GO:0045949
name: positive regulation of phosphorus utilization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of phosphorus utilization." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of phosphorus utilization." [GOC:curators]
synonym: "activation of phosphorus utilization" NARROW []
synonym: "stimulation of phosphorus utilization" NARROW []
synonym: "up regulation of phosphorus utilization" EXACT []
@@ -288126,7 +291469,7 @@
id: GO:0045950
name: negative regulation of mitotic recombination
namespace: biological_process
-def: "Any process that inhibits or decreases the rate of DNA recombination during mitosis." [GOC:go_curators, GOC:hjd]
+def: "Any process that inhibits or decreases the rate of DNA recombination during mitosis." [GOC:curators, GOC:hjd]
synonym: "down regulation of mitotic recombination" EXACT []
synonym: "down-regulation of mitotic recombination" EXACT []
synonym: "downregulation of mitotic recombination" EXACT []
@@ -288142,7 +291485,7 @@
id: GO:0045951
name: positive regulation of mitotic recombination
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of DNA recombination during mitosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of DNA recombination during mitosis." [GOC:curators]
synonym: "activation of mitotic recombination" NARROW []
synonym: "positive regulation of recombination within rDNA repeats" NARROW []
synonym: "stimulation of mitotic recombination" NARROW []
@@ -288159,7 +291502,7 @@
id: GO:0045952
name: regulation of juvenile hormone catabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:curators]
synonym: "regulation of juvenile hormone breakdown" EXACT []
synonym: "regulation of juvenile hormone catabolism" EXACT []
synonym: "regulation of juvenile hormone degradation" EXACT []
@@ -288221,7 +291564,7 @@
id: GO:0045955
name: negative regulation of calcium ion-dependent exocytosis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:curators]
synonym: "down regulation of calcium ion-dependent exocytosis" EXACT []
synonym: "down-regulation of calcium ion-dependent exocytosis" EXACT []
synonym: "downregulation of calcium ion-dependent exocytosis" EXACT []
@@ -288236,7 +291579,7 @@
id: GO:0045956
name: positive regulation of calcium ion-dependent exocytosis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis." [GOC:curators]
synonym: "activation of calcium ion-dependent exocytosis" NARROW []
synonym: "stimulation of calcium ion-dependent exocytosis" NARROW []
synonym: "up regulation of calcium ion-dependent exocytosis" EXACT []
@@ -288252,7 +291595,7 @@
id: GO:0045957
name: negative regulation of complement activation, alternative pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway." [GOC:curators]
synonym: "down regulation of complement activation, alternative pathway" EXACT []
synonym: "down-regulation of complement activation, alternative pathway" EXACT []
synonym: "downregulation of complement activation, alternative pathway" EXACT []
@@ -288269,7 +291612,7 @@
id: GO:0045958
name: positive regulation of complement activation, alternative pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of complement activation by the alternative pathway." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of complement activation by the alternative pathway." [GOC:curators]
synonym: "activation of complement activation, alternative pathway" NARROW []
synonym: "positive regulation of complement cascade, alternative pathway" EXACT [GOC:add]
synonym: "stimulation of complement activation, alternative pathway" NARROW []
@@ -288287,7 +291630,7 @@
id: GO:0045959
name: negative regulation of complement activation, classical pathway
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway." [GOC:curators]
synonym: "down regulation of complement activation, classical pathway" EXACT []
synonym: "down-regulation of complement activation, classical pathway" EXACT []
synonym: "downregulation of complement activation, classical pathway" EXACT []
@@ -288304,7 +291647,7 @@
id: GO:0045960
name: positive regulation of complement activation, classical pathway
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of complement activation by the classical pathway." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of complement activation by the classical pathway." [GOC:curators]
synonym: "activation of complement activation, classical pathway" NARROW []
synonym: "positive regulation of complement cascade, classical pathway" EXACT [GOC:add]
synonym: "stimulation of complement activation, classical pathway" NARROW []
@@ -288322,7 +291665,7 @@
id: GO:0045961
name: negative regulation of development, heterochronic
namespace: biological_process
-def: "Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and decreases the rate at which this time point is reached." [GOC:go_curators]
+def: "Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and decreases the rate at which this time point is reached." [GOC:curators]
synonym: "down regulation of development, heterochronic" EXACT []
synonym: "down-regulation of development, heterochronic" EXACT []
synonym: "downregulation of development, heterochronic" EXACT []
@@ -288333,7 +291676,7 @@
id: GO:0045962
name: positive regulation of development, heterochronic
namespace: biological_process
-def: "Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and increases the rate at which this time point is reached." [GOC:go_curators]
+def: "Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and increases the rate at which this time point is reached." [GOC:curators]
synonym: "activation of development, heterochronic" NARROW []
synonym: "stimulation of development, heterochronic" NARROW []
synonym: "up regulation of development, heterochronic" EXACT []
@@ -288345,7 +291688,7 @@
id: GO:0045963
name: negative regulation of dopamine metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:curators]
synonym: "down regulation of dopamine metabolic process" EXACT []
synonym: "down-regulation of dopamine metabolic process" EXACT []
synonym: "downregulation of dopamine metabolic process" EXACT []
@@ -288361,7 +291704,7 @@
id: GO:0045964
name: positive regulation of dopamine metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving dopamine." [GOC:curators]
synonym: "activation of dopamine metabolic process" NARROW []
synonym: "positive regulation of dopamine metabolism" EXACT []
synonym: "stimulation of dopamine metabolic process" NARROW []
@@ -288378,7 +291721,7 @@
id: GO:0045965
name: obsolete negative regulation of ecdysteroid metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." [GOC:go_curators]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "down regulation of ecdysteroid metabolic process" EXACT []
synonym: "down-regulation of ecdysteroid metabolic process" EXACT []
@@ -288392,7 +291735,7 @@
id: GO:0045966
name: obsolete positive regulation of ecdysteroid metabolic process
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." [GOC:curators]
comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "activation of ecdysteroid metabolic process" NARROW []
synonym: "positive regulation of ecdysteroid metabolism" EXACT []
@@ -288420,7 +291763,7 @@
id: GO:0045968
name: negative regulation of juvenile hormone biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:curators]
synonym: "down regulation of juvenile hormone biosynthetic process" EXACT []
synonym: "down-regulation of juvenile hormone biosynthetic process" EXACT []
synonym: "downregulation of juvenile hormone biosynthetic process" EXACT []
@@ -288441,7 +291784,7 @@
id: GO:0045969
name: positive regulation of juvenile hormone biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." [GOC:curators]
synonym: "activation of juvenile hormone biosynthetic process" NARROW []
synonym: "positive regulation of juvenile hormone anabolism" EXACT []
synonym: "positive regulation of juvenile hormone biosynthesis" EXACT []
@@ -288462,7 +291805,7 @@
id: GO:0045970
name: negative regulation of juvenile hormone catabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:curators]
synonym: "down regulation of juvenile hormone catabolic process" EXACT []
synonym: "down-regulation of juvenile hormone catabolic process" EXACT []
synonym: "downregulation of juvenile hormone catabolic process" EXACT []
@@ -288481,7 +291824,7 @@
id: GO:0045971
name: positive regulation of juvenile hormone catabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." [GOC:curators]
synonym: "activation of juvenile hormone catabolic process" NARROW []
synonym: "positive regulation of juvenile hormone breakdown" EXACT []
synonym: "positive regulation of juvenile hormone catabolism" EXACT []
@@ -288501,7 +291844,7 @@
id: GO:0045972
name: negative regulation of juvenile hormone secretion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone." [GOC:curators]
synonym: "down regulation of juvenile hormone secretion" EXACT []
synonym: "down-regulation of juvenile hormone secretion" EXACT []
synonym: "downregulation of juvenile hormone secretion" EXACT []
@@ -288518,7 +291861,7 @@
id: GO:0045973
name: positive regulation of juvenile hormone secretion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone." [GOC:curators]
synonym: "activation of juvenile hormone secretion" NARROW []
synonym: "stimulation of juvenile hormone secretion" NARROW []
synonym: "up regulation of juvenile hormone secretion" EXACT []
@@ -288535,14 +291878,14 @@
id: GO:0045974
name: regulation of translation, ncRNA-mediated
namespace: biological_process
-def: "Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein." [GOC:curators, GOC:dph, GOC:tb]
is_a: GO:0006417 ! regulation of translation
[Term]
id: GO:0045975
name: positive regulation of translation, ncRNA-mediated
namespace: biological_process
-def: "Any process, mediated by small non-coding RNAs, that activates or increases the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process, mediated by small non-coding RNAs, that activates or increases the rate that mRNAs are effectively translated into protein." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of mRNA translation, ncRNA-mediated" NARROW []
synonym: "stimulation of mRNA translation, ncRNA-mediated" NARROW []
synonym: "up regulation of mRNA translation, ncRNA-mediated" EXACT []
@@ -288555,7 +291898,7 @@
id: GO:0045976
name: negative regulation of mitotic cell cycle, embryonic
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of progression through the embryonic mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of progression through embryonic mitotic cell cycle" EXACT []
synonym: "down-regulation of progression through embryonic mitotic cell cycle" EXACT []
synonym: "downregulation of progression through embryonic mitotic cell cycle" EXACT []
@@ -288573,7 +291916,7 @@
id: GO:0045977
name: positive regulation of mitotic cell cycle, embryonic
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of progression through the embryonic mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of mitotic cell cycle, embryonic" NARROW []
synonym: "positive regulation of embryonic mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
synonym: "positive regulation of embryonic mitotic cell cycle progression" EXACT []
@@ -288592,7 +291935,7 @@
id: GO:0045978
name: negative regulation of nucleoside metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:curators]
synonym: "down regulation of nucleoside metabolic process" EXACT []
synonym: "down-regulation of nucleoside metabolic process" EXACT []
synonym: "downregulation of nucleoside metabolic process" EXACT []
@@ -288609,7 +291952,7 @@
id: GO:0045979
name: positive regulation of nucleoside metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleosides." [GOC:curators]
synonym: "activation of nucleoside metabolic process" NARROW []
synonym: "positive regulation of nucleoside metabolism" EXACT []
synonym: "stimulation of nucleoside metabolic process" NARROW []
@@ -288626,7 +291969,7 @@
id: GO:0045980
name: negative regulation of nucleotide metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:curators]
synonym: "down regulation of nucleotide metabolic process" EXACT []
synonym: "down-regulation of nucleotide metabolic process" EXACT []
synonym: "downregulation of nucleotide metabolic process" EXACT []
@@ -288644,7 +291987,7 @@
id: GO:0045981
name: positive regulation of nucleotide metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleotides." [GOC:curators]
synonym: "activation of nucleotide metabolic process" NARROW []
synonym: "positive regulation of nucleotide metabolism" EXACT []
synonym: "stimulation of nucleotide metabolic process" NARROW []
@@ -288662,12 +292005,12 @@
id: GO:0045982
name: negative regulation of purine nucleobase metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases." [GOC:curators]
synonym: "down regulation of purine base metabolic process" EXACT []
synonym: "down-regulation of purine base metabolic process" EXACT []
synonym: "downregulation of purine base metabolic process" EXACT []
synonym: "inhibition of purine base metabolic process" NARROW []
-synonym: "negative regulation of purine base metabolic process" EXACT [GOC:go_curators]
+synonym: "negative regulation of purine base metabolic process" EXACT [GOC:curators]
synonym: "negative regulation of purine base metabolism" EXACT []
is_a: GO:0006141 ! regulation of purine nucleobase metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
@@ -288680,7 +292023,7 @@
id: GO:0045983
name: positive regulation of purine nucleobase metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases." [GOC:curators]
synonym: "activation of purine base metabolic process" NARROW []
synonym: "positive regulation of purine base metabolic process" EXACT []
synonym: "positive regulation of purine base metabolism" EXACT []
@@ -288698,12 +292041,12 @@
id: GO:0045984
name: negative regulation of pyrimidine nucleobase metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:curators]
synonym: "down regulation of pyrimidine base metabolic process" EXACT []
synonym: "down-regulation of pyrimidine base metabolic process" EXACT []
synonym: "downregulation of pyrimidine base metabolic process" EXACT []
synonym: "inhibition of pyrimidine base metabolic process" NARROW []
-synonym: "negative regulation of pyrimidine base metabolic process" EXACT [GOC:go_curators]
+synonym: "negative regulation of pyrimidine base metabolic process" EXACT [GOC:curators]
synonym: "negative regulation of pyrimidine base metabolism" EXACT []
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
@@ -288715,9 +292058,9 @@
id: GO:0045985
name: positive regulation of pyrimidine nucleobase metabolic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving pyrimidine nucleobases." [GOC:curators]
synonym: "activation of pyrimidine base metabolic process" NARROW []
-synonym: "positive regulation of pyrimidine base metabolic process" EXACT [GOC:go_curators]
+synonym: "positive regulation of pyrimidine base metabolic process" EXACT [GOC:curators]
synonym: "positive regulation of pyrimidine base metabolism" EXACT []
synonym: "stimulation of pyrimidine base metabolic process" NARROW []
synonym: "up regulation of pyrimidine base metabolic process" EXACT []
@@ -288733,7 +292076,7 @@
id: GO:0045986
name: negative regulation of smooth muscle contraction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction." [GOC:curators]
synonym: "down regulation of smooth muscle contraction" EXACT []
synonym: "down-regulation of smooth muscle contraction" EXACT []
synonym: "downregulation of smooth muscle contraction" EXACT []
@@ -288749,7 +292092,7 @@
id: GO:0045987
name: positive regulation of smooth muscle contraction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of smooth muscle contraction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of smooth muscle contraction." [GOC:curators]
synonym: "activation of smooth muscle contraction" NARROW []
synonym: "stimulation of smooth muscle contraction" NARROW []
synonym: "up regulation of smooth muscle contraction" EXACT []
@@ -288765,7 +292108,7 @@
id: GO:0045988
name: negative regulation of striated muscle contraction
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction." [GOC:curators]
synonym: "down regulation of striated muscle contraction" EXACT []
synonym: "down-regulation of striated muscle contraction" EXACT []
synonym: "downregulation of striated muscle contraction" EXACT []
@@ -288780,7 +292123,7 @@
id: GO:0045989
name: positive regulation of striated muscle contraction
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of striated muscle contraction." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of striated muscle contraction." [GOC:curators]
synonym: "activation of striated muscle contraction" NARROW []
synonym: "stimulation of striated muscle contraction" NARROW []
synonym: "up regulation of striated muscle contraction" EXACT []
@@ -288796,7 +292139,7 @@
id: GO:0045990
name: carbon catabolite regulation of transcription
namespace: biological_process
-def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:go_curators, GOC:mah, PMID:18359269, PMID:9618445]
+def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources." [GOC:curators, GOC:mah, PMID:18359269, PMID:9618445]
synonym: "regulation of transcription by carbon catabolites" EXACT [GOC:mah]
is_a: GO:0006355 ! regulation of DNA-templated transcription
is_a: GO:0031670 ! cellular response to nutrient
@@ -288814,7 +292157,7 @@
id: GO:0045992
name: negative regulation of embryonic development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." [GOC:curators]
synonym: "down regulation of embryonic development" EXACT []
synonym: "down-regulation of embryonic development" EXACT []
synonym: "downregulation of embryonic development" EXACT []
@@ -288830,7 +292173,7 @@
id: GO:0045993
name: negative regulation of translational initiation by iron
namespace: biological_process
-def: "Any process involving iron that stops, prevents or reduces the rate of translational initiation." [GOC:go_curators]
+def: "Any process involving iron that stops, prevents or reduces the rate of translational initiation." [GOC:curators]
synonym: "down regulation of translational initiation by iron" EXACT []
synonym: "down-regulation of translational initiation by iron" EXACT []
synonym: "downregulation of translational initiation by iron" EXACT []
@@ -288842,7 +292185,7 @@
id: GO:0045994
name: positive regulation of translational initiation by iron
namespace: biological_process
-def: "Any process involving iron that activates or increases the rate of translational initiation." [GOC:go_curators]
+def: "Any process involving iron that activates or increases the rate of translational initiation." [GOC:curators]
synonym: "activation of translational initiation by iron" NARROW []
synonym: "stimulation of translational initiation by iron" NARROW []
synonym: "up regulation of translational initiation by iron" EXACT []
@@ -288855,7 +292198,7 @@
id: GO:0045995
name: regulation of embryonic development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of embryonic development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of embryonic development." [GOC:curators]
is_a: GO:2000026 ! regulation of multicellular organismal development
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009790 ! embryo development
@@ -288865,7 +292208,7 @@
id: GO:0045996
name: obsolete negative regulation of transcription by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription." [GOC:curators]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "down regulation of transcription by pheromones" EXACT []
synonym: "down-regulation of transcription by pheromones" EXACT []
@@ -288878,7 +292221,7 @@
id: GO:0045997
name: negative regulation of ecdysteroid biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:curators]
synonym: "down regulation of ecdysteroid biosynthetic process" EXACT []
synonym: "down-regulation of ecdysteroid biosynthetic process" EXACT []
synonym: "downregulation of ecdysteroid biosynthetic process" EXACT []
@@ -288898,7 +292241,7 @@
id: GO:0045998
name: positive regulation of ecdysteroid biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." [GOC:curators]
synonym: "activation of ecdysteroid biosynthetic process" NARROW []
synonym: "positive regulation of ecdysteroid anabolism" EXACT []
synonym: "positive regulation of ecdysteroid biosynthesis" EXACT []
@@ -288919,7 +292262,7 @@
id: GO:0045999
name: negative regulation of ecdysteroid secretion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid." [GOC:curators]
synonym: "down regulation of ecdysteroid secretion" EXACT []
synonym: "down-regulation of ecdysteroid secretion" EXACT []
synonym: "downregulation of ecdysteroid secretion" EXACT []
@@ -288934,7 +292277,7 @@
id: GO:0046000
name: positive regulation of ecdysteroid secretion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid." [GOC:curators]
synonym: "activation of ecdysteroid secretion" NARROW []
synonym: "stimulation of ecdysteroid secretion" NARROW []
synonym: "up regulation of ecdysteroid secretion" EXACT []
@@ -288950,7 +292293,7 @@
id: GO:0046001
name: negative regulation of preblastoderm mitotic cell cycle
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of progression through the preblastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of progression through the preblastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of progression through preblastoderm mitotic cell cycle" EXACT []
synonym: "down-regulation of progression through preblastoderm mitotic cell cycle" EXACT []
synonym: "downregulation of progression through preblastoderm mitotic cell cycle" EXACT []
@@ -288967,7 +292310,7 @@
id: GO:0046002
name: positive regulation of preblastoderm mitotic cell cycle
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of progression through the preblastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the rate or extent of progression through the preblastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of progression through preblastoderm mitotic cell cycle" NARROW []
synonym: "positive regulation of preblastoderm mitotic cell cycle progression" EXACT []
synonym: "positive regulation of progression through preblastoderm mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
@@ -288985,7 +292328,7 @@
id: GO:0046003
name: negative regulation of syncytial blastoderm mitotic cell cycle
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of progression through the syncytial blastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that stops, prevents or reduces the rate or extent of progression through the syncytial blastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "down regulation of progression through syncytial blastoderm mitotic cell cycle" EXACT []
synonym: "down-regulation of progression through syncytial blastoderm mitotic cell cycle" EXACT []
synonym: "downregulation of progression through syncytial blastoderm mitotic cell cycle" EXACT []
@@ -289002,7 +292345,7 @@
id: GO:0046004
name: positive regulation of syncytial blastoderm mitotic cell cycle
namespace: biological_process
-def: "Any process that activates or increases the rate or extent of progression through the syncytial blastoderm mitotic cell cycle." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the rate or extent of progression through the syncytial blastoderm mitotic cell cycle." [GOC:curators, GOC:dph, GOC:tb]
synonym: "activation of progression through syncytial blastoderm mitotic cell cycle" NARROW []
synonym: "positive regulation of progression through syncytial blastoderm mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
synonym: "positive regulation of syncytial blastoderm cell cycle progression" EXACT []
@@ -289020,7 +292363,7 @@
id: GO:0046005
name: positive regulation of circadian sleep/wake cycle, REM sleep
namespace: biological_process
-def: "Any process that activates or increases the duration or quality of rapid eye movement (REM) sleep." [GOC:go_curators]
+def: "Any process that activates or increases the duration or quality of rapid eye movement (REM) sleep." [GOC:curators]
synonym: "activation of circadian sleep/wake cycle, REM sleep" NARROW []
synonym: "positive regulation of REM sleep" EXACT []
synonym: "stimulation of circadian sleep/wake cycle, REM sleep" NARROW []
@@ -289037,7 +292380,7 @@
id: GO:0046006
name: regulation of activated T cell proliferation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of activated T cell proliferation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of activated T cell proliferation." [GOC:curators]
synonym: "regulation of activated T lymphocyte proliferation" EXACT []
synonym: "regulation of activated T-cell proliferation" EXACT []
synonym: "regulation of activated T-lymphocyte proliferation" EXACT []
@@ -289050,7 +292393,7 @@
id: GO:0046007
name: negative regulation of activated T cell proliferation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation." [GOC:go_curators]
+def: "Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation." [GOC:curators]
synonym: "down regulation of activated T cell proliferation" EXACT []
synonym: "down-regulation of activated T cell proliferation" EXACT []
synonym: "downregulation of activated T cell proliferation" EXACT []
@@ -289068,14 +292411,14 @@
id: GO:0046008
name: regulation of female receptivity, post-mating
namespace: biological_process
-def: "Any process that modulates the receptiveness of a female to male advances subsequent to mating." [GOC:go_curators]
+def: "Any process that modulates the receptiveness of a female to male advances subsequent to mating." [GOC:curators]
is_a: GO:0045924 ! regulation of female receptivity
[Term]
id: GO:0046009
name: positive regulation of female receptivity, post-mating
namespace: biological_process
-def: "Any process that increases the receptiveness of a female to male advances subsequent to mating." [GOC:go_curators]
+def: "Any process that increases the receptiveness of a female to male advances subsequent to mating." [GOC:curators]
synonym: "activation of female receptivity, post-mating" NARROW []
synonym: "stimulation of female receptivity, post-mating" NARROW []
synonym: "up regulation of female receptivity, post-mating" EXACT []
@@ -289088,7 +292431,7 @@
id: GO:0046010
name: positive regulation of circadian sleep/wake cycle, non-REM sleep
namespace: biological_process
-def: "Any process that activates or increases the duration or quality of non-rapid eye movement (NREM) sleep." [GOC:go_curators]
+def: "Any process that activates or increases the duration or quality of non-rapid eye movement (NREM) sleep." [GOC:curators]
synonym: "activation of circadian sleep/wake cycle, non-REM sleep" NARROW []
synonym: "positive regulation of non-REM sleep" EXACT []
synonym: "stimulation of circadian sleep/wake cycle, non-REM sleep" NARROW []
@@ -289105,14 +292448,14 @@
id: GO:0046011
name: regulation of oskar mRNA translation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of oskar mRNA translation. To ensure the localization of Oskar protein at the posterior pole of the oocyte, translation of oskar mRNA is repressed during its transport to the posterior pole and activated upon localization of the mRNA at the posterior cortex." [GOC:go_curators, PMID:12538512]
+def: "Any process that modulates the frequency, rate or extent of oskar mRNA translation. To ensure the localization of Oskar protein at the posterior pole of the oocyte, translation of oskar mRNA is repressed during its transport to the posterior pole and activated upon localization of the mRNA at the posterior cortex." [GOC:curators, PMID:12538512]
is_a: GO:0006417 ! regulation of translation
[Term]
id: GO:0046012
name: positive regulation of oskar mRNA translation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of oskar mRNA translation." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of oskar mRNA translation." [GOC:curators]
synonym: "activation of oskar mRNA translation" NARROW []
synonym: "stimulation of oskar mRNA translation" NARROW []
synonym: "up regulation of oskar mRNA translation" EXACT []
@@ -289125,7 +292468,7 @@
id: GO:0046013
name: regulation of T cell homeostatic proliferation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of resting T cell proliferation." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of resting T cell proliferation." [GOC:curators]
synonym: "regulation of resting T cell proliferation" EXACT []
synonym: "regulation of T lymphocyte homeostatic proliferation" EXACT []
synonym: "regulation of T-cell homeostatic proliferation" EXACT []
@@ -289139,7 +292482,7 @@
id: GO:0046014
name: negative regulation of T cell homeostatic proliferation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the rate or extent of resting T cell proliferation." [GOC:go_curators]
+def: "Any process that stops, prevents or reduces the rate or extent of resting T cell proliferation." [GOC:curators]
synonym: "down regulation of T cell homeostatic proliferation" EXACT []
synonym: "down-regulation of T cell homeostatic proliferation" EXACT []
synonym: "downregulation of T cell homeostatic proliferation" EXACT []
@@ -289158,14 +292501,14 @@
id: GO:0046015
name: regulation of transcription by glucose
namespace: biological_process
-def: "Any process involving glucose that modulates the frequency, rate or extent or transcription." [GOC:go_curators]
+def: "Any process involving glucose that modulates the frequency, rate or extent or transcription." [GOC:curators]
is_a: GO:0006355 ! regulation of DNA-templated transcription
[Term]
id: GO:0046016
name: positive regulation of transcription by glucose
namespace: biological_process
-def: "Any process involving glucose that activates or increases the rate of transcription." [GOC:go_curators]
+def: "Any process involving glucose that activates or increases the rate of transcription." [GOC:curators]
synonym: "activation of transcription by glucose" NARROW []
synonym: "stimulation of transcription by glucose" NARROW []
synonym: "up regulation of transcription by glucose" EXACT []
@@ -289178,7 +292521,7 @@
id: GO:0046017
name: obsolete regulation of transcription from RNA polymerase I promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "mitotic regulation of transcription from Pol I promoter" EXACT []
synonym: "regulation of transcription from Pol I promoter during mitosis" EXACT [GOC:dph, GOC:tb]
@@ -289192,7 +292535,7 @@
id: GO:0046018
name: obsolete positive regulation of transcription from RNA polymerase I promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "activation of transcription from RNA polymerase I promoter during mitosis" NARROW [GOC:mah]
synonym: "mitotic activation of transcription from Pol I promoter" EXACT []
@@ -289211,7 +292554,7 @@
id: GO:0046019
name: obsolete regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH]
+def: "OBSOLETE. Any process involving pheromones that modulates the frequency, rate or extent or transcription from an RNA polymerase II promoter." [GOC:curators, GOC:txnOH]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "regulation of transcription from Pol II promoter by pheromones" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12739" xsd:anyURI
@@ -289221,7 +292564,7 @@
id: GO:0046020
name: obsolete negative regulation of transcription from RNA polymerase II promoter by pheromones
namespace: biological_process
-def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:go_curators]
+def: "OBSOLETE. Any process involving pheromones that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:curators]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "down regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
synonym: "down-regulation of transcription from RNA polymerase II promoter by pheromones" EXACT []
@@ -289235,7 +292578,7 @@
id: GO:0046021
name: obsolete regulation of transcription from RNA polymerase II promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "mitotic regulation of transcription from Pol II promoter" EXACT []
synonym: "regulation of transcription from Pol II promoter, mitotic" EXACT []
@@ -289249,7 +292592,7 @@
id: GO:0046022
name: obsolete positive regulation of transcription from RNA polymerase II promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "activation of transcription from RNA polymerase II promoter during mitosis" NARROW [GOC:mah]
synonym: "mitotic activation of transcription from Pol II promoter" EXACT []
@@ -289268,7 +292611,7 @@
id: GO:0046023
name: obsolete regulation of transcription from RNA polymerase III promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. A cell cycle process that modulates the frequency, rate or extent of transcription from an RNA polymerase III promoter that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "mitotic regulation of transcription from Pol III promoter" EXACT []
synonym: "regulation of transcription from Pol III promoter, mitotic" EXACT []
@@ -289282,7 +292625,7 @@
id: GO:0046024
name: obsolete positive regulation of transcription from RNA polymerase III promoter during mitotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III that occurs during the mitotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III that occurs during the mitotic cell cycle." [GOC:curators]
comment: The reason for obsoletion is that 'during' should be captured using an annotation extension.
synonym: "activation of transcription from RNA polymerase III promoter during mitosis" NARROW [GOC:mah]
synonym: "mitotic activation of transcription from Pol III promoter" EXACT []
@@ -289341,8 +292684,8 @@
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.158
property_value: skos:exactMatch RHEA:14057
-property_value: skos:relatedMatch RHEA:77739
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29862" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31730" xsd:anyURI
[Term]
id: GO:0046028
@@ -289385,7 +292728,7 @@
id: GO:0046031
name: ADP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate." [GOC:curators]
synonym: "ADP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009179 ! purine ribonucleoside diphosphate metabolic process
@@ -289394,7 +292737,7 @@
id: GO:0046032
name: ADP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate." [GOC:curators]
synonym: "ADP breakdown" EXACT []
synonym: "ADP catabolism" EXACT []
synonym: "ADP degradation" EXACT []
@@ -289406,7 +292749,7 @@
id: GO:0046033
name: AMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving AMP, adenosine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving AMP, adenosine monophosphate." [GOC:curators]
synonym: "adenylate forming enzyme activity" RELATED []
synonym: "AMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
@@ -289416,7 +292759,7 @@
id: GO:0046034
name: ATP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC:go_curators]
+def: "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." [GOC:curators]
synonym: "ATP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process
@@ -289425,7 +292768,7 @@
id: GO:0046035
name: CMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving CMP, cytidine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving CMP, cytidine monophosphate." [GOC:curators]
synonym: "CMP metabolism" EXACT []
is_a: GO:0009173 ! pyrimidine ribonucleoside monophosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289435,7 +292778,7 @@
name: CTP metabolic process
namespace: biological_process
alt_id: GO:0006243
-def: "The chemical reactions and pathways involving CTP, cytidine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving CTP, cytidine triphosphate." [GOC:curators]
synonym: "CTP deamination" NARROW []
synonym: "CTP metabolism" EXACT []
is_a: GO:0009208 ! pyrimidine ribonucleoside triphosphate metabolic process
@@ -289445,7 +292788,7 @@
id: GO:0046037
name: GMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving GMP, guanosine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving GMP, guanosine monophosphate." [GOC:curators]
synonym: "GMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009167 ! purine ribonucleoside monophosphate metabolic process
@@ -289454,7 +292797,7 @@
id: GO:0046038
name: GMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of GMP, guanosine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of GMP, guanosine monophosphate." [GOC:curators]
synonym: "GMP breakdown" EXACT []
synonym: "GMP catabolism" EXACT []
synonym: "GMP degradation" EXACT []
@@ -289466,7 +292809,7 @@
id: GO:0046039
name: GTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving GTP, guanosine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving GTP, guanosine triphosphate." [GOC:curators]
synonym: "GTP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process
@@ -289475,7 +292818,7 @@
id: GO:0046040
name: IMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving IMP, inosine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving IMP, inosine monophosphate." [GOC:curators]
synonym: "IMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009167 ! purine ribonucleoside monophosphate metabolic process
@@ -289484,7 +292827,7 @@
id: GO:0046041
name: ITP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ITP, inosine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving ITP, inosine triphosphate." [GOC:curators]
synonym: "ITP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0009205 ! purine ribonucleoside triphosphate metabolic process
@@ -289493,7 +292836,7 @@
id: GO:0046042
name: ITP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ITP, inosine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of ITP, inosine triphosphate." [GOC:curators]
synonym: "ITP anabolism" EXACT []
synonym: "ITP biosynthesis" EXACT []
synonym: "ITP formation" EXACT []
@@ -289506,7 +292849,7 @@
id: GO:0046043
name: TDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving TDP, ribosylthymine diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving TDP, ribosylthymine diphosphate." [GOC:curators]
synonym: "TDP metabolism" EXACT []
is_a: GO:0009193 ! pyrimidine ribonucleoside diphosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289515,7 +292858,7 @@
id: GO:0046044
name: TMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving TMP, ribosylthymine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving TMP, ribosylthymine monophosphate." [GOC:curators]
synonym: "TMP metabolism" EXACT []
is_a: GO:0009173 ! pyrimidine ribonucleoside monophosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289524,7 +292867,7 @@
id: GO:0046045
name: TMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of TMP, ribosylthymine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of TMP, ribosylthymine monophosphate." [GOC:curators]
synonym: "TMP breakdown" EXACT []
synonym: "TMP catabolism" EXACT []
synonym: "TMP degradation" EXACT []
@@ -289536,7 +292879,7 @@
id: GO:0046046
name: TTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving TTP, ribosylthymine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving TTP, ribosylthymine triphosphate." [GOC:curators]
synonym: "TTP metabolism" EXACT []
is_a: GO:0009208 ! pyrimidine ribonucleoside triphosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289545,7 +292888,7 @@
id: GO:0046047
name: TTP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of TTP, ribosylthymine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of TTP, ribosylthymine triphosphate." [GOC:curators]
synonym: "TTP breakdown" EXACT []
synonym: "TTP catabolism" EXACT []
synonym: "TTP degradation" EXACT []
@@ -289558,7 +292901,7 @@
id: GO:0046048
name: UDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving UDP, uridine (5'-)diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving UDP, uridine (5'-)diphosphate." [GOC:curators]
synonym: "UDP metabolism" EXACT []
is_a: GO:0009193 ! pyrimidine ribonucleoside diphosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289567,7 +292910,7 @@
id: GO:0046049
name: UMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving UMP, uridine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving UMP, uridine monophosphate." [GOC:curators]
synonym: "UMP metabolism" EXACT []
is_a: GO:0009173 ! pyrimidine ribonucleoside monophosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289576,7 +292919,7 @@
id: GO:0046050
name: UMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of UMP, uridine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of UMP, uridine monophosphate." [GOC:curators]
synonym: "UMP breakdown" EXACT []
synonym: "UMP catabolism" EXACT []
synonym: "UMP degradation" EXACT []
@@ -289588,7 +292931,7 @@
id: GO:0046051
name: UTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving UTP, uridine (5'-)triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving UTP, uridine (5'-)triphosphate." [GOC:curators]
synonym: "UTP metabolism" EXACT []
is_a: GO:0009208 ! pyrimidine ribonucleoside triphosphate metabolic process
is_a: GO:0009218 ! pyrimidine ribonucleotide metabolic process
@@ -289597,7 +292940,7 @@
id: GO:0046052
name: UTP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of UTP, uridine (5'-)triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of UTP, uridine (5'-)triphosphate." [GOC:curators]
synonym: "UTP breakdown" EXACT []
synonym: "UTP catabolism" EXACT []
synonym: "UTP degradation" EXACT []
@@ -289610,7 +292953,7 @@
id: GO:0046053
name: dAMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dAMP, deoxyadenosine monophosphate (2'-deoxyadenosine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dAMP, deoxyadenosine monophosphate (2'-deoxyadenosine 5'-phosphate)." [GOC:curators]
synonym: "dAMP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009170 ! purine deoxyribonucleoside monophosphate metabolic process
@@ -289619,7 +292962,7 @@
id: GO:0046054
name: dGMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate)." [GOC:curators]
synonym: "dGMP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009170 ! purine deoxyribonucleoside monophosphate metabolic process
@@ -289628,7 +292971,7 @@
id: GO:0046055
name: dGMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dGMP, deoxyguanosine monophosphate (2'-deoxyguanosine 5'-phosphate)." [GOC:curators]
synonym: "dGMP breakdown" EXACT []
synonym: "dGMP catabolism" EXACT []
synonym: "dGMP degradation" EXACT []
@@ -289640,7 +292983,7 @@
id: GO:0046056
name: dADP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate)." [GOC:curators]
synonym: "dADP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009182 ! purine deoxyribonucleoside diphosphate metabolic process
@@ -289649,7 +292992,7 @@
id: GO:0046057
name: dADP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate)." [GOC:curators]
synonym: "dADP breakdown" EXACT []
synonym: "dADP catabolism" EXACT []
synonym: "dADP degradation" EXACT []
@@ -289661,7 +293004,7 @@
id: GO:0046058
name: cAMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate)." [GOC:curators]
synonym: "3',5' cAMP metabolic process" EXACT []
synonym: "3',5' cAMP metabolism" EXACT []
synonym: "3',5'-cAMP metabolic process" EXACT []
@@ -289679,7 +293022,7 @@
id: GO:0046059
name: dAMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dAMP, deoxyadenosine monophosphate (2'-deoxyadenosine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dAMP, deoxyadenosine monophosphate (2'-deoxyadenosine 5'-phosphate)." [GOC:curators]
synonym: "dAMP breakdown" EXACT []
synonym: "dAMP catabolism" EXACT []
synonym: "dAMP degradation" EXACT []
@@ -289691,7 +293034,7 @@
id: GO:0046060
name: dATP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate)." [GOC:curators]
synonym: "dATP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
@@ -289700,7 +293043,7 @@
id: GO:0046061
name: dATP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate)." [GOC:curators]
synonym: "dATP breakdown" EXACT []
synonym: "dATP catabolism" EXACT []
synonym: "dATP degradation" EXACT []
@@ -289712,7 +293055,7 @@
id: GO:0046062
name: dCDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dCDP, deoxycytidine 5'-diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dCDP, deoxycytidine 5'-diphosphate." [GOC:curators]
synonym: "dCDP metabolism" EXACT []
is_a: GO:0009196 ! pyrimidine deoxyribonucleoside diphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289721,7 +293064,7 @@
id: GO:0046063
name: dCMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dCMP, deoxycytidine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dCMP, deoxycytidine monophosphate." [GOC:curators]
synonym: "dCMP metabolism" EXACT []
is_a: GO:0009176 ! pyrimidine deoxyribonucleoside monophosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289730,7 +293073,7 @@
id: GO:0046064
name: dCMP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of dCMP, deoxycytidine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of dCMP, deoxycytidine monophosphate." [GOC:curators]
synonym: "dCMP anabolism" EXACT []
synonym: "dCMP biosynthesis" EXACT []
synonym: "dCMP formation" EXACT []
@@ -289743,7 +293086,7 @@
id: GO:0046065
name: dCTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dCTP, deoxycytidine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dCTP, deoxycytidine triphosphate." [GOC:curators]
synonym: "dCTP metabolism" EXACT []
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289752,7 +293095,7 @@
id: GO:0046066
name: dGDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate)." [GOC:curators]
synonym: "dGDP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009182 ! purine deoxyribonucleoside diphosphate metabolic process
@@ -289761,7 +293104,7 @@
id: GO:0046067
name: dGDP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate)." [GOC:curators]
synonym: "dGDP breakdown" EXACT []
synonym: "dGDP catabolism" EXACT []
synonym: "dGDP degradation" EXACT []
@@ -289773,7 +293116,7 @@
id: GO:0046068
name: cGMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate." [GOC:curators]
synonym: "cGMP metabolism" EXACT []
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0052652 ! cyclic purine nucleotide metabolic process
@@ -289782,7 +293125,7 @@
id: GO:0046069
name: cGMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate." [GOC:curators]
synonym: "cGMP breakdown" EXACT []
synonym: "cGMP catabolism" EXACT []
synonym: "cGMP degradation" EXACT []
@@ -289794,7 +293137,7 @@
id: GO:0046070
name: dGTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dGTP, guanosine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dGTP, guanosine triphosphate." [GOC:curators]
synonym: "dGTP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
@@ -289803,7 +293146,7 @@
id: GO:0046071
name: dGTP biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of dGTP, guanosine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of dGTP, guanosine triphosphate." [GOC:curators]
synonym: "dGTP anabolism" EXACT []
synonym: "dGTP biosynthesis" EXACT []
synonym: "dGTP formation" EXACT []
@@ -289816,7 +293159,7 @@
id: GO:0046072
name: dTDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dTDP, deoxyribosylthymine diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dTDP, deoxyribosylthymine diphosphate." [GOC:curators]
synonym: "dTDP metabolism" EXACT []
is_a: GO:0009196 ! pyrimidine deoxyribonucleoside diphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289825,7 +293168,7 @@
id: GO:0046073
name: dTMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate)." [GOC:curators]
synonym: "dTMP metabolism" EXACT []
is_a: GO:0009176 ! pyrimidine deoxyribonucleoside monophosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289834,7 +293177,7 @@
id: GO:0046074
name: dTMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dTMP, deoxyribosylthymine monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dTMP, deoxyribosylthymine monophosphate." [GOC:curators]
synonym: "dTMP breakdown" EXACT []
synonym: "dTMP catabolism" EXACT []
synonym: "dTMP degradation" EXACT []
@@ -289846,7 +293189,7 @@
id: GO:0046075
name: dTTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dTTP, deoxyribosylthymine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dTTP, deoxyribosylthymine triphosphate." [GOC:curators]
synonym: "dTTP metabolism" EXACT []
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289855,7 +293198,7 @@
id: GO:0046076
name: dTTP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dTTP, deoxyribosylthymine triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dTTP, deoxyribosylthymine triphosphate." [GOC:curators]
synonym: "dTTP breakdown" EXACT []
synonym: "dTTP catabolism" EXACT []
synonym: "dTTP degradation" EXACT []
@@ -289867,7 +293210,7 @@
id: GO:0046077
name: dUDP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dUDP, deoxyuridine (5'-)diphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dUDP, deoxyuridine (5'-)diphosphate." [GOC:curators]
synonym: "dUDP metabolism" EXACT []
is_a: GO:0009196 ! pyrimidine deoxyribonucleoside diphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289876,7 +293219,7 @@
id: GO:0046078
name: dUMP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dUMP, deoxyuridine (5'-)monophosphate (2'-deoxyuridine 5'-phosphate)." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dUMP, deoxyuridine (5'-)monophosphate (2'-deoxyuridine 5'-phosphate)." [GOC:curators]
synonym: "dUMP metabolism" EXACT []
is_a: GO:0009176 ! pyrimidine deoxyribonucleoside monophosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289885,7 +293228,7 @@
id: GO:0046079
name: dUMP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dUMP, deoxyuridine (5'-)monophosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dUMP, deoxyuridine (5'-)monophosphate." [GOC:curators]
synonym: "dUMP breakdown" EXACT []
synonym: "dUMP catabolism" EXACT []
synonym: "dUMP degradation" EXACT []
@@ -289897,7 +293240,7 @@
id: GO:0046080
name: dUTP metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate." [GOC:curators]
synonym: "dUTP metabolism" EXACT []
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -289906,7 +293249,7 @@
id: GO:0046081
name: dUTP catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate." [GOC:curators]
synonym: "dUTP breakdown" EXACT []
synonym: "dUTP catabolism" EXACT []
synonym: "dUTP degradation" EXACT []
@@ -289918,7 +293261,7 @@
id: GO:0046082
name: obsolete 5-methylcytosine biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 5-methylcytosine, a methylated base of DNA." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 5-methylcytosine, a methylated base of DNA." [GOC:curators]
comment: This term was obsoleted because itis redundant with DNA methylation-dependent heterochromatin formation ; GO:0006346 or its children.
synonym: "5-methylcytosine anabolism" EXACT []
synonym: "5-methylcytosine biosynthesis" EXACT []
@@ -289932,7 +293275,7 @@
id: GO:0046083
name: adenine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine." [GOC:go_curators]
+def: "The chemical reactions and pathways involving adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine." [GOC:curators]
synonym: "adenine metabolism" EXACT []
is_a: GO:0006144 ! purine nucleobase metabolic process
@@ -289940,7 +293283,7 @@
id: GO:0046084
name: adenine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine." [GOC:curators]
synonym: "adenine anabolism" EXACT []
synonym: "adenine biosynthesis" EXACT []
synonym: "adenine formation" EXACT []
@@ -289952,7 +293295,7 @@
id: GO:0046085
name: adenosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:go_curators]
+def: "The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:curators]
synonym: "adenosine metabolism" EXACT []
is_a: GO:0046128 ! purine ribonucleoside metabolic process
@@ -289960,7 +293303,7 @@
id: GO:0046086
name: adenosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes." [GOC:curators]
synonym: "adenosine anabolism" EXACT []
synonym: "adenosine biosynthesis" EXACT []
synonym: "adenosine formation" EXACT []
@@ -289972,7 +293315,7 @@
id: GO:0046087
name: cytidine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside." [GOC:go_curators]
+def: "The chemical reactions and pathways involving cytidine, cytosine riboside, a widely distributed nucleoside." [GOC:curators]
synonym: "cytidine metabolism" EXACT []
is_a: GO:0046131 ! pyrimidine ribonucleoside metabolic process
@@ -289980,7 +293323,7 @@
id: GO:0046088
name: obsolete cytidine biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of cytidine, cytosine riboside, a widely distributed nucleoside." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of cytidine, cytosine riboside, a widely distributed nucleoside." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "cytidine anabolism" EXACT []
synonym: "cytidine biosynthesis" EXACT []
@@ -289993,7 +293336,7 @@
id: GO:0046089
name: obsolete cytosine biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives." [GOC:go_curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives." [GOC:curators]
comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "cytosine anabolism" EXACT []
synonym: "cytosine biosynthesis" EXACT []
@@ -290006,27 +293349,29 @@
id: GO:0046090
name: deoxyadenosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyadenosine metabolism" EXACT []
+is_a: GO:0009120 ! 2'-deoxyribonucleoside metabolic process
is_a: GO:0046122 ! purine deoxyribonucleoside metabolic process
[Term]
id: GO:0046091
name: deoxyadenosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of deoxyadenosine, 2-deoxyribosyladenine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyadenosine anabolism" EXACT []
synonym: "deoxyadenosine biosynthesis" EXACT []
synonym: "deoxyadenosine formation" EXACT []
synonym: "deoxyadenosine synthesis" EXACT []
is_a: GO:0046090 ! deoxyadenosine metabolic process
+is_a: GO:0046120 ! 2'-deoxyribonucleoside biosynthetic process
is_a: GO:0046123 ! purine deoxyribonucleoside biosynthetic process
[Term]
id: GO:0046092
name: deoxycytidine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxycytidine metabolism" EXACT []
is_a: GO:0046125 ! pyrimidine deoxyribonucleoside metabolic process
@@ -290034,7 +293379,7 @@
id: GO:0046093
name: deoxycytidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of deoxycytidine, 2-deoxyribosylcytosine, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxycytidine anabolism" EXACT []
synonym: "deoxycytidine biosynthesis" EXACT []
synonym: "deoxycytidine formation" EXACT []
@@ -290046,27 +293391,29 @@
id: GO:0046094
name: deoxyinosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving deoxyinosine, hypoxanthine deoxyriboside." [GOC:go_curators]
+def: "The chemical reactions and pathways involving deoxyinosine, hypoxanthine deoxyriboside." [GOC:curators]
synonym: "deoxyinosine metabolism" EXACT []
+is_a: GO:0009120 ! 2'-deoxyribonucleoside metabolic process
is_a: GO:0046122 ! purine deoxyribonucleoside metabolic process
[Term]
id: GO:0046095
name: deoxyinosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of deoxyinosine, hypoxanthine deoxyriboside." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of deoxyinosine, hypoxanthine deoxyriboside." [GOC:curators]
synonym: "deoxyinosine anabolism" EXACT []
synonym: "deoxyinosine biosynthesis" EXACT []
synonym: "deoxyinosine formation" EXACT []
synonym: "deoxyinosine synthesis" EXACT []
is_a: GO:0046094 ! deoxyinosine metabolic process
+is_a: GO:0046120 ! 2'-deoxyribonucleoside biosynthetic process
is_a: GO:0046123 ! purine deoxyribonucleoside biosynthetic process
[Term]
id: GO:0046096
name: deoxyuridine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyuridine metabolism" EXACT []
is_a: GO:0046125 ! pyrimidine deoxyribonucleoside metabolic process
@@ -290074,7 +293421,7 @@
id: GO:0046097
name: deoxyuridine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of deoxyuridine, 2-deoxyribosyluracil, one of the four major nucleosides of DNA." [GOC:curators]
synonym: "deoxyuridine anabolism" EXACT []
synonym: "deoxyuridine biosynthesis" EXACT []
synonym: "deoxyuridine formation" EXACT []
@@ -290086,7 +293433,7 @@
id: GO:0046098
name: guanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:go_curators]
+def: "The chemical reactions and pathways involving guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:curators]
synonym: "guanine metabolism" EXACT []
is_a: GO:0006144 ! purine nucleobase metabolic process
@@ -290094,7 +293441,7 @@
id: GO:0046099
name: guanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important." [GOC:curators]
synonym: "guanine anabolism" EXACT []
synonym: "guanine biosynthesis" EXACT []
synonym: "guanine formation" EXACT []
@@ -290106,7 +293453,7 @@
id: GO:0046100
name: hypoxanthine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate." [GOC:go_curators]
+def: "The chemical reactions and pathways involving hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate." [GOC:curators]
synonym: "hypoxanthine metabolism" EXACT []
is_a: GO:0006144 ! purine nucleobase metabolic process
@@ -290114,7 +293461,7 @@
id: GO:0046101
name: hypoxanthine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate." [GOC:curators]
synonym: "hypoxanthine anabolism" EXACT []
synonym: "hypoxanthine biosynthesis" EXACT []
synonym: "hypoxanthine formation" EXACT []
@@ -290126,7 +293473,7 @@
id: GO:0046102
name: inosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:go_curators]
+def: "The chemical reactions and pathways involving inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:curators]
synonym: "inosine metabolism" EXACT []
is_a: GO:0046128 ! purine ribonucleoside metabolic process
@@ -290134,7 +293481,7 @@
id: GO:0046103
name: inosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of inosine, hypoxanthine riboside, a nucleoside found free but not in combination in nucleic acids except in the anticodons of some tRNAs." [GOC:curators]
synonym: "inosine anabolism" EXACT []
synonym: "inosine biosynthesis" EXACT []
synonym: "inosine formation" EXACT []
@@ -290146,7 +293493,7 @@
id: GO:0046104
name: thymidine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:curators]
synonym: "deoxyribosylthymine metabolic process" EXACT []
synonym: "deoxyribosylthymine metabolism" EXACT []
synonym: "thymidine metabolism" EXACT []
@@ -290156,7 +293503,7 @@
id: GO:0046105
name: thymidine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA." [GOC:curators]
synonym: "deoxyribosylthymine biosynthesis" EXACT []
synonym: "deoxyribosylthymine biosynthetic process" EXACT []
synonym: "thymidine anabolism" EXACT []
@@ -290170,7 +293517,7 @@
id: GO:0046106
name: thymine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base." [GOC:curators]
synonym: "thymine anabolism" EXACT []
synonym: "thymine biosynthesis" EXACT []
synonym: "thymine formation" EXACT []
@@ -290182,7 +293529,7 @@
id: GO:0046107
name: uracil biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA." [GOC:curators]
synonym: "uracil anabolism" EXACT []
synonym: "uracil biosynthesis" EXACT []
synonym: "uracil formation" EXACT []
@@ -290194,7 +293541,7 @@
id: GO:0046108
name: uridine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways involving uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:curators]
synonym: "uridine metabolism" EXACT []
is_a: GO:0046131 ! pyrimidine ribonucleoside metabolic process
@@ -290202,7 +293549,7 @@
id: GO:0046109
name: uridine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of uridine, uracil riboside, a ribonucleoside very widely distributed but occurring almost entirely as phosphoric esters in ribonucleotides and ribonucleic acids." [GOC:curators]
synonym: "uridine anabolism" EXACT []
synonym: "uridine biosynthesis" EXACT []
synonym: "uridine formation" EXACT []
@@ -290214,7 +293561,7 @@
id: GO:0046110
name: xanthine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways involving xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:curators]
synonym: "xanthine metabolism" EXACT []
is_a: GO:0006144 ! purine nucleobase metabolic process
@@ -290222,7 +293569,7 @@
id: GO:0046111
name: xanthine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids." [GOC:curators]
synonym: "xanthine anabolism" EXACT []
synonym: "xanthine biosynthesis" EXACT []
synonym: "xanthine formation" EXACT []
@@ -290257,7 +293604,7 @@
id: GO:0046114
name: guanosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of guanine, guanine riboside, a nucleoside with a wide species distribution." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of guanine, guanine riboside, a nucleoside with a wide species distribution." [GOC:curators]
synonym: "guanosine anabolism" EXACT []
synonym: "guanosine biosynthesis" EXACT []
synonym: "guanosine formation" EXACT []
@@ -290270,7 +293617,7 @@
name: guanosine catabolic process
namespace: biological_process
alt_id: GO:0006160
-def: "The chemical reactions and pathways resulting in the breakdown of guanine, guanine riboside, a nucleoside with a wide species distribution." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of guanine, guanine riboside, a nucleoside with a wide species distribution." [GOC:curators]
synonym: "guanosine breakdown" EXACT []
synonym: "guanosine catabolism" EXACT []
synonym: "guanosine degradation" EXACT []
@@ -290325,26 +293672,30 @@
[Term]
id: GO:0046120
-name: deoxyribonucleoside biosynthetic process
+name: 2'-deoxyribonucleoside biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside)." [GOC:ai]
synonym: "deoxyribonucleoside anabolism" EXACT []
synonym: "deoxyribonucleoside biosynthesis" EXACT []
+synonym: "deoxyribonucleoside biosynthetic process" EXACT []
synonym: "deoxyribonucleoside formation" EXACT []
synonym: "deoxyribonucleoside synthesis" EXACT []
-is_a: GO:0009120 ! deoxyribonucleoside metabolic process
+is_a: GO:0009120 ! 2'-deoxyribonucleoside metabolic process
is_a: GO:0009163 ! nucleoside biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0046121
-name: deoxyribonucleoside catabolic process
+name: 2'-deoxyribonucleoside catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside)." [GOC:ai]
synonym: "deoxyribonucleoside breakdown" EXACT []
+synonym: "deoxyribonucleoside catabolic process" EXACT []
synonym: "deoxyribonucleoside catabolism" EXACT []
synonym: "deoxyribonucleoside degradation" EXACT []
-is_a: GO:0009120 ! deoxyribonucleoside metabolic process
+is_a: GO:0009120 ! 2'-deoxyribonucleoside metabolic process
is_a: GO:0009164 ! nucleoside catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0046122
@@ -290352,7 +293703,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving any one of a family of organic molecules consisting of a purine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside)." [GOC:ai]
synonym: "purine deoxyribonucleoside metabolism" EXACT []
-is_a: GO:0009120 ! deoxyribonucleoside metabolic process
is_a: GO:0042278 ! purine nucleoside metabolic process
[Term]
@@ -290365,7 +293715,6 @@
synonym: "purine deoxyribonucleoside formation" EXACT []
synonym: "purine deoxyribonucleoside synthesis" EXACT []
is_a: GO:0042451 ! purine nucleoside biosynthetic process
-is_a: GO:0046120 ! deoxyribonucleoside biosynthetic process
is_a: GO:0046122 ! purine deoxyribonucleoside metabolic process
[Term]
@@ -290377,7 +293726,6 @@
synonym: "purine deoxyribonucleoside catabolism" EXACT []
synonym: "purine deoxyribonucleoside degradation" EXACT []
is_a: GO:0006152 ! purine nucleoside catabolic process
-is_a: GO:0046121 ! deoxyribonucleoside catabolic process
is_a: GO:0046122 ! purine deoxyribonucleoside metabolic process
[Term]
@@ -290387,7 +293735,7 @@
def: "The chemical reactions and pathways involving any one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside)." [GOC:ai]
synonym: "pyrimidine deoxyribonucleoside metabolism" EXACT []
is_a: GO:0006213 ! pyrimidine nucleoside metabolic process
-is_a: GO:0009120 ! deoxyribonucleoside metabolic process
+is_a: GO:0009120 ! 2'-deoxyribonucleoside metabolic process
[Term]
id: GO:0046126
@@ -290398,7 +293746,7 @@
synonym: "pyrimidine deoxyribonucleoside biosynthesis" EXACT []
synonym: "pyrimidine deoxyribonucleoside formation" EXACT []
synonym: "pyrimidine deoxyribonucleoside synthesis" EXACT []
-is_a: GO:0046120 ! deoxyribonucleoside biosynthetic process
+is_a: GO:0046120 ! 2'-deoxyribonucleoside biosynthetic process
is_a: GO:0046125 ! pyrimidine deoxyribonucleoside metabolic process
is_a: GO:0046134 ! pyrimidine nucleoside biosynthetic process
@@ -290410,7 +293758,7 @@
synonym: "pyrimidine deoxyribonucleoside breakdown" EXACT []
synonym: "pyrimidine deoxyribonucleoside catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside degradation" EXACT []
-is_a: GO:0046121 ! deoxyribonucleoside catabolic process
+is_a: GO:0046121 ! 2'-deoxyribonucleoside catabolic process
is_a: GO:0046125 ! pyrimidine deoxyribonucleoside metabolic process
is_a: GO:0046135 ! pyrimidine nucleoside catabolic process
@@ -290842,23 +294190,27 @@
name: alcohol catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [GOC:ai]
+subset: gocheck_do_not_annotate
synonym: "alcohol breakdown" EXACT []
synonym: "alcohol catabolism" EXACT []
synonym: "alcohol degradation" EXACT []
is_a: GO:0006066 ! alcohol metabolic process
is_a: GO:0044282 ! small molecule catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
[Term]
id: GO:0046165
name: alcohol biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom." [GOC:ai]
+subset: gocheck_do_not_annotate
synonym: "alcohol anabolism" EXACT []
synonym: "alcohol biosynthesis" EXACT []
synonym: "alcohol formation" EXACT []
synonym: "alcohol synthesis" EXACT []
is_a: GO:0006066 ! alcohol metabolic process
is_a: GO:0044283 ! small molecule biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
[Term]
id: GO:0046166
@@ -291311,6 +294663,10 @@
synonym: "spermidine degradation" EXACT []
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0008216 ! spermidine metabolic process
+property_value: skos:broadMatch MetaCyc:PWY-6117
+property_value: skos:broadMatch MetaCyc:PWY-6440
+property_value: skos:broadMatch MetaCyc:PWY-6441
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0046204
@@ -291360,6 +294716,10 @@
synonym: "spermine degradation" EXACT []
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0008215 ! spermine metabolic process
+property_value: skos:broadMatch MetaCyc:PWY-6117
+property_value: skos:broadMatch MetaCyc:PWY-6440
+property_value: skos:broadMatch MetaCyc:PWY-6441
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0046209
@@ -291659,7 +295019,7 @@
id: GO:0046233
name: obsolete 3-hydroxyphenylacetate biosynthetic process
namespace: biological_process
-def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 3-hydroxyphenylacetate, 1,3-benzenediol monoacetate, also known as resorcinol monoacetate." [GOC:curator]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 3-hydroxyphenylacetate, 1,3-benzenediol monoacetate, also known as resorcinol monoacetate." [GOC:curators]
comment: This term was made obsolete because 3-hydroxyphenylacetate is not synthesized by living organisms and GO does not cover non-biological processes.
synonym: "3-hydroxyphenylacetate anabolism" EXACT []
synonym: "3-hydroxyphenylacetate biosynthesis" EXACT []
@@ -292067,10 +295427,13 @@
synonym: "thiocyanate breakdown" EXACT []
synonym: "thiocyanate catabolism" EXACT []
synonym: "thiocyanate degradation" EXACT []
+xref: MetaCyc:P581-PWY
+xref: MetaCyc:PWY-743
is_a: GO:0018969 ! thiocyanate metabolic process
-is_a: GO:0042178 ! xenobiotic catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
-is_a: GO:0044282 ! small molecule catabolic process
+property_value: skos:narrowMatch MetaCyc:P581-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-743
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0046266
@@ -292457,6 +295820,10 @@
is_a: GO:0009441 ! glycolate metabolic process
is_a: GO:0034310 ! primary alcohol catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
+property_value: skos:broadMatch MetaCyc:GLYCOLATEMET-PWY
+property_value: skos:broadMatch MetaCyc:GLYOXDEG-PWY
+property_value: skos:broadMatch MetaCyc:PWY-8576
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0046297
@@ -293236,21 +296603,22 @@
[Term]
id: GO:0046357
-name: galactarate biosynthetic process
+name: D-galactarate biosynthetic process
namespace: biological_process
alt_id: GO:0042872
def: "The chemical reactions and pathways resulting in the formation of galactarate, the anion of galactaric acid." [GOC:pr, ISBN:0198506732]
synonym: "D-galactarate anabolism" RELATED []
-synonym: "D-galactarate biosynthesis" RELATED []
-synonym: "D-galactarate biosynthetic process" RELATED []
+synonym: "D-galactarate biosynthesis" EXACT []
synonym: "D-galactarate formation" RELATED []
-synonym: "D-galactarate synthesis" RELATED []
+synonym: "D-galactarate synthesis" EXACT []
synonym: "galactarate anabolism" EXACT []
synonym: "galactarate biosynthesis" EXACT []
synonym: "galactarate formation" EXACT []
synonym: "galactarate synthesis" EXACT []
+is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0019578 ! aldaric acid biosynthetic process
is_a: GO:0019580 ! galactarate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0046358
@@ -293626,20 +296994,25 @@
[Term]
id: GO:0046392
-name: galactarate catabolic process
+name: D-galactarate catabolic process
namespace: biological_process
alt_id: GO:0019582
-def: "The chemical reactions and pathways resulting in the breakdown of galactarate, the anion of galactaric acid." [GOC:ai, GOC:pr]
+def: "The chemical reactions and pathways resulting in the breakdown of D-galactarate, the anion of galactaric acid." [GOC:ai, GOC:pr]
synonym: "D-galactarate breakdown" RELATED []
-synonym: "D-galactarate catabolic process" RELATED []
synonym: "D-galactarate catabolism" RELATED []
synonym: "D-galactarate degradation" RELATED []
synonym: "galactarate breakdown" EXACT []
synonym: "galactarate catabolism" EXACT []
synonym: "galactarate degradation" EXACT []
xref: MetaCyc:GALACTARDEG-PWY
+xref: MetaCyc:PWY-6497
+is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019579 ! aldaric acid catabolic process
is_a: GO:0019580 ! galactarate metabolic process
+property_value: skos:narrowMatch MetaCyc:GALACTARDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-6497
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
[Term]
id: GO:0046394
@@ -293854,7 +297227,7 @@
id: GO:0046411
name: 2-keto-3-deoxygluconate transmembrane transport
namespace: biological_process
-def: "The process in which 2-keto-3-deoxygluconate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:go_curators]
+def: "The process in which 2-keto-3-deoxygluconate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:curators]
synonym: "2-keto-3-deoxygluconate transport" RELATED []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015749 ! monosaccharide transmembrane transport
@@ -294062,9 +297435,25 @@
xref: EC:2.5.1.74
xref: MetaCyc:RXN-11047
xref: RHEA:26478
+xref: RHEA:30099
+xref: RHEA:33211
+xref: RHEA:44800
+xref: RHEA:44804
+xref: RHEA:44808
+xref: RHEA:44812
+xref: RHEA:44816
+xref: RHEA:44820
is_a: GO:0004659 ! prenyltransferase activity
property_value: skos:exactMatch EC:2.5.1.74
property_value: skos:exactMatch RHEA:26478
+property_value: skos:narrowMatch RHEA:30099
+property_value: skos:narrowMatch RHEA:33211
+property_value: skos:narrowMatch RHEA:44800
+property_value: skos:narrowMatch RHEA:44804
+property_value: skos:narrowMatch RHEA:44808
+property_value: skos:narrowMatch RHEA:44812
+property_value: skos:narrowMatch RHEA:44816
+property_value: skos:narrowMatch RHEA:44820
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29428" xsd:anyURI
[Term]
@@ -294152,12 +297541,15 @@
[Term]
id: GO:0046436
-name: D-alanine metabolic process
+name: obsolete D-alanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving D-alanine, the D-enantiomer of the amino acid alanine, i.e. (2R)-2-aminopropanoic acid." [GOC:ai, GOC:jsg]
+def: "OBSOLETE. The chemical reactions and pathways involving D-alanine, the D-enantiomer of the amino acid alanine, i.e. (2R)-2-aminopropanoic acid." [GOC:ai, GOC:jsg]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "D-alanine metabolism" EXACT []
-is_a: GO:0006522 ! alanine metabolic process
-is_a: GO:0046416 ! D-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
+consider: GO:0030632
+consider: GO:0055130
[Term]
id: GO:0046437
@@ -294184,13 +297576,15 @@
[Term]
id: GO:0046439
-name: L-cysteine metabolic process
+name: obsolete L-cysteine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [GOC:ai, GOC:jsg, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways involving L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid." [GOC:ai, GOC:jsg, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "L-cysteine metabolism" EXACT []
-is_a: GO:0006534 ! cysteine metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0019344
+consider: GO:0019448
[Term]
id: GO:0046440
@@ -294673,7 +298067,7 @@
id: GO:0046482
name: para-aminobenzoic acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving para-aminobenzoic acid, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [ISBN:0198506732, PMID:11377864, PMID:11960743]
+def: "The chemical reactions and pathways involving para-aminobenzoic acid, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [PMID:11960743]
synonym: "4-aminobenzoic acid metabolic process" EXACT []
synonym: "4-aminobenzoic acid metabolism" EXACT []
synonym: "p-aminobenzoic acid metabolic process" EXACT []
@@ -294748,7 +298142,8 @@
synonym: "phosphoinositide metabolism" EXACT []
synonym: "PtdIns metabolic process" EXACT []
synonym: "PtdIns metabolism" EXACT []
-is_a: GO:0006650 ! glycerophospholipid metabolic process
+is_a: GO:0006793 ! phosphorus metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
id: GO:0046490
@@ -294835,15 +298230,13 @@
[Term]
id: GO:0046498
-name: S-adenosylhomocysteine metabolic process
+name: obsolete S-adenosylhomocysteine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving S-adenosylhomocysteine; the L-enantiomer is formed from S-adenosylmethionine and is a strong inhibitor of S-adenosylmethionine-mediated methylation reactions. It can be cleaved to form adenosine and homocysteine." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving S-adenosylhomocysteine; the L-enantiomer is formed from S-adenosylmethionine and is a strong inhibitor of S-adenosylmethionine-mediated methylation reactions. It can be cleaved to form adenosine and homocysteine." [ISBN:0198506732]
+comment: The reason for obsoletion is that the terms represent molecular functions and not biological processes.
synonym: "S-adenosylhomocysteine metabolism" EXACT []
-is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0006790 ! sulfur compound metabolic process
-is_a: GO:0046128 ! purine ribonucleoside metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15179" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0046499
@@ -294858,7 +298251,7 @@
id: GO:0046500
name: S-adenosylmethionine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism." [GOC:curators, ISBN:0198506732]
synonym: "S-adenosyl methionine metabolic process" EXACT []
synonym: "S-adenosyl methionine metabolism" EXACT []
synonym: "S-adenosylmethionine metabolism" EXACT []
@@ -294981,9 +298374,15 @@
xref: KEGG_REACTION:R02691
xref: MetaCyc:2.4.1.46-RXN
xref: RHEA:14945
+xref: RHEA:48480
+xref: RHEA:48492
+xref: RHEA:48496
is_a: GO:0035250 ! UDP-galactosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.46
property_value: skos:exactMatch RHEA:14945
+property_value: skos:narrowMatch RHEA:48480
+property_value: skos:narrowMatch RHEA:48492
+property_value: skos:narrowMatch RHEA:48496
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -295055,11 +298454,14 @@
[Term]
id: GO:0046516
-name: hypusine metabolic process
+name: obsolete hypusine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving hypusine, N6-(4-amino-2-hydroxybutyl)-L-lysine." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving hypusine, N6-(4-amino-2-hydroxybutyl)-L-lysine." [GOC:ai]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "hypusine metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0008612
[Term]
id: GO:0046517
@@ -295153,8 +298555,8 @@
xref: EC:5.3.1.23
xref: KEGG_REACTION:R04420
xref: MetaCyc:5.3.1.23-RXN
-xref: Reactome:R-HSA-1237096 "Methylthio-ribose-P = Methylthio-ribulose-P"
-xref: Reactome:R-HSA-1299507 "Methylthio-ribulose-P = Methylthio-ribose-P"
+xref: Reactome:R-HSA-1237096 "Methylthio-ribose-P => Methylthio-ribulose-P"
+xref: Reactome:R-HSA-1299507 "Methylthio-ribulose-P => Methylthio-ribose-P"
xref: RHEA:19989
is_a: GO:0016861 ! intramolecular oxidoreductase activity, interconverting aldoses and ketoses
property_value: skos:exactMatch EC:5.3.1.23
@@ -295262,7 +298664,7 @@
name: regulation of photoreceptor cell differentiation
namespace: biological_process
alt_id: GO:0045673
-def: "Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:curators]
synonym: "regulation of photoreceptor differentiation" EXACT []
is_a: GO:0045664 ! regulation of neuron differentiation
intersection_of: GO:0065007 ! biological regulation
@@ -295274,7 +298676,7 @@
name: negative regulation of photoreceptor cell differentiation
namespace: biological_process
alt_id: GO:0045674
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:curators]
synonym: "down regulation of photoreceptor cell differentiation" EXACT []
synonym: "down regulation of photoreceptor differentiation" EXACT []
synonym: "down-regulation of photoreceptor cell differentiation" EXACT []
@@ -295296,7 +298698,7 @@
name: positive regulation of photoreceptor cell differentiation
namespace: biological_process
alt_id: GO:0045675
-def: "Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:go_curators]
+def: "Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." [GOC:curators]
synonym: "activation of photoreceptor cell differentiation" NARROW []
synonym: "activation of photoreceptor differentiation" NARROW []
synonym: "positive regulation of photoreceptor differentiation" EXACT []
@@ -295628,9 +299030,17 @@
xref: EC:3.2.1.139
xref: MetaCyc:3.2.1.139-RXN
xref: RHEA:20005
+xref: RHEA:84887
+xref: RHEA:84891
+xref: RHEA:84895
+xref: RHEA:84899
is_a: GO:0046574 ! glucuronidase activity
property_value: skos:exactMatch EC:3.2.1.139
property_value: skos:exactMatch RHEA:20005
+property_value: skos:narrowMatch RHEA:84887
+property_value: skos:narrowMatch RHEA:84891
+property_value: skos:narrowMatch RHEA:84895
+property_value: skos:narrowMatch RHEA:84899
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30698" xsd:anyURI
@@ -295826,14 +299236,15 @@
id: GO:0046572
name: versicolorin B synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: versiconal = versicolorin B + H2O." [MetaCyc:RXN-9494, PMID:8784203]
+def: "Catalysis of the reaction: (2S-3S)-versiconal hemiacetal = versicolorin B + H2O." [PMID:8784203, RHEA:33859]
xref: EC:4.2.1.143
xref: MetaCyc:RXN-9494
xref: RHEA:33859
-is_a: GO:0016835 ! carbon-oxygen lyase activity
+is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.143
property_value: skos:exactMatch RHEA:33859
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31620" xsd:anyURI
[Term]
id: GO:0046573
@@ -295880,9 +299291,17 @@
xref: EC:1.1.3.20
xref: MetaCyc:RXN-4444
xref: RHEA:22756
+xref: RHEA:69484
+xref: RHEA:69488
+xref: RHEA:76475
+xref: RHEA:76479
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.1.3.20
property_value: skos:exactMatch RHEA:22756
+property_value: skos:narrowMatch RHEA:69484
+property_value: skos:narrowMatch RHEA:69488
+property_value: skos:narrowMatch RHEA:76475
+property_value: skos:narrowMatch RHEA:76479
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -296374,7 +299793,7 @@
id: GO:0046618
name: xenobiotic export from cell
namespace: biological_process
-def: "The directed movement of a xenobiotic from a cell, into the extracellular region. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
+def: "The directed movement of a xenobiotic from a cell, into the extracellular region. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:curators, GOC:krc]
synonym: "drug export" RELATED []
synonym: "xenobiotic export" RELATED []
is_a: GO:0042908 ! xenobiotic transport
@@ -296437,21 +299856,23 @@
synonym: "sphingolipid flippase activity" EXACT []
synonym: "sphingolipid floppase activity (cytosolic to exoplasmic leaflet)" EXACT []
synonym: "sphingolipid-translocating ATPase activity" RELATED []
-is_a: GO:0046624 ! sphingolipid transporter activity
+is_a: GO:0046624 ! sphingolipid intramembrane carrier activity
is_a: GO:0140328 ! floppase activity
relationship: part_of GO:0099039 ! sphingolipid translocation
property_value: skos:broadMatch RHEA:66132
[Term]
id: GO:0046624
-name: sphingolipid transporter activity
+name: sphingolipid intramembrane carrier activity
namespace: molecular_function
def: "Enables the directed movement of sphingolipids into, out of or within a cell, or between cells. Sphingolipids are a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid)." [GOC:ai, ISBN:0198506732]
subset: gocheck_do_not_annotate
+synonym: "sphingolipid intramembrane transporter activity" BROAD []
xref: Reactome:R-HSA-9695890 "SPNS2,MFSD2B transport S1P from cytosol to extracellular region"
xref: Reactome:R-HSA-9843721 "ABCC1,ABCG2 transport C18-S1P to extracellular region"
-is_a: GO:0005319 ! lipid transporter activity
+is_a: GO:0140303 ! intramembrane lipid carrier activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31121" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
[Term]
id: GO:0046625
@@ -297133,7 +300554,9 @@
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC:ai, GOC:ef]
subset: goslim_chembl
synonym: "antibiotic susceptibility/resistance" RELATED []
+xref: Reactome:R-HSA-9638771 "Action of antimicrobials"
xref: Reactome:R-HSA-9639775 "Antimicrobial action and antimicrobial resistance in Mtb"
+xref: Reactome:R-HSA-9913143 "Antimicrobial resistance"
is_a: GO:0042221 ! response to chemical
[Term]
@@ -297316,7 +300739,7 @@
def: "A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens." [PMID:11706042, PMID:9665271]
comment: Note that this term should not be used to refer to CD14 alone, but the multiprotein receptor complex that it is part of.
synonym: "LPS receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
is_a: GO:0098796 ! membrane protein complex
[Term]
@@ -298098,7 +301521,7 @@
id: GO:0046785
name: microtubule polymerization
namespace: biological_process
-def: "The addition of tubulin heterodimers to one or both ends of a microtubule." [GOC:ai, GOC:go_curators]
+def: "The addition of tubulin heterodimers to one or both ends of a microtubule." [GOC:ai, GOC:curators]
synonym: "microtubule assembly" EXACT []
synonym: "microtubule formation" RELATED []
is_a: GO:0031109 ! microtubule polymerization or depolymerization
@@ -298390,12 +301813,12 @@
[Term]
id: GO:0046820
-name: 4-amino-4-deoxychorismate synthase activity
+name: aminodeoxychorismate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamine + chorismate = 4-amino-4-deoxychorismate + L-glutamate. It is composed of two enzymatic activities (which may be present on one or two polypeptides); the first is a glutaminase which yields ammonia from glutamine, releasing glutamate. The ammonia is used by the second activity which catalyzes the amination of chorismate to form 4-amino-4-deoxychorismate." [EC:2.6.1.85, RHEA:11672]
comment: Note that the name 'para-aminobenzoic acid synthase' was initially given to the 'aminodeoxychorismate synthase' activity before the additional 4-amino-4-deoxychorismate lyase activity was discovered. It is the lyase activity that actually produces para-aminobenzoic acid from 4-amino-4-deoxychorismate.
+synonym: "4-amino-4-deoxychorismate synthase activity" EXACT []
synonym: "ADC synthase activity" RELATED [EC:2.6.1.85]
-synonym: "aminodeoxychorismate synthase activity" RELATED []
synonym: "chorismate:L-glutamine amido-ligase activity" RELATED [EC:2.6.1.85]
synonym: "p-aminobenzoate synthetase" RELATED []
synonym: "PabB activity" RELATED [EC:2.6.1.85]
@@ -298409,6 +301832,7 @@
property_value: skos:exactMatch EC:2.6.1.85
property_value: skos:exactMatch RHEA:11672
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0046821
@@ -298811,7 +302235,7 @@
synonym: "phosphoinositide phosphorylation" NARROW []
synonym: "PIP biosynthesis" EXACT []
synonym: "PtdInsP biosynthesis" EXACT []
-is_a: GO:0006661 ! phosphatidylinositol biosynthetic process
+is_a: GO:0046474 ! glycerophospholipid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14184" xsd:anyURI
[Term]
@@ -299339,10 +302763,14 @@
xref: MetaCyc:2.7.4.10-RXN
xref: Reactome:R-HSA-1008248 "Adenylate Kinase 3 is a GTP-AMP phosphotransferase"
xref: RHEA:13749
+xref: RHEA:29863
+xref: RHEA:29867
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch EC:2.7.4.10
property_value: skos:exactMatch RHEA:13749
+property_value: skos:narrowMatch RHEA:29863
+property_value: skos:narrowMatch RHEA:29867
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -299488,7 +302916,7 @@
id: GO:0046912
name: acyltransferase activity, acyl groups converted into alkyl on transfer
namespace: molecular_function
-def: "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer." [GOC:jl]
+def: "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer." [EC:2.3.3.-, GOC:jl]
synonym: "acyltransferase, acyl groups converted into alkyl on transfer" EXACT []
synonym: "transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer" EXACT []
xref: EC:2.3.3.-
@@ -299564,7 +302992,7 @@
synonym: "alpha(1,3)-fucosyltransferase activity" EXACT []
synonym: "alpha-(1,3)-fucosyltransferase activity" EXACT []
synonym: "alpha-1,3-fucosyltransferase activity" EXACT []
-xref: Reactome:R-HSA-9603984 "FUT4,5,9,(10,11) transfer Fuc to Type 2 chains to form LeX"
+xref: Reactome:R-HSA-9603984 "FUT4,5,9 transfer Fuc to Type 2 chains to form LeX"
xref: Reactome:R-HSA-9605609 "FUT3 transfers Fuc to Type 1 MSGG to form sLeA"
xref: Reactome:R-HSA-9605644 "FUT3 transfers Fuc to Type 1 DSGG to form dsLeA"
xref: Reactome:R-HSA-9605682 "FUT3,5,6,7 transfers Fuc to Type 2 MSGG to form sLeX"
@@ -299595,7 +303023,6 @@
xref: Reactome:R-HSA-5173192 "POFUT2 transfers fucose to TSR domain-containing proteins"
is_a: GO:0008417 ! fucosyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
-relationship: part_of GO:0036066 ! protein O-linked glycosylation via fucose
property_value: skos:exactMatch EC:2.4.1.221
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -299797,9 +303224,13 @@
xref: Reactome:R-HSA-9712084 "PI3K synthesizes PIP3 downstream of ALK mutants"
xref: Reactome:R-HSA-9860816 "Phospho-PI3K in p-Y713-PECAM1:CDH5:PIK3CA,B,D:p-Y464-PIK3R2:p-Y801,Y1054,Y1175-KDR:p-Y1063,Y1230-FLT4:CTNNB1 phosphorylates phosphoinositol-4,5-bisphosphate to yield phosphoinositol-3,4,5-trisphosphate"
xref: RHEA:21292
+xref: RHEA:43396
+xref: RHEA:55632
is_a: GO:0052742 ! phosphatidylinositol kinase activity
property_value: skos:exactMatch EC:2.7.1.153
property_value: skos:exactMatch RHEA:21292
+property_value: skos:narrowMatch RHEA:43396
+property_value: skos:narrowMatch RHEA:55632
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28336" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -299969,7 +303400,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism." [ISBN:0198506732]
comment: The reason for obsoletion is that this term is redundant to GO:1902224, ketone body metabolic process
synonym: "cellular ketone body metabolism" EXACT []
-xref: Reactome:R-HSA-74182 "Ketone body metabolism"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI
is_obsolete: true
replaced_by: GO:1902224
@@ -300138,7 +303568,7 @@
synonym: "3'-phosphoadenosine 5'-phosphosulphate transporter activity" EXACT []
synonym: "adenosine 3'-phosphate 5'-phosphosulfate transmembrane transporter activity" EXACT []
synonym: "PAPS transporter activity" EXACT []
-xref: Reactome:R-HSA-741449 "SLC35B2,3 transport cytosolic PAPS to Golgi lumen"
+xref: Reactome:R-HSA-741449 "SLC35B2,3 exchange cytosolic PAPS with Golgi PAP"
is_a: GO:0000295 ! adenine nucleotide transmembrane transporter activity
is_a: GO:0005346 ! purine ribonucleotide transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
@@ -300170,6 +303600,7 @@
namespace: biological_process
def: "The directed movement of substances from the cytosol to the endoplasmic reticulum of a cell." [GOC:ai]
synonym: "cytosol to ER transport" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
is_a: GO:0055085 ! transmembrane transport
@@ -300287,6 +303718,8 @@
synonym: "histone methyltransferase activity (H3-K27 specific)" EXACT []
synonym: "histone-H3K27 methyltransferase activity" EXACT []
xref: Reactome:R-HSA-3240295 "PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter"
+xref: Reactome:R-HSA-9764932 "PRC2 (EZH2) core complex methylates nucleosomes at CDH1 gene promoter"
+xref: Reactome:R-HSA-9909631 "Trimethylation of CD274 gene promoter by EZH2"
is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
is_a: GO:0140938 ! histone H3 methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24337" xsd:anyURI
@@ -300948,10 +304381,24 @@
xref: EC:1.1.1.201
xref: MetaCyc:1.1.1.201-RXN
xref: RHEA:20233
+xref: RHEA:68656
+xref: RHEA:68860
+xref: RHEA:68976
+xref: RHEA:68980
+xref: RHEA:69436
+xref: RHEA:69452
+xref: RHEA:69456
xref: Wikipedia:7beta-hydroxysteroid_dehydrogenase_(NADP+)
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.201
property_value: skos:exactMatch RHEA:20233
+property_value: skos:narrowMatch RHEA:68656
+property_value: skos:narrowMatch RHEA:68860
+property_value: skos:narrowMatch RHEA:68976
+property_value: skos:narrowMatch RHEA:68980
+property_value: skos:narrowMatch RHEA:69436
+property_value: skos:narrowMatch RHEA:69452
+property_value: skos:narrowMatch RHEA:69456
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -301330,9 +304777,11 @@
xref: EC:1.1.1.53
xref: MetaCyc:1.1.1.53-RXN
xref: RHEA:22400
+xref: RHEA:42004
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.53
property_value: skos:exactMatch RHEA:22400
+property_value: skos:narrowMatch RHEA:42004
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -301348,6 +304797,7 @@
xref: EC:1.1.1.64 {status="skos:exactMatch"}
xref: KEGG_REACTION:R01838
xref: MetaCyc:1.1.1.64-RXN
+xref: Reactome:R-HSA-193064 "HSD17B3-like proteins reducde ANDST to TEST"
xref: RHEA:14981
xref: Wikipedia:Testosterone_17beta-dehydrogenase_(NADP+)
is_a: GO:0072582 ! 17-beta-hydroxysteroid dehydrogenase (NADP+) activity
@@ -301703,9 +305153,33 @@
xref: Reactome:R-HSA-9020271 "GPX4-2 reduces 17(R)-Hp-DHA to 17(R)-HDHA"
xref: Reactome:R-HSA-9020273 "GPX4-2 reduces 17(S)-Hp-DHA to 17(S)-HDHA"
xref: RHEA:19057
+xref: RHEA:48620
+xref: RHEA:48888
+xref: RHEA:50708
+xref: RHEA:75835
+xref: RHEA:76687
+xref: RHEA:76691
+xref: RHEA:76695
+xref: RHEA:76699
+xref: RHEA:76703
+xref: RHEA:76707
+xref: RHEA:76711
+xref: RHEA:76715
is_a: GO:0004601 ! peroxidase activity
property_value: skos:exactMatch EC:1.11.1.12
property_value: skos:exactMatch RHEA:19057
+property_value: skos:narrowMatch RHEA:48620
+property_value: skos:narrowMatch RHEA:48888
+property_value: skos:narrowMatch RHEA:50708
+property_value: skos:narrowMatch RHEA:75835
+property_value: skos:narrowMatch RHEA:76687
+property_value: skos:narrowMatch RHEA:76691
+property_value: skos:narrowMatch RHEA:76695
+property_value: skos:narrowMatch RHEA:76699
+property_value: skos:narrowMatch RHEA:76703
+property_value: skos:narrowMatch RHEA:76707
+property_value: skos:narrowMatch RHEA:76711
+property_value: skos:narrowMatch RHEA:76715
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23399" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -302698,6 +306172,7 @@
synonym: "P2C reductase activity" RELATED [EC:1.5.1.21]
xref: EC:1.5.1.21
xref: MetaCyc:RXN-8166
+xref: Reactome:R-HSA-5693347 "CRYM reduces P2C to PPCA"
xref: RHEA:12524
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.5.1.21
@@ -302730,7 +306205,6 @@
synonym: "thiomorpholine-3-carboxylate:NAD(P)+ 5,6-oxidoreductase activity" RELATED [EC:1.5.1.25]
xref: EC:1.5.1.25
xref: MetaCyc:1.5.1.25-RXN
-xref: Reactome:R-HSA-5693347 "CRYM reduces P2C to PPCA"
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.5.1.25
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -303156,7 +306630,7 @@
id: GO:0047151
name: tRNA (uracil(54)-C5)-methyltransferase activity, 5,10-methylenetetrahydrofolate-dependent
namespace: molecular_function
-def: "Catalysis of the reaction: 5,10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH + H+ = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD+." [EC:2.1.1.74, MetaCyc:2.1.1.74-RXN]
+def: "Catalysis of the reaction: uridine54 in tRNA + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NAD(P)H + H+ = 5-methyluridine54 in tRNA + (6S)-5,6,7,8-tetrahydrofolate + NAD(P)+." [EC:2.1.1.74]
synonym: "5,10-methylenetetrahydrofolate:tRNA (uracil-5-)-methyltransferase activity" RELATED [EC:2.1.1.74]
synonym: "5,10-methylenetetrahydrofolate:tRNA-UPsiC (uracil-5-)-methyl-transferase activity" RELATED [EC:2.1.1.74]
synonym: "folate-dependent ribothymidyl synthase activity" RELATED [EC:2.1.1.74]
@@ -303167,9 +306641,11 @@
xref: KEGG_REACTION:R03704
xref: MetaCyc:2.1.1.74-RXN
xref: RHEA:16873
+xref: RHEA:62372
is_a: GO:0016300 ! tRNA (uridine) methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.74
-property_value: skos:exactMatch RHEA:16873
+property_value: skos:narrowMatch RHEA:16873
+property_value: skos:narrowMatch RHEA:62372
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26118" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -303316,9 +306792,15 @@
xref: EC:2.3.1.25
xref: MetaCyc:PLASMALOGEN-SYNTHASE-RXN
xref: RHEA:10344
+xref: RHEA:37627
+xref: RHEA:37711
+xref: RHEA:37819
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.25
property_value: skos:exactMatch RHEA:10344
+property_value: skos:narrowMatch RHEA:37627
+property_value: skos:narrowMatch RHEA:37711
+property_value: skos:narrowMatch RHEA:37819
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -303426,9 +306908,13 @@
xref: EC:2.3.1.116
xref: MetaCyc:2.3.1.116-RXN
xref: RHEA:20085
+xref: RHEA:67336
+xref: RHEA:67340
is_a: GO:0050736 ! O-malonyltransferase activity
property_value: skos:exactMatch EC:2.3.1.116
property_value: skos:exactMatch RHEA:20085
+property_value: skos:narrowMatch RHEA:67336
+property_value: skos:narrowMatch RHEA:67340
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303440,9 +306926,19 @@
xref: EC:2.3.1.121
xref: MetaCyc:2.3.1.121-RXN
xref: RHEA:16245
+xref: RHEA:37631
+xref: RHEA:37635
+xref: RHEA:37755
+xref: RHEA:37759
+xref: RHEA:37763
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.121
property_value: skos:exactMatch RHEA:16245
+property_value: skos:narrowMatch RHEA:37631
+property_value: skos:narrowMatch RHEA:37635
+property_value: skos:narrowMatch RHEA:37755
+property_value: skos:narrowMatch RHEA:37759
+property_value: skos:narrowMatch RHEA:37763
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303547,9 +307043,15 @@
xref: MetaCyc:2.3.1.135-RXN
xref: Reactome:R-HSA-975608 "LRAT esterifies RBP2:atROL and FACYLs to atREs"
xref: RHEA:17469
+xref: RHEA:55320
+xref: RHEA:56244
+xref: RHEA:56248
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.135
property_value: skos:exactMatch RHEA:17469
+property_value: skos:narrowMatch RHEA:55320
+property_value: skos:narrowMatch RHEA:56244
+property_value: skos:narrowMatch RHEA:56248
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -303647,9 +307149,11 @@
xref: EC:2.3.1.149
xref: MetaCyc:2.3.1.149-RXN
xref: RHEA:11048
+xref: RHEA:41396
is_a: GO:0016407 ! acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.149
property_value: skos:exactMatch RHEA:11048
+property_value: skos:narrowMatch RHEA:41396
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303727,9 +307231,35 @@
xref: MetaCyc:2.3.1.23-RXN
xref: Reactome:R-HSA-1482794 "CL and 1-acyl LPC are converted to MLCL and PC by TAZ (IM) (Reversible)"
xref: RHEA:12937
+xref: RHEA:33359
+xref: RHEA:35987
+xref: RHEA:37475
+xref: RHEA:37515
+xref: RHEA:37559
+xref: RHEA:37563
+xref: RHEA:37703
+xref: RHEA:37707
+xref: RHEA:37803
+xref: RHEA:37855
+xref: RHEA:37859
+xref: RHEA:37863
+xref: RHEA:37867
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.23
property_value: skos:exactMatch RHEA:12937
+property_value: skos:narrowMatch RHEA:33359
+property_value: skos:narrowMatch RHEA:35987
+property_value: skos:narrowMatch RHEA:37475
+property_value: skos:narrowMatch RHEA:37515
+property_value: skos:narrowMatch RHEA:37559
+property_value: skos:narrowMatch RHEA:37563
+property_value: skos:narrowMatch RHEA:37703
+property_value: skos:narrowMatch RHEA:37707
+property_value: skos:narrowMatch RHEA:37803
+property_value: skos:narrowMatch RHEA:37855
+property_value: skos:narrowMatch RHEA:37859
+property_value: skos:narrowMatch RHEA:37863
+property_value: skos:narrowMatch RHEA:37867
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303843,9 +307373,19 @@
xref: KEGG_REACTION:R01319
xref: MetaCyc:2.3.1.62-RXN
xref: RHEA:10332
+xref: RHEA:74799
+xref: RHEA:74803
+xref: RHEA:74807
+xref: RHEA:74811
+xref: RHEA:74823
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.62
property_value: skos:exactMatch RHEA:10332
+property_value: skos:narrowMatch RHEA:74799
+property_value: skos:narrowMatch RHEA:74803
+property_value: skos:narrowMatch RHEA:74807
+property_value: skos:narrowMatch RHEA:74811
+property_value: skos:narrowMatch RHEA:74823
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303857,9 +307397,17 @@
xref: EC:2.3.1.63
xref: MetaCyc:2.3.1.63-RXN
xref: RHEA:23992
+xref: RHEA:37715
+xref: RHEA:37783
+xref: RHEA:37811
+xref: RHEA:37839
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.63
property_value: skos:exactMatch RHEA:23992
+property_value: skos:narrowMatch RHEA:37715
+property_value: skos:narrowMatch RHEA:37783
+property_value: skos:narrowMatch RHEA:37811
+property_value: skos:narrowMatch RHEA:37839
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303883,9 +307431,13 @@
xref: EC:2.3.1.67
xref: MetaCyc:2.3.1.67-RXN
xref: RHEA:18461
+xref: RHEA:37699
+xref: RHEA:37719
is_a: GO:0016413 ! O-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.67
property_value: skos:exactMatch RHEA:18461
+property_value: skos:narrowMatch RHEA:37699
+property_value: skos:narrowMatch RHEA:37719
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -303948,12 +307500,40 @@
xref: MetaCyc:RXNQT-4193
xref: Reactome:R-HSA-5696424 "AWAT1 transfers acyl group from acyl-CoA to ARACOH, forming wax esters"
xref: Reactome:R-HSA-8848582 "AWAT2 transfers PALM from PALM-CoA to HXOL, forming palmityl palmitate ester"
+xref: RHEA:38167
+xref: RHEA:38171
+xref: RHEA:38227
+xref: RHEA:38231
+xref: RHEA:38235
+xref: RHEA:38239
+xref: RHEA:38243
+xref: RHEA:38247
+xref: RHEA:38251
xref: RHEA:38443
+xref: RHEA:55288
+xref: RHEA:81783
+xref: RHEA:81803
+xref: RHEA:81807
+xref: RHEA:81811
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.75
property_value: skos:exactMatch MetaCyc:2.3.1.75-RXN
property_value: skos:exactMatch RHEA:38443
property_value: skos:narrowMatch MetaCyc:RXNQT-4193
+property_value: skos:narrowMatch RHEA:38167
+property_value: skos:narrowMatch RHEA:38171
+property_value: skos:narrowMatch RHEA:38227
+property_value: skos:narrowMatch RHEA:38231
+property_value: skos:narrowMatch RHEA:38235
+property_value: skos:narrowMatch RHEA:38239
+property_value: skos:narrowMatch RHEA:38243
+property_value: skos:narrowMatch RHEA:38247
+property_value: skos:narrowMatch RHEA:38251
+property_value: skos:narrowMatch RHEA:55288
+property_value: skos:narrowMatch RHEA:81783
+property_value: skos:narrowMatch RHEA:81803
+property_value: skos:narrowMatch RHEA:81807
+property_value: skos:narrowMatch RHEA:81811
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
[Term]
@@ -303967,16 +307547,20 @@
xref: EC:2.3.1.77
xref: MetaCyc:2.3.1.77-RXN
xref: RHEA:16897
+xref: RHEA:78195
+xref: RHEA:78199
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.77
property_value: skos:exactMatch RHEA:16897
+property_value: skos:narrowMatch RHEA:78195
+property_value: skos:narrowMatch RHEA:78199
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047198
name: L-cysteine-S-conjugate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-substituted L-cysteine + acetyl-CoA = S-substituted N-acetyl-L-cysteine + CoA + H+." [EC:2.3.1.80, RHEA:19213]
+def: "Catalysis of the reaction: S-substituted L-cysteine + acetyl-CoA = S-substituted N-acetyl-L-cysteine + CoA + H+." [RHEA:19213]
synonym: "acetyl-CoA:S-substituted L-cysteine N-acetyltransferase activity" RELATED [EC:2.3.1.80]
synonym: "cysteine-S-conjugate N-acetyltransferase activity" EXACT []
xref: EC:2.3.1.80
@@ -303984,9 +307568,13 @@
xref: MetaCyc:2.3.1.80-RXN
xref: Reactome:R-HSA-5433066 "Unknown NAT transfers COCH3 to AFXBO-C, AFNBO-C"
xref: RHEA:19213
+xref: RHEA:75511
+xref: RHEA:75523
is_a: GO:0140085 ! L-amino-acid N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.80
property_value: skos:exactMatch RHEA:19213
+property_value: skos:narrowMatch RHEA:75511
+property_value: skos:narrowMatch RHEA:75523
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -304008,7 +307596,7 @@
id: GO:0047200
name: tetrahydrodipicolinate N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H2O = L-2-acetamido-6-oxopimelate + CoA." [EC:2.3.1.89, RHEA:13085]
+def: "Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H2O = L-2-acetamido-6-oxopimelate + CoA." [RHEA:13085]
synonym: "acetyl-CoA:(S)-2,3,4,5-tetrahydrodipicolinate-2,6-dicarboxylate N2-acetyltransferase activity" RELATED [EC:2.3.1.89]
synonym: "acetyl-CoA:(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate 2-N-acetyltransferase activity" RELATED [EC:2.3.1.89]
synonym: "acetyl-CoA:L-2,3,4,5-tetrahydrodipicolinate N2-acetyltransferase activity" RELATED [EC:2.3.1.89]
@@ -304226,9 +307814,21 @@
xref: EC:2.4.1.115
xref: MetaCyc:2.4.1.115-RXN
xref: RHEA:20093
+xref: RHEA:60100
+xref: RHEA:61500
+xref: RHEA:61504
+xref: RHEA:61508
+xref: RHEA:61512
+xref: RHEA:74139
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.115
property_value: skos:exactMatch RHEA:20093
+property_value: skos:narrowMatch RHEA:60100
+property_value: skos:narrowMatch RHEA:61500
+property_value: skos:narrowMatch RHEA:61504
+property_value: skos:narrowMatch RHEA:61508
+property_value: skos:narrowMatch RHEA:61512
+property_value: skos:narrowMatch RHEA:74139
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -304411,7 +308011,6 @@
synonym: "uridine diphosphoacetylglucosamine-mucin beta(1->3)-acetylglucosaminyltransferase (elongating)" RELATED [EC:2.4.1.146]
xref: EC:2.4.1.146
xref: MetaCyc:2.4.1.146-RXN
-xref: Reactome:R-HSA-5617037 "POMGNT1 transfers GlcNAc from UDP-GlcNAc to Man-O-Ser-DAG1"
xref: Reactome:R-HSA-5617096 "Defective POMGNT1 does not transfer GlcNAc from UDP-GlcNAc to Man-O-Ser-DAG1"
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
@@ -304431,6 +308030,7 @@
synonym: "uridine diphosphoacetylglucosamine-mucin beta(1->3)-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.147]
xref: EC:2.4.1.147
xref: MetaCyc:2.4.1.147-RXN
+xref: Reactome:R-HSA-914010 "B3GNT6 transfers GlcNAc to Tn antigen"
xref: RHEA:46880
xref: RHEA:46884
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
@@ -304578,9 +308178,15 @@
xref: EC:2.4.1.165
xref: MetaCyc:2.4.1.165-RXN
xref: RHEA:81947
+xref: RHEA:81955
+xref: RHEA:81971
+xref: RHEA:82011
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.165
property_value: skos:exactMatch RHEA:81947
+property_value: skos:narrowMatch RHEA:81955
+property_value: skos:narrowMatch RHEA:81971
+property_value: skos:narrowMatch RHEA:82011
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18752" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -304671,10 +308277,10 @@
synonym: "uridine diphosphoacetylgalactosamine-chondroitin acetylgalactosaminyltransferase II activity" RELATED [EC:2.4.1.175]
xref: EC:2.4.1.175
xref: MetaCyc:RXN-16325
-xref: Reactome:R-HSA-1971482 "The addition of GalNAc to the terminal glucuronate residue forms chondroitin"
-xref: Reactome:R-HSA-1971487 "CHPF,CHSY3 transfer GalNAc to chondroitin"
+xref: Reactome:R-HSA-1971482 "CSGALNACTs transfer GalNAc to CS linker glycan"
+xref: Reactome:R-HSA-1971487 "Chondroitin polymerase complex transfers GalNAc to CS chain"
xref: Reactome:R-HSA-3595176 "Defective CHSY1 does not transfer GalNAc to chondroitin"
-xref: Reactome:R-HSA-9632033 "CHSY1 transfers GalNAc to chondroitin"
+xref: Reactome:R-HSA-9632033 "CSGALNACTs transfer GalNAc to CS chain"
is_a: GO:0008376 ! acetylgalactosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.175
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -305117,7 +308723,7 @@
id: GO:0047263
name: obsolete N-acylsphingosine galactosyltransferase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: ceramide + UDP-galactose = D-galactosylceramide + UDP." [GOC:curator]
+def: "OBSOLETE. Catalysis of the reaction: ceramide + UDP-galactose = D-galactosylceramide + UDP." [GOC:curators]
comment: The reason for obsoletion is that this term is equivalent to GO:0003851.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28173" xsd:anyURI
@@ -305550,6 +309156,7 @@
synonym: "monosialoganglioside sialyltransferase" EXACT [EC:2.4.3.2]
xref: EC:2.4.3.2
xref: MetaCyc:RXN-18256
+xref: Reactome:R-HSA-981497 "ST3GAL1-4 transfers sialic acid to the T antigen at the alpha 3 position"
xref: RHEA:52380
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.2
@@ -305585,10 +309192,20 @@
xref: KEGG_REACTION:R04635
xref: MetaCyc:2.4.99.7-RXN
xref: Reactome:R-HSA-981809 "ST6GALNAC3/4 transfers sialic acid to the sialyl T antigen to form the disialyl T antigen"
+xref: RHEA:48316
xref: RHEA:53896
+xref: RHEA:56088
+xref: RHEA:65280
+xref: RHEA:65284
+xref: RHEA:65288
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.7
property_value: skos:exactMatch RHEA:53896
+property_value: skos:narrowMatch RHEA:48316
+property_value: skos:narrowMatch RHEA:56088
+property_value: skos:narrowMatch RHEA:65280
+property_value: skos:narrowMatch RHEA:65284
+property_value: skos:narrowMatch RHEA:65288
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -305689,39 +309306,47 @@
id: GO:0047296
name: homospermidine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 putrescine = NH3 + sym-homospermidine." [EC:2.5.1.44]
+def: "Catalysis of the reaction: 2 putrescine = sym-homospermidine + NH4+." [RHEA:18645]
synonym: "putrescine:putrescine 4-aminobutyltransferase (ammonia-forming)" RELATED [EC:2.5.1.44]
-xref: EC:2.5.1.44
xref: MetaCyc:2.5.1.44-RXN
xref: RHEA:18645
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
-property_value: skos:exactMatch EC:2.5.1.44
+property_value: skos:broadMatch EC:2.5.1.44
property_value: skos:exactMatch RHEA:18645
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047297
-name: asparagine-oxo-acid transaminase activity
+name: L-asparagine:oxo-acid transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 2-oxo acid + L-asparagine = an amino acid + 2-oxosuccinamate." [RHEA:19813]
+def: "Catalysis of the reaction: L-asparagine + a 2-oxocarboxylate = 2-oxosuccinamate + an L-alpha-amino acid." [RHEA:19813]
synonym: "asparagine--oxo-acid aminotransferase activity" RELATED [EC:2.6.1.14]
synonym: "asparagine-keto acid aminotransferase activity" RELATED [EC:2.6.1.14]
synonym: "asparagine-oxo-acid aminotransferase activity" EXACT []
+synonym: "asparagine-oxo-acid transaminase activity" EXACT []
synonym: "L-asparagine:2-oxo-acid aminotransferase activity" RELATED [EC:2.6.1.14]
xref: EC:2.6.1.14
xref: MetaCyc:2.6.1.14-RXN
xref: RHEA:19813
-is_a: GO:0008483 ! transaminase activity
+xref: RHEA:52528
+xref: RHEA:68376
+xref: RHEA:68380
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.14
property_value: skos:exactMatch RHEA:19813
+property_value: skos:narrowMatch RHEA:52528
+property_value: skos:narrowMatch RHEA:68376
+property_value: skos:narrowMatch RHEA:68380
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047298
-name: (S)-3-amino-2-methylpropionate transaminase activity
+name: (S)-3-amino-2-methylpropionate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3-oxopropanoate + L-glutamate." [EC:2.6.1.22, RHEA:13993]
+def: "Catalysis of the reaction: (S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3-oxopropanoate + L-glutamate." [RHEA:13993]
synonym: "(S)-3-amino-2-methylpropanoate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.22]
synonym: "(S)-3-amino-2-methylpropionate aminotransferase activity" EXACT []
+synonym: "(S)-3-amino-2-methylpropionate transaminase activity" EXACT []
synonym: "beta-aminobutyric transaminase activity" RELATED [EC:2.6.1.22]
synonym: "beta-aminoisobutyrate-alpha-ketoglutarate transaminase activity" RELATED [EC:2.6.1.22]
synonym: "L-3-aminoisobutyrate aminotransferase activity" RELATED [EC:2.6.1.22]
@@ -305736,32 +309361,36 @@
property_value: skos:exactMatch EC:2.6.1.22
property_value: skos:exactMatch RHEA:13993
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047299
-name: tryptophan-phenylpyruvate transaminase activity
+name: L-tryptophan:phenylpyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: keto-phenylpyruvate + L-tryptophan = 3-(indol-3-yl)pyruvate + L-phenylalanine." [EC:2.6.1.28, RHEA:13741]
+def: "Catalysis of the reaction: 3-phenylpyruvate + L-tryptophan = indole-3-pyruvate + L-phenylalanine." [RHEA:13741]
synonym: "L-tryptophan-alpha-ketoisocaproate aminotransferase activity" RELATED [EC:2.6.1.28]
synonym: "L-tryptophan:phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.28]
synonym: "tryptophan--phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.28]
synonym: "tryptophan-phenylpyruvate aminotransferase activity" EXACT []
+synonym: "tryptophan-phenylpyruvate transaminase activity" EXACT []
xref: EC:2.6.1.28
xref: KEGG_REACTION:R01376
xref: MetaCyc:2.6.1.28-RXN
xref: RHEA:13741
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.28
property_value: skos:exactMatch RHEA:13741
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047300
-name: pyridoxamine-pyruvate transaminase activity
+name: pyridoxamine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyridoxamine + pyruvate = L-alanine + pyridoxal." [EC:2.6.1.30, RHEA:12841]
+def: "Catalysis of the reaction: pyridoxamine + pyruvate = L-alanine + pyridoxal." [RHEA:12841]
synonym: "pyridoxamine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.30]
synonym: "pyridoxamine-pyruvate aminotransferase activity" EXACT []
+synonym: "pyridoxamine-pyruvate transaminase activity" EXACT []
synonym: "pyridoxamine-pyruvic transaminase" BROAD [EC:2.6.1.30]
synonym: "pyridoxamine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.30]
synonym: "pyridoxamineu-pyruvic transaminase activity" RELATED [EC:2.6.1.30]
@@ -305773,32 +309402,36 @@
property_value: skos:exactMatch EC:2.6.1.30
property_value: skos:exactMatch RHEA:12841
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047301
-name: valine-3-methyl-2-oxovalerate transaminase activity
+name: L-valine:3-methyl-2-oxovalerate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + L-valine = 3-methyl-2-oxobutanoate + L-isoleucine." [EC:2.6.1.32, RHEA:11468]
+def: "Catalysis of the reaction: (S)-3-methyl-2-oxopentanoate + L-valine = 3-methyl-2-oxobutanoate + L-isoleucine." [RHEA:11468]
synonym: "L-valine:(S)-3-methyl-2-oxopentanoate aminotransferase activity" RELATED [EC:2.6.1.32]
synonym: "valine--3-methyl-2-oxovalerate aminotransferase activity" RELATED [EC:2.6.1.32]
synonym: "valine--isoleucine aminotransferase activity" RELATED [EC:2.6.1.32]
synonym: "valine--isoleucine transaminase activity" RELATED [EC:2.6.1.32]
synonym: "valine-2-keto-methylvalerate aminotransferase activity" RELATED [EC:2.6.1.32]
synonym: "valine-3-methyl-2-oxovalerate aminotransferase activity" EXACT []
+synonym: "valine-3-methyl-2-oxovalerate transaminase activity" EXACT []
xref: EC:2.6.1.32
xref: KEGG_REACTION:R02200
xref: MetaCyc:2.6.1.32-RXN
xref: RHEA:11468
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.32
property_value: skos:exactMatch RHEA:11468
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047302
-name: UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity
+name: UDP-N-acetylbacillosamine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose = L-glutamate + UDP-2-acetamido-4-dehydro-2,6-dideoxy-beta-D-glucose." [PMID:16286454, RHEA:31663]
+def: "Catalysis of the reaction: UDP-N-acetylbacillosamine + 2-oxoglutarate = UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-hex-4-ulose + L-glutamate." [PMID:16286454, RHEA:31663]
+synonym: "UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity" BROAD []
synonym: "UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.34]
synonym: "UDP-4-amino-2-acetamido-2,4,6-trideoxyglucose aminotransferase activity" EXACT []
synonym: "UDP-4-amino-2-acetamido-2,4,6-trideoxyglucose transaminase activity" EXACT []
@@ -305811,30 +309444,33 @@
property_value: skos:exactMatch EC:2.6.1.34
property_value: skos:exactMatch RHEA:31663
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047303
-name: glycine-oxaloacetate transaminase activity
+name: glycine:oxaloacetate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycine + oxaloacetate = L-aspartate + glyoxylate." [EC:2.6.1.35, RHEA:17141]
+def: "Catalysis of the reaction: glycine + oxaloacetate = L-aspartate + glyoxylate." [RHEA:17141]
synonym: "glycine--oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.35]
synonym: "glycine-oxalacetate aminotransferase activity" RELATED [EC:2.6.1.35]
synonym: "glycine-oxaloacetate aminotransferase activity" EXACT []
+synonym: "glycine-oxaloacetate transaminase activity" EXACT []
synonym: "glycine:oxaloacetate aminotransferase activity" RELATED [EC:2.6.1.35]
xref: EC:2.6.1.35
xref: KEGG_REACTION:R00373
xref: MetaCyc:2.6.1.35-RXN
xref: RHEA:17141
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.35
property_value: skos:exactMatch RHEA:17141
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047304
-name: 2-aminoethylphosphonate-pyruvate transaminase activity
+name: 2-aminoethylphosphonate:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2-aminoethyl)phosphonate + pyruvate = L-alanine + phosphonoacetaldehyde." [EC:2.6.1.37, RHEA:17021]
+def: "Catalysis of the reaction: (2-aminoethyl)phosphonate + pyruvate = L-alanine + phosphonoacetaldehyde." [RHEA:17021]
synonym: "(2-aminoethyl)phosphonate aminotransferase activity" RELATED [EC:2.6.1.37]
synonym: "(2-aminoethyl)phosphonate transaminase activity" RELATED [EC:2.6.1.37]
synonym: "(2-aminoethyl)phosphonate--pyruvate aminotransferase activity" RELATED [EC:2.6.1.37]
@@ -305843,6 +309479,7 @@
synonym: "2-aminoethylphosphonate aminotransferase activity" RELATED [EC:2.6.1.37]
synonym: "2-aminoethylphosphonate--pyruvate aminotransferase activity" RELATED [EC:2.6.1.37]
synonym: "2-aminoethylphosphonate-pyruvate aminotransferase activity" EXACT []
+synonym: "2-aminoethylphosphonate-pyruvate transaminase activity" EXACT []
xref: EC:2.6.1.37
xref: KEGG_REACTION:R04152
xref: MetaCyc:2.6.1.37-RXN
@@ -305851,20 +309488,21 @@
property_value: skos:exactMatch EC:2.6.1.37
property_value: skos:exactMatch RHEA:17021
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047305
-name: (R)-3-amino-2-methylpropionate-pyruvate transaminase activity
+name: (R)-3-amino-2-methylpropionate:pyruvate transaminase activity
namespace: molecular_function
alt_id: GO:0047314
-def: "Catalysis of the reaction: (2R)-3-amino-2-methylpropanoate + pyruvate = 2-methyl-3-oxopropanoate + L-alanine." [EC:2.6.1.40, RHEA:18393]
-comment: Note that this function was EC:2.6.1.61.
+def: "Catalysis of the reaction: (R)-3-amino-2-methylpropanoate + pyruvate = 2-methyl-3-oxopropanoate + L-alanine." [RHEA:18393]
synonym: "(R)-3-amino-2-methylpropanoate aminotransferase activity" EXACT []
synonym: "(R)-3-amino-2-methylpropanoate transaminase activity" EXACT []
synonym: "(R)-3-amino-2-methylpropanoate:pyruvate aminotransferase activity" RELATED [EC:2.6.1.40]
synonym: "(R)-3-amino-2-methylpropionate transaminase activity" EXACT []
synonym: "(R)-3-amino-2-methylpropionate--pyruvate aminotransferase activity" RELATED [EC:2.6.1.40]
synonym: "(R)-3-amino-2-methylpropionate-pyruvate aminotransferase activity" EXACT []
+synonym: "(R)-3-amino-2-methylpropionate-pyruvate transaminase activity" EXACT []
synonym: "beta-aminoisobutyrate--pyruvate transaminase activity" RELATED [EC:2.6.1.40]
synonym: "beta-aminoisobutyrate-pyruvate aminotransferase activity" RELATED [EC:2.6.1.40]
synonym: "D-3-aminoisobutyrate--pyruvate aminotransferase activity" RELATED [EC:2.6.1.40]
@@ -305881,33 +309519,37 @@
property_value: skos:exactMatch EC:2.6.1.40
property_value: skos:exactMatch RHEA:18393
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047306
-name: D-methionine-pyruvate transaminase activity
+name: D-methionine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-methionine + pyruvate = 4-methylthio-2-oxobutanoate + L-alanine." [EC:2.6.1.41, RHEA:23836]
+def: "Catalysis of the reaction: D-methionine + pyruvate = 4-methylthio-2-oxobutanoate + L-alanine." [RHEA:23836]
synonym: "D-methionine aminotransferase activity" RELATED [EC:2.6.1.41]
synonym: "D-methionine transaminase activity" RELATED [EC:2.6.1.41]
synonym: "D-methionine--pyruvate aminotransferase activity" RELATED [EC:2.6.1.41]
synonym: "D-methionine-pyruvate aminotransferase activity" EXACT []
+synonym: "D-methionine-pyruvate transaminase activity" EXACT []
synonym: "D-methionine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.41]
xref: EC:2.6.1.41
xref: KEGG_REACTION:R03001
xref: MetaCyc:2.6.1.41-RXN
xref: RHEA:23836
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.41
property_value: skos:exactMatch RHEA:23836
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047307
-name: diaminobutyrate-pyruvate transaminase activity
+name: L-2,4-diaminobutyrate:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2,4-diaminobutyrate + pyruvate = L-alanine + L-aspartate 4-semialdehyde." [EC:2.6.1.46, RHEA:12380]
+def: "Catalysis of the reaction: L-2,4-diaminobutyrate + pyruvate = L-alanine + L-aspartate 4-semialdehyde." [RHEA:12380]
synonym: "diaminobutyrate--pyruvate aminotransferase activity" RELATED [EC:2.6.1.46]
synonym: "diaminobutyrate-pyruvate aminotransferase activity" EXACT []
+synonym: "diaminobutyrate-pyruvate transaminase activity" EXACT []
synonym: "L-2,4-diaminobutanoate:pyruvate aminotransferase activity" RELATED [EC:2.6.1.46]
synonym: "L-diaminobutyric acid transaminase activity" RELATED [EC:2.6.1.46]
xref: EC:2.6.1.46
@@ -305918,12 +309560,13 @@
property_value: skos:exactMatch EC:2.6.1.46
property_value: skos:exactMatch RHEA:12380
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047308
-name: alanine-oxomalonate transaminase activity
+name: L-alanine:oxomalonate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + oxomalonate = aminomalonate + pyruvate." [EC:2.6.1.47, RHEA:18809]
+def: "Catalysis of the reaction: L-alanine + oxomalonate = aminomalonate + pyruvate." [RHEA:18809]
synonym: "alanine--oxomalonate aminotransferase activity" RELATED [EC:2.6.1.47]
synonym: "alanine-ketomalonate (mesoxalate) transaminase activity" RELATED [EC:2.6.1.47]
synonym: "alanine-oxomalonate aminotransferase activity" EXACT []
@@ -305933,19 +309576,21 @@
xref: KEGG_REACTION:R02970
xref: MetaCyc:2.6.1.47-RXN
xref: RHEA:18809
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.47
property_value: skos:exactMatch RHEA:18809
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047309
-name: dihydroxyphenylalanine transaminase activity
+name: dihydroxyphenylalanine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-dopa = 3,4-dihydroxyphenylpyruvate + L-glutamate." [EC:2.6.1.49, RHEA:15273]
+def: "Catalysis of the reaction: L-dopa + 2-oxoglutarate = 3-(3,4-dihydroxyphenyl)pyruvate + L-glutamate." [RHEA:15273]
synonym: "3,4-dihydroxy-L-phenylalanine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.49]
synonym: "aspartate-DOPP transaminase (ADT)" RELATED [EC:2.6.1.49]
synonym: "dihydroxyphenylalanine aminotransferase activity" EXACT []
+synonym: "dihydroxyphenylalanine transaminase activity" EXACT []
synonym: "DOPA aminotransferase activity" RELATED [EC:2.6.1.49]
synonym: "dopa transaminase activity" RELATED [EC:2.6.1.49]
synonym: "glutamate-DOPP transaminase (GDT)" RELATED [EC:2.6.1.49]
@@ -305955,19 +309600,20 @@
xref: KEGG_REACTION:R02077
xref: MetaCyc:2.6.1.49-RXN
xref: RHEA:15273
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.49
property_value: skos:exactMatch RHEA:15273
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047310
-name: glutamine-scyllo-inositol transaminase activity
+name: L-glutamine:scyllo-inositol transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4,6/3,5-pentahydroxycyclohexanone + L-glutamine = 1-amino-1-deoxy-scyllo-inositol + 2-oxoglutaramate." [EC:2.6.1.50, RHEA:22920]
+def: "Catalysis of the reaction: scyllo-inosose + L-glutamine = 1-amino-1-deoxy-scyllo-inositol + 2-oxoglutaramate." [RHEA:22920]
synonym: "glutamine scyllo-inosose aminotransferase activity" RELATED [EC:2.6.1.50]
synonym: "glutamine--scyllo-inosose aminotransferase activity" RELATED [EC:2.6.1.50]
synonym: "glutamine--scyllo-inosose transaminase activity" RELATED [EC:2.6.1.50]
+synonym: "glutamine-scyllo-inositol transaminase activity" EXACT []
synonym: "glutamine-scyllo-inosose aminotransferase activity" EXACT []
synonym: "glutamine-scyllo-inosose transaminase activity" EXACT []
synonym: "L-glutamine-keto-scyllo-inositol aminotransferase activity" RELATED [EC:2.6.1.50]
@@ -305977,17 +309623,19 @@
xref: KEGG_REACTION:R02781
xref: MetaCyc:2.6.1.50-RXN
xref: RHEA:22920
-is_a: GO:0070548 ! L-glutamine aminotransferase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.50
property_value: skos:exactMatch RHEA:22920
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047311
-name: 1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol transaminase activity
+name: 1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol + pyruvate = 1D-1-guanidino-1-deoxy-3-dehydro-scyllo-inositol + L-alanine." [EC:2.6.1.56, RHEA:15497]
+def: "Catalysis of the reaction: 1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol + pyruvate = 1D-1-guanidino-1-deoxy-3-dehydro-scyllo-inositol + L-alanine." [RHEA:15497]
synonym: "1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol aminotransferase activity" EXACT []
+synonym: "1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol transaminase activity" EXACT []
synonym: "1D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol:pyruvate aminotransferase activity" RELATED [EC:2.6.1.56]
synonym: "guanidinoaminodideoxy-scyllo-inositol-pyruvate aminotransferase activity" RELATED [EC:2.6.1.56]
synonym: "L-alanine-N-amidino-3-(or 5-)keto-scyllo-inosamine transaminase activity" RELATED [EC:2.6.1.56]
@@ -305999,53 +309647,64 @@
property_value: skos:exactMatch EC:2.6.1.56
property_value: skos:exactMatch RHEA:15497
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047312
-name: L-phenylalanine-pyruvate transaminase activity
+name: L-phenylalanine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + L-phenylalanine = phenylpyruvate + L-alanine." [RHEA:13053]
+def: "Catalysis of the reaction: L-phenylalanine + pyruvate = 3-phenylpyruvate + L-alanine." [RHEA:13053]
synonym: "histidine aminotransferase activity" RELATED [GOC:kad]
synonym: "histidine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.58, GOC:kad]
synonym: "L-histidine:pyruvate aminotransferase activity" RELATED [GOC:kad]
synonym: "L-phenylalanine(L-histidine):pyruvate aminotransferase activity" BROAD [EC:2.6.1.58]
+synonym: "L-phenylalanine-pyruvate transaminase activity" EXACT []
synonym: "L-phenylalanine:pyruvate aminotransferase activity" EXACT []
-synonym: "L-phenylalanine:pyruvate transaminase activity" EXACT [GOC:kad]
synonym: "phenylalanine (histidine) aminotransferase activity" BROAD [EC:2.6.1.58]
synonym: "phenylalanine(histidine) aminotransferase activity" BROAD []
synonym: "phenylalanine(histidine) transaminase activity" BROAD [EC:2.6.1.58]
synonym: "phenylalanine(histidine):pyruvate aminotransferase activity" BROAD [EC:2.6.1.58]
xref: KEGG_REACTION:R00692
xref: MetaCyc:2.6.1.58-RXN
-xref: Reactome:R-HSA-893593 "phenylalanine + pyruvate => 3-(indol-3-yl)pyruvate + alanine"
+xref: Reactome:R-HSA-893593 "phenylalanine + pyruvate => keto-phenylpyruvate + alanine"
xref: RHEA:13053
-is_a: GO:0008793 ! aromatic-amino-acid transaminase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:broadMatch EC:2.6.1.58
property_value: skos:exactMatch RHEA:13053
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047313
-name: aromatic-amino-acid-glyoxylate transaminase activity
+name: aromatic-amino-acid:glyoxylate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glyoxylate + an aromatic amino acid = L-glycine + an aromatic oxo acid." [EC:2.6.1.60, MetaCyc:2.6.1.60-RXN]
+def: "Catalysis of the reaction: an aromatic L-alpha-amino acid + glyoxylate = an aromatic oxo-acid + glycine." [RHEA:10900]
synonym: "aromatic-amino-acid--glyoxylate aminotransferase activity" RELATED [EC:2.6.1.60]
synonym: "aromatic-amino-acid-glyoxylate aminotransferase activity" EXACT []
+synonym: "aromatic-amino-acid-glyoxylate transaminase activity" EXACT []
synonym: "aromatic-amino-acid:glyoxylate aminotransferase activity" RELATED [EC:2.6.1.60]
xref: EC:2.6.1.60
xref: MetaCyc:2.6.1.60-RXN
xref: RHEA:10900
-is_a: GO:0008483 ! transaminase activity
+xref: RHEA:69116
+xref: RHEA:69120
+xref: RHEA:69124
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.60
property_value: skos:exactMatch RHEA:10900
+property_value: skos:narrowMatch RHEA:69116
+property_value: skos:narrowMatch RHEA:69120
+property_value: skos:narrowMatch RHEA:69124
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047315
-name: kynurenine-glyoxylate transaminase activity
+name: L-kynurenine:glyoxylate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-kynurenine + glyoxylate = 4-(2-aminophenyl)-2,4-dioxobutanoate + glycine." [EC:2.6.1.63, RHEA:19249]
+def: "Catalysis of the reaction: L-kynurenine + glyoxylate = 4-(2-aminophenyl)-2,4-dioxobutanoate + glycine." [RHEA:19249]
synonym: "kynurenine--glyoxylate aminotransferase activity" RELATED [EC:2.6.1.63]
synonym: "kynurenine-glyoxylate aminotransferase activity" EXACT []
+synonym: "kynurenine-glyoxylate transaminase activity" EXACT []
synonym: "L-kynurenine:glyoxylate aminotransferase (cyclizing)" RELATED [EC:2.6.1.63]
xref: EC:2.6.1.63
xref: KEGG_REACTION:R01957
@@ -306055,34 +309714,38 @@
property_value: skos:exactMatch EC:2.6.1.63
property_value: skos:exactMatch RHEA:19249
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047316
-name: glutamine-phenylpyruvate transaminase activity
+name: L-glutamine:phenylpyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: keto-phenylpyruvate + L-glutamine = 2-oxoglutaramate + L-phenylalanine." [EC:2.6.1.64, RHEA:17593]
+def: "Catalysis of the reaction: 3-phenylpyruvate + L-glutamine = 2-oxoglutaramate + L-phenylalanine." [RHEA:17593]
synonym: "glutamine transaminase K activity" RELATED [EC:2.6.1.64]
synonym: "glutamine--phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.64]
synonym: "glutamine-phenylpyruvate aminotransferase activity" EXACT []
+synonym: "glutamine-phenylpyruvate transaminase activity" EXACT []
synonym: "L-glutamine:phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.64]
xref: EC:2.6.1.64
xref: KEGG_REACTION:R01375
xref: MetaCyc:2.6.1.64-RXN
xref: RHEA:17593
-is_a: GO:0070548 ! L-glutamine aminotransferase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.64
property_value: skos:exactMatch RHEA:17593
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047317
-name: N6-acetyl-beta-lysine transaminase activity
+name: N6-acetyl-beta-lysine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + 3-amino-6-acetamidohexanoate = L-glutamate + 3-oxo-6-acetamidohexanoate." [EC:2.6.1.65, MetaCyc:2.6.1.65-RXN]
+def: "Catalysis of the reaction: 2-oxoglutarate + 3-amino-6-acetamidohexanoate = L-glutamate + 3-oxo-6-acetamidohexanoate." [RHEA:16889]
synonym: "6-acetamido-3-aminohexanoate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.65]
synonym: "epsilon-acetyl-beta-lysine aminotransferase activity" RELATED [EC:2.6.1.65]
synonym: "N(6)-acetyl-beta-lysine aminotransferase activity" RELATED [EC:2.6.1.65]
synonym: "N6-acetyl-beta-lysine aminotransferase activity" EXACT []
+synonym: "N6-acetyl-beta-lysine transaminase activity" EXACT []
xref: EC:2.6.1.65
xref: MetaCyc:2.6.1.65-RXN
xref: RHEA:16889
@@ -306090,29 +309753,33 @@
property_value: skos:exactMatch EC:2.6.1.65
property_value: skos:exactMatch RHEA:16889
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047319
-name: aspartate-phenylpyruvate transaminase activity
+name: L-aspartate:phenylpyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: keto-phenylpyruvate + L-aspartate = L-phenylalanine + oxaloacetate." [RHEA:14097]
+def: "Catalysis of the reaction: L-aspartate + 3-phenylpyruvate = oxaloacetate + L-phenylalanine." [RHEA:14097]
synonym: "aspartate--phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.70]
+synonym: "aspartate-phenylpyruvate transaminase activity" EXACT []
synonym: "aspartate:phenylpyruvate aminotransferase activity" EXACT []
synonym: "L-aspartate:phenylpyruvate aminotransferase activity" RELATED [EC:2.6.1.70]
xref: EC:2.6.1.70
xref: KEGG_REACTION:R00695
xref: MetaCyc:2.6.1.70-RXN
xref: RHEA:14097
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.70
property_value: skos:exactMatch RHEA:14097
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047320
-name: D-4-hydroxyphenylglycine transaminase activity
+name: D-4-hydroxyphenylglycine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + D-4-hydroxyphenylglycine = 4-hydroxyphenylglyoxylate + L-glutamate." [EC:2.6.1.72, RHEA:15589]
+def: "Catalysis of the reaction: 2-oxoglutarate + D-4-hydroxyphenylglycine = 4-hydroxyphenylglyoxylate + L-glutamate." [RHEA:15589]
synonym: "D-4-hydroxyphenylglycine aminotransferase activity" EXACT []
+synonym: "D-4-hydroxyphenylglycine transaminase activity" EXACT []
synonym: "D-4-hydroxyphenylglycine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.72]
synonym: "D-hydroxyphenylglycine aminotransferase activity" RELATED [EC:2.6.1.72]
xref: EC:2.6.1.72
@@ -306123,6 +309790,7 @@
property_value: skos:exactMatch EC:2.6.1.72
property_value: skos:exactMatch RHEA:15589
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047321
@@ -306190,7 +309858,6 @@
synonym: "STK2" RELATED [EC:2.7.11.4]
xref: EC:2.7.11.4
xref: MetaCyc:2.7.11.4-RXN
-xref: Reactome:R-HSA-5693148 "BCKDK phosphorylates BCKDH"
xref: Reactome:R-HSA-9912480 "BCKDK loss-of-function mutations do not phosphorylate BCKDH"
xref: RHEA:17301
is_a: GO:0004674 ! protein serine/threonine kinase activity
@@ -306299,7 +309966,7 @@
id: GO:0047329
name: phosphoramidate-hexose phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: hexose + phosphoramidate = hexose 1-phosphate + NH3." [EC:2.7.1.62, MetaCyc:2.7.1.62-RXN]
+def: "Catalysis of the reaction: phosphoramidate + a D-hexose + H+ = alpha-D-hexose 1-phosphate + NH4+." [RHEA:10972]
synonym: "phosphoramidate-hexose transphosphorylase activity" RELATED [EC:2.7.1.62]
synonym: "phosphoramidate:hexose 1-phosphotransferase activity" RELATED [EC:2.7.1.62]
synonym: "phosphoramidic-hexose transphosphorylase activity" RELATED [EC:2.7.1.62]
@@ -306687,6 +310354,7 @@
xref: EC:2.7.7.40
xref: KEGG_REACTION:R02921
xref: MetaCyc:2.7.7.40-RXN
+xref: Reactome:R-HSA-9940844 "CRPPA dimer transfers cytidylyl to Rbt5P"
xref: RHEA:12456
is_a: GO:0070567 ! cytidylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.40
@@ -307120,12 +310788,16 @@
xref: Reactome:R-HSA-426043 "2-AG hydrolysis to arachidonate by MAGL"
xref: Reactome:R-HSA-5694462 "ABHD6,12 hydrolyse 3AG"
xref: RHEA:15245
+xref: RHEA:34019
+xref: RHEA:44688
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:broadMatch EC:3.1.1.79
property_value: skos:exactMatch EC:3.1.1.23
property_value: skos:exactMatch MetaCyc:RXN-19280
property_value: skos:exactMatch RHEA:15245
+property_value: skos:narrowMatch RHEA:34019
+property_value: skos:narrowMatch RHEA:44688
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
[Term]
@@ -307227,9 +310899,11 @@
xref: KEGG_REACTION:R04043
xref: MetaCyc:3.1.1.71-RXN
xref: RHEA:11552
+xref: RHEA:38563
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.71
property_value: skos:exactMatch RHEA:11552
+property_value: skos:narrowMatch RHEA:38563
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -307335,6 +311009,7 @@
synonym: "branched-chain oxo-acid dehydrogenase phosphatase activity" EXACT []
xref: EC:3.1.3.52
xref: MetaCyc:3.1.3.52-RXN
+xref: Reactome:R-HSA-5693153 "PPM1K dephosphorylates p-BCKDH"
xref: RHEA:77247
is_a: GO:0004721 ! phosphoprotein phosphatase activity
property_value: skos:exactMatch EC:3.1.3.52
@@ -307686,9 +311361,13 @@
xref: EC:3.2.2.10
xref: MetaCyc:3.2.2.10-RXN
xref: RHEA:13425
+xref: RHEA:30075
+xref: RHEA:52704
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
property_value: skos:exactMatch EC:3.2.2.10
property_value: skos:exactMatch RHEA:13425
+property_value: skos:narrowMatch RHEA:30075
+property_value: skos:narrowMatch RHEA:52704
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -307767,7 +311446,7 @@
id: GO:0047411
name: 2-(acetamidomethylene)succinate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H2O + 2-(acetamidomethylene)succinate = CO2 + NH3 + succinate semialdehyde + acetate." [EC:3.5.1.29, MetaCyc:3.5.1.29-RXN]
+def: "Catalysis of the reaction: 2-(acetamidomethylene)succinate + 2 H2O + H+ = succinate semialdehyde + acetate + NH4+ + CO2." [RHEA:10432]
synonym: "2-(acetamidomethylene)succinate amidohydrolase (deaminating, decarboxylating)" RELATED [EC:3.5.1.29]
synonym: "alpha-(N-acetylaminomethylene)succinic acid hydrolase activity" RELATED [EC:3.5.1.29]
xref: EC:3.5.1.29
@@ -307789,9 +311468,19 @@
xref: EC:3.5.1.60
xref: MetaCyc:3.5.1.60-RXN
xref: RHEA:17505
+xref: RHEA:45060
+xref: RHEA:45064
+xref: RHEA:45452
+xref: RHEA:63124
+xref: RHEA:63128
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.60
property_value: skos:exactMatch RHEA:17505
+property_value: skos:narrowMatch RHEA:45060
+property_value: skos:narrowMatch RHEA:45064
+property_value: skos:narrowMatch RHEA:45452
+property_value: skos:narrowMatch RHEA:63124
+property_value: skos:narrowMatch RHEA:63128
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -307858,16 +311547,24 @@
xref: EC:3.5.1.76
xref: MetaCyc:3.5.1.76-RXN
xref: RHEA:10352
+xref: RHEA:67196
+xref: RHEA:67200
+xref: RHEA:67204
+xref: RHEA:67208
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.76
property_value: skos:exactMatch RHEA:10352
+property_value: skos:narrowMatch RHEA:67196
+property_value: skos:narrowMatch RHEA:67200
+property_value: skos:narrowMatch RHEA:67204
+property_value: skos:narrowMatch RHEA:67208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047417
name: N-carbamoyl-D-amino acid hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + N-carbamoyl-D-amino acid = CO2 + NH3 + D-amino acid." [EC:3.5.1.77, MetaCyc:3.5.1.77-RXN]
+def: "Catalysis of the reaction: an N-carbamoyl-D-amino acid + H2O + 2 H+ = a D-alpha-amino acid + NH4+ + CO2." [RHEA:11000]
synonym: "N-carbamoyl-D-amino acid amidohydrolase activity" RELATED [EC:3.5.1.77]
xref: EC:3.5.1.77
xref: MetaCyc:3.5.1.77-RXN
@@ -307974,7 +311671,7 @@
id: GO:0047424
name: methylenediurea deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H2O + methylenediurea = CO2 + 2 NH3 + N-hydroxymethylurea." [EC:3.5.3.21, MetaCyc:3.5.3.21-RXN, RHEA:15929]
+def: "Catalysis of the reaction: methylenediurea + 2 H2O + 2 H+ = N-(hydroxymethyl)urea + 2 NH4+ + CO2." [RHEA:15929]
synonym: "methylenediurea aminohydrolase activity" RELATED [EC:3.5.3.21]
synonym: "methylenediurease activity" RELATED [EC:3.5.3.21]
xref: EC:3.5.3.21
@@ -308007,7 +311704,7 @@
id: GO:0047426
name: ricinine nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + ricinine = NH3 + 3-carboxy-4-methoxy-N-methyl-2-pyridone." [EC:3.5.5.2]
+def: "Catalysis of the reaction: ricinine + 2 H2O = 4-methoxy-1-methyl-2-oxo-1,2-dihydropyridine-3-carboxylate + NH4+." [RHEA:22704]
synonym: "ricinine aminohydrolase activity" RELATED [EC:3.5.5.2]
xref: EC:3.5.5.2
xref: MetaCyc:3.5.5.2-RXN
@@ -308028,16 +311725,18 @@
xref: KEGG_REACTION:R00486
xref: MetaCyc:3.5.5.4-RXN
xref: RHEA:11188
+xref: RHEA:47936
is_a: GO:0000257 ! nitrilase activity
property_value: skos:exactMatch EC:3.5.5.4
property_value: skos:exactMatch RHEA:11188
+property_value: skos:narrowMatch RHEA:47936
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047428
name: arylacetonitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H2O + 4-chlorophenylacetonitrile = 4-chlorophenylacetate + NH3." [EC:3.5.5.5]
+def: "Catalysis of the reaction: 4-chlorophenylacetonitrile + 2 H2O = 4-chlorophenylacetate + NH4+." [RHEA:20657]
synonym: "arylacetonitrile aminohydrolase activity" RELATED [EC:3.5.5.5]
xref: EC:3.5.5.5
xref: MetaCyc:3.5.5.5-RXN
@@ -308333,9 +312032,11 @@
xref: MetaCyc:RXN-9988
xref: Reactome:R-HSA-4084976 "NANS converts ManNAc-6-P to Neu5Ac-9-P"
xref: RHEA:13421
+xref: RHEA:80835
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
property_value: skos:exactMatch EC:2.5.1.57
property_value: skos:exactMatch RHEA:13421
+property_value: skos:narrowMatch RHEA:80835
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -308379,7 +312080,7 @@
id: GO:0047447
name: erythro-3-hydroxyaspartate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: erythro-3-hydroxy-L-aspartate = NH3 + oxaloacetic acid." [EC:4.3.1.20, MetaCyc:4.3.1.20-RXN]
+def: "Catalysis of the reaction: 3-hydroxy-L-aspartate = oxaloacetate + NH4+." [RHEA:19757]
synonym: "3-hydroxyaspartate dehydratase activity" BROAD [EC:4.3.1.20]
synonym: "erythro-3-hydroxy-L(s)-aspartate hydro-lyase (deaminating) activity" RELATED [EC:4.3.1.20]
synonym: "erythro-3-hydroxy-Ls-aspartate ammonia-lyase (oxaloacetate-forming)" RELATED [EC:4.3.1.20]
@@ -308721,9 +312422,11 @@
xref: EC:5.1.3.9
xref: MetaCyc:5.1.3.9-RXN
xref: RHEA:23932
+xref: RHEA:25257
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
property_value: skos:exactMatch EC:5.1.3.9
property_value: skos:exactMatch RHEA:23932
+property_value: skos:narrowMatch RHEA:25257
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -308844,11 +312547,13 @@
id: GO:0047473
name: D-alanine [D-alanyl carrier protein] ligase activity
namespace: molecular_function
-def: "Catalysis of the ATP-dependent activation of D-alanine and its transfer as a thiol ester to the phosphopantheinyl prosthetic group of a D-alanyl carrier protein, according to the reaction: ATP + D-alanine + a [D-alaninyl carrier protein] = a D-alanyl-[D-alanyl carrier protein] + AMP + diphosphate." [GOC:pg]
+def: "Catalysis of the ATP-dependent activation of D-alanine and its transfer as a thiol ester to the phosphopantheinyl prosthetic group of a D-alanyl carrier protein, according to the reaction: holo-[D-alanyl-carrier protein] + D-alanine + ATP = D-alanyl-[D-alanyl-carrier protein] + AMP + diphosphate." [RHEA:55132]
synonym: "D-alanine-activating enzyme activity" RELATED []
synonym: "D-alanine-D-alanyl carrier protein ligase activity" RELATED []
synonym: "D-alanine-poly(phosphoribitol) ligase activity" BROAD []
synonym: "D-alanine:poly(phosphoribitol) ligase (AMP-forming)" BROAD []
+xref: EC:6.2.1.54
+xref: RHEA:55132
is_a: GO:0016878 ! acid-thiol ligase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14237" xsd:anyURI
@@ -308887,7 +312592,6 @@
xref: MetaCyc:RXN-10819
xref: RHEA:20956
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.30
property_value: skos:exactMatch RHEA:20956
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -308905,7 +312609,6 @@
xref: MetaCyc:6.2.1.28-RXN
xref: RHEA:21776
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.28
property_value: skos:exactMatch RHEA:21776
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -309388,10 +313091,12 @@
xref: EC:2.7.4.13
xref: MetaCyc:DEOXYNUCLEOSIDE-PHOSPHATE-KINASE-RXN
xref: RHEA:11216
+xref: RHEA:62120
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch EC:2.7.4.13
property_value: skos:exactMatch RHEA:11216
+property_value: skos:narrowMatch RHEA:62120
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29533" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -309774,13 +313479,17 @@
id: GO:0047530
name: 2,4-diaminopentanoate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,4-diaminopentanoate + H2O + NAD(P)+ = 2-amino-4-oxopentanoate + NH3 + NAD(P)H + H+." [EC:1.4.1.12, MetaCyc:24-DIAMINOPENTANOATE-DEHYDROGENASE-RXN]
+def: "Catalysis of the reaction: (2R,4S)-2,4-diaminopentanoate + NADP+ + H2O = (2R)-2-amino-4-oxopentanoate + NH4+ + NADPH + H+." [EC:1.4.1.12]
synonym: "2,4-diaminopentanoate:NAD(P)+ oxidoreductase (deaminating)" RELATED [EC:1.4.1.12]
synonym: "2,4-diaminopentanoic acid C4 dehydrogenase activity" RELATED [EC:1.4.1.12]
xref: EC:1.4.1.12
xref: MetaCyc:24-DIAMINOPENTANOATE-DEHYDROGENASE-RXN
+xref: RHEA:24192
+xref: RHEA:24196
is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.4.1.12
+property_value: skos:narrowMatch RHEA:24192
+property_value: skos:narrowMatch RHEA:24196
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -309859,10 +313568,11 @@
[Term]
id: GO:0047536
-name: 2-aminoadipate transaminase activity
+name: L-2-aminoadipate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-2-aminoadipate = 2-oxoadipate + L-glutamate." [EC:2.6.1.39, RHEA:12601]
+def: "Catalysis of the reaction: L-2-aminoadipate + 2-oxoglutarate = 2-oxoadipate + L-glutamate." [RHEA:12601]
synonym: "2-aminoadipate aminotransferase activity" EXACT []
+synonym: "2-aminoadipate transaminase activity" EXACT []
synonym: "2-aminoadipic aminotransferase activity" RELATED [EC:2.6.1.39]
synonym: "alpha-aminoadipate aminotransferase activity" RELATED [EC:2.6.1.39]
synonym: "glutamate-alpha-ketoadipate transaminase activity" RELATED [EC:2.6.1.39]
@@ -309878,13 +313588,15 @@
property_value: skos:exactMatch EC:2.6.1.39
property_value: skos:exactMatch RHEA:12601
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047537
-name: 2-aminohexanoate transaminase activity
+name: L-2-aminohexanoate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-aminohexanoate + 2-oxoglutarate = 2-oxohexanoate + L-glutamate." [EC:2.6.1.67, MetaCyc:2-AMINOHEXANOATE-AMINOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: L-2-aminohexanoate + 2-oxoglutarate = 2-oxohexanoate + L-glutamate." [RHEA:23600]
synonym: "2-aminohexanoate aminotransferase activity" EXACT []
+synonym: "2-aminohexanoate transaminase activity" EXACT []
synonym: "L-2-aminohexanoate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.67]
synonym: "leucine L-norleucine: 2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.67]
synonym: "norleucine (leucine) aminotransferase activity" RELATED [EC:2.6.1.67]
@@ -309897,6 +313609,7 @@
property_value: skos:exactMatch EC:2.6.1.67
property_value: skos:exactMatch RHEA:23600
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047538
@@ -309958,7 +313671,6 @@
xref: MetaCyc:2-FUROATE--COA-LIGASE-RXN
xref: RHEA:19269
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.31
property_value: skos:exactMatch RHEA:19269
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -310039,9 +313751,13 @@
xref: MetaCyc:2-HYDROXYGLUTARATE-DEHYDROGENASE-RXN
xref: Reactome:R-HSA-880050 "(S)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2"
xref: RHEA:21252
+xref: RHEA:30087
+xref: RHEA:57172
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: skos:exactMatch EC:1.1.99.2
property_value: skos:exactMatch RHEA:21252
+property_value: skos:narrowMatch RHEA:30087
+property_value: skos:narrowMatch RHEA:57172
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30707" xsd:anyURI
@@ -310146,10 +313862,12 @@
xref: EC:1.2.1.23
xref: MetaCyc:2-OXOALDEHYDE-DEHYDROGENASE-NAD+-RXN
xref: RHEA:22276
+xref: RHEA:52004
xref: Wikipedia:2-oxoaldehyde_dehydrogenase_(NAD+)
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.2.1.23
property_value: skos:exactMatch RHEA:22276
+property_value: skos:narrowMatch RHEA:52004
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -310518,9 +314236,11 @@
xref: EC:1.3.99.4
xref: MetaCyc:3-OXOSTEROID-1-DEHYDROGENASE-RXN
xref: RHEA:13329
+xref: RHEA:51052
is_a: GO:0033765 ! steroid dehydrogenase activity, acting on the CH-CH group of donors
property_value: skos:exactMatch EC:1.3.99.4
property_value: skos:exactMatch RHEA:13329
+property_value: skos:narrowMatch RHEA:51052
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -310625,19 +314345,21 @@
[Term]
id: GO:0047578
-name: 4-hydroxyglutamate transaminase activity
+name: (4S)-4-hydroxy-L-glutamate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxy-L-glutamate + 2-oxoglutarate = 4-hydroxy-2-oxoglutarate + L-glutamate." [EC:2.6.1.23, MetaCyc:4-HYDROXYGLUTAMATE-AMINOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: (4S)-4-hydroxy-L-glutamate + 2-oxoglutarate = (4R)-4-hydroxy-2-oxoglutarate + L-glutamate." [RHEA:31235]
synonym: "4-hydroxy-L-glutamate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.23]
synonym: "4-hydroxyglutamate aminotransferase activity" EXACT []
+synonym: "4-hydroxyglutamate transaminase activity" EXACT []
xref: EC:2.6.1.23
xref: MetaCyc:4-HYDROXYGLUTAMATE-AMINOTRANSFERASE-RXN
xref: Reactome:R-HSA-6784393 "PXLP-K279-GOT2 dimer transaminates 4-OH-L-glutamate to 4-hydroxy-2-oxoglutarate (HOG)"
-xref: RHEA:10480
+xref: RHEA:31235
is_a: GO:0008483 ! transaminase activity
property_value: skos:exactMatch EC:2.6.1.23
-property_value: skos:exactMatch RHEA:10480
+property_value: skos:exactMatch RHEA:31235
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047579
@@ -310792,7 +314514,7 @@
id: GO:0047588
name: 5-aminopentanamidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-aminopentanamide + H2O = 5-aminopentanoate + NH3." [EC:3.5.1.30, MetaCyc:5-AMINOPENTANAMIDASE-RXN]
+def: "Catalysis of the reaction: 5-aminopentanamide + H2O = 5-aminopentanoate + NH4+." [RHEA:15677]
synonym: "5-aminonorvaleramidase activity" RELATED [EC:3.5.1.30]
synonym: "5-aminopentanamide amidohydrolase activity" RELATED [EC:3.5.1.30]
synonym: "5-aminovaleramidase activity" RELATED [EC:3.5.1.30]
@@ -310806,11 +314528,12 @@
[Term]
id: GO:0047589
-name: 5-aminovalerate transaminase activity
+name: 5-aminovalerate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + 5-aminopentanoate = 5-oxopentanoate + L-glutamate." [EC:2.6.1.48, RHEA:10212]
+def: "Catalysis of the reaction: 5-aminopentanoate + 2-oxoglutarate = 5-oxopentanoate + L-glutamate." [RHEA:10212]
synonym: "5-aminopentanoate:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.48]
synonym: "5-aminovalerate aminotransferase activity" EXACT []
+synonym: "5-aminovalerate transaminase activity" EXACT []
synonym: "delta-aminovalerate aminotransferase activity" RELATED [EC:2.6.1.48]
synonym: "delta-aminovalerate transaminase activity" RELATED [EC:2.6.1.48]
xref: EC:2.6.1.48
@@ -310821,6 +314544,7 @@
property_value: skos:exactMatch EC:2.6.1.48
property_value: skos:exactMatch RHEA:10212
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047590
@@ -311196,7 +314920,7 @@
xref: KEGG_REACTION:R00394
xref: MetaCyc:ACID--COA-LIGASE-GDP-FORMING-RXN
xref: RHEA:10968
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.10
property_value: skos:exactMatch RHEA:10968
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -311350,10 +315074,14 @@
xref: MetaCyc:ACYLGLYCEROL-KINASE-RXN
xref: Reactome:R-HSA-5696074 "AGK:Mg2+ phosphorylates MAG, DAG"
xref: RHEA:19293
+xref: RHEA:33747
+xref: RHEA:39847
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.94
property_value: skos:exactMatch RHEA:19293
+property_value: skos:narrowMatch RHEA:33747
+property_value: skos:narrowMatch RHEA:39847
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -311393,7 +315121,7 @@
id: GO:0047623
name: adenosine-phosphate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an adenosine-phosphate + H20 = an inosine phosphate + NH3. Catalyzes the deamination of AMP, ADP or ATP." [EC:3.5.4.17]
+def: "Catalysis of the reaction: an adenosine-phosphate + H20 = an inosine phosphate + NH4+. Catalyzes the deamination of AMP, ADP or ATP." [EC:3.5.4.17]
comment: Consider instead annotating to one of the more specific terms: AMP deaminase activity ; GO:0003876, ADP deaminase activity ; GO:0047629, or ATP deaminase activity ; GO:0047692.
synonym: "adenine nucleotide deaminase activity" RELATED [EC:3.5.4.17]
synonym: "adenosine (phosphate) deaminase activity" RELATED [EC:3.5.4.17]
@@ -311485,7 +315213,7 @@
id: GO:0047629
name: ADP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ADP + H2O = IDP + NH3." [EC:3.5.4.7, MetaCyc:ADP-DEAMINASE-RXN]
+def: "Catalysis of the reaction: ADP + H2O + H+ = IDP + NH4+." [RHEA:12741]
synonym: "adenosine diphosphate deaminase activity" RELATED [EC:3.5.4.7]
synonym: "adenosinepyrophosphate deaminase activity" RELATED [EC:3.5.4.7]
synonym: "ADP aminohydrolase activity" RELATED [EC:3.5.4.7]
@@ -311539,7 +315267,7 @@
id: GO:0047632
name: agmatine deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: agmatine + H2O = N-carbamoylputrescine + NH3." [EC:3.5.3.12, MetaCyc:AGMATINE-DEIMINASE-RXN]
+def: "Catalysis of the reaction: agmatine + H2O = N-carbamoylputrescine + NH4+." [RHEA:18037]
synonym: "agmatine amidinohydrolase" BROAD [EC:3.5.3.12]
synonym: "agmatine iminohydrolase activity" RELATED [EC:3.5.3.12]
xref: EC:3.5.3.12
@@ -311588,9 +315316,9 @@
[Term]
id: GO:0047635
-name: alanine-oxo-acid transaminase activity
+name: L-alanine:oxo-acid transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-alanine + a 2-oxo acid = pyruvate + an L-amino acid." [EC:2.6.1.12, MetaCyc:ALANINE--OXO-ACID-AMINOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: L-alanine + a 2-oxocarboxylate = an L-alpha-amino acid + pyruvate." [RHEA:19953]
synonym: "alanine--oxo-acid aminotransferase activity" RELATED [EC:2.6.1.12]
synonym: "alanine-keto acid aminotransferase activity" RELATED [EC:2.6.1.12]
synonym: "alanine-oxo acid aminotransferase activity" RELATED [EC:2.6.1.12]
@@ -311600,11 +315328,36 @@
synonym: "leucine-alanine transaminase activity" RELATED [EC:2.6.1.12]
xref: EC:2.6.1.12
xref: MetaCyc:ALANINE--OXO-ACID-AMINOTRANSFERASE-RXN
+xref: RHEA:13833
xref: RHEA:19953
-is_a: GO:0008483 ! transaminase activity
+xref: RHEA:65912
+xref: RHEA:65920
+xref: RHEA:68372
+xref: RHEA:77303
+xref: RHEA:77307
+xref: RHEA:77319
+xref: RHEA:77327
+xref: RHEA:77347
+xref: RHEA:77355
+xref: RHEA:81635
+xref: RHEA:82415
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.12
property_value: skos:exactMatch RHEA:19953
+property_value: skos:narrowMatch RHEA:13833
+property_value: skos:narrowMatch RHEA:65912
+property_value: skos:narrowMatch RHEA:65920
+property_value: skos:narrowMatch RHEA:68372
+property_value: skos:narrowMatch RHEA:77303
+property_value: skos:narrowMatch RHEA:77307
+property_value: skos:narrowMatch RHEA:77319
+property_value: skos:narrowMatch RHEA:77327
+property_value: skos:narrowMatch RHEA:77347
+property_value: skos:narrowMatch RHEA:77355
+property_value: skos:narrowMatch RHEA:81635
+property_value: skos:narrowMatch RHEA:82415
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047636
@@ -311671,11 +315424,21 @@
xref: MetaCyc:ALCOHOL-OXIDASE-RXN
xref: MetaCyc:METHANOL-OXIDASE-RXN
xref: RHEA:19829
+xref: RHEA:25311
+xref: RHEA:31679
+xref: RHEA:43504
+xref: RHEA:69492
+xref: RHEA:69496
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.1.3.13
property_value: skos:exactMatch MetaCyc:ALCOHOL-OXIDASE-RXN
property_value: skos:exactMatch RHEA:19829
property_value: skos:narrowMatch MetaCyc:METHANOL-OXIDASE-RXN
+property_value: skos:narrowMatch RHEA:25311
+property_value: skos:narrowMatch RHEA:31679
+property_value: skos:narrowMatch RHEA:43504
+property_value: skos:narrowMatch RHEA:69492
+property_value: skos:narrowMatch RHEA:69496
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
[Term]
@@ -311689,9 +315452,13 @@
xref: EC:1.1.1.121
xref: MetaCyc:ALDOSE-1-DEHYDROGENASE-RXN
xref: RHEA:15917
+xref: RHEA:42392
+xref: RHEA:62076
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.121
property_value: skos:exactMatch RHEA:15917
+property_value: skos:narrowMatch RHEA:42392
+property_value: skos:narrowMatch RHEA:62076
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -311773,9 +315540,27 @@
xref: EC:1.1.99.20
xref: MetaCyc:ALKAN-1-OL-DEHYDROGENASE-ACCEPTOR-RXN
xref: RHEA:14685
+xref: RHEA:17085
+xref: RHEA:33567
+xref: RHEA:33571
+xref: RHEA:48076
+xref: RHEA:51148
+xref: RHEA:76451
+xref: RHEA:76455
+xref: RHEA:76459
+xref: RHEA:76463
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: skos:exactMatch EC:1.1.99.20
property_value: skos:exactMatch RHEA:14685
+property_value: skos:narrowMatch RHEA:17085
+property_value: skos:narrowMatch RHEA:33567
+property_value: skos:narrowMatch RHEA:33571
+property_value: skos:narrowMatch RHEA:48076
+property_value: skos:narrowMatch RHEA:51148
+property_value: skos:narrowMatch RHEA:76451
+property_value: skos:narrowMatch RHEA:76455
+property_value: skos:narrowMatch RHEA:76459
+property_value: skos:narrowMatch RHEA:76463
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -311841,10 +315626,12 @@
xref: KEGG_REACTION:R04126
xref: MetaCyc:ALKYLGLYCEROL-KINASE-RXN
xref: RHEA:16937
+xref: RHEA:41672
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.93
property_value: skos:exactMatch RHEA:16937
+property_value: skos:narrowMatch RHEA:41672
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -311883,7 +315670,7 @@
id: GO:0047652
name: allantoate deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: allantoate + H2O + H+ = CO2 + NH3 + ureidoglycine." [EC:3.5.3.9, MetaCyc:ALLANTOATE-DEIMINASE-RXN]
+def: "Catalysis of the reaction: allantoate + H2O + 2 H+ = (S)-2-ureidoglycine + NH4+ + CO2." [RHEA:27485]
synonym: "allantoate amidinohydrolase (decarboxylating)" RELATED [EC:3.5.3.9]
synonym: "allantoate amidohydrolase activity" RELATED [EC:3.5.3.9]
xref: EC:3.5.3.9
@@ -311924,9 +315711,13 @@
xref: EC:4.4.1.4
xref: MetaCyc:ALLIIN-LYASE-RXN
xref: RHEA:20141
+xref: RHEA:54688
+xref: RHEA:69348
is_a: GO:0016846 ! carbon-sulfur lyase activity
property_value: skos:exactMatch EC:4.4.1.4
property_value: skos:exactMatch RHEA:20141
+property_value: skos:narrowMatch RHEA:54688
+property_value: skos:narrowMatch RHEA:69348
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312036,9 +315827,35 @@
xref: EC:5.1.1.10
xref: MetaCyc:AMINO-ACID-RACEMASE-RXN
xref: RHEA:18317
+xref: RHEA:45560
+xref: RHEA:51884
+xref: RHEA:59188
+xref: RHEA:59272
+xref: RHEA:59276
+xref: RHEA:59280
+xref: RHEA:59396
+xref: RHEA:59400
+xref: RHEA:59404
+xref: RHEA:59804
+xref: RHEA:59808
+xref: RHEA:60516
+xref: RHEA:62772
is_a: GO:0016855 ! racemase and epimerase activity, acting on amino acids and derivatives
property_value: skos:exactMatch EC:5.1.1.10
property_value: skos:exactMatch RHEA:18317
+property_value: skos:narrowMatch RHEA:45560
+property_value: skos:narrowMatch RHEA:51884
+property_value: skos:narrowMatch RHEA:59188
+property_value: skos:narrowMatch RHEA:59272
+property_value: skos:narrowMatch RHEA:59276
+property_value: skos:narrowMatch RHEA:59280
+property_value: skos:narrowMatch RHEA:59396
+property_value: skos:narrowMatch RHEA:59400
+property_value: skos:narrowMatch RHEA:59404
+property_value: skos:narrowMatch RHEA:59804
+property_value: skos:narrowMatch RHEA:59808
+property_value: skos:narrowMatch RHEA:60516
+property_value: skos:narrowMatch RHEA:62772
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312081,7 +315898,7 @@
id: GO:0047664
name: aminoimidazolase activity
namespace: molecular_function
-def: "Catalysis of the reaction:4-aminoimidazole + H20 = imidazol-4-one + NH3." [RHEA:22348]
+def: "Catalysis of the reaction: 4-aminoimidazole + H2O + H+ = imidazol-4-one + NH4+." [RHEA:22348]
synonym: "4-aminoimidazole aminohydrolase activity" RELATED [EC:3.5.4.8]
synonym: "4-aminoimidazole hydrolase activity" RELATED [EC:3.5.4.8]
xref: EC:3.5.4.8
@@ -312094,9 +315911,9 @@
[Term]
id: GO:0047665
-name: aminolevulinate transaminase activity
+name: aminolevulinate:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-aminolevulinate + pyruvate = 4,5-dioxopentanoate + L-alanine." [EC:2.6.1.43, RHEA:12480]
+def: "Catalysis of the reaction: 5-aminolevulinate + pyruvate = 4,5-dioxopentanoate + L-alanine." [RHEA:12480]
synonym: "4,5-dioxovalerate aminotransferase activity" RELATED [EC:2.6.1.43]
synonym: "4,5-dioxovaleric acid aminotransferase activity" RELATED [EC:2.6.1.43]
synonym: "4,5-dioxovaleric acid transaminase activity" RELATED [EC:2.6.1.43]
@@ -312106,7 +315923,7 @@
synonym: "alanine-dioxovalerate aminotransferase activity" RELATED [EC:2.6.1.43]
synonym: "alanine-gamma,delta-dioxovalerate aminotransferase activity" RELATED [EC:2.6.1.43]
synonym: "alanine:4,5-dioxovalerate aminotransferase activity" RELATED [EC:2.6.1.43]
-synonym: "aminolevulinate aminotransferase activity" EXACT []
+synonym: "aminolevulinate aminotransferase activity" BROAD []
synonym: "aminolevulinic acid transaminase activity" RELATED [EC:2.6.1.43]
synonym: "dioxovalerate transaminase activity" RELATED [EC:2.6.1.43]
synonym: "DOVA transaminase activity" RELATED [EC:2.6.1.43]
@@ -312123,6 +315940,7 @@
property_value: skos:exactMatch EC:2.6.1.43
property_value: skos:exactMatch RHEA:12480
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047666
@@ -312393,9 +316211,11 @@
xref: EC:1.1.1.91
xref: MetaCyc:ARYL-ALCOHOL-DEHYDROGENASE-NADP+-RXN
xref: RHEA:17761
+xref: RHEA:58776
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.91
property_value: skos:exactMatch RHEA:17761
+property_value: skos:narrowMatch RHEA:58776
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312410,9 +316230,33 @@
xref: EC:1.1.3.7
xref: MetaCyc:ARYL-ALCOHOL-OXIDASE-RXN
xref: RHEA:17541
+xref: RHEA:80379
+xref: RHEA:80383
+xref: RHEA:80431
+xref: RHEA:80435
+xref: RHEA:80439
+xref: RHEA:80443
+xref: RHEA:80447
+xref: RHEA:80451
+xref: RHEA:80455
+xref: RHEA:80459
+xref: RHEA:80463
+xref: RHEA:80467
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.1.3.7
property_value: skos:exactMatch RHEA:17541
+property_value: skos:narrowMatch RHEA:80379
+property_value: skos:narrowMatch RHEA:80383
+property_value: skos:narrowMatch RHEA:80431
+property_value: skos:narrowMatch RHEA:80435
+property_value: skos:narrowMatch RHEA:80439
+property_value: skos:narrowMatch RHEA:80443
+property_value: skos:narrowMatch RHEA:80447
+property_value: skos:narrowMatch RHEA:80451
+property_value: skos:narrowMatch RHEA:80455
+property_value: skos:narrowMatch RHEA:80459
+property_value: skos:narrowMatch RHEA:80463
+property_value: skos:narrowMatch RHEA:80467
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312425,9 +316269,31 @@
xref: EC:1.2.1.30
xref: MetaCyc:1.2.1.30-RXN
xref: RHEA:19229
+xref: RHEA:68868
+xref: RHEA:68872
+xref: RHEA:68876
+xref: RHEA:68880
+xref: RHEA:68884
+xref: RHEA:68888
+xref: RHEA:68892
+xref: RHEA:68896
+xref: RHEA:68900
+xref: RHEA:68904
+xref: RHEA:68908
is_a: GO:0033721 ! aldehyde dehydrogenase (NADP+) activity
property_value: skos:exactMatch EC:1.2.1.30
property_value: skos:exactMatch RHEA:19229
+property_value: skos:narrowMatch RHEA:68868
+property_value: skos:narrowMatch RHEA:68872
+property_value: skos:narrowMatch RHEA:68876
+property_value: skos:narrowMatch RHEA:68880
+property_value: skos:narrowMatch RHEA:68884
+property_value: skos:narrowMatch RHEA:68888
+property_value: skos:narrowMatch RHEA:68892
+property_value: skos:narrowMatch RHEA:68896
+property_value: skos:narrowMatch RHEA:68900
+property_value: skos:narrowMatch RHEA:68904
+property_value: skos:narrowMatch RHEA:68908
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312475,9 +316341,13 @@
xref: EC:2.8.2.22
xref: MetaCyc:ARYLSULFATE-SULFOTRANSFERASE-RXN
xref: RHEA:51072
+xref: RHEA:79263
+xref: RHEA:79267
is_a: GO:0008146 ! sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.22
property_value: skos:exactMatch RHEA:51072
+property_value: skos:narrowMatch RHEA:79263
+property_value: skos:narrowMatch RHEA:79267
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312562,15 +316432,14 @@
id: GO:0047692
name: ATP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ITP + NH3." [EC:3.5.4.18, MetaCyc:ATP-DEAMINASE-RXN]
+def: "Catalysis of the reaction: ATP + H2O + H+ = ITP + NH4+." [RHEA:13037]
synonym: "adenosine triphosphate deaminase activity" RELATED [EC:3.5.4.18]
synonym: "ATP aminohydrolase activity" RELATED [EC:3.5.4.18]
xref: EC:3.5.4.18
xref: MetaCyc:ATP-DEAMINASE-RXN
-xref: RHEA:13037
is_a: GO:0047623 ! adenosine-phosphate deaminase activity
+property_value: skos:broadMatch RHEA:13037
property_value: skos:exactMatch EC:3.5.4.18
-property_value: skos:exactMatch RHEA:13037
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -312679,7 +316548,7 @@
id: GO:0047698
name: beta-alanyl-CoA ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-alanyl-CoA = acryloyl-CoA + NH3." [EC:4.3.1.6, MetaCyc:BETA-ALANYL-COA-AMMONIA-LYASE-RXN]
+def: "Catalysis of the reaction: beta-alanyl-CoA = acryloyl-CoA + NH4+." [RHEA:12416]
synonym: "b-alanyl-CoA ammonia-lyase activity" EXACT []
synonym: "beta-alanyl coenzyme A ammonia-lyase activity" RELATED [EC:4.3.1.6]
synonym: "beta-alanyl-CoA ammonia-lyase (acryloyl-CoA-forming)" RELATED [EC:4.3.1.6]
@@ -312831,7 +316700,6 @@
xref: MetaCyc:BIOTIN--COA-LIGASE-RXN
xref: RHEA:19681
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.11
property_value: skos:exactMatch RHEA:19681
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -312900,7 +316768,7 @@
id: GO:0047711
name: blasticidin-S deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: blasticidin S + H2O = deaminohydroxyblasticidin S + NH3." [EC:3.5.4.23, MetaCyc:BLASTICIDIN-S-DEAMINASE-RXN]
+def: "Catalysis of the reaction: blasticidin S + H2O + H+ = deaminohydroxyblasticidin S + NH4+." [RHEA:10148]
synonym: "blasticidin-S aminohydrolase activity" RELATED [EC:3.5.4.23]
xref: EC:3.5.4.23
xref: MetaCyc:BLASTICIDIN-S-DEAMINASE-RXN
@@ -313153,16 +317021,17 @@
id: GO:0047726
name: iron-cytochrome-c reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ferrocytochrome c + Fe3+ = ferricytochrome c + Fe2+." [EC:1.9.98.1, MetaCyc:IRON--CYTOCHROME-C-REDUCTASE-RXN]
-synonym: "ferrocytochrome-c:Fe3+ oxidoreductase activity" RELATED [EC:1.9.98.1]
-synonym: "iron-cytochrome c reductase activity" RELATED [EC:1.9.98.1]
-xref: EC:1.9.98.1
+def: "Catalysis of the reaction: Fe3+ + Fe(II)-[cytochrome c] = Fe2+ + Fe(III)-[cytochrome c]." [EC:1.16.2.1, RHEA:15617]
+synonym: "ferrocytochrome-c:Fe3+ oxidoreductase activity" RELATED [EC:1.16.2.1]
+synonym: "iron-cytochrome c reductase activity" RELATED [EC:1.16.2.1]
+xref: EC:1.16.2.1
xref: MetaCyc:IRON--CYTOCHROME-C-REDUCTASE-RXN
xref: RHEA:15617
-is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
-property_value: skos:exactMatch EC:1.9.98.1
+is_a: GO:0016722 ! oxidoreductase activity, acting on metal ions
+property_value: skos:exactMatch EC:1.16.2.1
property_value: skos:exactMatch RHEA:15617
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31488" xsd:anyURI
[Term]
id: GO:0047727
@@ -313191,9 +317060,11 @@
xref: KEGG_REACTION:R02395
xref: MetaCyc:CARNITINE-3-DEHYDROGENASE-RXN
xref: RHEA:19265
+xref: RHEA:25330
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.108
property_value: skos:exactMatch RHEA:19265
+property_value: skos:narrowMatch RHEA:25330
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -313337,9 +317208,11 @@
xref: EC:1.1.99.18
xref: MetaCyc:CELLOBIOSE-DEHYDROGENASE-ACCEPTOR-RXN
xref: RHEA:23484
+xref: RHEA:59316
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: skos:exactMatch EC:1.1.99.18
property_value: skos:exactMatch RHEA:23484
+property_value: skos:narrowMatch RHEA:59316
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -313393,10 +317266,11 @@
[Term]
id: GO:0047740
-name: cephalosporin-C transaminase activity
+name: cephalosporin-C:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (7R)-7-(5-carboxylato-5-oxopentanamido)deacetylcephalosporanate + D-glutamate = 2-oxoglutarate + cephalosporin C." [EC:2.6.1.74, RHEA:14553]
+def: "Catalysis of the reaction: (7R)-7-(5-carboxylato-5-oxopentanamido)deacetylcephalosporanate + D-glutamate = 2-oxoglutarate + cephalosporin C." [RHEA:14553]
synonym: "cephalosporin C aminotransferase activity" RELATED [EC:2.6.1.74]
+synonym: "cephalosporin-C transaminase activity" EXACT []
synonym: "cephalosporin-C:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.74]
synonym: "L-alanine:cephalosporin-C aminotransferase activity" RELATED [EC:2.6.1.74]
xref: EC:2.6.1.74
@@ -313407,6 +317281,7 @@
property_value: skos:exactMatch EC:2.6.1.74
property_value: skos:exactMatch RHEA:14553
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047741
@@ -313493,9 +317368,11 @@
xref: EC:3.1.1.14
xref: MetaCyc:CHLOROPHYLLASE-RXN
xref: RHEA:19605
+xref: RHEA:38011
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.14
property_value: skos:exactMatch RHEA:19605
+property_value: skos:narrowMatch RHEA:38011
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -313535,7 +317412,6 @@
xref: RHEA:47128
xref: RHEA:47136
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.7
property_value: skos:narrowMatch RHEA:22976
property_value: skos:narrowMatch RHEA:23532
@@ -313612,7 +317488,16 @@
xref: MetaCyc:CHOLESTENONE-5-ALPHA-REDUCTASE-RXN
xref: MetaCyc:RXN-4229
xref: MetaCyc:RXN-711
+xref: RHEA:21952
+xref: RHEA:24552
+xref: RHEA:50816
+xref: RHEA:50820
xref: RHEA:54384
+xref: RHEA:54416
+xref: RHEA:69987
+xref: RHEA:69991
+xref: RHEA:84191
+xref: RHEA:84195
is_a: GO:0003865 ! 3-oxo-5-alpha-steroid 4-dehydrogenase activity
is_a: GO:0035671 ! enone reductase activity
property_value: skos:exactMatch EC:1.3.1.22
@@ -313621,6 +317506,15 @@
property_value: skos:narrowMatch MetaCyc:CHOLESTENONE-5-ALPHA-REDUCTASE-RXN
property_value: skos:narrowMatch MetaCyc:RXN-4229
property_value: skos:narrowMatch MetaCyc:RXN-711
+property_value: skos:narrowMatch RHEA:21952
+property_value: skos:narrowMatch RHEA:24552
+property_value: skos:narrowMatch RHEA:50816
+property_value: skos:narrowMatch RHEA:50820
+property_value: skos:narrowMatch RHEA:54416
+property_value: skos:narrowMatch RHEA:69987
+property_value: skos:narrowMatch RHEA:69991
+property_value: skos:narrowMatch RHEA:84191
+property_value: skos:narrowMatch RHEA:84195
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25314" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
@@ -313681,7 +317575,7 @@
synonym: "chondroitin 4-sulphotransferase activity" EXACT []
xref: EC:2.8.2.5
xref: MetaCyc:CHONDROITIN-4-SULFOTRANSFERASE-RXN
-xref: Reactome:R-HSA-1971483 "Chondroitin can be sulfated on position 4 of GalNAc by CHST9, 11, 12 and 13"
+xref: Reactome:R-HSA-1971483 "CHST11,12,13,9 transfer sulfate to (4-)GalNAc"
xref: RHEA:16101
is_a: GO:0034481 ! chondroitin sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.5
@@ -313700,7 +317594,7 @@
synonym: "urunosyl C-5 epimerase activity" RELATED [EC:5.1.3.19]
xref: EC:5.1.3.19
xref: MetaCyc:CHONDROITIN-GLUCURONATE-5-EPIMERASE-RXN
-xref: Reactome:R-HSA-2022052 "Dermatan-sulfate epimerase (DSE) converts chondroitin sulfate (CS) to dermatan sulfate (DS)"
+xref: Reactome:R-HSA-2022052 "DSE converts GlcA to IdoA"
xref: RHEA:21084
is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and derivatives
property_value: skos:exactMatch EC:5.1.3.19
@@ -314039,7 +317933,7 @@
xref: KEGG_REACTION:R01322
xref: MetaCyc:CITRATE--COA-LIGASE-RXN
xref: RHEA:21472
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.18
property_value: skos:exactMatch RHEA:21472
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -314062,7 +317956,7 @@
id: GO:0047781
name: citrullinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + citrulline = NH3 + CO2 + L-ornithine." [EC:3.5.1.20, MetaCyc:CITRULLINASE-RXN]
+def: "Catalysis of the reaction: L-citrulline + H2O + 2 H+ = L-ornithine + NH4+ + CO2." [RHEA:11940]
synonym: "citrulline hydrolase activity" RELATED [EC:3.5.1.20]
synonym: "citrulline ureidase activity" RELATED [EC:3.5.1.20]
synonym: "L-citrulline 5-N-carbamoyldihydrolase activity" RELATED [EC:3.5.1.20]
@@ -314200,6 +318094,19 @@
xref: MetaCyc:CORTISONE-BETA-REDUCTASE-RXN
xref: MetaCyc:RXN-23672
xref: MetaCyc:RXN-9726
+xref: RHEA:11524
+xref: RHEA:14037
+xref: RHEA:46632
+xref: RHEA:46636
+xref: RHEA:46640
+xref: RHEA:46644
+xref: RHEA:46652
+xref: RHEA:46656
+xref: RHEA:46660
+xref: RHEA:46664
+xref: RHEA:46668
+xref: RHEA:46672
+xref: RHEA:47080
xref: RHEA:54412
is_a: GO:0035671 ! enone reductase activity
property_value: skos:exactMatch EC:1.3.1.3
@@ -314208,6 +318115,19 @@
property_value: skos:narrowMatch MetaCyc:CHOLESTENONE-5-BETA-REDUCTASE-RXN
property_value: skos:narrowMatch MetaCyc:CORTISONE-BETA-REDUCTASE-RXN
property_value: skos:narrowMatch MetaCyc:RXN-9726
+property_value: skos:narrowMatch RHEA:11524
+property_value: skos:narrowMatch RHEA:14037
+property_value: skos:narrowMatch RHEA:46632
+property_value: skos:narrowMatch RHEA:46636
+property_value: skos:narrowMatch RHEA:46640
+property_value: skos:narrowMatch RHEA:46644
+property_value: skos:narrowMatch RHEA:46652
+property_value: skos:narrowMatch RHEA:46656
+property_value: skos:narrowMatch RHEA:46660
+property_value: skos:narrowMatch RHEA:46664
+property_value: skos:narrowMatch RHEA:46668
+property_value: skos:narrowMatch RHEA:46672
+property_value: skos:narrowMatch RHEA:47080
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27695" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -314248,7 +318168,7 @@
id: GO:0047790
name: creatinine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: creatinine + H2O = N-methylhydantoin + NH3." [EC:3.5.4.21, MetaCyc:CREATININE-DEAMINASE-RXN]
+def: "Catalysis of the reaction: creatinine + H2O + H+ = N-methylhydantoin + NH4+." [RHEA:12681]
synonym: "creatinine desiminase activity" RELATED [EC:3.5.4.21]
synonym: "creatinine hydrolase" BROAD [EC:3.5.4.21]
synonym: "creatinine iminohydrolase activity" RELATED [EC:3.5.4.21]
@@ -314374,9 +318294,11 @@
xref: KEGG_REACTION:R02234
xref: MetaCyc:CYCLOHEXANONE-DEHYDROGENASE-RXN
xref: RHEA:21780
+xref: RHEA:80151
is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
property_value: skos:exactMatch EC:1.3.99.14
property_value: skos:exactMatch RHEA:21780
+property_value: skos:narrowMatch RHEA:80151
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -314434,28 +318356,31 @@
[Term]
id: GO:0047801
-name: L-cysteine transaminase activity
+name: L-cysteine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteine + 2-oxoglutarate = mercaptopyruvate + L-glutamate." [RHEA:17441]
+def: "Catalysis of the reaction: L-cysteine + 2-oxoglutarate = 2-oxo-3-sulfanylpropanoate + L-glutamate." [RHEA:17441]
synonym: "cysteine aminotransferase activity" BROAD []
synonym: "cysteine transaminase activity" EXACT [EC:2.6.1.3]
+synonym: "L-cysteine transaminase activity" BROAD []
synonym: "L-cysteine:2-oxoglutarate aminotransferase activity" EXACT []
xref: EC:2.6.1.3
xref: MetaCyc:CYSTEINE-AMINOTRANSFERASE-RXN
xref: Reactome:R-HSA-9012597 "GOT2 dimer transfers amino group from L-Cys to 2OG to form 3MPYR and Glu"
xref: RHEA:17441
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.3
property_value: skos:exactMatch RHEA:17441
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047802
-name: cysteine-conjugate transaminase activity
+name: cysteine-conjugate:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + S-(4-bromophenyl)-L-cysteine = (4-bromophenylsulfanyl)pyruvate + L-glutamate." [EC:2.6.1.75, RHEA:13485]
+def: "Catalysis of the reaction: 2-oxoglutarate + S-(4-bromophenyl)-L-cysteine = (4-bromophenylsulfanyl)pyruvate + L-glutamate." [RHEA:13485]
synonym: "cysteine conjugate aminotransferase activity" RELATED [EC:2.6.1.75]
synonym: "cysteine-conjugate alpha-ketoglutarate transaminase (CAT-1)" RELATED [EC:2.6.1.75]
+synonym: "cysteine-conjugate transaminase activity" EXACT []
synonym: "S-(4-bromophenyl)-L-cysteine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.75]
xref: EC:2.6.1.75
xref: KEGG_REACTION:R04338
@@ -314465,6 +318390,7 @@
property_value: skos:exactMatch EC:2.6.1.75
property_value: skos:exactMatch RHEA:13485
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047803
@@ -314498,12 +318424,26 @@
xref: EC:4.4.1.13
xref: MetaCyc:CYSTATHIONINE-BETA-LYASE-RXN
xref: MetaCyc:RXN-6763
+xref: RHEA:13965
xref: RHEA:18121
+xref: RHEA:22424
+xref: RHEA:64740
+xref: RHEA:64744
+xref: RHEA:64748
+xref: RHEA:64752
+xref: RHEA:64756
is_a: GO:0016846 ! carbon-sulfur lyase activity
property_value: skos:exactMatch EC:4.4.1.13
property_value: skos:exactMatch MetaCyc:RXN-6763
property_value: skos:exactMatch RHEA:18121
property_value: skos:narrowMatch MetaCyc:CYSTATHIONINE-BETA-LYASE-RXN
+property_value: skos:narrowMatch RHEA:13965
+property_value: skos:narrowMatch RHEA:22424
+property_value: skos:narrowMatch RHEA:64740
+property_value: skos:narrowMatch RHEA:64744
+property_value: skos:narrowMatch RHEA:64748
+property_value: skos:narrowMatch RHEA:64752
+property_value: skos:narrowMatch RHEA:64756
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27673" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -314598,20 +318538,23 @@
xref: KEGG_REACTION:R00297
xref: MetaCyc:D-2-HYDROXY-ACID-DEHYDROGENASE-RXN
xref: RHEA:15089
+xref: RHEA:62968
is_a: GO:0004457 ! lactate dehydrogenase activity
is_a: GO:0033719 ! (2R)-oxo-acid reductase activity
property_value: skos:exactMatch EC:1.1.99.6
property_value: skos:exactMatch RHEA:15089
+property_value: skos:narrowMatch RHEA:62968
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30132" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0047810
-name: D-alanine-2-oxoglutarate aminotransferase activity
+name: D-alanine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate." [EC:2.6.1.21]
+def: "Catalysis of the reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate." [RHEA:15869]
synonym: "D-alanine aminotransferase activity" EXACT []
synonym: "D-alanine transaminase activity" BROAD [EC:2.6.1.21]
+synonym: "D-alanine-2-oxoglutarate aminotransferase activity" EXACT []
synonym: "D-alanine-D-glutamate transaminase activity" RELATED [EC:2.6.1.21]
synonym: "D-amino acid aminotransferase activity" BROAD [EC:2.6.1.21]
synonym: "D-amino acid transaminase activity" BROAD [EC:2.6.1.21]
@@ -314622,10 +318565,11 @@
xref: EC:2.6.1.21
xref: MetaCyc:D-ALANINE-AMINOTRANSFERASE-RXN
xref: RHEA:15869
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.21
property_value: skos:exactMatch RHEA:15869
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047811
@@ -314653,10 +318597,11 @@
xref: EC:2.3.1.36
xref: MetaCyc:D-AMINO-ACID-N-ACETYLTRANSFERASE-RXN
xref: RHEA:20704
-is_a: GO:0008080 ! N-acetyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.36
property_value: skos:exactMatch RHEA:20704
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0047813
@@ -315024,9 +318969,15 @@
xref: EC:1.1.1.122
xref: MetaCyc:D-THREO-ALDOSE-1-DEHYDROGENASE-RXN
xref: RHEA:19645
+xref: RHEA:81515
+xref: RHEA:81519
+xref: RHEA:81523
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.122
property_value: skos:exactMatch RHEA:19645
+property_value: skos:narrowMatch RHEA:81515
+property_value: skos:narrowMatch RHEA:81519
+property_value: skos:narrowMatch RHEA:81523
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -315057,9 +319008,11 @@
xref: MetaCyc:D-TRYPTOPHAN-N-MALONYLTRANSFERASE-RXN
xref: RHEA:23320
is_a: GO:0050735 ! N-malonyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.112
property_value: skos:exactMatch RHEA:23320
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0047837
@@ -315320,9 +319273,19 @@
xref: EC:6.2.1.23
xref: MetaCyc:DICARBOXYLATE--COA-LIGASE-RXN
xref: RHEA:14289
-is_a: GO:0016878 ! acid-thiol ligase activity
+xref: RHEA:40239
+xref: RHEA:40287
+xref: RHEA:40291
+xref: RHEA:40295
+xref: RHEA:49600
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.23
property_value: skos:exactMatch RHEA:14289
+property_value: skos:narrowMatch RHEA:40239
+property_value: skos:narrowMatch RHEA:40287
+property_value: skos:narrowMatch RHEA:40291
+property_value: skos:narrowMatch RHEA:40295
+property_value: skos:narrowMatch RHEA:49600
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -315453,25 +319416,20 @@
name: diiodophenylpyruvate reductase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: 3-(3,5-diiodo-4-hydroxyphenyl)lactate + NAD+ = 3-(3,5-diiodo-4-hydroxyphenyl)pyruvate + H+ + NADH." [RHEA:20293]
-synonym: "2-oxo acid reductase activity" RELATED [EC:1.1.1.96]
-synonym: "3-(3,5-diiodo-4-hydroxyphenyl)lactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.96]
-synonym: "aromatic alpha-keto acid" RELATED [EC:1.1.1.96]
-synonym: "KAR" RELATED [EC:1.1.1.96]
-xref: EC:1.1.1.96
xref: KEGG_REACTION:R03431
xref: MetaCyc:DIIODOPHENYLPYRUVATE-REDUCTASE-RXN
xref: RHEA:20293
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-property_value: skos:exactMatch EC:1.1.1.96
property_value: skos:exactMatch RHEA:20293
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30138" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31488" xsd:anyURI
[Term]
id: GO:0047861
-name: diiodotyrosine transaminase activity
+name: 3,5-diiodo-L-tyrosine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + 3,5-diiodo-L-tyrosine = 3-(3,5-diiodo-4-hydroxyphenyl)pyruvate + L-glutamate." [EC:2.6.1.24, RHEA:19781]
+def: "Catalysis of the reaction: 2-oxoglutarate + 3,5-diiodo-L-tyrosine = 3-(3,5-diiodo-4-hydroxyphenyl)pyruvate + L-glutamate." [RHEA:19781]
synonym: "3,5-diiodo-L-tyrosine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.24]
synonym: "diiodotyrosine aminotransferase activity" EXACT []
synonym: "halogenated tyrosine aminotransferase activity" RELATED [EC:2.6.1.24]
@@ -315484,6 +319442,7 @@
property_value: skos:exactMatch EC:2.6.1.24
property_value: skos:exactMatch RHEA:19781
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047862
@@ -315752,9 +319711,19 @@
xref: EC:3.2.1.123
xref: MetaCyc:ENDOGLYCOSYLCERAMIDASE-RXN
xref: RHEA:22288
+xref: RHEA:65540
+xref: RHEA:65544
+xref: RHEA:65548
+xref: RHEA:65552
+xref: RHEA:65556
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
property_value: skos:exactMatch EC:3.2.1.123
property_value: skos:exactMatch RHEA:22288
+property_value: skos:narrowMatch RHEA:65540
+property_value: skos:narrowMatch RHEA:65544
+property_value: skos:narrowMatch RHEA:65548
+property_value: skos:narrowMatch RHEA:65552
+property_value: skos:narrowMatch RHEA:65556
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -315871,7 +319840,7 @@
id: GO:0047883
name: ethanolamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethanolamine + H2O + O2 = glycolaldehyde + NH3 + H2O2." [RHEA:18581]
+def: "Catalysis of the reaction: ethanolamine + O2 + H2O = glycolaldehyde + H2O2 + NH4+." [RHEA:18581]
synonym: "ethanolamine:oxygen oxidoreductase (deaminating)" RELATED [EC:1.4.3.8]
xref: EC:1.4.3.8
xref: MetaCyc:ETHANOLAMINE-OXIDASE-RXN
@@ -316056,9 +320025,11 @@
xref: EC:2.4.1.91
xref: MetaCyc:FLAVONOL-3-O-GLUCOSYLTRANSFERASE-RXN
xref: RHEA:22300
+xref: RHEA:61180
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.91
property_value: skos:exactMatch RHEA:22300
+property_value: skos:narrowMatch RHEA:61180
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -316672,7 +320643,7 @@
name: glucosaminate ammonia-lyase activity
namespace: molecular_function
alt_id: GO:0050443
-def: "Catalysis of the reaction: D-glucosaminate = 2-dehydro-3-deoxy-D-gluconate + NH3." [EC:4.3.1.9]
+def: "Catalysis of the reaction: 2-amino-2-deoxy-D-gluconate = 2-dehydro-3-deoxy-D-gluconate + NH4+." [RHEA:12488]
comment: Note that this function was EC:4.3.1.21.
synonym: "2-amino-2-deoxy-D-gluconate ammonia-lyase activity" RELATED [EC:4.3.1.9]
synonym: "2-amino-2-deoxy-D-gluconate hydro-lyase (deaminating) activity" RELATED [EC:4.3.1.9]
@@ -316933,9 +320904,9 @@
[Term]
id: GO:0047945
-name: L-glutamine:pyruvate aminotransferase activity
+name: L-glutamine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine." [EC:2.6.1.15, RHEA:10400]
+def: "Catalysis of the reaction: L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine." [RHEA:10400]
synonym: "gamma-glutaminyltransferase activity" RELATED [EC:2.6.1.15]
synonym: "glutaminase II activity" RELATED [EC:2.6.1.15]
synonym: "glutamine transaminase activity" BROAD [EC:2.6.1.15]
@@ -316948,26 +320919,29 @@
synonym: "glutamine-oxo acid aminotransferase activity" BROAD [EC:2.6.1.15]
synonym: "glutamine-pyruvate transaminase activity" BROAD [EC:2.6.1.15]
synonym: "L-glutamine transaminase L" RELATED [EC:2.6.1.15]
+synonym: "L-glutamine:pyruvate aminotransferase activity" EXACT []
xref: EC:2.6.1.15
xref: KEGG_REACTION:R00576
xref: MetaCyc:GLUTAMINE--PYRUVATE-AMINOTRANSFERASE-RXN
xref: Reactome:R-HSA-893616 "glutamine + pyruvate => 2-oxoglutaramate + alanine"
xref: RHEA:10400
-is_a: GO:0070548 ! L-glutamine aminotransferase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.15
property_value: skos:exactMatch RHEA:10400
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047946
-name: glutamine N-acyltransferase activity
+name: L-glutamine N-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + L-glutamine = CoA + N-acyl-L-glutamine." [EC:2.3.1.68, MetaCyc:GLUTAMINE-N-ACYLTRANSFERASE-RXN]
+def: "Catalysis of the reaction: acyl-CoA + L-glutamine = CoA + N-acyl-L-glutamine." [RHEA:18469]
synonym: "acyl-CoA:L-glutamine N-acyltransferase activity" RELATED [EC:2.3.1.68]
+synonym: "glutamine N-acyltransferase activity" BROAD []
xref: EC:2.3.1.68
xref: MetaCyc:GLUTAMINE-N-ACYLTRANSFERASE-RXN
xref: RHEA:18469
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0140085 ! L-amino-acid N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.68
property_value: skos:exactMatch RHEA:18469
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -317000,7 +320974,7 @@
xref: KEGG_REACTION:R02402
xref: MetaCyc:GLUTARATE--COA-LIGASE-RXN
xref: RHEA:14169
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.6
property_value: skos:exactMatch RHEA:14169
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -317020,16 +320994,17 @@
id: GO:0047950
name: glutathione oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 glutathione + O2 = glutathione disulfide + H2O2." [EC:1.8.3.3, RHEA:24112]
+def: "Catalysis of the reaction: 2 glutathione + O2 = glutathione disulfide + H2O2." [RHEA:24112]
synonym: "glutathione:oxygen oxidoreductase activity" RELATED [EC:1.8.3.3]
xref: EC:1.8.3.3
xref: KEGG_REACTION:R00120
xref: MetaCyc:GLUTATHIONE-OXIDASE-RXN
xref: RHEA:24112
-is_a: GO:0016670 ! oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
+is_a: GO:0016972 ! thiol oxidase activity
property_value: skos:exactMatch EC:1.8.3.3
property_value: skos:exactMatch RHEA:24112
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
[Term]
id: GO:0047951
@@ -317160,29 +321135,31 @@
[Term]
id: GO:0047958
-name: glycine:2-oxoglutarate aminotransferase activity
+name: glycine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycine + 2-oxoglutarate = glyoxylate + L-glutamate." [EC:2.6.1.4, MetaCyc:GLYCINE-AMINOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: glycine + 2-oxoglutarate = glyoxylate + L-glutamate." [RHEA:14089]
synonym: "glutamate-glyoxylate transaminase activity" EXACT []
synonym: "glutamic-glyoxylic transaminase activity" RELATED [EC:2.6.1.4]
synonym: "glycine aminotransferase activity" BROAD []
synonym: "glycine transaminase activity" BROAD [EC:2.6.1.4]
+synonym: "glycine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "glyoxylate-glutamate aminotransferase activity" RELATED [EC:2.6.1.4]
synonym: "glyoxylate-glutamic transaminase activity" RELATED [EC:2.6.1.4]
synonym: "L-glutamate:glyoxylate aminotransferase activity" EXACT []
xref: EC:2.6.1.4
xref: MetaCyc:GLYCINE-AMINOTRANSFERASE-RXN
xref: RHEA:14089
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.4
property_value: skos:exactMatch RHEA:14089
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0047959
name: glycine dehydrogenase (cytochrome) activity
namespace: molecular_function
-def: "Catalysis of the reaction: glycine + H2O + 2 ferricytochrome c = glyoxylate + NH3 + 2 ferrocytochrome c." [EC:1.4.2.1, MetaCyc:GLYCINE-DEHYDROGENASE-CYTOCHROME-RXN]
+def: "Catalysis of the reaction: 2 Fe(III)-[cytochrome c] + glycine + H2O = 2 Fe(II)-[cytochrome c] + glyoxylate + NH4+ + 2 H+." [RHEA:16909]
synonym: "glycine-cytochrome c reductase activity" RELATED [EC:1.4.2.1]
synonym: "glycine:ferricytochrome-c oxidoreductase (deaminating)" RELATED [EC:1.4.2.1]
synonym: "reductase, glycine-cytochrome c" RELATED [EC:1.4.2.1]
@@ -317214,7 +321191,7 @@
id: GO:0047961
name: glycine N-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + glycine = CoA + N-acylglycine." [EC:2.3.1.13, MetaCyc:GLYCINE-N-ACYLTRANSFERASE-RXN]
+def: "Catalysis of the reaction: acyl-CoA + glycine = CoA + N-acylglycine." [RHEA:19869]
synonym: "acyl-CoA:glycine N-acyltransferase activity" RELATED [EC:2.3.1.13]
synonym: "glycine acyltransferase activity" RELATED [EC:2.3.1.13]
synonym: "glycine-N-acylase activity" RELATED [EC:2.3.1.13]
@@ -317222,10 +321199,15 @@
xref: MetaCyc:GLYCINE-N-ACYLTRANSFERASE-RXN
xref: Reactome:R-HSA-2534040 "Unknown NAT N-acylates Gly in GNAT1"
xref: RHEA:19869
-is_a: GO:0016410 ! N-acyltransferase activity
+xref: RHEA:49788
+xref: RHEA:64244
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.13
property_value: skos:exactMatch RHEA:19869
+property_value: skos:narrowMatch RHEA:49788
+property_value: skos:narrowMatch RHEA:64244
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0047962
@@ -317443,7 +321425,7 @@
id: GO:0047974
name: guanosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanosine + H2O = xanthosine + NH3." [EC:3.5.4.15, MetaCyc:GUANOSINE-DEAMINASE-RXN]
+def: "Catalysis of the reaction: guanosine + H2O + H+ = xanthosine + NH4+." [RHEA:12861]
synonym: "guanosine aminase activity" RELATED [EC:3.5.4.15]
synonym: "guanosine aminohydrolase activity" RELATED [EC:3.5.4.15]
xref: EC:3.5.4.15
@@ -317564,7 +321546,7 @@
id: GO:0047981
name: L-histidine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidine + acetyl-CoA = N(alpha)-acetyl-L-histidine + CoA + H+." [EC:2.3.1.33, RHEA:24596]
+def: "Catalysis of the reaction: L-histidine + acetyl-CoA = N(alpha)-acetyl-L-histidine + CoA + H+." [RHEA:24596]
synonym: "acetyl-CoA:L-histidine N-acetyltransferase activity" RELATED [EC:2.3.1.33]
synonym: "acetylhistidine synthetase activity" RELATED [EC:2.3.1.33]
synonym: "histidine acetyltransferase activity" RELATED [EC:2.3.1.33]
@@ -317582,7 +321564,7 @@
id: GO:0047982
name: homocysteine desulfhydrase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-homocysteine + H2O = sulfide + NH3 + 2-oxobutanoate." [EC:4.4.1.2, MetaCyc:HOMOCYSTEINE-DESULFHYDRASE-RXN]
+def: "Catalysis of the reaction: L-homocysteine + H2O = 2-oxobutanoate + hydrogen sulfide + NH4+ + H+." [RHEA:14501]
synonym: "homocysteine desulfurase activity" RELATED [EC:4.4.1.2]
synonym: "L-homocysteine hydrogen-sulfide-lyase (deaminating)" RELATED [EC:4.4.1.2]
synonym: "L-homocysteine hydrogen-sulfide-lyase (deaminating; 2-oxobutanoate-forming)" RELATED [EC:4.4.1.2]
@@ -318058,8 +322040,8 @@
synonym: "receptor agonist activity" RELATED [GOC:molecular_function_refactoring]
synonym: "signaling molecule" BROAD []
synonym: "signaling receptor ligand activity" EXACT []
-xref: Reactome:R-HSA-163625 "Glucagon binds to Glucagon receptor"
xref: Reactome:R-HSA-381612 "GLP1R binds GLP1"
+xref: Reactome:R-HSA-8848663 "ADIPOQ trimer binds ADIPOR dimers"
is_a: GO:0030546 ! signaling receptor activator activity
relationship: has_part GO:0005102 ! signaling receptor binding
relationship: part_of GO:0007165 ! signal transduction
@@ -318373,7 +322355,9 @@
namespace: cellular_component
def: "The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it." [GOC:jid]
xref: Wikipedia:Apoplast
-is_a: GO:0005576 ! extracellular region
+is_a: GO:0110165 ! cellular anatomical structure
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0048047
@@ -319382,17 +323366,16 @@
id: GO:0048180
name: activin complex
namespace: cellular_component
-def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit." [GOC:go_curators]
+def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits, inhibin beta-A and inhibin beta-B (sometimes known as activin beta or activin/inhibin beta). There are three forms of activin complex, activin A, which is composed of 2 inhibin beta-A subunits, activin B, which is composed of 2 inhibin beta-B subunits, and activin AB, which is composed of an inhibin beta-A and an inhibin beta-B subunit." [GOC:curators]
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'.
subset: goslim_pir
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
[Term]
id: GO:0048183
name: activin AB complex
namespace: cellular_component
-def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits (sometimes known as activin beta or activin/inhibin beta), inhibin beta-A and inhibin beta-B." [GOC:go_curators]
+def: "A nonsteroidal regulator, composed of two covalently linked inhibin beta subunits (sometimes known as activin beta or activin/inhibin beta), inhibin beta-A and inhibin beta-B." [GOC:curators]
comment: Note that the actions of the activin complex are the opposite of those of the inhibin complex, which is a dimer of an inhibin beta-A or inhibin beta-B subunit and a inhibin alpha subunit. See 'inhibin complex ; GO:0043511'.
synonym: "inhibin beta-A" NARROW []
synonym: "inhibin beta-B" NARROW []
@@ -319994,6 +323977,7 @@
synonym: "mitochondrial iron ion transmembrane transport" RELATED []
synonym: "mitochondrial iron ion transport" RELATED []
synonym: "mitochondrial iron transport" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034755 ! iron ion transmembrane transport
created_by: al
creation_date: 2016-02-10T11:24:22Z
@@ -320059,17 +324043,18 @@
[Term]
id: GO:0048258
-name: 3-ketoglucose-reductase activity
+name: obsolete 3-ketoglucose-reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP+ + 3-dehydro-alpha-D-glucose = NADPH + alpha-D-glucose." [MetaCyc:KETOGLUCOSE-REDUCTASE-RXN]
-xref: MetaCyc:KETOGLUCOSE-REDUCTASE-RXN
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: NADP+ + 3-dehydro-alpha-D-glucose = NADPH + alpha-D-glucose." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0048259
name: regulation of receptor-mediated endocytosis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:go_curators, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:curators, GOC:tb]
synonym: "regulation of receptor mediated endocytosis" EXACT [GOC:tb]
is_a: GO:0030100 ! regulation of endocytosis
intersection_of: GO:0065007 ! biological regulation
@@ -320080,7 +324065,7 @@
id: GO:0048260
name: positive regulation of receptor-mediated endocytosis
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:go_curators, GOC:tb]
+def: "Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:curators, GOC:tb]
synonym: "activation of receptor mediated endocytosis" NARROW []
synonym: "positive regulation of receptor mediated endocytosis" EXACT [GOC:tb]
synonym: "stimulation of receptor mediated endocytosis" NARROW []
@@ -320097,7 +324082,7 @@
id: GO:0048261
name: negative regulation of receptor-mediated endocytosis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport." [GOC:curators]
synonym: "down regulation of receptor mediated endocytosis" EXACT []
synonym: "down-regulation of receptor mediated endocytosis" EXACT []
synonym: "downregulation of receptor mediated endocytosis" EXACT []
@@ -320154,7 +324139,8 @@
def: "Any process that results in a change in the behavior of an organism as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli." [GOC:jid]
synonym: "behavioural response to pain" EXACT []
is_a: GO:0007610 ! behavior
-relationship: part_of GO:0048265 ! response to pain
+is_a: GO:0048265 ! response to pain
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31407" xsd:anyURI
[Term]
id: GO:0048268
@@ -320656,7 +324642,7 @@
id: GO:0048317
name: seed morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the seed are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the seed are generated and organized." [GOC:curators]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0090698 ! post-embryonic plant morphogenesis
relationship: part_of GO:0048316 ! seed development
@@ -320672,7 +324658,7 @@
id: GO:0048319
name: axial mesoderm morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the axial mesoderm are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the axial mesoderm are generated and organized." [GOC:curators]
is_a: GO:0048332 ! mesoderm morphogenesis
relationship: part_of GO:0048318 ! axial mesoderm development
@@ -320816,7 +324802,7 @@
id: GO:0048332
name: mesoderm morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the mesoderm are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the mesoderm are generated and organized." [GOC:curators]
is_a: GO:0048729 ! tissue morphogenesis
relationship: part_of GO:0007498 ! mesoderm development
@@ -320911,7 +324897,7 @@
id: GO:0048340
name: paraxial mesoderm morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the paraxial mesoderm are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the paraxial mesoderm are generated and organized." [GOC:curators]
is_a: GO:0048332 ! mesoderm morphogenesis
is_a: GO:0072132 ! mesenchyme morphogenesis
relationship: part_of GO:0048339 ! paraxial mesoderm development
@@ -321176,7 +325162,7 @@
id: GO:0048366
name: leaf development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048827 ! phyllome development
[Term]
@@ -321184,7 +325170,7 @@
name: shoot system development
namespace: biological_process
alt_id: GO:0022621
-def: "The process whose specific outcome is the progression of the shoot system over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the shoot system over time, from its formation to the mature structure." [GOC:curators]
synonym: "shoot development" EXACT []
is_a: GO:0048731 ! system development
@@ -321192,7 +325178,7 @@
id: GO:0048368
name: lateral mesoderm development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure." [GOC:curators]
synonym: "lateral plate mesoderm development" EXACT []
is_a: GO:0007498 ! mesoderm development
is_a: GO:0060485 ! mesenchyme development
@@ -321201,7 +325187,7 @@
id: GO:0048369
name: lateral mesoderm morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the lateral mesoderm are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the lateral mesoderm are generated and organized." [GOC:curators]
synonym: "lateral plate mesoderm morphogenesis" EXACT []
is_a: GO:0048332 ! mesoderm morphogenesis
is_a: GO:0072132 ! mesenchyme morphogenesis
@@ -321443,7 +325429,7 @@
id: GO:0048388
name: endosomal lumen acidification
namespace: biological_process
-def: "Any process that reduces the pH of the endosomal lumen, measured by the concentration of the hydrogen ion." [GOC:jid]
+def: "Any process that reduces the pH of the endosomal lumen, corresponding to an increase in hydrogen ion concentration." [GOC:jid]
is_a: GO:0051452 ! intracellular pH reduction
relationship: part_of GO:0007032 ! endosome organization
@@ -321458,7 +325444,7 @@
id: GO:0048390
name: intermediate mesoderm morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the intermediate mesoderm are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the intermediate mesoderm are generated and organized." [GOC:curators]
is_a: GO:0048332 ! mesoderm morphogenesis
relationship: part_of GO:0048389 ! intermediate mesoderm development
@@ -321639,7 +325625,7 @@
name: floral organ development
namespace: biological_process
alt_id: GO:0048433
-def: "The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure." [GOC:go_curators, GOC:PO_curators, PO:0025395]
+def: "The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure." [GOC:curators, GOC:PO_curators, PO:0025395]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0099402 ! plant organ development
relationship: part_of GO:0009908 ! flower development
@@ -321649,7 +325635,7 @@
name: floral whorl development
namespace: biological_process
alt_id: GO:0048413
-def: "The process whose specific outcome is the progression of a floral whorl over time, from its formation to the mature structure. A floral whorl is a circular arrangement of parts of a flower arising from a stem of a plant." [GOC:dph, GOC:go_curators, GOC:PO_curators, GOC:tb, PO:0025023]
+def: "The process whose specific outcome is the progression of a floral whorl over time, from its formation to the mature structure. A floral whorl is a circular arrangement of parts of a flower arising from a stem of a plant." [GOC:curators, GOC:dph, GOC:PO_curators, GOC:tb, PO:0025023]
comment: Consider instead annotating to one of the more specific child terms, or to 'floral organ development ; GO:0048438' or one of its child terms.
synonym: "collective phyllome structure development" BROAD [GOC:PO_curators, PO:0025023]
is_a: GO:0003006 ! developmental process involved in reproduction
@@ -321661,7 +325647,7 @@
name: flower morphogenesis
namespace: biological_process
alt_id: GO:0048411
-def: "The process in which the anatomical structures of the flower are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the flower are generated and organized." [GOC:curators]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0010016 ! shoot system morphogenesis
is_a: GO:0090698 ! post-embryonic plant morphogenesis
@@ -321672,7 +325658,7 @@
name: carpel development
namespace: biological_process
alt_id: GO:0048429
-def: "The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style." [GOC:curators]
is_a: GO:0048437 ! floral organ development
is_a: GO:0048827 ! phyllome development
relationship: part_of GO:0048467 ! gynoecium development
@@ -321682,7 +325668,7 @@
name: petal development
namespace: biological_process
alt_id: GO:0048417
-def: "The process whose specific outcome is the progression of the petal over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the petal over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048437 ! floral organ development
is_a: GO:0048827 ! phyllome development
relationship: part_of GO:0048465 ! corolla development
@@ -321692,7 +325678,7 @@
name: sepal development
namespace: biological_process
alt_id: GO:0048421
-def: "The process whose specific outcome is the progression of the sepal over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the sepal over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048437 ! floral organ development
is_a: GO:0048827 ! phyllome development
relationship: part_of GO:0048464 ! flower calyx development
@@ -321702,7 +325688,7 @@
name: stamen development
namespace: biological_process
alt_id: GO:0048425
-def: "The process whose specific outcome is the progression of the stamen over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the stamen over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048437 ! floral organ development
is_a: GO:0048827 ! phyllome development
relationship: part_of GO:0048466 ! androecium development
@@ -321712,7 +325698,7 @@
name: floral organ morphogenesis
namespace: biological_process
alt_id: GO:0048434
-def: "The process in which the anatomical structures of the floral organ are generated and organized." [GOC:go_curators, GOC:PO_curators, PO:0025395]
+def: "The process in which the anatomical structures of the floral organ are generated and organized." [GOC:curators, GOC:PO_curators, PO:0025395]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0090697 ! post-embryonic plant organ morphogenesis
relationship: part_of GO:0048437 ! floral organ development
@@ -321722,7 +325708,7 @@
name: carpel morphogenesis
namespace: biological_process
alt_id: GO:0048430
-def: "The process in which the anatomical structures of the carpel are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the carpel are generated and organized." [GOC:curators]
is_a: GO:0048444 ! floral organ morphogenesis
relationship: part_of GO:0048440 ! carpel development
@@ -321731,7 +325717,7 @@
name: petal morphogenesis
namespace: biological_process
alt_id: GO:0048418
-def: "The process in which the anatomical structures of the petal are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the petal are generated and organized." [GOC:curators]
is_a: GO:0048444 ! floral organ morphogenesis
relationship: part_of GO:0048441 ! petal development
@@ -321740,7 +325726,7 @@
name: sepal morphogenesis
namespace: biological_process
alt_id: GO:0048422
-def: "The process in which the anatomical structures of the sepal are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the sepal are generated and organized." [GOC:curators]
is_a: GO:0048444 ! floral organ morphogenesis
relationship: part_of GO:0048442 ! sepal development
@@ -321749,7 +325735,7 @@
name: stamen morphogenesis
namespace: biological_process
alt_id: GO:0048426
-def: "The process in which the anatomical structures of the stamen are generated and organized." [GOC:go_curators]
+def: "The process in which the anatomical structures of the stamen are generated and organized." [GOC:curators]
is_a: GO:0048444 ! floral organ morphogenesis
relationship: part_of GO:0048443 ! stamen development
@@ -321836,7 +325822,7 @@
name: floral whorl morphogenesis
namespace: biological_process
alt_id: GO:0048414
-def: "The process in which the anatomical structures of the floral whorl are generated and organized." [GOC:go_curators, GOC:PO_curators, PO:0025023]
+def: "The process in which the anatomical structures of the floral whorl are generated and organized." [GOC:curators, GOC:PO_curators, PO:0025023]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0090698 ! post-embryonic plant morphogenesis
relationship: part_of GO:0048438 ! floral whorl development
@@ -321908,28 +325894,28 @@
id: GO:0048464
name: flower calyx development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the flower calyx over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the flower calyx over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048438 ! floral whorl development
[Term]
id: GO:0048465
name: corolla development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the corolla over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the corolla over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048438 ! floral whorl development
[Term]
id: GO:0048466
name: androecium development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the androecium over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the androecium over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0048438 ! floral whorl development
[Term]
id: GO:0048467
name: gynoecium development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the gynoecium over time, from its formation to the mature structure. The gynoecium is the collective name for the carpels of a flower." [GOC:go_curators, PO:0008062]
+def: "The process whose specific outcome is the progression of the gynoecium over time, from its formation to the mature structure. The gynoecium is the collective name for the carpels of a flower." [GOC:curators, PO:0008062]
synonym: "pistil development" EXACT []
is_a: GO:0048438 ! floral whorl development
@@ -321937,7 +325923,7 @@
id: GO:0048468
name: cell development
namespace: biological_process
-def: "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." [GOC:go_curators]
+def: "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." [GOC:curators]
subset: goslim_candida
synonym: "terminal differentiation" RELATED [GOC:dph, GOC:tb]
is_a: GO:0048856 ! anatomical structure development
@@ -321949,7 +325935,7 @@
id: GO:0048469
name: cell maturation
namespace: biological_process
-def: "The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state." [GOC:go_curators]
+def: "The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state." [GOC:curators]
subset: goslim_pir
synonym: "functional differentiation" RELATED [GOC:dph]
is_a: GO:0048869 ! cellular developmental process
@@ -322370,7 +326356,7 @@
id: GO:0048512
name: circadian behavior
namespace: biological_process
-def: "The specific behavior of an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:go_curators, GOC:pr]
+def: "The specific behavior of an organism that recurs with a regularity of approximately 24 hours." [GOC:bf, GOC:curators, GOC:pr]
synonym: "circadian rhythm behavior" EXACT []
is_a: GO:0007622 ! rhythmic behavior
is_a: GO:0007623 ! circadian rhythm
@@ -322623,7 +326609,7 @@
id: GO:0048532
name: anatomical structure arrangement
namespace: biological_process
-def: "The process that gives rise to the configuration of the constituent parts of an anatomical structure. This process pertains to the physical shaping of a rudimentary structure. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:go_curators]
+def: "The process that gives rise to the configuration of the constituent parts of an anatomical structure. This process pertains to the physical shaping of a rudimentary structure. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:curators]
synonym: "anatomical structure organization" BROAD []
synonym: "anatomical structure structural organization" EXACT []
synonym: "organization of an anatomical structure" EXACT []
@@ -322756,7 +326742,7 @@
id: GO:0048545
name: response to steroid hormone
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC:curators]
synonym: "response to steroid hormone stimulus" EXACT [GOC:dos]
is_a: GO:0009725 ! response to hormone
is_a: GO:0033993 ! response to lipid
@@ -322766,7 +326752,7 @@
name: digestive tract morphogenesis
namespace: biological_process
alt_id: GO:0048547
-def: "The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:dph, GOC:go_curators, PMID:12618131]
+def: "The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:curators, GOC:dph, PMID:12618131]
synonym: "alimentary canal morphogenesis" EXACT []
synonym: "digestive tube morphogenesis" EXACT []
synonym: "gastrointestinal tract morphogenesis" EXACT []
@@ -322779,7 +326765,7 @@
id: GO:0048548
name: regulation of pinocytosis
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:curators]
is_a: GO:0030100 ! regulation of endocytosis
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006907 ! pinocytosis
@@ -322789,7 +326775,7 @@
id: GO:0048549
name: positive regulation of pinocytosis
namespace: biological_process
-def: "Any process that activates, maintains or increases the rate of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:go_curators]
+def: "Any process that activates, maintains or increases the rate of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:curators]
synonym: "activation of pinocytosis" NARROW []
synonym: "stimulation of pinocytosis" NARROW []
synonym: "up regulation of pinocytosis" EXACT []
@@ -322805,7 +326791,7 @@
id: GO:0048550
name: negative regulation of pinocytosis
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes." [GOC:curators]
synonym: "down regulation of pinocytosis" EXACT []
synonym: "down-regulation of pinocytosis" EXACT []
synonym: "downregulation of pinocytosis" EXACT []
@@ -322840,7 +326826,7 @@
name: embryonic digestive tract morphogenesis
namespace: biological_process
alt_id: GO:0048558
-def: "The process in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:go_curators]
+def: "The process in which the anatomical structures of the digestive tract are generated and organized during embryonic development. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:curators]
synonym: "embryonic gut morphogenesis" BROAD [GOC:dph]
is_a: GO:0048562 ! embryonic organ morphogenesis
relationship: part_of GO:0048546 ! digestive tract morphogenesis
@@ -322895,7 +326881,7 @@
name: photosystem I assembly
namespace: biological_process
alt_id: GO:0010251
-def: "The aggregation, arrangement and bonding together of a set of components to form a photosystem I complex on the thylakoid membrane." [GOC:go_curators]
+def: "The aggregation, arrangement and bonding together of a set of components to form a photosystem I complex on the thylakoid membrane." [GOC:curators]
is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0019684 ! photosynthesis, light reaction
@@ -322903,7 +326889,7 @@
id: GO:0048565
name: digestive tract development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed." [GOC:curators]
synonym: "gut development" BROAD [GOC:dph]
synonym: "intestinal development" NARROW []
synonym: "intestine development" NARROW []
@@ -322914,7 +326900,7 @@
id: GO:0048566
name: embryonic digestive tract development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus." [GOC:curators]
is_a: GO:0048565 ! digestive tract development
is_a: GO:0048568 ! embryonic organ development
@@ -323198,7 +327184,7 @@
id: GO:0048588
name: developmental cell growth
namespace: biological_process
-def: "The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another." [GOC:go_curators, GOC:isa_complete]
+def: "The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another." [GOC:curators, GOC:isa_complete]
subset: gocheck_do_not_annotate
synonym: "developmental growth of a unicellular organism" EXACT []
is_a: GO:0016049 ! cell growth
@@ -323210,7 +327196,7 @@
id: GO:0048589
name: developmental growth
namespace: biological_process
-def: "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:go_curators]
+def: "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." [GOC:curators]
is_a: GO:0040007 ! growth
intersection_of: GO:0040007 ! growth
intersection_of: part_of GO:0032502 ! developmental process
@@ -323271,7 +327257,7 @@
id: GO:0048599
name: oocyte development
namespace: biological_process
-def: "The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." [GOC:curators]
is_a: GO:0007281 ! germ cell development
relationship: part_of GO:0009994 ! oocyte differentiation
@@ -323279,7 +327265,7 @@
id: GO:0048600
name: oocyte fate commitment
namespace: biological_process
-def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into an oocyte." [GOC:go_curators]
+def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into an oocyte." [GOC:curators]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0045165 ! cell fate commitment
relationship: part_of GO:0009994 ! oocyte differentiation
@@ -323288,7 +327274,7 @@
id: GO:0048601
name: oocyte morphogenesis
namespace: biological_process
-def: "The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte." [GOC:go_curators]
+def: "The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte." [GOC:curators]
synonym: "oocyte morphogenesis during differentiation" EXACT []
is_a: GO:0000902 ! cell morphogenesis
is_a: GO:0003006 ! developmental process involved in reproduction
@@ -323438,7 +327424,7 @@
id: GO:0048623
name: seed germination on parent plant
namespace: biological_process
-def: "The process in which a seed germinates before being shed from the parent plant." [GOC:go_curators]
+def: "The process in which a seed germinates before being shed from the parent plant." [GOC:curators]
synonym: "non-vegetative vivipary" BROAD []
synonym: "pre-harvest sprouting" EXACT []
synonym: "vivipary" BROAD []
@@ -323448,7 +327434,7 @@
id: GO:0048624
name: plantlet formation on parent plant
namespace: biological_process
-def: "The process in which a new plantlet develops from a meristem on the plant body. As part of this process, when the plantlet is large enough to live independently, the physical connection between the new plantlet and the main plant is severed." [GOC:go_curators]
+def: "The process in which a new plantlet develops from a meristem on the plant body. As part of this process, when the plantlet is large enough to live independently, the physical connection between the new plantlet and the main plant is severed." [GOC:curators]
synonym: "vegetative vivipary" BROAD []
synonym: "vivipary" BROAD []
is_a: GO:0003006 ! developmental process involved in reproduction
@@ -323557,7 +327543,7 @@
id: GO:0048634
name: regulation of muscle organ development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of muscle development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of muscle development." [GOC:curators]
is_a: GO:0050793 ! regulation of developmental process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0007517 ! muscle organ development
@@ -323567,7 +327553,7 @@
id: GO:0048635
name: negative regulation of muscle organ development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development." [GOC:curators]
synonym: "down regulation of muscle development" EXACT []
synonym: "down-regulation of muscle development" EXACT []
synonym: "downregulation of muscle development" EXACT []
@@ -323583,7 +327569,7 @@
id: GO:0048636
name: positive regulation of muscle organ development
namespace: biological_process
-def: "Any process that activates, maintains or increases the rate of muscle development." [GOC:go_curators]
+def: "Any process that activates, maintains or increases the rate of muscle development." [GOC:curators]
synonym: "activation of muscle development" NARROW []
synonym: "stimulation of muscle development" NARROW []
synonym: "up regulation of muscle development" EXACT []
@@ -323600,7 +327586,7 @@
id: GO:0048638
name: regulation of developmental growth
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of developmental growth." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of developmental growth." [GOC:curators]
is_a: GO:0040008 ! regulation of growth
is_a: GO:0050793 ! regulation of developmental process
intersection_of: GO:0065007 ! biological regulation
@@ -323611,7 +327597,7 @@
id: GO:0048639
name: positive regulation of developmental growth
namespace: biological_process
-def: "Any process that activates, maintains or increases the rate of developmental growth." [GOC:go_curators]
+def: "Any process that activates, maintains or increases the rate of developmental growth." [GOC:curators]
synonym: "activation of developmental growth" NARROW []
synonym: "stimulation of developmental growth" NARROW []
synonym: "up regulation of developmental growth" EXACT []
@@ -323628,7 +327614,7 @@
id: GO:0048640
name: negative regulation of developmental growth
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth." [GOC:curators]
synonym: "down regulation of developmental growth" EXACT []
synonym: "down-regulation of developmental growth" EXACT []
synonym: "downregulation of developmental growth" EXACT []
@@ -323644,7 +327630,7 @@
id: GO:0048641
name: regulation of skeletal muscle tissue development
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of skeletal muscle tissue development." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of skeletal muscle tissue development." [GOC:curators]
is_a: GO:0016202 ! regulation of striated muscle tissue development
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0007519 ! skeletal muscle tissue development
@@ -323654,7 +327640,7 @@
id: GO:0048642
name: negative regulation of skeletal muscle tissue development
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development." [GOC:go_curators]
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development." [GOC:curators]
synonym: "down regulation of skeletal muscle development" EXACT []
synonym: "down-regulation of skeletal muscle development" EXACT []
synonym: "downregulation of skeletal muscle development" EXACT []
@@ -323669,7 +327655,7 @@
id: GO:0048643
name: positive regulation of skeletal muscle tissue development
namespace: biological_process
-def: "Any process that activates, maintains or increases the rate of skeletal muscle tissue development." [GOC:go_curators]
+def: "Any process that activates, maintains or increases the rate of skeletal muscle tissue development." [GOC:curators]
synonym: "activation of skeletal muscle development" NARROW []
synonym: "stimulation of skeletal muscle development" NARROW []
synonym: "up regulation of skeletal muscle development" EXACT []
@@ -326576,7 +330562,7 @@
id: GO:0050001
name: D-glutaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + L-glutamine = NH3 + D-glutamate." [EC:3.5.1.35, MetaCyc:D-GLUTAMINASE-RXN]
+def: "Catalysis of the reaction: D-glutamine + H2O = D-glutamate + NH4+." [RHEA:22840]
synonym: "D-glutamine amidohydrolase activity" RELATED [EC:3.5.1.35]
xref: EC:3.5.1.35
xref: MetaCyc:D-GLUTAMINASE-RXN
@@ -326630,10 +330616,18 @@
synonym: "uridine diphosphoglucose-isoflavone 7-O-glucosyltransferase activity" RELATED [EC:2.4.1.170]
xref: EC:2.4.1.170
xref: MetaCyc:ISOFLAVONE-7-O-GLUCOSYLTRANSFERASE-RXN
+xref: RHEA:17497
+xref: RHEA:55416
+xref: RHEA:56048
+xref: RHEA:56056
xref: RHEA:56344
is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.170
property_value: skos:exactMatch RHEA:56344
+property_value: skos:narrowMatch RHEA:17497
+property_value: skos:narrowMatch RHEA:55416
+property_value: skos:narrowMatch RHEA:56048
+property_value: skos:narrowMatch RHEA:56056
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -326979,7 +330973,7 @@
id: GO:0050025
name: L-glutamate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutamate + O2 + H2O = 2-oxoglutarate + NH3 + H2O2." [RHEA:20728]
+def: "Catalysis of the reaction: L-glutamate + O2 + H2O = 2-oxoglutarate + H2O2 + NH4+." [RHEA:20728]
synonym: "glutamate (acceptor) dehydrogenase activity" RELATED [EC:1.4.3.11]
synonym: "glutamate oxidase activity" RELATED [EC:1.4.3.11]
synonym: "glutamic acid oxidase activity" RELATED [EC:1.4.3.11]
@@ -327049,7 +331043,6 @@
name: L-lysine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + L-lysine + O2 = 6-amino-2-oxohexanoate + H2O2 + NH4+." [RHEA:14437]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-lysine alpha-oxidase activity" RELATED [EC:1.4.3.14]
synonym: "L-lysine:oxygen 2-oxidoreductase (deaminating)" RELATED [EC:1.4.3.14]
synonym: "L-lysyl-alpha-oxidase activity" RELATED [EC:1.4.3.14]
@@ -327062,8 +331055,8 @@
property_value: skos:exactMatch KEGG_REACTION:R00447
property_value: skos:exactMatch MetaCyc:L-LYSINE-OXIDASE-RXN
property_value: skos:exactMatch RHEA:14437
-property_value: skos:relatedMatch MetaCyc:PWY-5311
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0050030
@@ -327349,12 +331342,16 @@
xref: EC:1.14.19.20
xref: MetaCyc:RXN-16378
xref: MetaCyc:RXN-4209
+xref: RHEA:46556
+xref: RHEA:46560
xref: RHEA:54320
is_a: GO:0070704 ! sterol desaturase activity
property_value: skos:exactMatch EC:1.14.19.20
property_value: skos:exactMatch MetaCyc:RXN-16378
property_value: skos:exactMatch RHEA:54320
property_value: skos:narrowMatch MetaCyc:RXN-4209
+property_value: skos:narrowMatch RHEA:46556
+property_value: skos:narrowMatch RHEA:46560
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21133" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27381" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -327409,7 +331406,7 @@
id: GO:0050050
name: L-leucine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-leucine + acetyl-CoA = N-acetyl-L-leucine + CoA + H+." [EC:2.3.1.66, RHEA:20089]
+def: "Catalysis of the reaction: L-leucine + acetyl-CoA = N-acetyl-L-leucine + CoA + H+." [RHEA:20089]
synonym: "acetyl-CoA:L-leucine N-acetyltransferase activity" RELATED [EC:2.3.1.66]
synonym: "leucine acetyltransferase activity" RELATED [EC:2.3.1.66]
xref: EC:2.3.1.66
@@ -327607,10 +331604,24 @@
xref: EC:1.2.1.48
xref: MetaCyc:LONG-CHAIN-ALDEHYDE-DEHYDROGENASE-RXN
xref: RHEA:10652
+xref: RHEA:33739
+xref: RHEA:36135
+xref: RHEA:39015
+xref: RHEA:39803
+xref: RHEA:40095
+xref: RHEA:44020
+xref: RHEA:44172
xref: UM-BBD_reactionID:r1404
is_a: GO:0102673 ! fatty aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.2.1.48
property_value: skos:exactMatch RHEA:10652
+property_value: skos:narrowMatch RHEA:33739
+property_value: skos:narrowMatch RHEA:36135
+property_value: skos:narrowMatch RHEA:39015
+property_value: skos:narrowMatch RHEA:39803
+property_value: skos:narrowMatch RHEA:40095
+property_value: skos:narrowMatch RHEA:44020
+property_value: skos:narrowMatch RHEA:44172
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28142" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -327627,9 +331638,11 @@
xref: EC:1.2.1.50
xref: MetaCyc:LONG-CHAIN-FATTY-ACYL-COA-REDUCTASE-RXN
xref: RHEA:15437
+xref: RHEA:27270
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.2.1.50
property_value: skos:exactMatch RHEA:15437
+property_value: skos:narrowMatch RHEA:27270
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25060" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25804" xsd:anyURI
@@ -327664,25 +331677,26 @@
[Term]
id: GO:0050065
-name: lysine-pyruvate 6-transaminase activity
+name: L-lysine:pyruvate 6-transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + pyruvate = L-alanine + L-allysine." [EC:2.6.1.71, RHEA:19393]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: L-lysine + pyruvate = (S)-2-amino-6-oxohexanoate + L-alanine." [RHEA:19393]
synonym: "L-lysine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.71]
synonym: "Lys-AT" RELATED [EC:2.6.1.71]
synonym: "lysine--pyruvate 6-aminotransferase activity" EXACT []
+synonym: "lysine-pyruvate 6-transaminase activity" EXACT []
synonym: "lysine-pyruvate aminotransferase activity" RELATED [EC:2.6.1.71]
xref: EC:2.6.1.71
xref: KEGG_REACTION:R00453
xref: MetaCyc:LYSINE--PYRUVATE-6-AMINOTRANSFERASE-RXN
xref: RHEA:19393
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.71
property_value: skos:exactMatch KEGG_REACTION:R00453
property_value: skos:exactMatch MetaCyc:LYSINE--PYRUVATE-6-AMINOTRANSFERASE-RXN
property_value: skos:exactMatch RHEA:19393
-property_value: skos:relatedMatch MetaCyc:PWY-5324
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0050066
@@ -327820,7 +331834,7 @@
xref: EC:6.2.1.9
xref: MetaCyc:MALATE--COA-LIGASE-RXN
xref: RHEA:26193
-is_a: GO:0016878 ! acid-thiol ligase activity
+is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch EC:6.2.1.9
property_value: skos:exactMatch RHEA:26193
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -328143,20 +332157,22 @@
[Term]
id: GO:0050094
-name: methionine-glyoxylate transaminase activity
+name: L-methionine:glyoxylate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-methionine + glyoxylate = 4-methylthio-2-oxobutanoate + glycine." [EC:2.6.1.73, RHEA:22884]
+def: "Catalysis of the reaction: glyoxylate + L-methionine = 4-methylsulfanyl-2-oxobutanoate + glycine." [RHEA:22884]
synonym: "L-methionine:glyoxylate aminotransferase activity" RELATED [EC:2.6.1.73]
synonym: "methionine-glyoxylate aminotransferase activity" RELATED [EC:2.6.1.73]
+synonym: "methionine-glyoxylate transaminase activity" EXACT []
synonym: "MGAT activity" RELATED [EC:2.6.1.73]
xref: EC:2.6.1.73
xref: KEGG_REACTION:R00652
xref: MetaCyc:METHIONINE--GLYOXYLATE-TRANSAMINASE-RXN
xref: RHEA:22884
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0010326 ! L-methionine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.73
property_value: skos:exactMatch RHEA:22884
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0050095
@@ -328667,9 +332683,13 @@
xref: MetaCyc:N-ACYLNEURAMINATE-9-PHOSPHATASE-RXN
xref: Reactome:R-HSA-4084989 "NANP dephosphorylates Neu5Ac-9-P to Neu5Ac"
xref: RHEA:13057
+xref: RHEA:80839
+xref: RHEA:83303
is_a: GO:0016791 ! phosphatase activity
property_value: skos:exactMatch EC:3.1.3.29
property_value: skos:exactMatch RHEA:13057
+property_value: skos:narrowMatch RHEA:80839
+property_value: skos:narrowMatch RHEA:83303
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -328789,9 +332809,11 @@
xref: EC:1.5.3.2
xref: MetaCyc:N-METHYL-L-AMINO-ACID-OXIDASE-RXN
xref: RHEA:11472
+xref: RHEA:28006
is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.5.3.2
property_value: skos:exactMatch RHEA:11472
+property_value: skos:narrowMatch RHEA:28006
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -328825,9 +332847,11 @@
xref: MetaCyc:N6-HYDROXYLYSINE-O-ACETYLTRANSFERASE-RXN
xref: RHEA:22388
is_a: GO:0016413 ! O-acetyltransferase activity
+is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.102
property_value: skos:exactMatch RHEA:22388
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
[Term]
id: GO:0050134
@@ -328875,10 +332899,22 @@
xref: EC:1.6.5.9
xref: MetaCyc:1.6.99.5-RXN
xref: RHEA:46160
+xref: RHEA:60660
+xref: RHEA:61984
+xref: RHEA:69695
+xref: RHEA:74075
+xref: RHEA:74079
+xref: RHEA:83235
is_a: GO:0003954 ! NADH dehydrogenase activity
is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity
property_value: skos:exactMatch EC:1.6.5.9
property_value: skos:exactMatch RHEA:46160
+property_value: skos:narrowMatch RHEA:60660
+property_value: skos:narrowMatch RHEA:61984
+property_value: skos:narrowMatch RHEA:69695
+property_value: skos:narrowMatch RHEA:74075
+property_value: skos:narrowMatch RHEA:74079
+property_value: skos:narrowMatch RHEA:83235
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25784" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -328970,7 +333006,7 @@
id: GO:0050142
name: nitrogenase (flavodoxin) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6 reduced flavodoxin + 6 H+ + N2 + n ATP = 6 oxidized flavodoxin + 2 NH3 + n ADP + n phosphate." [EC:1.19.6.1, MetaCyc:NITROGENASE-FLAVODOXIN-RXN]
+def: "Catalysis of the reaction: N2 + 4 reduced [flavodoxin] + 16 ATP + 16 H2O = 4 oxidized [flavodoxin] + H2 + 2 NH4+ + 16 ADP + 16 phosphate + 18 H+." [RHEA:15645]
synonym: "reduced flavodoxin:dinitrogen oxidoreductase (ATP-hydrolysing)" RELATED [EC:1.19.6.1]
xref: EC:1.19.6.1
xref: MetaCyc:NITROGENASE-FLAVODOXIN-RXN
@@ -329061,10 +333097,14 @@
xref: Reactome:R-HSA-2162066 "carbovir + IMP => carbovir monophosphate + inosine"
xref: Reactome:R-HSA-9754916 "NT5C2 tetramer phosphorylates RBV"
xref: RHEA:19961
+xref: RHEA:69572
+xref: RHEA:69580
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch EC:2.7.1.77
property_value: skos:exactMatch RHEA:19961
+property_value: skos:narrowMatch RHEA:69572
+property_value: skos:narrowMatch RHEA:69580
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -329439,26 +333479,30 @@
[Term]
id: GO:0050170
-name: peptidyl-glutaminase activity
+name: protein-glutaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-N-peptidyl-L-glutamine + H2O = alpha-N-peptidyl-L-glutamate + NH3." [EC:3.5.1.43, MetaCyc:PEPTIDYL-GLUTAMINASE-RXN]
+def: "Catalysis of the reaction: [protein]-C-terminal-L-glutamine + H2O = [protein]-C-terminal-L-glutamate + NH4+." [RHEA:10032]
synonym: "peptideglutaminase activity" RELATED [EC:3.5.1.43]
synonym: "peptidoglutaminase activity" RELATED [EC:3.5.1.43]
synonym: "peptidoglutaminase I activity" NARROW [EC:3.5.1.43]
+synonym: "peptidyl-glutaminase activity" EXACT []
synonym: "peptidyl-L-glutamine amidohydrolase activity" RELATED [EC:3.5.1.43]
xref: EC:3.5.1.43
xref: MetaCyc:PEPTIDYL-GLUTAMINASE-RXN
xref: RHEA:10032
+xref: RHEA:47952
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.43
property_value: skos:exactMatch RHEA:10032
+property_value: skos:narrowMatch RHEA:47952
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0050171
-name: phenol beta-glucosyltransferase activity
+name: obsolete phenol beta-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-glucose + a phenol = UDP + an aryl beta-D-glucoside." [EC:2.4.1.35, MetaCyc:PHENOL-BETA-GLUCOSYLTRANSFERASE-RXN]
+def: "OBSOLETE. Catalysis of the reaction: UDP-glucose + a phenol = UDP + an aryl beta-D-glucoside." [EC:2.4.1.35]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
synonym: "phenol b-glucosyltransferase activity" EXACT []
synonym: "phenol-beta-D-glucosyltransferase activity" RELATED [EC:2.4.1.35]
synonym: "UDP glucosyltransferase activity" RELATED [EC:2.4.1.35]
@@ -329469,9 +333513,9 @@
synonym: "uridine diphosphoglucosyltransferase activity" RELATED [EC:2.4.1.35]
xref: EC:2.4.1.35
xref: MetaCyc:PHENOL-BETA-GLUCOSYLTRANSFERASE-RXN
-is_a: GO:0035251 ! UDP-glucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.35
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0050172
@@ -329544,7 +333588,7 @@
id: GO:0050176
name: L-phenylalanine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-phenylalanine + acetyl-CoA = N-acetyl-L-phenylalanine + CoA + H+." [EC:2.3.1.53, RHEA:17801]
+def: "Catalysis of the reaction: L-phenylalanine + acetyl-CoA = N-acetyl-L-phenylalanine + CoA + H+." [RHEA:17801]
synonym: "acetyl-CoA-L-phenylalanine alpha-N-acetyltransferase activity" RELATED [EC:2.3.1.53]
synonym: "acetyl-CoA:L-phenylalanine N-acetyltransferase activity" RELATED [EC:2.3.1.53]
synonym: "phenylalanine N-acetyltransferase activity" EXACT []
@@ -329706,6 +333750,7 @@
xref: MetaCyc:RXN-8360
xref: MetaCyc:RXN-9669
xref: RHEA:46332
+xref: RHEA:66456
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
property_value: skos:exactMatch EC:1.14.19.22
property_value: skos:exactMatch MetaCyc:RXN-9669
@@ -329718,6 +333763,7 @@
property_value: skos:narrowMatch MetaCyc:RXN-8328
property_value: skos:narrowMatch MetaCyc:RXN-8330
property_value: skos:narrowMatch MetaCyc:RXN-8360
+property_value: skos:narrowMatch RHEA:66456
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23540" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -329942,7 +333988,6 @@
xref: Reactome:R-HSA-389622 "phytanate + CoA-SH + ATP => phytanoyl-CoA + AMP + pyrophosphate"
xref: RHEA:21380
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.24
property_value: skos:exactMatch RHEA:21380
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -330009,7 +334054,7 @@
xref: EC:2.7.1.52
xref: KEGG_REACTION:R03161
xref: MetaCyc:FUCOKINASE-RXN
-xref: Reactome:R-HSA-6787540 "FUK phosphorylates beta-Fuc to Fuc1P"
+xref: Reactome:R-HSA-6787540 "FCSK phosphorylates beta-Fuc to Fuc1P"
xref: RHEA:13241
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
@@ -330047,7 +334092,6 @@
xref: MetaCyc:OXALATE--COA-LIGASE-RXN
xref: RHEA:18293
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch EC:6.2.1.8
property_value: skos:exactMatch RHEA:18293
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -330116,9 +334160,17 @@
xref: EC:1.14.19.77
xref: MetaCyc:RXN-17732
xref: RHEA:22956
+xref: RHEA:61960
+xref: RHEA:61964
+xref: RHEA:61968
+xref: RHEA:61972
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
property_value: skos:exactMatch EC:1.14.19.77
property_value: skos:exactMatch RHEA:22956
+property_value: skos:narrowMatch RHEA:61960
+property_value: skos:narrowMatch RHEA:61964
+property_value: skos:narrowMatch RHEA:61968
+property_value: skos:narrowMatch RHEA:61972
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24969" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -330197,22 +334249,20 @@
id: GO:0050212
name: progesterone 11-alpha-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH2 + O2 + progesterone = 11alpha-hydroxyprogesterone + A + H2O." [RHEA:18205]
-synonym: "progesterone 11-alpha-hydroxylase activity" RELATED [EC:1.14.99.14]
+def: "Catalysis of the reaction: progesterone + reduced [NADPH-hemoprotein reductase] + O2 = 11alpha-hydroxyprogesterone + oxidized [NADPH-hemoprotein reductase] + H2O + H+." [PMID:39766209, RHEA:86055]
+synonym: "progesterone 11-alpha-hydroxylase activity" RELATED [EC:1.14.14.197]
synonym: "progesterone 11a-monooxygenase activity" EXACT []
-synonym: "progesterone 11alpha-hydroxylase activity" RELATED [EC:1.14.99.14]
-synonym: "progesterone 11alpha-monooxygenase activity" RELATED [EC:1.14.99.14]
-synonym: "progesterone,hydrogen-donor:oxygen oxidoreductase (11alpha-hydroxylating)" RELATED [EC:1.14.99.14]
-xref: EC:1.14.99.14
+synonym: "progesterone 11alpha-hydroxylase activity" RELATED [EC:1.14.14.197]
+synonym: "progesterone 11alpha-monooxygenase activity" RELATED [EC:1.14.14.197]
+synonym: "progesterone,hydrogen-donor:oxygen oxidoreductase (11alpha-hydroxylating)" RELATED [EC:1.14.14.197]
xref: KEGG_REACTION:R02214
xref: MetaCyc:PROGESTERONE-11-ALPHA-MONOOXYGENASE-RXN
-xref: PMID:39766209
-xref: RHEA:18205
+xref: RHEA:86055
is_a: GO:0050214 ! progesterone monooxygenase activity
-property_value: skos:exactMatch EC:1.14.99.14
-property_value: skos:exactMatch RHEA:18205
+property_value: skos:exactMatch RHEA:86055
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29311" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31423" xsd:anyURI
[Term]
id: GO:0050213
@@ -330484,11 +334534,13 @@
synonym: "acrasinase activity" RELATED [EC:3.5.4.11]
xref: EC:3.5.4.11
xref: MetaCyc:PTERIN-DEAMINASE-RXN
+xref: RHEA:11904
xref: RHEA:36055
is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
is_a: GO:0019239 ! deaminase activity
property_value: skos:exactMatch EC:3.5.4.11
property_value: skos:exactMatch RHEA:36055
+property_value: skos:narrowMatch RHEA:11904
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30157" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -330661,7 +334713,7 @@
id: GO:0050239
name: pyrithiamine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(4-amino-2-methylpyrimid-5-ylmethyl)-3-(beta-hydroxyethyl)-2-methylpyridinium bromide + H2O = 1-(4-hydroxy-2-methylpyrimid-5-ylmethyl)-3-(beta-hydroxyethyl)-2-methylpyridinium bromide + NH3." [EC:3.5.4.20, MetaCyc:PYRITHIAMIN-DEAMINASE-RXN]
+def: "Catalysis of the reaction: 1-(4-amino-2-methylpyrimid-5-ylmethyl)-3-(2-hydroxyethyl)-2-methylpyridinium + H2O + H+ = 1-(4-hydroxy-2-methylpyrimid-5-ylmethyl)-3-(2-hydroxyethyl)-2-methylpyridinium + NH4+." [RHEA:14537]
synonym: "1-(4-amino-2-methylpyrimid-5-ylmethyl)-3-(beta-hydroxyethyl)-2-methylpyridinium-bromide aminohydrolase activity" RELATED [EC:3.5.4.20]
xref: EC:3.5.4.20
xref: MetaCyc:PYRITHIAMIN-DEAMINASE-RXN
@@ -330868,10 +334920,14 @@
xref: Reactome:R-HSA-2465919 "AWAT2 transfers PALM to 11cROL forming 11cRPALM"
xref: Reactome:R-HSA-8848585 "AWAT2 transfers PALM from PALM-CoA to atROL, forming atR-PALM"
xref: RHEA:11488
+xref: RHEA:38175
+xref: RHEA:55284
is_a: GO:0008374 ! O-acyltransferase activity
relationship: part_of GO:0042572 ! retinol metabolic process
property_value: skos:exactMatch EC:2.3.1.76
property_value: skos:exactMatch RHEA:11488
+property_value: skos:narrowMatch RHEA:38175
+property_value: skos:narrowMatch RHEA:55284
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -331076,10 +335132,12 @@
synonym: "YeiK" RELATED [EC:3.2.2.8]
xref: EC:3.2.2.8
xref: MetaCyc:RIBOSYLPYRIMIDINE-NUCLEOSIDASE-RXN
+xref: RHEA:27958
xref: RHEA:56816
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
property_value: skos:exactMatch EC:3.2.2.8
property_value: skos:exactMatch RHEA:56816
+property_value: skos:narrowMatch RHEA:27958
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -331347,7 +335405,7 @@
id: GO:0050279
name: sepiapterin deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sepiapterin + H2O = xanthopterin-B2 + NH3." [EC:3.5.4.24, MetaCyc:SEPIAPTERIN-DEAMINASE-RXN]
+def: "Catalysis of the reaction: L-sepiapterin + H2O + H+ = (S)-xanthopterin-B2 + NH4+." [RHEA:14025]
synonym: "sepiapterin aminohydrolase activity" RELATED [EC:3.5.4.24]
xref: EC:3.5.4.24
xref: MetaCyc:SEPIAPTERIN-DEAMINASE-RXN
@@ -331375,19 +335433,21 @@
[Term]
id: GO:0050281
-name: L-serine-glyoxylate transaminase activity
+name: L-serine:glyoxylate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine + glyoxylate = 3-hydroxypyruvate + glycine." [EC:2.6.1.45]
+def: "Catalysis of the reaction: L-serine + glyoxylate = 3-hydroxypyruvate + glycine." [RHEA:19125]
+synonym: "L-serine-glyoxylate transaminase activity" EXACT []
synonym: "L-serine:glyoxylate aminotransferase activity" RELATED [EC:2.6.1.45]
synonym: "serine--glyoxylate aminotransferase activity" EXACT []
synonym: "SGAT activity" RELATED [EC:2.6.1.45]
xref: EC:2.6.1.45
xref: MetaCyc:SERINE--GLYOXYLATE-AMINOTRANSFERASE-RXN
xref: RHEA:19125
-is_a: GO:0008483 ! transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.45
property_value: skos:exactMatch RHEA:19125
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0050282
@@ -331410,7 +335470,7 @@
id: GO:0050283
name: serine-sulfate ammonia-lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-serine O-sulfate + H2O = pyruvate + NH3 + sulfate." [EC:4.3.1.10, MetaCyc:SERINE-SULFATE-AMMONIA-LYASE-RXN]
+def: "Catalysis of the reaction: -serine O-sulfate + H2O = sulfate + pyruvate + NH4+ + H+." [RHEA:15605]
synonym: "(L-SOS)lyase activity" RELATED [EC:4.3.1.10]
synonym: "L-serine-O-sulfate ammonia-lyase (pyruvate-forming)" RELATED [EC:4.3.1.10]
synonym: "serine-sulphate ammonia-lyase activity" EXACT []
@@ -331552,9 +335612,21 @@
xref: MetaCyc:SPHINGOSINE-N-ACYLTRANSFERASE-RXN
xref: Reactome:R-HSA-428185 "Ceramide synthases transfer acyl-CoA onto sphingoid"
xref: RHEA:23768
+xref: RHEA:36687
+xref: RHEA:36691
+xref: RHEA:37115
+xref: RHEA:37123
+xref: RHEA:45284
+xref: RHEA:64044
is_a: GO:0016410 ! N-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.24
property_value: skos:exactMatch RHEA:23768
+property_value: skos:narrowMatch RHEA:36687
+property_value: skos:narrowMatch RHEA:36691
+property_value: skos:narrowMatch RHEA:37115
+property_value: skos:narrowMatch RHEA:37123
+property_value: skos:narrowMatch RHEA:45284
+property_value: skos:narrowMatch RHEA:64044
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -331606,10 +335678,12 @@
xref: Reactome:R-HSA-176517 "SULTs transfer (SO4)2- group to PREG"
xref: Reactome:R-HSA-176521 "beta-estradiol + PAPS => beta-estradiol 3-sulfate + PAP"
xref: Reactome:R-HSA-176631 "dehydroepiandrosterone (DHEA) + PAPS => DHEA sulfate + PAP"
+xref: RHEA:52372
xref: RHEA:68460
is_a: GO:0008146 ! sulfotransferase activity
property_value: skos:exactMatch EC:2.8.2.15
property_value: skos:exactMatch RHEA:68460
+property_value: skos:narrowMatch RHEA:52372
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -331757,23 +335831,25 @@
id: GO:0050303
name: L-lysine 6-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-lysine + NAD+ = L-1-piperideine-6-carboxylate + NH4+ + NADH + 2 H+." [RHEA:12408]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: L-lysine + NAD+ = L-1-piperideine-6-carboxylate + NH4+ + NADH + 2 H+. (S)-(2-aminoethyl)-L-cysteine can act as a substrate, and NADP+ can act as the acceptor." [EC:1.4.1.18]
synonym: "L-lysine epsilon-dehydrogenase activity" RELATED [EC:1.4.1.18]
synonym: "L-lysine:NAD+ 6-oxidoreductase (deaminating)" RELATED [EC:1.4.1.18]
synonym: "LysDH activity" RELATED [EC:1.4.1.18]
xref: EC:1.4.1.18
xref: MetaCyc:LYSINE-6-DEHYDROGENASE-RXN
xref: RHEA:12408
+xref: RHEA:64792
+xref: RHEA:64800
is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.4.1.18
-property_value: skos:exactMatch MetaCyc:LYSINE-6-DEHYDROGENASE-RXN
-property_value: skos:exactMatch RHEA:12408
-property_value: skos:relatedMatch MetaCyc:PWY-5314
-property_value: skos:relatedMatch RHEA:64792
-property_value: skos:relatedMatch RHEA:64800
+property_value: skos:narrowMatch MetaCyc:LYSINE-6-DEHYDROGENASE-RXN
+property_value: skos:narrowMatch RHEA:12408
+property_value: skos:narrowMatch RHEA:64792
+property_value: skos:narrowMatch RHEA:64800
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31730" xsd:anyURI
[Term]
id: GO:0050304
@@ -332084,13 +336160,14 @@
[Term]
id: GO:0050322
-name: taurine-2-oxoglutarate transaminase activity
+name: taurine:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: taurine + 2-oxoglutarate = sulfoacetaldehyde + L-glutamate." [PMID:16535664, RHEA:16353]
synonym: "taurine aminotransferase activity" EXACT []
synonym: "taurine transaminase activity" EXACT []
synonym: "taurine--alpha-ketoglutarate aminotransferase activity" RELATED [EC:2.6.1.55]
synonym: "taurine--glutamate transaminase activity" RELATED [EC:2.6.1.55]
+synonym: "taurine-2-oxoglutarate transaminase activity" EXACT []
synonym: "taurine:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.55]
xref: EC:2.6.1.55
xref: MetaCyc:RXN-2301
@@ -332099,6 +336176,7 @@
property_value: skos:exactMatch EC:2.6.1.55
property_value: skos:exactMatch RHEA:16353
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0050323
@@ -332111,9 +336189,11 @@
xref: KEGG_REACTION:R07167
xref: MetaCyc:TAURINE-DEHYDROGENASE-RXN
xref: RHEA:18709
+xref: RHEA:81555
is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
property_value: skos:exactMatch EC:1.4.99.2
property_value: skos:exactMatch RHEA:18709
+property_value: skos:narrowMatch RHEA:81555
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -332446,9 +336526,17 @@
xref: EC:1.3.1.44
xref: MetaCyc:TRANS-2-ENOYL-COA-REDUCTASE-NAD+-RXN
xref: RHEA:18177
+xref: RHEA:46072
+xref: RHEA:46076
+xref: RHEA:46080
+xref: RHEA:63232
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.44
property_value: skos:exactMatch RHEA:18177
+property_value: skos:narrowMatch RHEA:46072
+property_value: skos:narrowMatch RHEA:46076
+property_value: skos:narrowMatch RHEA:46080
+property_value: skos:narrowMatch RHEA:63232
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -332723,7 +336811,7 @@
id: GO:0050360
name: tryptophan 2'-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + O2 = 3-indoleglycolaldehyde + CO2 + NH3." [EC:1.13.99.3, MetaCyc:TRYPTOPHAN-2-DIOXYGENASE-RXN]
+def: "Catalysis of the reaction: L-tryptophan + O2 + H+ = 3-indoleglycolaldehyde + NH4+ + CO2." [RHEA:22620]
synonym: "indole-3-alkane alpha-hydroxylase activity" RELATED [EC:1.13.99.3]
synonym: "indolyl-3-alkan alpha-hydroxylase activity" RELATED [EC:1.13.99.3]
synonym: "L-tryptophan:oxygen 2'-oxidoreductase (side-chain-cleaving)" RELATED [EC:1.13.99.3]
@@ -332760,30 +336848,33 @@
[Term]
id: GO:0050362
-name: L-tryptophan:2-oxoglutarate aminotransferase activity
+name: L-tryptophan:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + 2-oxoglutarate = indolepyruvate + L-glutamate." [EC:2.6.1.27, MetaCyc:TRYPTOPHAN-AMINOTRANSFERASE-RXN]
+def: "Catalysis of the reaction: L-tryptophan + 2-oxoglutarate = indole-3-pyruvate + L-glutamate." [RHEA:14093]
synonym: "5-hydroxytryptophan-ketoglutaric transaminase activity" RELATED [EC:2.6.1.27]
synonym: "hydroxytryptophan aminotransferase activity" RELATED [EC:2.6.1.27]
synonym: "L-phenylalanine-2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.27]
synonym: "L-tryptophan aminotransferase activity" BROAD [EC:2.6.1.27]
synonym: "L-tryptophan transaminase activity" BROAD [EC:2.6.1.27]
+synonym: "L-tryptophan:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "tryptophan aminotransferase activity" EXACT []
synonym: "tryptophan transaminase activity" BROAD [EC:2.6.1.27]
xref: EC:2.6.1.27
xref: MetaCyc:TRYPTOPHAN-AMINOTRANSFERASE-RXN
xref: RHEA:14093
-is_a: GO:0070529 ! L-tryptophan aminotransferase activity
+is_a: GO:0008793 ! aromatic-amino-acid:2-oxoglutarate transaminase activity
property_value: skos:exactMatch EC:2.6.1.27
property_value: skos:exactMatch RHEA:14093
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0050363
-name: L-tryptophan dehydrogenase (NAD+) activity
+name: L-tryptophan dehydrogenase [NAD(P)+] activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + NAD+ + H2O = indole-3-pyruvate + NH4+ + NADH + H+." [RHEA:13473]
+def: "Catalysis of the reaction: L-tryptophan + NAD(P)+ + H2O = indole-3-pyruvate + NH4+ + NAD(P)H + H+." [EC:1.4.1.19]
synonym: "L-Trp-dehydrogenase activity" RELATED [EC:1.4.1.19]
+synonym: "L-tryptophan dehydrogenase (NAD+) activity" NARROW []
synonym: "L-tryptophan dehydrogenase activity" RELATED [EC:1.4.1.19]
synonym: "L-tryptophan:NAD(P)+ oxidoreductase (deaminating)" RELATED [EC:1.4.1.19]
synonym: "NAD(P)+-L-tryptophan dehydrogenase activity" RELATED [EC:1.4.1.19]
@@ -332793,12 +336884,14 @@
xref: EC:1.4.1.19
xref: MetaCyc:TRYPTOPHAN-DEHYDROGENASE-RXN
xref: RHEA:13473
+xref: RHEA:13477
is_a: GO:0050018 ! amino-acid dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.4.1.19
-property_value: skos:exactMatch RHEA:13473
-property_value: skos:relatedMatch RHEA:13477
+property_value: skos:narrowMatch RHEA:13473
+property_value: skos:narrowMatch RHEA:13477
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31730" xsd:anyURI
[Term]
id: GO:0050364
@@ -333036,8 +337129,7 @@
id: GO:0050378
name: UDP-glucuronate 4-epimerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-alpha-D-glucuronate = UDP-alpha-D-galacturonate." [EC:5.1.3.6, RHEA:11404]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
+def: "Catalysis of the reaction: UDP-alpha-D-glucuronate = UDP-alpha-D-galacturonate." [RHEA:11404]
synonym: "UDP glucuronic epimerase activity" RELATED [EC:5.1.3.6]
synonym: "UDP-D-galacturonic acid 4-epimerase activity" RELATED [EC:5.1.3.6]
synonym: "UDP-galacturonate 4-epimerase activity" RELATED [EC:5.1.3.6]
@@ -333054,8 +337146,8 @@
property_value: skos:exactMatch KEGG_REACTION:R01385
property_value: skos:exactMatch MetaCyc:UDP-GLUCURONATE-4-EPIMERASE-RXN
property_value: skos:exactMatch RHEA:11404
-property_value: skos:relatedMatch MetaCyc:PWY-4861
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0050379
@@ -333646,7 +337738,7 @@
id: GO:0050414
name: formimidoylaspartate deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formimidoyl-L-aspartate + H2O = N-formyl-L-aspartate + NH3." [EC:3.5.3.5, MetaCyc:FORMIMINOASPARTATE-DEIMINASE-RXN]
+def: "Catalysis of the reaction: N-formimidoyl-L-aspartate + H2O = N-formyl-L-aspartate + NH4+." [RHEA:13661]
synonym: "formiminoaspartate deiminase activity" EXACT []
synonym: "N-formimidoyl-L-aspartate iminohydrolase activity" RELATED [EC:3.5.3.5]
xref: EC:3.5.3.5
@@ -333680,7 +337772,7 @@
id: GO:0050416
name: formimidoylglutamate deiminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formimidoyl-L-glutamate + H2O = N-formyl-L-glutamate + NH3." [EC:3.5.3.13, MetaCyc:FORMIMINOGLUTAMATE-DEIMINASE-RXN]
+def: "Catalysis of the reaction: N-formimidoyl-L-glutamate + H2O = N-formyl-L-glutamate + NH4+." [RHEA:22832]
synonym: "formiminoglutamate deiminase activity" EXACT []
synonym: "formiminoglutamic iminohydrolase activity" RELATED [EC:3.5.3.13]
synonym: "N-formimidoyl-L-glutamate iminohydrolase activity" RELATED [EC:3.5.3.13]
@@ -333696,7 +337788,7 @@
id: GO:0050417
name: glutamin-(asparagin-)ase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + L-glutamine = NH3 + L-glutamate; and H2O + L-asparagine = NH3 + L-aspartate." [EC:3.5.1.38]
+def: "Catalysis of the reactions: H2O + L-glutamine = NH4 + L-glutamate; and H2O + L-asparagine = NH4 + L-aspartate." [EC:3.5.1.38]
synonym: "glutaminase-(asparagin-)ase activity" EXACT []
synonym: "glutaminase-asparaginase activity" RELATED [EC:3.5.1.38]
synonym: "L-ASNase/L-GLNase activity" RELATED [EC:3.5.1.38]
@@ -333714,7 +337806,7 @@
id: GO:0050418
name: hydroxylamine reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor." [EC:1.7.99.1]
+def: "Catalysis of the reaction: an acceptor + NH4+ + H2O = hydroxylamine + a reduced acceptor + H+." [RHEA:22052]
synonym: "ammonia:(acceptor) oxidoreductase activity" RELATED [EC:1.7.99.1]
synonym: "ammonia:acceptor oxidoreductase activity" RELATED [EC:1.7.99.1]
synonym: "hydroxylamine (acceptor) reductase activity" RELATED [EC:1.7.99.1]
@@ -333869,6 +337961,7 @@
synonym: "phosphoadenosine phosphosulfate metabolic process" EXACT []
synonym: "phosphoadenosine phosphosulfate metabolism" EXACT []
xref: Reactome:R-HSA-156584 "Cytosolic sulfonation of small molecules"
+xref: Reactome:R-HSA-174362 "Transport and metabolism of PAPS"
is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0009150 ! purine ribonucleotide metabolic process
is_a: GO:0034035 ! purine ribonucleoside bisphosphate metabolic process
@@ -334864,9 +338957,15 @@
xref: EC:3.1.1.25
xref: MetaCyc:14-LACTONASE-RXN
xref: RHEA:12745
+xref: RHEA:44900
+xref: RHEA:52644
+xref: RHEA:52648
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.25
property_value: skos:exactMatch RHEA:12745
+property_value: skos:narrowMatch RHEA:44900
+property_value: skos:narrowMatch RHEA:52644
+property_value: skos:narrowMatch RHEA:52648
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -335002,7 +339101,7 @@
synonym: "spHAS" RELATED [EC:2.4.1.212]
xref: EC:2.4.1.212
xref: MetaCyc:2.4.1.212-RXN
-xref: Reactome:R-HSA-2160851 "HAS1,2,3 mediate the polymerization of HA"
+xref: Reactome:R-HSA-2160851 "HAS1,2,3 mediate the polymerization and export of HA"
xref: RHEA:12528
is_a: GO:0008194 ! UDP-glycosyltransferase activity
is_a: GO:0016758 ! hexosyltransferase activity
@@ -335120,12 +339219,9 @@
synonym: "UDP-N-acetyl-D-glucosamine:beta-D-glucuronosyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.224]
xref: EC:2.4.1.224
xref: MetaCyc:2.4.1.224-RXN
-xref: Reactome:R-HSA-2022851 "EXT1:EXT2 transfer GlcNAc to the heparan chain"
-xref: Reactome:R-HSA-2022919 "EXT1:EXT2 transfers GlcNAc to the terminal GlcA residue"
+xref: Reactome:R-HSA-2022851 "EXT1:EXT2 transfers GlcNAc to the heparan chain"
xref: Reactome:R-HSA-3656254 "Defective EXT2 (in EXT1:EXT2) does not transfer GlcNAc to the heparan chain"
xref: Reactome:R-HSA-3656261 "Defective EXT1 (in EXT1:EXT2) does not transfer GlcNAc to the heparan chain"
-xref: Reactome:R-HSA-9036283 "Defective EXT1 (in EXT1:EXT2) does not transfer GlcNAc to the terminal GlcA residue"
-xref: Reactome:R-HSA-9036290 "Defective EXT2 (in EXT1:EXT2) does not transfer GlcNAc to heparan"
xref: RHEA:16213
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
property_value: skos:exactMatch EC:2.4.1.224
@@ -335144,7 +339240,7 @@
synonym: "UDP-alpha-D-glucuronate:N-acetyl-alpha-D-glucosaminyl-(1->4)-beta-D-glucuronosyl-proteoglycan 4-beta-glucuronosyltransferase activity" RELATED [EC:2.4.1.225]
xref: EC:2.4.1.225
xref: MetaCyc:2.4.1.225-RXN
-xref: Reactome:R-HSA-2022856 "EXT1:EXT2 transfers GlcNAc to heparan"
+xref: Reactome:R-HSA-2022856 "EXT1:EXT2 transfers GlcA to heparan"
xref: Reactome:R-HSA-2076392 "EXT1:EXT2 transfers GlcA to heparan"
xref: Reactome:R-HSA-3656257 "Defective EXT1 (in EXT1:EXT2) does not transfer GlcA to heparan"
xref: Reactome:R-HSA-3656267 "Defective EXT2 (in EXT1:EXT2) does not transfer GlcA to heparan"
@@ -335167,9 +339263,8 @@
synonym: "N-acetylgalactosaminyl-proteoglycan 3-b-glucuronosyltransferase activity" EXACT []
xref: EC:2.4.1.226
xref: MetaCyc:RXN-16324
-xref: Reactome:R-HSA-1971491 "CHPF,CHPF2,CHSY3 transfer GlcA to chondroitin"
+xref: Reactome:R-HSA-1971491 "Chondroitin polymerase complex transfers GlcA to CS chain"
xref: Reactome:R-HSA-3595178 "Defective CHSY1 does not transfer GlcA to chondroitin"
-xref: Reactome:R-HSA-9632034 "CHSY1 transfers GlcA to chondroitin"
is_a: GO:0015020 ! glucuronosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.226
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -335233,7 +339328,7 @@
id: GO:0050514
name: homospermidine synthase (spermidine-specific) activity
namespace: molecular_function
-def: "Catalysis of the reaction: spermidine + putrescine = sym-homospermidine + propane-1,3-diamine." [EC:2.5.1.45]
+def: "Catalysis of the reaction: spermidine + putrescine = sym-homospermidine + propane-1,3-diamine." [RHEA:11236]
synonym: "spermidine:putrescine 4-aminobutyltransferase (propane-1,3-diamine-forming)" RELATED [EC:2.5.1.45]
xref: EC:2.5.1.45
xref: MetaCyc:2.5.1.45-RXN
@@ -335621,9 +339716,29 @@
xref: EC:3.5.1.87
xref: MetaCyc:3.5.1.87-RXN
xref: RHEA:17581
+xref: RHEA:72783
+xref: RHEA:72787
+xref: RHEA:72823
+xref: RHEA:72827
+xref: RHEA:83911
+xref: RHEA:83915
+xref: RHEA:84011
+xref: RHEA:84015
+xref: RHEA:84019
+xref: RHEA:84023
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.87
property_value: skos:exactMatch RHEA:17581
+property_value: skos:narrowMatch RHEA:72783
+property_value: skos:narrowMatch RHEA:72787
+property_value: skos:narrowMatch RHEA:72823
+property_value: skos:narrowMatch RHEA:72827
+property_value: skos:narrowMatch RHEA:83911
+property_value: skos:narrowMatch RHEA:83915
+property_value: skos:narrowMatch RHEA:84011
+property_value: skos:narrowMatch RHEA:84015
+property_value: skos:narrowMatch RHEA:84019
+property_value: skos:narrowMatch RHEA:84023
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -336003,9 +340118,11 @@
xref: EC:6.1.1.24
xref: MetaCyc:6.1.1.24-RXN
xref: RHEA:18397
+xref: RHEA:64612
is_a: GO:0004812 ! aminoacyl-tRNA ligase activity
property_value: skos:exactMatch EC:6.1.1.24
property_value: skos:exactMatch RHEA:18397
+property_value: skos:narrowMatch RHEA:64612
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -336129,7 +340246,7 @@
id: GO:0050568
name: protein-glutamine glutaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein L-glutamine + H2O = protein L-glutamate + NH3." [EC:3.5.1.44, MetaCyc:CHEBDEAMID-RXN]
+def: "Catalysis of the reaction: L-glutaminyl-[protein] + H2O = L-glutamyl-[protein] + NH4+." [RHEA:16441]
synonym: "destabilase activity" RELATED [EC:3.5.1.44]
synonym: "glutaminyl-peptide glutaminase activity" RELATED [EC:3.5.1.44]
synonym: "glutaminylpeptide glutaminase activity" RELATED [EC:3.5.1.44]
@@ -336188,6 +340305,7 @@
xref: EC:1.1.1.263
xref: KEGG_REACTION:R05682
xref: MetaCyc:1.1.1.263-RXN
+xref: Reactome:R-HSA-9773976 "AKR1E2 reduces 1,5-aF to 1,5-aG"
xref: RHEA:20665
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.263
@@ -336269,7 +340387,7 @@
synonym: "GDP-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing)" RELATED [EC:1.1.1.271]
xref: EC:1.1.1.271
xref: MetaCyc:1.1.1.271-RXN
-xref: Reactome:R-HSA-6787642 "TSTA3 dimer reduces GDP-KDGal to GDP-Fuc"
+xref: Reactome:R-HSA-6787642 "GFUS dimer reduces GDP-KDGal to GDP-Fuc"
xref: RHEA:18885
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
relationship: part_of GO:0042350 ! GDP-L-fucose biosynthetic process
@@ -336288,11 +340406,19 @@
synonym: "L-sulfolactate dehydrogenase activity" RELATED [EC:1.1.1.272]
xref: EC:1.1.1.272
xref: MetaCyc:1.1.1.272-RXN
+xref: RHEA:12873
xref: RHEA:35735
+xref: RHEA:57704
+xref: RHEA:64468
+xref: RHEA:83043
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
is_a: GO:0033719 ! (2R)-oxo-acid reductase activity
property_value: skos:exactMatch EC:1.1.1.272
property_value: skos:exactMatch RHEA:35735
+property_value: skos:narrowMatch RHEA:12873
+property_value: skos:narrowMatch RHEA:57704
+property_value: skos:narrowMatch RHEA:64468
+property_value: skos:narrowMatch RHEA:83043
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30138" xsd:anyURI
[Term]
@@ -336860,6 +340986,7 @@
xref: MetaCyc:RXN66-14
xref: Reactome:R-HSA-194674 "4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol is reduced to 4,4-dimethylcholesta-8(9),24-dien-3beta-ol [LBR]"
xref: Reactome:R-HSA-194698 "4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol is reduced to 4,4-dimethylcholesta-8(9),24-dien-3beta-ol [TM7SF2]"
+xref: Reactome:R-HSA-9946140 "TM7SF2 reduces 4,4-diMeCholesta-8,14-dien-3-ol to 4,4-diMe5-cholest-8-en-3-ol"
xref: RHEA:18561
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.70
@@ -337459,6 +341586,7 @@
synonym: "chondroitin sulphate proteoglycan biosynthesis" EXACT []
synonym: "chondroitin sulphate proteoglycan biosynthetic process" EXACT []
xref: MetaCyc:PWY-6567
+xref: Reactome:R-HSA-2022870 "CS-GAG biosynthesis"
is_a: GO:0030166 ! proteoglycan biosynthetic process
is_a: GO:0050654 ! chondroitin sulfate proteoglycan metabolic process
is_a: GO:0180064 ! protein O-linked glycosylation via xylose
@@ -337480,6 +341608,7 @@
synonym: "dermatan sulphate proteoglycan biosynthesis" EXACT []
synonym: "dermatan sulphate proteoglycan biosynthetic process" EXACT []
xref: MetaCyc:PWY-6568
+xref: Reactome:R-HSA-2022923 "DS-GAG biosynthesis"
is_a: GO:0030166 ! proteoglycan biosynthetic process
is_a: GO:0050655 ! dermatan sulfate proteoglycan metabolic process
is_a: GO:0180064 ! protein O-linked glycosylation via xylose
@@ -337592,7 +341721,8 @@
xref: KEGG_REACTION:R10869
xref: MetaCyc:RXN-7953
xref: MetaCyc:RXN-7954
-xref: Reactome:R-HSA-2018659 "Chondroitin 4-sulfate (C4S) can be further sulfated on position 6 by CHST15"
+xref: Reactome:R-HSA-2018659 "CHST15 transfers sulfate to (6-)GalNAc-4-sulfate"
+xref: Reactome:R-HSA-9941312 "CHST15 transfers sulfate to (6-)GalNAc-4-sulfate"
xref: RHEA:54300
xref: RHEA:54304
is_a: GO:0008146 ! sulfotransferase activity
@@ -337931,6 +342061,9 @@
synonym: "downregulation of antiviral response" EXACT []
synonym: "inhibition of antiviral response" NARROW []
synonym: "negative regulation of antiviral response" EXACT [GOC:dph]
+xref: Reactome:R-HSA-164938 "Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters"
+xref: Reactome:R-HSA-164944 "Nef and signal transduction"
+xref: Reactome:R-HSA-168276 "NS1 Mediated Effects on Host Pathways"
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
@@ -338383,6 +342516,7 @@
def: "Binding to a low-density lipoprotein receptor." [GOC:ai]
synonym: "LDL receptor binding" EXACT []
synonym: "low-density lipoprotein receptor binding" EXACT [GOC:dph]
+xref: Reactome:R-HSA-2423785 "CR:atREs binds apoE and HSPG"
is_a: GO:0070325 ! lipoprotein particle receptor binding
[Term]
@@ -338450,7 +342584,7 @@
id: GO:0050761
name: depsipeptide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:go_curators]
+def: "The chemical reactions and pathways involving depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:curators]
subset: goslim_pir
synonym: "depsipeptide metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
@@ -338459,7 +342593,7 @@
id: GO:0050762
name: depsipeptide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the breakdown of depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:curators]
synonym: "depsipeptide breakdown" EXACT []
synonym: "depsipeptide catabolism" EXACT []
synonym: "depsipeptide degradation" EXACT []
@@ -338470,7 +342604,7 @@
id: GO:0050763
name: depsipeptide biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of depsipeptides, a linear or cyclic compound composed of both amino acids and hydroxy acids in peptide and ester bonds respectively." [GOC:curators]
synonym: "depsipeptide anabolism" EXACT []
synonym: "depsipeptide biosynthesis" EXACT []
synonym: "depsipeptide formation" EXACT []
@@ -338808,7 +342942,7 @@
name: regulation of biological process
namespace: biological_process
alt_id: GO:0050791
-def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:curators]
subset: gocheck_do_not_annotate
subset: goslim_candida
subset: goslim_pir
@@ -338837,7 +342971,7 @@
id: GO:0050792
name: regulation of viral process
namespace: biological_process
-def: "Any process that modulates the rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts." [GOC:go_curators, GOC:tb]
+def: "Any process that modulates the rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts." [GOC:curators, GOC:tb]
synonym: "regulation of viral reproduction" NARROW [GOC:bf, GOC:jl]
is_a: GO:0050789 ! regulation of biological process
intersection_of: GO:0065007 ! biological regulation
@@ -338848,7 +342982,7 @@
id: GO:0050793
name: regulation of developmental process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:curators]
is_a: GO:0050789 ! regulation of biological process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0032502 ! developmental process
@@ -338859,7 +342993,7 @@
name: regulation of cellular process
namespace: biological_process
alt_id: GO:0051244
-def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:curators]
subset: gocheck_do_not_annotate
synonym: "regulation of cellular physiological process" EXACT []
is_a: GO:0050789 ! regulation of biological process
@@ -338871,7 +343005,7 @@
id: GO:0050795
name: regulation of behavior
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:go_curators, GOC:pr]
+def: "Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." [GOC:curators, GOC:pr]
synonym: "regulation of behaviour" EXACT []
is_a: GO:0051239 ! regulation of multicellular organismal process
intersection_of: GO:0065007 ! biological regulation
@@ -341682,7 +345816,7 @@
id: GO:0051037
name: obsolete regulation of transcription involved in meiotic cell cycle
namespace: biological_process
-def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle." [GOC:go_curators]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of transcription as part of a meiotic cell cycle." [GOC:curators]
comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "meiotic regulation of transcription" EXACT []
synonym: "regulation of transcription, meiotic" EXACT [GOC:mah]
@@ -341970,7 +346104,7 @@
id: GO:0051056
name: regulation of small GTPase mediated signal transduction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction." [GOC:curators]
synonym: "regulation of small GTPase-mediated signal transduction" EXACT []
xref: Reactome:R-HSA-9012999 "RHO GTPase cycle"
is_a: GO:1902531 ! regulation of intracellular signal transduction
@@ -342337,7 +346471,6 @@
def: "OBSOLETE. The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release." [GOC:rb]
comment: This term represent a GO-CAM model
synonym: "chaperone cofactor-independent protein folding" EXACT [GOC:rb]
-xref: Reactome:R-HSA-390450 "Folding of actin by CCT/TriC"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21869" xsd:anyURI
is_obsolete: true
replaced_by: GO:0006457
@@ -342383,7 +346516,6 @@
synonym: "regulation of sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "regulation of thyroid hormone receptor activity" NARROW []
synonym: "regulation of transcription factor activity" BROAD [GOC:dph, GOC:tb]
-xref: Reactome:R-HSA-9708530 "Regulation of BACH1 activity"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30856" xsd:anyURI
is_obsolete: true
@@ -342625,7 +346757,6 @@
xref: MetaCyc:DCARNCOALIG-RXN
xref: RHEA:30543
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016881 ! acid-amino acid ligase activity
property_value: skos:exactMatch RHEA:30543
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -342633,14 +346764,21 @@
id: GO:0051109
name: crotonobetaine-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: CoA + crotono-betaine + ATP = AMP + diphosphate + crotonobetainyl-CoA." [MetaCyc:CROTCOALIG-RXN]
+def: "Catalysis of the reaction: (R)-carnitine + ATP + CoA = (R)-carnitinyl-CoA + AMP + diphosphate. Also catalyzes the transfer of CoA to crotonobetaine and gamma-butyrobetaine." [EC:6.2.1.48]
synonym: "crotonobetaine-CoA synthase activity" EXACT []
synonym: "crotonobetaine/carnitine-CoA ligase activity" BROAD []
+xref: EC:6.2.1.48
xref: MetaCyc:CROTCOALIG-RXN
+xref: RHEA:28514
xref: RHEA:30079
+xref: RHEA:55960
is_a: GO:0016405 ! CoA-ligase activity
-property_value: skos:exactMatch RHEA:30079
+property_value: skos:exactMatch EC:6.2.1.48
+property_value: skos:narrowMatch RHEA:28514
+property_value: skos:narrowMatch RHEA:30079
+property_value: skos:narrowMatch RHEA:55960
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31616" xsd:anyURI
[Term]
id: GO:0051110
@@ -342762,8 +346900,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: 12S-5Z,8Z,10E,14Z-12-hydro(pero)xy-eicosa-5,8,10,14-tetraenoic acid = (5Z,9E,14Z)-(8,11R,12S)-11,12-epoxy-8-hydroxyicosa-5,9,14-trienoate. 12S-5Z,8Z,10E,14Z-12-hydro(pero)xy-eicosa-5,8,10,14-tetraenoic acid is also known as 12S-HpETE, and (5Z,9E,14Z)-(8,11R,12S)-11,12-epoxy-8-hydroxyicosa-5,9,14-trienoate as hepoxilin A3." [PMID:15123652]
comment: The reason for obsoletion is that this term is equivalent to hydroperoxy icosatetraenoate isomerase activity.
-xref: Reactome:R-HSA-2161794 "Arachidonate is converted to HXA3/B3 by ALOX12"
-xref: Reactome:R-HSA-8942208 "ALOXE3 isomerises 12R-HpETE to HXA3"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
is_obsolete: true
replaced_by: GO:0106255
@@ -342775,7 +346911,6 @@
def: "OBSOLETE. The chemical reactions and pathways involving hepoxilins, a class of bioactive icosanoids with roles in the regulation of cell physiology." [PMID:15123652]
comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "hepoxilin metabolism" EXACT []
-xref: Reactome:R-HSA-2142696 "Synthesis of Hepoxilins (HX) and Trioxilins (TrX)"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30524" xsd:anyURI
is_obsolete: true
@@ -343456,6 +347591,7 @@
synonym: "nucleus export" EXACT []
synonym: "substance nuclear export" EXACT []
is_a: GO:0006913 ! nucleocytoplasmic transport
+is_a: GO:0010496 ! intercellular transport
[Term]
id: GO:0051169
@@ -343476,6 +347612,7 @@
synonym: "nuclear import" EXACT []
synonym: "nuclear translocation" EXACT []
is_a: GO:0006913 ! nucleocytoplasmic transport
+is_a: GO:0010496 ! intercellular transport
created_by: jl
creation_date: 2013-12-19T15:26:34Z
@@ -343935,6 +348072,7 @@
synonym: "release of stored calcium ion (Ca2+)" BROAD []
synonym: "release of stored calcium ion (Ca2+) into cytoplasm" BROAD []
synonym: "release of stored calcium ion (Ca2+) into cytosol" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0097553 ! calcium ion transmembrane import into cytosol
[Term]
@@ -344641,22 +348779,26 @@
xref: KEGG_REACTION:R02864
xref: MetaCyc:SIROHEME-FERROCHELAT-RXN
xref: RHEA:24360
-is_a: GO:0004325 ! ferrochelatase activity
+is_a: GO:0016829 ! lyase activity
property_value: skos:exactMatch EC:4.99.1.4
property_value: skos:exactMatch RHEA:24360
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31620" xsd:anyURI
[Term]
id: GO:0051267
-name: CP2 mannose-ethanolamine phosphotransferase activity
+name: obsolete CP2 mannose-ethanolamine phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethanolamine phosphate + Man-alpha-(1,2)-Man-alpha-(1,2)-Man-alpha-(1,6)-R = Man-alpha-(1,2)-Man-alpha-6-P-EtN-(1,2)-Man-alpha-(1,6)-R; R is Man-alpha(1,4)-GlcNH2-inositol-phosphate-lipid. This reaction is the transfer of ethanolamine phosphate to C6 of second mannose in the GPI lipid precursor CP2." [PMID:14985347, PMID:15452134]
+def: "OBSOLETE. Catalysis of the reaction: ethanolamine phosphate + Man-alpha-(1,2)-Man-alpha-(1,2)-Man-alpha-(1,6)-R = Man-alpha-(1,2)-Man-alpha-6-P-EtN-(1,2)-Man-alpha-(1,6)-R; R is Man-alpha(1,4)-GlcNH2-inositol-phosphate-lipid. This reaction is the transfer of ethanolamine phosphate to C6 of second mannose in the GPI lipid precursor CP2." [PMID:14985347, PMID:15452134]
+comment: This term was obsoleted because it represents the same process as its parent, mannose-ethanolamine phosphotransferase activity ; GO:0051377.
synonym: "addition of ethanolamine phosphate to mannose of GPI precursor CP2" EXACT []
synonym: "CP2 ethanolamine phosphate transferase activity" EXACT []
synonym: "CP2 EtN-P transferase activity" EXACT []
synonym: "CP2 phosphoethanolamine transferase activity" EXACT []
synonym: "gpi7 activity" RELATED []
-is_a: GO:0051377 ! mannose-ethanolamine phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31641" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0051377
[Term]
id: GO:0051268
@@ -344938,7 +349080,7 @@
id: GO:0051289
name: protein homotetramerization
namespace: biological_process
-def: "The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits." [GOC:go_curators]
+def: "The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits." [GOC:curators]
synonym: "protein homotetramer assembly" EXACT []
synonym: "protein homotetramer biosynthesis" EXACT []
synonym: "protein homotetramer biosynthetic process" EXACT []
@@ -344950,7 +349092,7 @@
id: GO:0051290
name: protein heterotetramerization
namespace: biological_process
-def: "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical." [GOC:go_curators]
+def: "The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical." [GOC:curators]
synonym: "protein heterotetramer assembly" EXACT []
synonym: "protein heterotetramer biosynthesis" EXACT []
synonym: "protein heterotetramer biosynthetic process" EXACT []
@@ -345070,7 +349212,7 @@
id: GO:0051301
name: cell division
namespace: biological_process
-def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:di, GOC:go_curators, GOC:pr]
+def: "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." [GOC:curators, GOC:di, GOC:pr]
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
subset: goslim_chembl
subset: goslim_drosophila
@@ -345082,7 +349224,7 @@
id: GO:0051302
name: regulation of cell division
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells." [GOC:curators]
is_a: GO:0050794 ! regulation of cellular process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0051301 ! cell division
@@ -346144,10 +350286,12 @@
namespace: molecular_function
def: "Catalysis of the reaction: a cytidine in tRNA + acetyl-CoA + ATP + H2O = ADP + an N4-acetylcytidine in tRNA + CoA + H+ + phosphate." [PMID:15037780, RHEA:53876]
synonym: "tRNA N4-acetyltransferase activity" EXACT []
+xref: RHEA:43788
xref: RHEA:53876
is_a: GO:0008080 ! N-acetyltransferase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: skos:exactMatch RHEA:53876
+property_value: skos:narrowMatch RHEA:43788
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26617" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29506" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30121" xsd:anyURI
@@ -346919,7 +351063,7 @@
id: GO:0051452
name: intracellular pH reduction
namespace: biological_process
-def: "Any process that reduces the internal pH of a cell, measured by the concentration of the hydrogen ion." [GOC:ai]
+def: "Any process that reduces the internal pH of a cell, corresponding to an increase in hydrogen ion concentration." [GOC:ai]
synonym: "cell pH reduction" EXACT []
synonym: "cellular acidification" EXACT []
synonym: "intracellular acidification" RELATED []
@@ -346931,12 +351075,16 @@
id: GO:0051453
name: regulation of intracellular pH
namespace: biological_process
-def: "Any process that modulates the internal pH of a cell, measured by the concentration of the hydrogen ion." [GOC:ai, GOC:dph, GOC:tb]
+def: "Any process that modulates the internal pH of a cell, corresponding to a change in hydrogen ion concentration." [GOC:ai, GOC:dph, GOC:tb]
synonym: "cell pH regulation" EXACT []
+synonym: "cellular hydrogen ion homeostasis" EXACT [GOC:dph, GOC:tb]
synonym: "cellular pH regulation" EXACT []
synonym: "pH regulation in cell" EXACT []
+synonym: "proton homeostasis" EXACT []
synonym: "regulation of cell pH" EXACT []
-is_a: GO:0030641 ! regulation of cellular pH
+synonym: "regulation of cellular pH" EXACT []
+is_a: GO:0006885 ! regulation of pH
+is_a: GO:0030003 ! intracellular monoatomic cation homeostasis
is_a: GO:0065008 ! regulation of biological quality
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
@@ -346944,7 +351092,7 @@
id: GO:0051454
name: intracellular pH elevation
namespace: biological_process
-def: "Any process that increases the internal pH of a cell, measured by the concentration of the hydrogen ion." [GOC:ai]
+def: "Any process that increases the internal pH of a cell, corresponding to a decrease in hydrogen ion concentration." [GOC:ai]
synonym: "cell pH elevation" EXACT []
synonym: "cellular alkalinization" EXACT []
synonym: "elevation of cellular pH" EXACT []
@@ -347559,9 +351707,15 @@
xref: EC:3.1.1.96
xref: MetaCyc:RXN-15041
xref: RHEA:13953
+xref: RHEA:69791
+xref: RHEA:69795
+xref: RHEA:69799
is_a: GO:0002161 ! aminoacyl-tRNA deacylase activity
property_value: skos:exactMatch EC:3.1.1.96
property_value: skos:exactMatch RHEA:13953
+property_value: skos:narrowMatch RHEA:69791
+property_value: skos:narrowMatch RHEA:69795
+property_value: skos:narrowMatch RHEA:69799
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29746" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -348608,17 +352762,16 @@
[Term]
id: GO:0051600
-name: regulation of endocytosis by exocyst localization
+name: obsolete regulation of endocytosis by exocyst localization
namespace: biological_process
-def: "Any process in which an exocyst is transported to, or maintained in, a specific location that results in the modulation of endocytosis. An exocyst is a protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse." [GOC:ai, GOC:dph, GOC:tb]
+def: "OBSOLETE. Any process in which an exocyst is transported to, or maintained in, a specific location that results in the modulation of endocytosis. An exocyst is a protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse." [GOC:ai, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this represents a phenotype.
synonym: "regulation of endocytosis by exocyst localisation" EXACT [GOC:mah]
synonym: "regulation of site selection of endocytosis" RELATED []
synonym: "relocation of endocytosis" RELATED []
synonym: "spatial regulation of endocytosis" RELATED []
-is_a: GO:0030100 ! regulation of endocytosis
-is_a: GO:0051601 ! exocyst localization
-intersection_of: GO:0051601 ! exocyst localization
-intersection_of: regulates GO:0006897 ! endocytosis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31201" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0051601
@@ -348667,6 +352820,7 @@
subset: goslim_pombe
subset: goslim_prokaryote
subset: goslim_yeast
+xref: Reactome:R-HSA-9918432 "Maturation of DENV proteins"
is_a: GO:0019538 ! protein metabolic process
relationship: part_of GO:0010467 ! gene expression
@@ -349797,6 +353951,7 @@
synonym: "growth of symbiont in host vacuole" NARROW []
synonym: "interaction with host" EXACT []
xref: Reactome:R-HSA-9635486 "Infection with Mycobacterium tuberculosis"
+xref: Reactome:R-HSA-9640148 "Infection with Enterobacteria"
xref: Reactome:R-HSA-9658195 "Leishmania infection"
is_a: GO:0044403 ! biological process involved in symbiotic interaction
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI
@@ -350069,7 +354224,6 @@
def: "OBSOLETE. Catalysis of the reaction: C-terminal protein amino acid methyl ester + H2O = protein amino acid + methanol." [PMID:10318862, PMID:8650216]
comment: This seems to be outside the scope of GO: it represent a specific protein and a 'domain.
synonym: "protein phosphatase methylesterase activity" NARROW []
-xref: Reactome:R-HSA-8856951 "PP2A demethylation by PPME1"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27558" xsd:anyURI
is_obsolete: true
replaced_by: GO:0051723
@@ -350086,6 +354240,7 @@
xref: EC:3.1.1.89
xref: MetaCyc:RXN-12322
xref: Reactome:R-HSA-5367022 "DPH7 hydrolyzes a methyl group on Me-diphthine EEF2"
+xref: Reactome:R-HSA-8856951 "PP2A demethylation by PPME1"
xref: RHEA:48548
is_a: GO:0052689 ! carboxylic ester hydrolase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -350111,6 +354266,7 @@
synonym: "oxidized nicotinamide adenine dinucleotide transmembrane transporter activity" EXACT []
synonym: "reduced NAD transporter activity" EXACT []
synonym: "reduced nicotinamide adenine dinucleotide transmembrane transporter activity" EXACT []
+xref: Reactome:R-HSA-9938195 "SLC25A51 mediates mitochondrial uptake of NAD+"
is_a: GO:0000295 ! adenine nucleotide transmembrane transporter activity
relationship: part_of GO:0035352 ! NAD transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21577" xsd:anyURI
@@ -350455,10 +354611,20 @@
synonym: "delta3,5-delta2,4-dienoyl-CoA isomerase activity" EXACT []
synonym: "delta5-delta2,4-dienoyl-CoA isomerase activity" RELATED []
xref: EC:5.3.3.21
+xref: RHEA:45224
xref: RHEA:45240
+xref: RHEA:45244
+xref: RHEA:47468
+xref: RHEA:84515
+xref: RHEA:84543
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
property_value: skos:exactMatch EC:5.3.3.21
property_value: skos:exactMatch RHEA:45240
+property_value: skos:narrowMatch RHEA:45224
+property_value: skos:narrowMatch RHEA:45244
+property_value: skos:narrowMatch RHEA:47468
+property_value: skos:narrowMatch RHEA:84515
+property_value: skos:narrowMatch RHEA:84543
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -350897,7 +355063,7 @@
id: GO:0051788
name: response to misfolded protein
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a misfolded protein stimulus." [GOC:go_curators]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a misfolded protein stimulus." [GOC:curators]
is_a: GO:0035966 ! response to topologically incorrect protein
[Term]
@@ -352246,8 +356412,12 @@
xref: Reactome:R-HSA-1222755 "Peroxynitrite is reduced to nitrite by Tpx"
xref: Reactome:R-HSA-1500804 "Peroxynitrite is reduced by AhpE"
xref: RHEA:10008
+xref: RHEA:62624
+xref: RHEA:62640
is_a: GO:0004601 ! peroxidase activity
property_value: skos:exactMatch RHEA:10008
+property_value: skos:narrowMatch RHEA:62624
+property_value: skos:narrowMatch RHEA:62640
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22598" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23121" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -353029,25 +357199,29 @@
[Term]
id: GO:0051975
-name: L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
+name: obsolete L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-lysine via the intermediates alpha-aminoadipic acid and saccharopine. This pathway is used by yeast and fungi to synthesize the essential amino acid L-lysine, and pathway intermediates are often incorporated into secondary metabolic processes. The pathway proceeds as follows: alpha-ketoglutarate is converted to homocitrate, which is metabolized to 3-carboxyhex-2-enedioate and then homoisocitrate. This is then decarboxylated to form alpha-ketoadipate, which is then converted to alpha-aminoadipate. This is then reduced to form alpha-aminoadipate 6-semialdehyde, which is metabolized to saccharopine and finally L-lysine." [MetaCyc:LYSINE-AMINOAD-PWY]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-lysine via the intermediates alpha-aminoadipic acid and saccharopine. This pathway is used by yeast and fungi to synthesize the essential amino acid L-lysine, and pathway intermediates are often incorporated into secondary metabolic processes. The pathway proceeds as follows: alpha-ketoglutarate is converted to homocitrate, which is metabolized to 3-carboxyhex-2-enedioate and then homoisocitrate. This is then decarboxylated to form alpha-ketoadipate, which is then converted to alpha-aminoadipate. This is then reduced to form alpha-aminoadipate 6-semialdehyde, which is metabolized to saccharopine and finally L-lysine." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine biosynthesis via aminoadipic acid and saccharopine" EXACT []
synonym: "lysine biosynthetic process via aminoadipic acid and saccharopine" EXACT []
-xref: MetaCyc:LYSINE-AMINOAD-PWY
-is_a: GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0051976
-name: L-lysine biosynthetic process via alpha-aminoadipate and N2-acetyl-alpha-aminoadipate
+name: obsolete L-lysine biosynthetic process via alpha-aminoadipate and N2-acetyl-alpha-aminoadipate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-lysine via the intermediates alpha-aminoadipic acid and N2-acetyl-alpha-aminoadipate. This pathway of prokaryotic lysine biosynthesis via alpha-aminoadipate was discovered in the hyper-thermophilic Gram-negative eubacterium Thermus thermophilus. The pathway proceeds as follows: alpha-ketoglutarate is converted to homocitrate, which is metabolized to 3-carboxyhex-2-enedioate and then homoisocitrate. This is then decarboxylated to form alpha-ketoadipate, which is then converted to alpha-aminoadipate. This undergoes acetylation, to form N2-acetyl-alpha-aminoadipate, and is then phosphorylated to give N2-acetyl-alpha-aminoadipyl-delta-phosphate. This is converted to N2-acetyl-alpha-aminoadipate semialdehyde, which is then converted to N2-acetyl-L-lysine. A final deacetylation reaction produces L-lysine." [MetaCyc:PWY-3081]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-lysine via the intermediates alpha-aminoadipic acid and N2-acetyl-alpha-aminoadipate. This pathway of prokaryotic lysine biosynthesis via alpha-aminoadipate was discovered in the hyper-thermophilic Gram-negative eubacterium Thermus thermophilus. The pathway proceeds as follows: alpha-ketoglutarate is converted to homocitrate, which is metabolized to 3-carboxyhex-2-enedioate and then homoisocitrate. This is then decarboxylated to form alpha-ketoadipate, which is then converted to alpha-aminoadipate. This undergoes acetylation, to form N2-acetyl-alpha-aminoadipate, and is then phosphorylated to give N2-acetyl-alpha-aminoadipyl-delta-phosphate. This is converted to N2-acetyl-alpha-aminoadipate semialdehyde, which is then converted to N2-acetyl-L-lysine. A final deacetylation reaction produces L-lysine." [GOC:curators]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "lysine biosynthesis via aminoadipic acid and N2-acetyl-alpha-aminoadipate" EXACT []
synonym: "lysine biosynthetic process via aminoadipic acid and N2-acetyl-alpha-aminoadipate" EXACT []
-xref: MetaCyc:PWY-3081
-is_a: GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30820" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009085
[Term]
id: GO:0051977
@@ -353063,7 +357237,6 @@
namespace: molecular_function
def: "Enables the directed movement of lysophospholipids from one side of a membrane to the other. A lysophospholipid is a phospholipid that lacks one of its fatty acyl chains; it is an intermediate formed during digestion of dietary and biliary phospholipids." [GOC:ai]
synonym: "lysophospholipid transporter activity" BROAD []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0015370 ! solute:sodium symporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
is_a: GO:0170055 ! lipid transmembrane transporter activity
@@ -353214,10 +357387,16 @@
xref: Reactome:R-HSA-880007 "(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2"
xref: Reactome:R-HSA-880053 "2-oxoglutarate + NADPH + H+ => (R)-2-hydroxyglutarate + NADP+ [mutant IDH1]"
xref: RHEA:38295
+xref: RHEA:51192
+xref: RHEA:51612
+xref: RHEA:57168
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
property_value: skos:exactMatch EC:1.1.99.39
property_value: skos:exactMatch MetaCyc:RXN-14932
property_value: skos:exactMatch RHEA:38295
+property_value: skos:narrowMatch RHEA:51192
+property_value: skos:narrowMatch RHEA:51612
+property_value: skos:narrowMatch RHEA:57168
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
[Term]
@@ -353268,11 +357447,13 @@
[Term]
id: GO:0051994
-name: P-methyltransferase activity
+name: obsolete P-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a methyl group to the phosphorus atom of an acceptor molecule." [GOC:ai]
-is_a: GO:0008168 ! methyltransferase activity
+def: "OBSOLETE. Catalysis of the transfer of a methyl group to the phosphorus atom of an acceptor molecule." [GOC:ai]
+comment: This term was obsoleted because it represents a specific substrate.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25591" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
created_by: ai
creation_date: 2010-07-16T04:39:34Z
@@ -353298,6 +357479,8 @@
synonym: "squalene synthetase activity" RELATED [EC:2.5.1.21]
xref: EC:2.5.1.21
xref: MetaCyc:RXN66-281
+xref: Reactome:R-HSA-191402 "Reduction of presqualene diphosphate to form squalene"
+xref: Reactome:R-HSA-191405 "Two FAPP molecules dimerize to form presqualene diphosphate"
xref: RHEA:32295
xref: RHEA:32299
is_a: GO:0004659 ! prenyltransferase activity
@@ -353863,6 +358046,7 @@
synonym: "negative regulation by symbiont of host programmed cell death" EXACT []
synonym: "suppression by symbiont of host PCD" EXACT []
synonym: "suppression by symbiont of host programmed cell death" EXACT []
+xref: Reactome:R-HSA-9636569 "Suppression of autophagy"
is_a: GO:0052040 ! symbiont-mediated perturbation of host programmed cell death
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23652" xsd:anyURI
@@ -355005,8 +359189,8 @@
synonym: "modulation by symbiont of host apoptotic process" EXACT []
synonym: "modulation by virus of host apoptosis" NARROW []
synonym: "regulation by virus of host apoptosis" NARROW []
+xref: Reactome:R-HSA-9920951 "Dengue virus modulates apoptosis"
xref: VZ:1518 "Apoptosis modulation"
-is_a: GO:0051709 ! regulation of killing of cells of another organism
is_a: GO:0052040 ! symbiont-mediated perturbation of host programmed cell death
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25986" xsd:anyURI
@@ -358266,6 +362450,7 @@
synonym: "modulation by organism of immune response of other organism involved in symbiotic interaction" BROAD []
synonym: "modulation by symbiont of host immune response" EXACT []
synonym: "perturbation of host immune response" EXACT []
+xref: Reactome:R-HSA-9920588 "Dengue virus activates/modulates innate and adaptive immune responses"
is_a: GO:0052031 ! symbiont-mediated perturbation of host defense response
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25569" xsd:anyURI
@@ -358685,7 +362870,7 @@
id: GO:0052595
name: aliphatic amine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an aliphatic amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide + H+." [MetaCyc:AMINEOXID-RXN]
+def: "Catalysis of the reaction: an aliphatic amine + H2O + O2 = an aldehyde + NH4+ + H2O2 + H+." [MetaCyc:AMINEOXID-RXN]
synonym: "aliphatic-amine oxidase activity" EXACT []
synonym: "aliphatic-amine:oxygen oxidoreductase(deaminating) activity" EXACT []
xref: MetaCyc:AMINEOXID-RXN
@@ -359189,9 +363374,13 @@
xref: Reactome:R-HSA-6809778 "PI(3,5)P2 is dephosphorylated to PI5P by MTMR2:SBF1"
xref: Reactome:R-HSA-6809944 "PI(3,5)P2 is dephosphorylated to PI5P by the MTMR2:SBF2 tetramer at the plasma membrane"
xref: RHEA:39019
+xref: RHEA:45632
+xref: RHEA:45636
is_a: GO:0106018 ! phosphatidylinositol-3,5-bisphosphate phosphatase activity
property_value: skos:exactMatch EC:3.1.3.95
property_value: skos:exactMatch RHEA:39019
+property_value: skos:narrowMatch RHEA:45632
+property_value: skos:narrowMatch RHEA:45636
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -359385,9 +363574,19 @@
xref: MetaCyc:RXNQT-4375
xref: Reactome:R-HSA-8878654 "ACP6 hydrolyses MYS-LPA"
xref: RHEA:33155
+xref: RHEA:39835
+xref: RHEA:53592
+xref: RHEA:53596
+xref: RHEA:53600
+xref: RHEA:53604
is_a: GO:0016791 ! phosphatase activity
property_value: skos:exactMatch EC:3.1.3.106
property_value: skos:exactMatch RHEA:33155
+property_value: skos:narrowMatch RHEA:39835
+property_value: skos:narrowMatch RHEA:53592
+property_value: skos:narrowMatch RHEA:53596
+property_value: skos:narrowMatch RHEA:53600
+property_value: skos:narrowMatch RHEA:53604
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26658" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -359549,44 +363748,51 @@
[Term]
id: GO:0052654
-name: L-leucine-2-oxoglutarate transaminase activity
+name: L-leucine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-leucine = 4-methyl-2-oxopentanoate + L-glutamatic acid." [RHEA:18321]
+def: "Catalysis of the reaction:L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate." [RHEA:18321]
subset: goslim_chembl
synonym: "L-leucine aminotransferase activity" EXACT []
+synonym: "L-leucine-2-oxoglutarate transaminase activity" EXACT []
+xref: EC:2.6.1.6
xref: KEGG_REACTION:R01090
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERLEU-RXN
xref: RHEA:18321
-is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
+is_a: GO:0004084 ! branched-chain-amino-acid:2-oxoglutarate transaminase activity
+property_value: skos:exactMatch EC:2.6.1.6
property_value: skos:exactMatch RHEA:18321
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0052655
-name: L-valine-2-oxoglutarate transaminase activity
+name: L-valine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-valine = 3-methyl-2-oxobutanoic acid + L-glutamatic acid." [RHEA:24813]
+def: "Catalysis of the reaction: L-valine + 2-oxoglutarate = 3-methyl-2-oxobutanoate + L-glutamate." [RHEA:24813]
subset: goslim_chembl
synonym: "L-valine aminotransferase activity" EXACT []
+synonym: "L-valine-2-oxoglutarate transaminase activity" EXACT []
xref: KEGG_REACTION:R01214
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERVAL-RXN
xref: RHEA:24813
-is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
+is_a: GO:0004084 ! branched-chain-amino-acid:2-oxoglutarate transaminase activity
property_value: skos:exactMatch RHEA:24813
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0052656
-name: L-isoleucine-2-oxoglutarate transaminase activity
+name: L-isoleucine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + L-isoleucine = (S)-3-methyl-2-oxopentanoic acid + L-glutamic acid." [RHEA:24801]
+def: "Catalysis of the reaction: L-isoleucine + 2-oxoglutarate = (S)-3-methyl-2-oxopentanoate + L-glutamate." [RHEA:24801]
subset: goslim_chembl
synonym: "L-isoleucine aminotransferase activity" EXACT []
+synonym: "L-isoleucine-2-oxoglutarate transaminase activity" EXACT []
xref: KEGG_REACTION:R02199
xref: MetaCyc:BRANCHED-CHAINAMINOTRANSFERILEU-RXN
xref: RHEA:24801
-is_a: GO:0004084 ! branched-chain-amino-acid transaminase activity
+is_a: GO:0004084 ! branched-chain-amino-acid:2-oxoglutarate transaminase activity
property_value: skos:exactMatch RHEA:24801
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -360064,27 +364270,26 @@
synonym: "perillyl-CoA synthetase activity" BROAD [UM-BBD_reactionID:r0731]
xref: KEGG_REACTION:R06368
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
[Term]
id: GO:0052687
-name: (3R)-3-isopropenyl-6-oxoheptanoate:CoA ligase (ADP-forming) activity
+name: obsolete (3R)-3-isopropenyl-6-oxoheptanoate:CoA ligase (ADP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-isopropenyl-6-oxoheptanoate + CoA-SH + ATP = H2O + ADP + phosphate + (3R)-3-isopropenyl-6-oxoheptanoyl-CoA." [KEGG_REACTION:R06396]
+def: "OBSOLETE. Catalysis of the reaction: (3R)-3-isopropenyl-6-oxoheptanoate + CoA-SH + ATP = H2O + ADP + phosphate + (3R)-3-isopropenyl-6-oxoheptanoyl-CoA." [KEGG_REACTION:R06396]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "3-isopropenyl-6-oxoheptanoyl-CoA synthetase activity" BROAD [UM-BBD_reactionID:r0737]
-xref: KEGG_REACTION:R06396
-is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0052688
-name: (3R)-3-isopropenyl-6-oxoheptanoate:CoA ligase (AMP-forming) activity
+name: obsolete (3R)-3-isopropenyl-6-oxoheptanoate:CoA ligase (AMP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-isopropenyl-6-oxoheptanoate + CoA-SH + ATP = H2O + AMP + diphosphate + (3R)-3-isopropenyl-6-oxoheptanoyl-CoA." [KEGG_REACTION:R06515]
+def: "OBSOLETE. Catalysis of the reaction: (3R)-3-isopropenyl-6-oxoheptanoate + CoA-SH + ATP = H2O + AMP + diphosphate + (3R)-3-isopropenyl-6-oxoheptanoyl-CoA." [KEGG_REACTION:R06515]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "3-isopropenyl-6-oxoheptanoyl-CoA synthetase activity" BROAD [UM-BBD_reactionID:r0737]
-xref: KEGG_REACTION:R06515
-is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0052689
@@ -360193,7 +364398,6 @@
synonym: "cellular glucuronide biosynthetic process" EXACT []
synonym: "cellular glucuronoside biosynthesis" EXACT []
synonym: "cellular glucuronoside biosynthetic process" EXACT []
-xref: Reactome:R-HSA-156588 "Glucuronidation"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28506" xsd:anyURI
is_obsolete: true
creation_date: 2011-07-27T05:28:18Z
@@ -360530,10 +364734,12 @@
[Term]
id: GO:0052715
-name: mannosyl-diinositol phosphorylceramide phospholipase activity
+name: obsolete mannosyl-diinositol phosphorylceramide phospholipase activity
namespace: molecular_function
-def: "Catalysis of the reaction: mannosyl-diinositol phosphorylceramide + H2O = C26-phytoceramide + mannosyldiphosphorylinositol." [GOC:ai]
-is_a: GO:0052713 ! inositol phosphorylceramide phospholipase activity
+def: "OBSOLETE. Catalysis of the reaction: mannosyl-diinositol phosphorylceramide + H2O = C26-phytoceramide + mannosyldiphosphorylinositol." [GOC:ai]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
created_by: ai
creation_date: 2011-08-05T08:02:57Z
@@ -360560,7 +364766,7 @@
id: GO:0052717
name: tRNA-specific adenosine-34 deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine-34 + H2O = inosine-34 + NH3, in a tRNA-Ala molecule." [PMID:17875641, RHEA:43168]
+def: "Catalysis of the reaction: adenosine34 in tRNA + H2O + H+ = inosine34 in tRNA + NH4+." [PMID:17875641, RHEA:43168]
synonym: "tRNA(Ala)-A34 deaminase activity" EXACT []
xref: EC:3.5.4.33
xref: RHEA:43168
@@ -360873,20 +365079,28 @@
[Term]
id: GO:0052735
-name: tRNA (cytidine-3-)-methyltransferase activity
+name: tRNA (cytidine-N3)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a cytidine in tRNA + S-adenosyl-L-methionine = an N3-methylcytidine in tRNA + H+ + S-adenosyl-L-homocysteine." [RHEA:60908]
synonym: "S-adenosyl-L-methionine:tRNA (cytosine-3-)-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:tRNA cytosine-3-methyltransferase activity" EXACT []
synonym: "transfer ribonucleate cytosine 3-methyltransferase activity" EXACT []
+synonym: "tRNA (cytidine-3-)-methyltransferase activity" EXACT []
synonym: "tRNA (cytosine 3)-methyltransferase activity" EXACT []
synonym: "tRNA (cytosine-3-)-methyltransferase activity" EXACT []
synonym: "tRNA cytosine 3-methyltransferase activity" EXACT []
synonym: "tRNA cytosine-3-methyltransferase activity" EXACT []
+xref: RHEA:50956
+xref: RHEA:50960
xref: RHEA:60908
+xref: RHEA:60912
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
property_value: skos:exactMatch RHEA:60908
+property_value: skos:narrowMatch RHEA:50956
+property_value: skos:narrowMatch RHEA:50960
+property_value: skos:narrowMatch RHEA:60912
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25722" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26109" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -360933,7 +365147,6 @@
def: "OBSOLETE. Catalysis of the reaction: phosphatidylserine + H2O = 2-acyl-sn-glycero-3-phosphoserine + fatty acid." [KEGG_REACTION:R04034]
comment: The reason for obsoletion is that this molecular function is equivalent to phospholipase A1 activity.
xref: KEGG_REACTION:R04034
-xref: Reactome:R-HSA-8869425 "PLA1A hydrolyses PS to 2-acyl LPS"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28816" xsd:anyURI
is_obsolete: true
replaced_by: GO:0008970
@@ -361075,7 +365288,7 @@
id: GO:0052750
name: versatile peroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: reactive black 5 + hydrogen peroxide = oxidized reactive black 5 + 2 H2O." [RHEA:22396]
+def: "Catalysis of the reaction: reactive black 5 + H2O2 = oxidized reactive black 5 + 2 H2O." [RHEA:22396]
synonym: "reactive-black-5:hydrogen-peroxide oxidoreductase activity" BROAD [EC:1.11.1.16]
xref: EC:1.11.1.16
xref: KEGG_REACTION:R07612
@@ -361100,15 +365313,12 @@
[Term]
id: GO:0052752
-name: reduced coenzyme F420:heterodisulfide oxidoreductase activity
+name: obsolete reduced coenzyme F420:heterodisulfide oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: reduced coenzyme F420 + CoB-S-S-CoM = coenzyme F420 + CoM-SH + CoB-SH." [GOC:mengo_curators, PMID:9914308]
-synonym: "coenzyme F420-dependent heterodisulfide oxidoreductase activity" EXACT [PMID:9914308]
-synonym: "F420-dependent heterodisulfide oxidoreductase activity" EXACT [PMID:9914308]
-synonym: "F420H2:heterodisulfide oxidoreductase activity" EXACT []
-is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
-created_by: ai
-creation_date: 2011-09-21T04:21:16Z
+def: "OBSOLETE. Catalysis of the reaction: reduced coenzyme F420 + CoB-S-S-CoM = coenzyme F420 + CoM-SH + CoB-SH." [GOC:mengo_curators, PMID:9914308]
+comment: The reason for obsoletion is that this reaction MF has no EC or RHEA xref and no annotations.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0052753
@@ -361123,17 +365333,17 @@
[Term]
id: GO:0052754
-name: GTP:coenzyme F420 guanyltransferase activity
+name: obsolete GTP:coenzyme F420 guanyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + factor gamma-F420-2 + H+ = coenzyme F390-G + diphosphate." [GOC:mengo_curators, MetaCyc:RXN-18273]
+def: "OBSOLETE. Catalysis of the reaction: GTP + factor gamma-F420-2 + H+ = coenzyme F390-G + diphosphate." [GOC:mengo_curators]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "coenzyme F390-G synthetase activity" EXACT []
synonym: "GTP:coenzyme F420 guanylyltransferase activity" EXACT []
-xref: MetaCyc:RXN-18273
-is_a: GO:0070568 ! guanylyltransferase activity
-property_value: skos:exactMatch MetaCyc:RXN-18273
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28324" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28503" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
created_by: ai
creation_date: 2011-09-22T03:25:30Z
@@ -361412,19 +365622,15 @@
[Term]
id: GO:0052776
-name: chitin catabolic process to fructose 6-phosphate via glucosamine
+name: obsolete chitin catabolic process to fructose 6-phosphate via glucosamine
namespace: biological_process
-def: "The pathway resulting in the breakdown of chitin into fructose 6-phosphate, via glucosamine; acetate is also produced during the process." [GOC:bf, GOC:mengo_curators, MetaCyc:PWY-6855, PMID:15136574, PMID:16232910, PMID:16736587]
+def: "OBSOLETE. The pathway resulting in the breakdown of chitin into fructose 6-phosphate, via glucosamine; acetate is also produced during the process." [GOC:bf, GOC:mengo_curators, PMID:15136574, PMID:16232910, PMID:16736587]
+comment: The reason for obsoletion is that the term is too specific and represents a GO-CAM model.
synonym: "diacetylchitobiose catabolic process to glucosamine and acetate" EXACT []
-xref: MetaCyc:PWY-6855
-is_a: GO:0006032 ! chitin catabolic process
-is_a: GO:0006083 ! acetate metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
-is_a: GO:0019637 ! organophosphate metabolic process
-relationship: has_part GO:0050119 ! N-acetylglucosamine deacetylase activity
-relationship: has_part GO:0052761 ! exo-1,4-beta-D-glucosaminidase activity
-relationship: has_part GO:0052773 ! diacetylchitobiose deacetylase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31633" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006032
[Term]
id: GO:0052777
@@ -361734,7 +365940,7 @@
xref: EC:1.8.98.3
xref: MetaCyc:RXN-15618
xref: RHEA:42808
-is_a: GO:0016002 ! sulfite reductase activity
+is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
property_value: skos:exactMatch EC:1.8.98.3
property_value: skos:exactMatch MetaCyc:RXN-15618
property_value: skos:exactMatch RHEA:42808
@@ -361849,9 +366055,29 @@
synonym: "medium-chain fatty aldehyde dehydrogenase activity" RELATED []
synonym: "medium-chain-aldehyde dehydrogenase activity" EXACT []
synonym: "medium-chain-aldehyde:NAD+ oxidoreductase activity" RELATED []
+xref: RHEA:44100
+xref: RHEA:44104
+xref: RHEA:44108
+xref: RHEA:44168
+xref: RHEA:59920
+xref: RHEA:67248
+xref: RHEA:67260
+xref: RHEA:67276
+xref: RHEA:69759
xref: RHEA:69763
+xref: RHEA:69767
is_a: GO:0102673 ! fatty aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch RHEA:69763
+property_value: skos:narrowMatch RHEA:44100
+property_value: skos:narrowMatch RHEA:44104
+property_value: skos:narrowMatch RHEA:44108
+property_value: skos:narrowMatch RHEA:44168
+property_value: skos:narrowMatch RHEA:59920
+property_value: skos:narrowMatch RHEA:67248
+property_value: skos:narrowMatch RHEA:67260
+property_value: skos:narrowMatch RHEA:67276
+property_value: skos:narrowMatch RHEA:69759
+property_value: skos:narrowMatch RHEA:69767
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28090" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28142" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -361869,10 +366095,32 @@
synonym: "medium-chain-acyl-CoA hydrolase activity" RELATED []
xref: EC:3.1.2.19
xref: MetaCyc:3.1.2.19-RXN
+xref: RHEA:30135
+xref: RHEA:30143
+xref: RHEA:40059
+xref: RHEA:40115
+xref: RHEA:40223
+xref: RHEA:55048
+xref: RHEA:59952
+xref: RHEA:65172
+xref: RHEA:65212
+xref: RHEA:65216
+xref: RHEA:65232
xref: RHEA:68184
is_a: GO:0047617 ! fatty acyl-CoA hydrolase activity
property_value: skos:exactMatch RHEA:68184
property_value: skos:narrowMatch EC:3.1.2.19
+property_value: skos:narrowMatch RHEA:30135
+property_value: skos:narrowMatch RHEA:30143
+property_value: skos:narrowMatch RHEA:40059
+property_value: skos:narrowMatch RHEA:40115
+property_value: skos:narrowMatch RHEA:40223
+property_value: skos:narrowMatch RHEA:55048
+property_value: skos:narrowMatch RHEA:59952
+property_value: skos:narrowMatch RHEA:65172
+property_value: skos:narrowMatch RHEA:65212
+property_value: skos:narrowMatch RHEA:65216
+property_value: skos:narrowMatch RHEA:65232
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26441" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -361889,9 +366137,55 @@
synonym: "long-chain acyl-thioester hydrolase activity" RELATED []
synonym: "long-chain hydrolase activity" RELATED []
synonym: "long-chain-acyl-CoA hydrolase activity" RELATED []
+xref: RHEA:16645
+xref: RHEA:30139
+xref: RHEA:40119
+xref: RHEA:40131
+xref: RHEA:40135
+xref: RHEA:40139
+xref: RHEA:40143
+xref: RHEA:40147
+xref: RHEA:40151
+xref: RHEA:40415
+xref: RHEA:40419
+xref: RHEA:40723
+xref: RHEA:40783
+xref: RHEA:54976
+xref: RHEA:55044
+xref: RHEA:59940
+xref: RHEA:59948
+xref: RHEA:65240
xref: RHEA:67680
+xref: RHEA:67696
+xref: RHEA:67700
+xref: RHEA:67712
+xref: RHEA:83071
+xref: RHEA:83355
is_a: GO:0047617 ! fatty acyl-CoA hydrolase activity
property_value: skos:exactMatch RHEA:67680
+property_value: skos:narrowMatch RHEA:16645
+property_value: skos:narrowMatch RHEA:30139
+property_value: skos:narrowMatch RHEA:40119
+property_value: skos:narrowMatch RHEA:40131
+property_value: skos:narrowMatch RHEA:40135
+property_value: skos:narrowMatch RHEA:40139
+property_value: skos:narrowMatch RHEA:40143
+property_value: skos:narrowMatch RHEA:40147
+property_value: skos:narrowMatch RHEA:40151
+property_value: skos:narrowMatch RHEA:40415
+property_value: skos:narrowMatch RHEA:40419
+property_value: skos:narrowMatch RHEA:40723
+property_value: skos:narrowMatch RHEA:40783
+property_value: skos:narrowMatch RHEA:54976
+property_value: skos:narrowMatch RHEA:55044
+property_value: skos:narrowMatch RHEA:59940
+property_value: skos:narrowMatch RHEA:59948
+property_value: skos:narrowMatch RHEA:65240
+property_value: skos:narrowMatch RHEA:67696
+property_value: skos:narrowMatch RHEA:67700
+property_value: skos:narrowMatch RHEA:67712
+property_value: skos:narrowMatch RHEA:83071
+property_value: skos:narrowMatch RHEA:83355
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26441" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -361908,9 +366202,13 @@
synonym: "very long-chain acyl-thioester hydrolase activity" RELATED []
synonym: "very long-chain hydrolase activity" RELATED []
synonym: "very long-chain-acyl-CoA hydrolase activity" RELATED []
+xref: RHEA:40787
+xref: RHEA:40791
xref: RHEA:67072
is_a: GO:0047617 ! fatty acyl-CoA hydrolase activity
property_value: skos:exactMatch RHEA:67072
+property_value: skos:narrowMatch RHEA:40787
+property_value: skos:narrowMatch RHEA:40791
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26441" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -362011,7 +366309,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = myo-inositol 1,3,4,5,6-pentakisphosphate + phosphate." [GOC:curators]
comment: The reason for obsoletion is that this term is equivalent to inositol hexakisphosphate 3-phosphatase activity.
-xref: Reactome:R-HSA-1855225 "IP6 is dephosphorylated to I(1,2,4,5,6)P5 by MINPP1 in the ER lumen"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30385" xsd:anyURI
is_obsolete: true
@@ -362121,9 +366418,15 @@
xref: EC:3.1.3.25
xref: MetaCyc:RXN-10949
xref: RHEA:24056
+xref: RHEA:44152
+xref: RHEA:44156
+xref: RHEA:44160
is_a: GO:0052745 ! inositol phosphate phosphatase activity
property_value: skos:exactMatch EC:3.1.3.25
property_value: skos:exactMatch RHEA:24056
+property_value: skos:narrowMatch RHEA:44152
+property_value: skos:narrowMatch RHEA:44156
+property_value: skos:narrowMatch RHEA:44160
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: ai
@@ -362354,6 +366657,7 @@
xref: KEGG_REACTION:R09541
xref: MetaCyc:RXN0-6555
xref: Reactome:R-HSA-917811 "STEAP3,STEAP4 reduce Fe3+ to Fe2+"
+xref: Reactome:R-HSA-9927945 "YqjH reduces FeEnt"
xref: RHEA:28795
is_a: GO:0000293 ! ferric-chelate reductase activity
is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor
@@ -362391,6 +366695,7 @@
synonym: "NADHX epimerase activity" NARROW []
synonym: "NADPHX epimerase activity" NARROW []
xref: EC:5.1.99.6
+xref: Reactome:R-HSA-6806966 "APOA1BP dimer epimerises R-NAD(P)HX to S-NAD(P)HX"
xref: RHEA:32215
xref: RHEA:32227
is_a: GO:0016854 ! racemase and epimerase activity
@@ -362405,7 +366710,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: (R)-NADPHX = (S)-NADPHX." [PMID:21994945]
comment: This term was obsoleted because it represents the same activity as NADHX epimerase activity ; GO:0052856.
-xref: Reactome:R-HSA-6806966 "APOA1BP dimer epimerises R-NAD(P)HX to S-NAD(P)HX"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
is_obsolete: true
replaced_by: GO:0052856
@@ -362565,9 +366869,11 @@
id: GO:0052868
name: protein-lysine lysyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein-lysine + protein-lysine = protein N6-(lysyl)-L-lysine + protein. This reaction is the addition of lysine group from one protein to a lysine residue in a second protein, producing N6-(lysyl)-L-lysine." [PMID:20729861]
+def: "Catalysis of the reaction: D-beta-lysine + L-lysyl-[protein] + ATP = N6-((3R)-3,6-diaminohexanoyl)-L-lysyl-[protein] + AMP + diphosphate + H+n. This reaction is the addition of lysine group from one protein to a lysine residue in a second protein, producing N6-(lysyl)-L-lysine." [PMID:20729861, RHEA:83435]
+xref: RHEA:83435
is_a: GO:0016755 ! aminoacyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31478" xsd:anyURI
created_by: ai
creation_date: 2012-01-11T03:05:27Z
@@ -362931,8 +367237,32 @@
xref: KEGG_REACTION:R09359
xref: MetaCyc:RXN-11732
xref: RHEA:54660
+xref: RHEA:77427
+xref: RHEA:77447
+xref: RHEA:77451
+xref: RHEA:77455
+xref: RHEA:77459
+xref: RHEA:77463
+xref: RHEA:77499
+xref: RHEA:77503
+xref: RHEA:77507
+xref: RHEA:77511
+xref: RHEA:77515
+xref: RHEA:77519
is_a: GO:0047606 ! (S)-hydroxynitrile lyase activity
property_value: skos:exactMatch RHEA:54660
+property_value: skos:narrowMatch RHEA:77427
+property_value: skos:narrowMatch RHEA:77447
+property_value: skos:narrowMatch RHEA:77451
+property_value: skos:narrowMatch RHEA:77455
+property_value: skos:narrowMatch RHEA:77459
+property_value: skos:narrowMatch RHEA:77463
+property_value: skos:narrowMatch RHEA:77499
+property_value: skos:narrowMatch RHEA:77503
+property_value: skos:narrowMatch RHEA:77507
+property_value: skos:narrowMatch RHEA:77511
+property_value: skos:narrowMatch RHEA:77515
+property_value: skos:narrowMatch RHEA:77519
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16166" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -363079,23 +367409,29 @@
synonym: "N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity" NARROW [EC:1.5.3.13]
xref: EC:1.5.3.13
xref: KEGG_REACTION:R03899
-xref: MetaCyc:RXN-12090
+xref: MetaCyc:RXN-10460
+xref: MetaCyc:RXN-12091
+xref: MetaCyc:RXN-9940
+xref: Reactome:R-HSA-141348 "PAO:FAD oxidises NASPM to PTCN"
+xref: Reactome:R-HSA-141351 "PAOX:FAD oxidises NASPN to SPM"
xref: RHEA:25800
xref: RHEA:25812
xref: RHEA:25868
is_a: GO:0046592 ! polyamine oxidase activity
property_value: skos:exactMatch EC:1.5.3.13
property_value: skos:exactMatch KEGG_REACTION:R03899
-property_value: skos:exactMatch MetaCyc:RXN-12090
+property_value: skos:narrowMatch MetaCyc:RXN-10460
+property_value: skos:narrowMatch MetaCyc:RXN-12091
+property_value: skos:narrowMatch MetaCyc:RXN-9940
property_value: skos:narrowMatch RHEA:25800
property_value: skos:narrowMatch RHEA:25812
property_value: skos:narrowMatch RHEA:25868
-property_value: skos:relatedMatch MetaCyc:RXN-9940
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24701" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25837" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31136" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0052904
@@ -363103,8 +367439,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: H2O + N(1)-acetylspermidine + O2 = 3-acetamidopropanal + H2O2 + putrescine." [GOC:curators]
comment: This term was obsoleted because it represents a specific substrate of N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity ; GO:0052903.
-xref: Reactome:R-HSA-141348 "PAO:FAD oxidises NASPM to PTCN"
-xref: Reactome:R-HSA-141351 "PAOX:FAD oxidises NASPN to SPM"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24701" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
is_obsolete: true
@@ -363543,12 +367877,14 @@
xref: MetaCyc:RXN-11332
xref: MetaCyc:RXN-2861
xref: RHEA:51004
+xref: RHEA:51008
is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
property_value: skos:exactMatch EC:1.1.2.7
property_value: skos:exactMatch KEGG_REACTION:R10713
property_value: skos:exactMatch MetaCyc:RXN-11332
property_value: skos:exactMatch RHEA:51004
property_value: skos:narrowMatch MetaCyc:RXN-2861
+property_value: skos:narrowMatch RHEA:51008
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -363572,10 +367908,28 @@
xref: KEGG_REACTION:R05198
xref: KEGG_REACTION:R05285
xref: MetaCyc:RXN-11333
+xref: RHEA:43432
xref: RHEA:51020
+xref: RHEA:55944
+xref: RHEA:62200
+xref: RHEA:62204
+xref: RHEA:79319
+xref: RHEA:79323
+xref: RHEA:79331
+xref: RHEA:79335
+xref: RHEA:79359
is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
property_value: skos:exactMatch EC:1.1.2.8
property_value: skos:exactMatch RHEA:51020
+property_value: skos:narrowMatch RHEA:43432
+property_value: skos:narrowMatch RHEA:55944
+property_value: skos:narrowMatch RHEA:62200
+property_value: skos:narrowMatch RHEA:62204
+property_value: skos:narrowMatch RHEA:79319
+property_value: skos:narrowMatch RHEA:79323
+property_value: skos:narrowMatch RHEA:79331
+property_value: skos:narrowMatch RHEA:79335
+property_value: skos:narrowMatch RHEA:79359
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -363973,6 +368327,7 @@
namespace: cellular_component
def: "Flagellar filaments located in the periplasmic space; characterized in spirochetes, in which they are essential for shape and motility. Composed of a core surrounded by two sheath layers, the flagella rotate to allow migration of the cell through viscous media, which would not be possible using external flagella." [GOC:jid, GOC:rph, PMID:15175283, PMID:1624463]
is_a: GO:0009288 ! bacterial-type flagellum
+is_a: GO:0043264 ! extracellular membraneless organelle
relationship: part_of GO:0042597 ! periplasmic space
[Term]
@@ -363993,17 +368348,21 @@
[Term]
id: GO:0055042
-name: 5-valerolactone hydrolase activity
+name: obsolete 5-valerolactone hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-valerolactone + H2O = 5-hydroxyvalerate." [GOC:jid, GOC:mlg]
-is_a: GO:0046573 ! lactonohydrolase activity
+def: "OBSOLETE. Catalysis of the reaction: 5-valerolactone + H2O = 5-hydroxyvalerate." [GOC:jid, GOC:mlg]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0055043
-name: 5-oxovalerate dehydrogenase activity
+name: obsolete 5-oxovalerate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-oxovalerate + NADP+ + H2O = glutarate + NADPH + H+." [GOC:jid, GOC:mlg]
-is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: 5-oxovalerate + NADP+ + H2O = glutarate + NADPH + H+." [GOC:jid, GOC:mlg]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0055044
@@ -364118,9 +368477,11 @@
def: "Enables the transfer of the D-enantiomer of the hexose monosaccharide glucose from one side of a membrane to the other." [GOC:jid, GOC:jsg, GOC:mah]
xref: Reactome:R-HSA-429094 "SLC2A6,8,10,12 transport Glc from extracellular region to cytosol"
xref: Reactome:R-HSA-450095 "GLUT2 (SLC2A2) transports Glc from cytosol to extracellular region"
+xref: Reactome:R-HSA-499981 "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2"
xref: Reactome:R-HSA-5339524 "GLUT1 (SLC2A1) tetramer transports Glc from extracellular region to cytosol"
xref: Reactome:R-HSA-5632804 "SLC2A1 tetramer does not transport Glc from extracellular region to cytosol"
xref: Reactome:R-HSA-5632871 "Defective SLC2A10 does not transport Glc from extracellular region to cytosol"
+xref: Reactome:R-HSA-5653873 "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen"
xref: Reactome:R-HSA-8981553 "GLUT14 (SLC2A14) tetramer transports Glc from extracellular region to cytosol"
xref: Reactome:R-HSA-8981564 "GLUT3 (SLC2A3) tetramer transports Glc from extracellular region to cytosol"
xref: Reactome:R-HSA-8981570 "GLUT4 (SLC2A4) tetramer transports Glc from extracellular region to cytosol"
@@ -364585,6 +368946,7 @@
name: Golgi to secretory granule transport
namespace: biological_process
def: "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex." [GOC:curators]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
[Term]
@@ -364781,15 +369143,19 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins." [GOC:ecd]
synonym: "pyrrolidine-2-carboxylic acid biosynthetic process" BROAD []
+xref: MetaCyc:ORN-AMINOPENTANOATE-CAT-PWY
xref: MetaCyc:PROSYN-PWY
xref: MetaCyc:PWY-3341
-xref: MetaCyc:PWY-4281 {status="skos:narrowMatch"}
+xref: MetaCyc:PWY-4281
xref: MetaCyc:PWY-4981
is_a: GO:0006560 ! L-proline metabolic process
is_a: GO:0009084 ! L-glutamine family amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:ORN-AMINOPENTANOATE-CAT-PWY
property_value: skos:narrowMatch MetaCyc:PROSYN-PWY
property_value: skos:narrowMatch MetaCyc:PWY-3341
+property_value: skos:narrowMatch MetaCyc:PWY-4281
property_value: skos:narrowMatch MetaCyc:PWY-4981
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: jid
creation_date: 2009-10-22T01:59:56Z
@@ -364797,10 +369163,12 @@
id: GO:0055130
name: D-alanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-alanine, the D-enantiomer of the amino acid alanine." [GOC:ecd]
+def: "The chemical reactions and pathways resulting in the breakdown of D-alanine." [GOC:curators]
synonym: "(2R)-2-aminopropanoic acid catabolic process" EXACT []
+xref: MetaCyc:PWY-8448
is_a: GO:0019478 ! D-amino acid catabolic process
-is_a: GO:0046436 ! D-alanine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
created_by: jid
creation_date: 2009-10-22T02:02:42Z
@@ -365679,10 +370047,10 @@
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
synonym: "binding, bridging" EXACT []
-synonym: "protein complex scaffold activity" BROAD []
-synonym: "protein-containing complex scaffold activity" BROAD []
+xref: Reactome:R-HSA-2564826 "4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold"
is_a: GO:0003674 ! molecular_function
relationship: has_part GO:0005488 ! binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31509" xsd:anyURI
[Term]
id: GO:0060091
@@ -366191,10 +370559,11 @@
id: GO:0060138
name: fetal process involved in parturition
namespace: biological_process
-def: "A reproductive process occurring in the embryo that results in birth." [GOC:dph]
+def: "A reproductive process occurring in the fetus that results in birth." [GOC:dph]
is_a: GO:0048609 ! multicellular organismal reproductive process
relationship: part_of GO:0007567 ! parturition
relationship: part_of GO:0009792 ! embryo development ending in birth or egg hatching
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31526" xsd:anyURI
[Term]
id: GO:0060140
@@ -366213,6 +370582,7 @@
def: "A process in which a symbiont initiates, promotes, or enhances the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual host cells. Syncytia are produced by viruses that are able to fuse directly at the cell surface without requiring endocytosis." [GOC:dph]
synonym: "positive regulation of syncytium formation by virus" EXACT []
synonym: "syncytium formation induced by viral infection" EXACT [VZ:5957]
+xref: Reactome:R-HSA-9733458 "Induction of Cell-Cell Fusion"
xref: VZ:5957
is_a: GO:0044068 ! symbiont-mediated perturbation of host cellular process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28791" xsd:anyURI
@@ -366222,23 +370592,21 @@
name: regulation of syncytium formation by plasma membrane fusion
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:dph]
-is_a: GO:0050793 ! regulation of developmental process
is_a: GO:0051128 ! regulation of cellular component organization
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0000768 ! syncytium formation by plasma membrane fusion
-relationship: regulates GO:0000768 ! syncytium formation by plasma membrane fusion
+intersection_of: regulates GO:0000768 ! syncytium formation by cell-cell fusion
+relationship: regulates GO:0000768 ! syncytium formation by cell-cell fusion
[Term]
id: GO:0060143
name: positive regulation of syncytium formation by plasma membrane fusion
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:dph]
-is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:0051130 ! positive regulation of cellular component organization
is_a: GO:0060142 ! regulation of syncytium formation by plasma membrane fusion
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0000768 ! syncytium formation by plasma membrane fusion
-relationship: positively_regulates GO:0000768 ! syncytium formation by plasma membrane fusion
+intersection_of: positively_regulates GO:0000768 ! syncytium formation by cell-cell fusion
+relationship: positively_regulates GO:0000768 ! syncytium formation by cell-cell fusion
[Term]
id: GO:0060144
@@ -367080,6 +371448,7 @@
name: lipase activator activity
namespace: molecular_function
def: "Binds to and increases the activity of a lipase, an enzyme that catalyzes of the hydrolysis of a lipid." [GOC:BHF, GOC:dph, GOC:tb]
+xref: Reactome:R-HSA-163549 "phosphorylated HSL dimer + FABP4 -> phosphorylated HSL dimer:FABP4 complex"
is_a: GO:0008047 ! enzyme activator activity
relationship: positively_regulates GO:0016298 ! lipase activity
@@ -367861,9 +372230,9 @@
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reaction involving the removal of one or more phosphate groups from a phosphatidylinositol." [GOC:dph, GOC:tb]
synonym: "regulation of phosphoinositide dephosphorylation" EXACT []
+is_a: GO:0019216 ! regulation of lipid metabolic process
is_a: GO:0035303 ! regulation of dephosphorylation
is_a: GO:0060255 ! regulation of macromolecule metabolic process
-is_a: GO:1903725 ! regulation of phospholipid metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0046856 ! phosphatidylinositol dephosphorylation
relationship: regulates GO:0046856 ! phosphatidylinositol dephosphorylation
@@ -370825,9 +375194,10 @@
namespace: molecular_function
def: "Binds to and modulates the activity of an ATP hydrolysis activity." [GOC:dph, GOC:tb]
synonym: "ATP hydrolysis regulator activity" EXACT []
-is_a: GO:0098772 ! molecular function regulator activity
-relationship: regulates GO:0140657 ! ATP-dependent activity
+is_a: GO:0060589 ! nucleoside-triphosphatase regulator activity
+relationship: regulates GO:0016887 ! ATP hydrolysis activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20955" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31398" xsd:anyURI
created_by: dph
creation_date: 2009-05-08T02:49:24Z
@@ -380099,7 +384469,7 @@
id: GO:0061402
name: obsolete positive regulation of transcription from RNA polymerase II promoter in response to acidic pH
namespace: biological_process
-def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7." [GOC:dph, GOC:go_curators]
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7." [GOC:curators, GOC:dph]
comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "positive regulation of transcription from RNA polymerase II promoter in response to acidity" BROAD []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26004" xsd:anyURI
@@ -381106,12 +385476,14 @@
[Term]
id: GO:0061502
-name: early endosome to recycling endosome transport
+name: obsolete early endosome to recycling endosome transport
namespace: biological_process
-def: "The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the recycling endosomes." [GOC:dph, GOC:kmv, PMID:21474295]
-is_a: GO:0098927 ! vesicle-mediated transport between endosomal compartments
-relationship: occurs_in GO:0005737 ! cytoplasm
+def: "OBSOLETE. The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the recycling endosomes." [GOC:dph, GOC:kmv, PMID:21474295]
+comment: This term is described by another GO term
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26386" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31240" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0032456
created_by: dph
creation_date: 2013-01-04T07:24:56Z
@@ -381546,12 +385918,22 @@
synonym: "S-adenosyl-L-methionine:2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone-O-methyltransferase" RELATED []
xref: EC:2.1.1.64
xref: Reactome:R-HSA-2162186 "COQ3 methylates DeMQ10H2"
+xref: RHEA:17049
+xref: RHEA:28679
xref: RHEA:44380
+xref: RHEA:44400
+xref: RHEA:44404
+xref: RHEA:44412
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
relationship: part_of GO:0006744 ! ubiquinone biosynthetic process
property_value: skos:exactMatch EC:2.1.1.64
property_value: skos:exactMatch RHEA:44380
+property_value: skos:narrowMatch RHEA:17049
+property_value: skos:narrowMatch RHEA:28679
+property_value: skos:narrowMatch RHEA:44400
+property_value: skos:narrowMatch RHEA:44404
+property_value: skos:narrowMatch RHEA:44412
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25680" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29420" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -382196,9 +386578,15 @@
xref: EC:2.10.1.1
xref: Reactome:R-HSA-947531 "Molybdenum ion transfer onto molybdopterin"
xref: RHEA:35047
+xref: RHEA:78687
+xref: RHEA:79031
+xref: RHEA:79035
is_a: GO:0016740 ! transferase activity
property_value: skos:exactMatch EC:2.10.1.1
property_value: skos:exactMatch RHEA:35047
+property_value: skos:narrowMatch RHEA:78687
+property_value: skos:narrowMatch RHEA:79031
+property_value: skos:narrowMatch RHEA:79035
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
creation_date: 2014-02-10T14:30:31Z
@@ -382277,7 +386665,6 @@
synonym: "N-terminal propionyltransferase activity" EXACT [PMID:23043182]
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140096 ! catalytic activity, acting on a protein
-relationship: part_of GO:0061606 ! N-terminal protein amino acid propionylation
created_by: dph
creation_date: 2014-02-11T14:24:35Z
@@ -382287,6 +386674,7 @@
namespace: molecular_function
def: "Combining with a nuclear import signal (NIS) on a cargo to be transported, to mediate transport of the cargo through the nuclear pore, from the cytoplasm to the nuclear lumen. The cargo can be either a RNA or a protein." [GOC:dph, GOC:pg, GOC:vw, PMID:28713609, Wikipedia:Nuclear_transport]
synonym: "importin activity" RELATED []
+xref: Reactome:R-HSA-2065550 "SREBP1A,1C,2 binds Importin beta-1"
is_a: GO:0140142 ! nucleocytoplasmic carrier activity
intersection_of: GO:0140142 ! nucleocytoplasmic carrier activity
intersection_of: part_of GO:0051170 ! import into nucleus
@@ -382714,6 +387102,15 @@
xref: Reactome:R-HSA-9762091 "NFE2L2 is ubiquitinated by BTRC:SKP1:CUL1:RBX1"
xref: Reactome:R-HSA-9766645 "CUL3:RBX1 ubiquitinates KEAP1"
xref: Reactome:R-HSA-990526 "Recruitment of ITCH and K48 ubiquitination of MAVS"
+xref: Reactome:R-HSA-9929490 "CD274 ubiquitination by SPOP:CUL3:RBX1 complex"
+xref: Reactome:R-HSA-9931298 "Ubiquitination of CD274 by ERAD complex"
+xref: Reactome:R-HSA-9931430 "MIB2-mediated K63-ubiquitination of CD274"
+xref: Reactome:R-HSA-9932510 "BTRC:CUL1:SKP1:RBX1 (SCF-beta-TrCP1) ubiquitinylates phosphorylated PER1,2,3"
+xref: Reactome:R-HSA-9932512 "FBXL3:CUL1:SKP1:RBX1 ubiquitinylates phosphorylated CRY1,2"
+xref: Reactome:R-HSA-9945766 "NS3 is ubiquitinated"
+xref: Reactome:R-HSA-9946390 "NS1 dimer is ubiquitinated"
+xref: Reactome:R-HSA-9948362 "LTN1 K48 polyubiquitinates the nascent peptide in NEMF:60S ribosomal subunit:peptidyl-tRNA with nascent peptide"
+xref: Reactome:R-HSA-9954737 "RCHY1 K48 polyubiquitinates alanine-tailed nascent peptide"
is_a: GO:0004842 ! ubiquitin-protein transferase activity
is_a: GO:0061659 ! ubiquitin-like protein ligase activity
property_value: skos:narrowMatch EC:2.3.2.26
@@ -382949,6 +387346,7 @@
namespace: molecular_function
def: "Isoenergetic transfer of ISG15 from one protein to another via the reaction X-ISG15 + Y = Y-ISG15 + X, where both the X-ISG15 and Y-ISG15 linkages are thioester bonds between the C-terminal amino acid of ISG15 and a sulfhydryl side group of a cysteine residue." [GOC:dph]
synonym: "E2" BROAD [GOC:dph]
+xref: Reactome:R-HSA-1169404 "Transfer of ISG15 from E1 to E2 (UBCH8)"
is_a: GO:0042296 ! ISG15 transferase activity
is_a: GO:0061650 ! ubiquitin-like protein conjugating enzyme activity
created_by: dph
@@ -383052,6 +387450,13 @@
namespace: molecular_function
def: "Catalysis of the transfer of a ISG15 to a substrate protein via the reaction X-ISG15 + S = X + S-ISG15, where X is either an E2 or E3 enzyme, the X-ISG15 linkage is a thioester bond, and the S-ISG15 linkage is an isopeptide bond between the C-terminal amino acid of ISG15 and the epsilon-amino group of lysine residues in the substrate." [GOC:dph]
synonym: "E3" BROAD [GOC:dph]
+xref: Reactome:R-HSA-1169394 "ISGylation of IRF3"
+xref: Reactome:R-HSA-1169395 "ISGylation of viral protein NS1"
+xref: Reactome:R-HSA-1169398 "ISGylation of host protein filamin B"
+xref: Reactome:R-HSA-1169402 "ISGylation of E2 conjugating enzymes"
+xref: Reactome:R-HSA-1169405 "ISGylation of protein phosphatase 1 beta (PP2CB)"
+xref: Reactome:R-HSA-1169406 "ISGylation of host proteins"
+xref: Reactome:R-HSA-9833973 "ISGylation of PKR"
is_a: GO:0042296 ! ISG15 transferase activity
is_a: GO:0061659 ! ubiquitin-like protein ligase activity
created_by: dph
@@ -383204,6 +387609,7 @@
name: importin-alpha family protein binding
namespace: molecular_function
def: "Binding to a member of the importin-alpha family." [PMID:15350979, PMID:17170104, PMID:23734157]
+xref: Reactome:R-HSA-2065539 "SREBP1A,1C,2:Importin beta-1 dissociates"
is_a: GO:0005515 ! protein binding
created_by: dph
creation_date: 2015-01-10T18:25:22Z
@@ -383315,7 +387721,7 @@
is_a: GO:0030163 ! protein catabolic process
relationship: has_part GO:0005102 ! signaling receptor binding
relationship: has_part GO:0051087 ! protein-folding chaperone binding
-relationship: has_part GO:0140597 ! protein carrier chaperone
+relationship: has_part GO:0140597 ! protein carrier activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20850" xsd:anyURI
created_by: dph
creation_date: 2015-03-04T14:35:26Z
@@ -383461,8 +387867,7 @@
name: pituitary gonadotropin complex
namespace: cellular_component
def: "A protein complex that is a protein hormone secreted by gonadotrope cells of the anterior pituitary of vertebrates. capable of regulating normal growth, sexual development, and reproductive function." [GOC:dph, PMID:11420129]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: dph
creation_date: 2015-05-06T13:11:18Z
@@ -383472,6 +387877,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: N(6)-glutaryl-L-lysyl-[protein] + NAD+ + H2O = 2''-O-glutaryl-ADP-D-ribose + nicotinamide + L-lysyl-[protein]." [PMID:24703693, RHEA:47664]
comment: This reaction is the removal of a glutaryl group from a glutarylated lysine residue of a protein or peptide.
+xref: Reactome:R-HSA-9955504 "SIRT5 deglutarylates CPS1"
xref: RHEA:47664
is_a: GO:0141218 ! NAD-dependent protein lysine deacylase activity
property_value: skos:exactMatch RHEA:47664
@@ -383632,6 +388038,7 @@
def: "Catalysis of the reaction: L-threonine + hydrogencarbonate + ATP = L-threonylcarbamoyladenylate + diphosphate + H2O." [RHEA:36407]
xref: EC:2.7.7.87
xref: MetaCyc:RXN-14569
+xref: Reactome:R-HSA-9611218 "YRDC synthesizes threonylcarbamoyladenylate"
xref: RHEA:36407
is_a: GO:0016779 ! nucleotidyltransferase activity
property_value: skos:exactMatch EC:2.7.7.87
@@ -383649,7 +388056,8 @@
synonym: "t6A synthase activity" EXACT []
xref: EC:2.3.1.234
xref: MetaCyc:RXN-14570
-xref: Reactome:R-HSA-6784494 "EKC complex threonylcarbamoylates A37 of tRNAs"
+xref: Reactome:R-HSA-6784494 "KEOPS (EKC) complex threonylcarbamoylates A37 of tRNAs"
+xref: Reactome:R-HSA-9611197 "OSGEPL1 threonylcarbamoylates adenosine-37 in tRNA"
xref: RHEA:37059
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
@@ -383687,6 +388095,7 @@
namespace: molecular_function
def: "Combining selectively with extracellular folic acid and delivering it into the cell via endocytosis." [GOC:BHF, GOC:hal]
synonym: "folate receptor activity" EXACT []
+xref: Reactome:R-HSA-8940134 "FOLR2 binds FOLA"
is_a: GO:0038024 ! cargo receptor activity
relationship: has_part GO:0005542 ! folic acid binding
relationship: part_of GO:0015884 ! folic acid transport
@@ -383935,8 +388344,8 @@
synonym: "peptide-lysine-acetyltransferase activity" EXACT []
synonym: "peptide-lysine-N-acetylase activity" EXACT []
synonym: "peptide-lysine-N-acetyltransferase activity" EXACT []
-synonym: "protein acetylase activity" BROAD []
-synonym: "protein acetyltransferase activity" BROAD []
+synonym: "protein acetylase activity" EXACT []
+synonym: "protein acetyltransferase activity" EXACT []
synonym: "protein-lysine-N-acetylase activity" EXACT []
xref: EC:2.3.1.48
xref: Reactome:R-HSA-6811508 "ING2-bound EP300 acetylates TP53"
@@ -383947,10 +388356,13 @@
xref: Reactome:R-HSA-9701531 "p-Y705,S727 STAT3 is acetylated"
xref: Reactome:R-HSA-9756494 "CREBBP acetylates SARS-CoV-2 N at K375"
xref: Reactome:R-HSA-9825747 "CREBBP acetylates HINT1 dimer"
+xref: Reactome:R-HSA-9920716 "CLOCK acetylates BMAL1 on lysine-538"
xref: RHEA:45948
+xref: RHEA:74151
is_a: GO:0034212 ! protein N-acetyltransferase activity
property_value: skos:exactMatch EC:2.3.1.48
property_value: skos:exactMatch RHEA:45948
+property_value: skos:narrowMatch RHEA:74151
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30180" xsd:anyURI
created_by: dph
creation_date: 2015-09-10T10:22:19Z
@@ -384631,7 +389043,7 @@
id: GO:0061795
name: Golgi lumen acidification
namespace: biological_process
-def: "Any process that reduces the pH of the Golgi lumen, measured by the concentration of the hydrogen ion." [GOC:dph, PMID:23447592]
+def: "Any process that reduces the pH of the Golgi lumen, corresponding to an increase in hydrogen ion concentration." [GOC:dph, PMID:23447592]
synonym: "Golgi apparatus lumen acidification" EXACT []
is_a: GO:0051452 ! intracellular pH reduction
created_by: dph
@@ -385187,7 +389599,7 @@
name: telomeric G-quadruplex DNA binding
namespace: molecular_function
def: "Binding to telomeric G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures in telomeres." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:16142245, PMID:9512530]
-is_a: GO:0042162 ! telomeric DNA binding
+is_a: GO:0042162 ! telomeric repeat DNA binding
is_a: GO:0051880 ! G-quadruplex DNA binding
[Term]
@@ -385957,6 +390369,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: glutathione = 5-oxoproline + L-cysteinylglycine." [PMID:23070364, PMID:27913623]
xref: EC:4.3.2.7
+xref: Reactome:R-HSA-6785928 "CHAC1,2 cleaves GSH to OPRO and CysGly"
xref: RHEA:47724
is_a: GO:0016842 ! amidine-lyase activity
property_value: skos:exactMatch EC:4.3.2.7
@@ -386049,7 +390462,6 @@
namespace: biological_process
def: "The binding and fusion of a sperm, with the plasma membrane of the oocyte as part of the process of double fertilization forming a zygote and endosperm." [PMID:21123745]
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0045026 ! plasma membrane fusion
relationship: part_of GO:0009567 ! double fertilization forming a zygote and endosperm
created_by: dph
creation_date: 2017-09-05T18:43:24Z
@@ -386206,6 +390618,12 @@
name: mRNA (adenine-N1-)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenine in mRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine in mRNA." [PMID:29072297]
+xref: Reactome:R-HSA-9937508 "TRMT61B methylates adenosine-1472 of MT-CO1 mRNA"
+xref: Reactome:R-HSA-9937512 "TRMT61B methylates adenosine-371 of MT-ND1 mRNA"
+xref: Reactome:R-HSA-9937518 "TRMT61B methylates adenosine-333, adenosine-458, and adenosine-707 of MT-CO3 mRNA"
+xref: Reactome:R-HSA-9937521 "TRMT61B methylates adenosine-185 of MT-CO2 mRNA"
+xref: Reactome:R-HSA-9937529 "TRMT61B methylates adenosine-616 and adenosine-617 of MT-CYB mRNA"
+xref: Reactome:R-HSA-9937535 "TRMT61B methylates adenosine-252 of MT-ND4L mRNA"
is_a: GO:0008174 ! mRNA methyltransferase activity
created_by: dph
creation_date: 2017-11-08T13:26:35Z
@@ -386713,12 +391131,14 @@
name: regulation of small molecule metabolic process
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a small molecule metabolic process." [GOC:vw]
+subset: gocheck_do_not_annotate
synonym: "regulation of small molecule metabolism" EXACT []
xref: Reactome:R-HSA-9861718 "Regulation of pyruvate metabolism"
is_a: GO:0019222 ! regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0044281 ! small molecule metabolic process
relationship: regulates GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: dph
creation_date: 2018-03-19T14:11:54Z
@@ -386727,12 +391147,14 @@
name: positive regulation of small molecule metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process." [GOC:vw]
+subset: gocheck_do_not_annotate
synonym: "positive regulation of small molecule metabolism" EXACT []
is_a: GO:0009893 ! positive regulation of metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0044281 ! small molecule metabolic process
relationship: positively_regulates GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: dph
creation_date: 2018-03-19T14:25:10Z
@@ -386741,12 +391163,14 @@
name: negative regulation of small molecule metabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process." [GOC:vw]
+subset: gocheck_do_not_annotate
synonym: "negative regulation of small molecule metabolism" EXACT []
is_a: GO:0009892 ! negative regulation of metabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0044281 ! small molecule metabolic process
relationship: negatively_regulates GO:0044281 ! small molecule metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: dph
creation_date: 2018-03-19T14:27:23Z
@@ -387024,10 +391448,12 @@
[Term]
id: GO:0062045
-name: L-lysine alpha-aminotransferase activity
+name: L-lysine:pyruvate alpha-transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-lysine + pyruvate= epsilon-amino-alpha-ketocaproic acid (KAC) + alanine." [PMID:27758894, PMID:28330936]
-is_a: GO:0008483 ! transaminase activity
+synonym: "L-lysine alpha-aminotransferase activity" BROAD []
+is_a: GO:0140385 ! amino acid transaminase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: dph
creation_date: 2018-05-11T12:13:57Z
@@ -387611,10 +392037,12 @@
xref: MetaCyc:PEPTIDE-ASPARTATE-BETA-DIOXYGENASE-RXN
xref: Reactome:R-HSA-9631355 "ASPH:Fe2+ hydroxylates an aspartate residue of F9"
xref: RHEA:11508
+xref: RHEA:54276
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:1.14.11.16
property_value: skos:exactMatch RHEA:11508
+property_value: skos:narrowMatch RHEA:54276
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17842" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
@@ -387644,10 +392072,18 @@
name: RNA 2'-O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + RNA = S-adenosyl-L-homocysteine + RNA containing 2'-O-methylribonucleotide." [PMID:30626973, RHEA:58956]
+xref: RHEA:42724
+xref: RHEA:48628
+xref: RHEA:56884
xref: RHEA:58956
+xref: RHEA:65380
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
property_value: skos:exactMatch RHEA:58956
+property_value: skos:narrowMatch RHEA:42724
+property_value: skos:narrowMatch RHEA:48628
+property_value: skos:narrowMatch RHEA:56884
+property_value: skos:narrowMatch RHEA:65380
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
creation_date: 2019-01-23T14:23:00Z
@@ -388044,7 +392480,7 @@
id: GO:0062146
name: 4-chloro-allylglycine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chloro-L-lysine + AH2 + O2 = A + formaldehyde + H2O + L-2-amino-4-chloropent-4-enoate + NH4(+)." [PMID:30867596, RHEA:59888]
+def: "Catalysis of the reaction: 4-chloro-L-lysine + AH2 + O2 = A + formaldehyde + H2O + L-2-amino-4-chloropent-4-enoate + NH4+." [PMID:30867596, RHEA:59888]
xref: RHEA:59888
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: skos:exactMatch RHEA:59888
@@ -388161,6 +392597,7 @@
name: curli secretion complex
namespace: cellular_component
def: "A protein-containing complex that serves as a channel for the secretion of curli. Curli are a fibers that serve as a major component of the extracellular matrix of pellicle biofilms." [PMID:25219853]
+is_a: GO:0140392 ! extracellular protein-containing complex
is_a: GO:1902495 ! transmembrane transporter complex
relationship: part_of GO:0009279 ! cell outer membrane
created_by: dph
@@ -388306,8 +392743,7 @@
def: "A protein-containing complex composed of six subunits of each of the three homologous polypeptide chains C1QA, C1QB, and C1QB. It is a subunit of the complement C1 complex. In addition to complement activation, C1q appears to have roles in homeostasis and cellular development, superoxide (O2-) production by neutrophils, blood coagulation and neurological synapse pruning." [PMID:29449492]
synonym: "C1q" EXACT []
synonym: "Complement 1q" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: dph
creation_date: 2019-11-12T13:21:57Z
@@ -389313,11 +393749,12 @@
[Term]
id: GO:0070007
-name: glutamic-type endopeptidase activity
+name: obsolete glutamic-type endopeptidase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism involving a glutamate/glutamine catalytic dyad." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE, https://www.ebi.ac.uk/merops/about/glossary.shtml#ENDOPEPTIDASE]
-is_a: GO:0004175 ! endopeptidase activity
-is_a: GO:0070002 ! glutamic-type peptidase activity
+def: "OBSOLETE. Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism involving a glutamate/glutamine catalytic dyad." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE, https://www.ebi.ac.uk/merops/about/glossary.shtml#ENDOPEPTIDASE]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0070008
@@ -389591,9 +394028,10 @@
[Term]
id: GO:0070039
-name: rRNA (guanosine-2'-O-)-methyltransferase activity
+name: rRNA (guanosine-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylguanosine." [GOC:imk, GOC:mah]
+synonym: "rRNA (guanosine-2'-O-)-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-6793096 "MRM3 (RNMTL1) methylates guanosine-1370 of 16S rRNA yielding 2'-O-methylguanosine-1370"
xref: Reactome:R-HSA-6793122 "MRM1 methylates guanosine-1145 of 16S rRNA yielding 2'-O-methylguanosine-1145"
is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity
@@ -389820,7 +394258,6 @@
synonym: "exosome" EXACT [GOC:pr]
synonym: "extracellular vesicular exosome" EXACT [GOC:vesicles]
is_a: GO:1903561 ! extracellular vesicle
-relationship: part_of GO:0005615 ! extracellular space
[Term]
id: GO:0070063
@@ -390463,6 +394900,7 @@
def: "The process resulting in the release of a polypeptide chain from the ribosome in a mitochondrion, usually in response to a termination codon (note that mitochondria use variants of the universal genetic code that differ between different taxa)." [GOC:mah, http://mitogenome.org/index.php/Genetic_Code_of_mitochondria]
synonym: "mitochondrial translation termination" EXACT [GOC:mah]
xref: Reactome:R-HSA-5419276 "Mitochondrial translation termination"
+xref: Reactome:R-HSA-9937383 "Mitochondrial ribosome-associated quality control"
is_a: GO:0006415 ! translational termination
intersection_of: GO:0006415 ! translational termination
intersection_of: occurs_in GO:0005739 ! mitochondrion
@@ -390984,11 +395422,15 @@
[Term]
id: GO:0070178
-name: D-serine metabolic process
+name: obsolete D-serine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid." [CHEBI:16523, GOC:jsg, GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways involving D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid." [CHEBI:16523, GOC:jsg, GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "D-serine metabolism" EXACT []
-is_a: GO:0046416 ! D-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
+consider: GO:0036088
+consider: GO:0070179
[Term]
id: GO:0070179
@@ -391000,7 +395442,6 @@
synonym: "D-serine formation" EXACT []
synonym: "D-serine synthesis" EXACT []
is_a: GO:0046437 ! D-amino acid biosynthetic process
-is_a: GO:0070178 ! D-serine metabolic process
[Term]
id: GO:0070180
@@ -391151,7 +395592,7 @@
name: growth hormone receptor complex
namespace: cellular_component
def: "A receptor complex that consists of two identical subunits and binds growth hormone." [GOC:BHF, GOC:mah, GOC:vk, PMID:11445442]
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
[Term]
id: GO:0070196
@@ -391494,12 +395935,14 @@
[Term]
id: GO:0070226
-name: sulfur:ferric ion oxidoreductase activity
+name: obsolete sulfur:ferric ion oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a perthiol + 4 Fe3+ + 3 H2O = sulfite + a thiol + 4 Fe2+ + 8 H+." [MetaCyc:SULFFEOXIDO-RXN]
+def: "OBSOLETE. Catalysis of the reaction: S-sulfanylglutathione + 4 Fe3+ + 3 H2O = sulfite + 4 Fe2+ + glutathione + 6 H+." [GOC:curators]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "hydrogen sulfide:ferric ion oxidoreductase" EXACT [MetaCyc:SULFFEOXIDO-RXN]
-xref: MetaCyc:SULFFEOXIDO-RXN
-is_a: GO:0016667 ! oxidoreductase activity, acting on a sulfur group of donors
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31518" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0070227
@@ -391898,7 +396341,6 @@
xref: Reactome:R-HSA-389632 "pristanate + CoA-SH + ATP => pristanoyl-CoA + AMP + pyrophosphate"
xref: RHEA:47264
is_a: GO:0016405 ! CoA-ligase activity
-is_a: GO:0016878 ! acid-thiol ligase activity
property_value: skos:exactMatch RHEA:47264
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -392079,6 +396521,8 @@
def: "A gasdermin-dependent inflammatory response that is associated with the generation of pyrogenic mediators such as IL-1beta and IL-18. Gasdermins are activated by caspase-1 or caspase-4/11, or by certain granzymes. In some, but not all cells, it can lead to pyroptotic programmed cell death." [PMID:18846107, PMID:21760595, PMID:33883744]
synonym: "pyroptosis" BROAD []
xref: Reactome:R-HSA-5620971 "Pyroptosis"
+xref: Reactome:R-HSA-9960519 "CASP4-mediated substrate cleavage"
+xref: Reactome:R-HSA-9960525 "CASP5-mediated substrate cleavage"
is_a: GO:0006954 ! inflammatory response
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27753" xsd:anyURI
@@ -392132,7 +396576,7 @@
id: GO:0070275
name: aerobic ammonia oxidation to nitrite via pyruvic oxime
namespace: biological_process
-def: "The metabolic process in which ammonia (NH3) is oxidized to nitrite (NO2) in the presence of oxygen. Hydroxylamine is produced enzymatically, and, in the presence of pyruvate, forms pyruvic oxime in a spontaneous, non-enzymatic reaction; pyruvic oxime is then converted to nitrite." [MetaCyc:PWY-2242]
+def: "The metabolic process in which ammonia (NH4+) is oxidized to nitrite (NO2) in the presence of oxygen. Hydroxylamine is produced enzymatically, and, in the presence of pyruvate, forms pyruvic oxime in a spontaneous, non-enzymatic reaction; pyruvic oxime is then converted to nitrite." [MetaCyc:PWY-2242]
xref: MetaCyc:PWY-2242
is_a: GO:0019329 ! ammonia oxidation
@@ -392265,9 +396709,29 @@
xref: MetaCyc:RXN-12116
xref: Reactome:R-HSA-2466831 "A2PE hydrolyses to A2E"
xref: RHEA:33159
+xref: RHEA:45532
+xref: RHEA:45536
+xref: RHEA:45552
+xref: RHEA:45556
+xref: RHEA:45608
+xref: RHEA:45612
+xref: RHEA:45616
+xref: RHEA:45620
+xref: RHEA:56544
+xref: RHEA:56548
is_a: GO:0004630 ! D-type glycerophospholipase activity
property_value: skos:exactMatch EC:3.1.4.54
property_value: skos:exactMatch RHEA:33159
+property_value: skos:narrowMatch RHEA:45532
+property_value: skos:narrowMatch RHEA:45536
+property_value: skos:narrowMatch RHEA:45552
+property_value: skos:narrowMatch RHEA:45556
+property_value: skos:narrowMatch RHEA:45608
+property_value: skos:narrowMatch RHEA:45612
+property_value: skos:narrowMatch RHEA:45616
+property_value: skos:narrowMatch RHEA:45620
+property_value: skos:narrowMatch RHEA:56544
+property_value: skos:narrowMatch RHEA:56548
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27559" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -394225,7 +398689,7 @@
id: GO:0070472
name: regulation of uterine smooth muscle contraction
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of uterine smooth muscle contraction." [GOC:go_curators]
+def: "Any process that modulates the frequency, rate or extent of uterine smooth muscle contraction." [GOC:curators]
synonym: "regulation of myometrial contraction" EXACT [GOC:sl]
synonym: "regulation of myometrial smooth muscle contraction" EXACT [GOC:sl]
synonym: "regulation of myometrium contraction" EXACT [GOC:sl]
@@ -394238,7 +398702,7 @@
id: GO:0070473
name: negative regulation of uterine smooth muscle contraction
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of uterine smooth muscle contraction." [GOC:go_curators]
+def: "Any process that decreases the frequency, rate or extent of uterine smooth muscle contraction." [GOC:curators]
synonym: "down regulation of uterine smooth muscle contraction" EXACT [GOC:mah]
synonym: "down-regulation of uterine smooth muscle contraction" EXACT [GOC:mah]
synonym: "downregulation of uterine smooth muscle contraction" EXACT [GOC:mah]
@@ -394257,7 +398721,7 @@
id: GO:0070474
name: positive regulation of uterine smooth muscle contraction
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of uterine smooth muscle contraction." [GOC:go_curators]
+def: "Any process that increases the frequency, rate or extent of uterine smooth muscle contraction." [GOC:curators]
synonym: "activation of uterine smooth muscle contraction" NARROW [GOC:mah]
synonym: "positive regulation of myometrial contraction" EXACT [GOC:sl]
synonym: "positive regulation of myometrial smooth muscle contraction" EXACT [GOC:sl]
@@ -394756,10 +399220,21 @@
name: 11-beta-hydroxysteroid dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD+ = an 11-oxosteroid + NADH + H+." [PMID:15761036, RHEA:53116]
+xref: Reactome:R-HSA-194023 "HSD11B2,HSD11B1 dimer oxidise CORT to COR"
+xref: RHEA:42204
+xref: RHEA:50208
xref: RHEA:53116
+xref: RHEA:69368
+xref: RHEA:69408
+xref: RHEA:84083
xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch RHEA:53116
+property_value: skos:narrowMatch RHEA:42204
+property_value: skos:narrowMatch RHEA:50208
+property_value: skos:narrowMatch RHEA:69368
+property_value: skos:narrowMatch RHEA:69408
+property_value: skos:narrowMatch RHEA:84083
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21915" xsd:anyURI
[Term]
@@ -394774,11 +399249,15 @@
xref: Reactome:R-HSA-9757706 "HSD11B1 hydrogenates PREDN to PREDL in hepatic cell"
xref: Reactome:R-HSA-9759259 "HSD11B2 dehydrogenates PREDL to PREDN"
xref: RHEA:11388
+xref: RHEA:42200
+xref: RHEA:84079
xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.146
property_value: skos:exactMatch MetaCyc:11-BETA-HYDROXYSTEROID-DEHYDROGENASE-RXN
property_value: skos:exactMatch RHEA:11388
+property_value: skos:narrowMatch RHEA:42200
+property_value: skos:narrowMatch RHEA:84079
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28173" xsd:anyURI
@@ -394817,10 +399296,14 @@
[Term]
id: GO:0070529
-name: L-tryptophan aminotransferase activity
+name: obsolete L-tryptophan transaminase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an amino group from L-tryptophan to an acceptor, usually a 2-oxo acid." [GOC:mah]
-is_a: GO:0008483 ! transaminase activity
+def: "OBSOLETE. Catalysis of the transfer of an amino group from L-tryptophan to an acceptor, usually a 2-oxo acid." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+synonym: "L-tryptophan aminotransferase activity" EXACT []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0047299
[Term]
id: GO:0070530
@@ -394972,10 +399455,14 @@
[Term]
id: GO:0070548
-name: L-glutamine aminotransferase activity
+name: obsolete L-glutamine transaminase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an amino group from L-glutamine to an acceptor, usually a 2-oxo acid." [GOC:mah]
-is_a: GO:0008483 ! transaminase activity
+def: "OBSOLETE. Catalysis of the transfer of an amino group from L-glutamine to an acceptor, usually a 2-oxo acid." [GOC:mah]
+comment: This term was obsoleted because it is too general. Consider other glutamine transaminase activity terms.
+synonym: "L-glutamine aminotransferase activity" EXACT []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+is_obsolete: true
+consider: GO:0047945
[Term]
id: GO:0070549
@@ -395173,6 +399660,7 @@
name: adenylyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an adenylyl group to an acceptor." [GOC:mah]
+xref: Reactome:R-HSA-9935837 "The TRAMP:RNA exosome oligoadenylates pre-rRNA 5' external transcribed spacer (5'ETS) fragment"
is_a: GO:0016779 ! nucleotidyltransferase activity
created_by: mah
creation_date: 2009-04-15T11:04:22Z
@@ -395258,9 +399746,9 @@
def: "Catalysis of the hydrolysis of a dipeptide by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE]
synonym: "metallo-exo-dipeptidase activity" EXACT [GOC:rb]
synonym: "metalloexodipeptidase activity" EXACT [GOC:mah]
-xref: Reactome:R-HSA-2022398 "ACE:Zn2+ hydrolyzes Angiotensin-(1-9) to Angiotensin-(1-7)"
-xref: Reactome:R-HSA-2022405 "ACE:Zn2+ hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
-xref: Reactome:R-HSA-2065355 "Secreted ACE:Zn2+ hydrolyzes Angiotensin-(1-10) to Angiotensin-(1-8)"
+xref: Reactome:R-HSA-2022398 "ACE:Zn2+ hydrolyzes AGT(25-33) (Angiotensin-(1-9)) to AGT(25-31) (Angiotensin-(1-7))"
+xref: Reactome:R-HSA-2022405 "ACE:Zn2+ hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-32) (Angiotensin-(1-8))"
+xref: Reactome:R-HSA-2065355 "Secreted ACE:Zn2+ hydrolyzes AGT(25-34) (Angiotensin-(1-10)) to AGT(25-32) (Angiotensin-(1-8))"
is_a: GO:0008235 ! metalloexopeptidase activity
is_a: GO:0016805 ! dipeptidase activity
created_by: mah
@@ -395465,6 +399953,7 @@
synonym: "calcium ion membrane transport" EXACT []
synonym: "transmembrane calcium transport" EXACT [GOC:mah]
xref: Reactome:R-HSA-3295583 "TRP channels"
+xref: Reactome:R-HSA-425561 "Sodium/Calcium exchangers"
is_a: GO:0006816 ! calcium ion transport
is_a: GO:0098655 ! monoatomic cation transmembrane transport
created_by: mah
@@ -396609,9 +401098,10 @@
[Term]
id: GO:0070677
-name: rRNA (cytosine-2'-O-)-methyltransferase activity
+name: rRNA (cytosine-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylcytosine." [GOC:mah, PMID:19400805]
+synonym: "rRNA (cytosine-2'-O-)-methyltransferase activity" EXACT []
is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity
is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
property_value: skos:broadMatch RHEA:58956
@@ -397344,8 +401834,7 @@
synonym: "IL23A" NARROW [GOC:add]
synonym: "p19" NARROW [GOC:add]
synonym: "p40" NARROW [GOC:add]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: mah
creation_date: 2009-06-23T01:06:02Z
@@ -397359,8 +401848,7 @@
synonym: "IL-27 complex" EXACT [GOC:add]
synonym: "IL27" NARROW [GOC:add]
synonym: "p28" NARROW [GOC:add]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: mah
creation_date: 2009-06-23T01:09:58Z
@@ -397374,8 +401862,7 @@
synonym: "IL-35 complex" EXACT [GOC:add]
synonym: "IL12A" NARROW [GOC:add]
synonym: "p35" NARROW [GOC:add]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: mah
creation_date: 2009-06-23T01:13:14Z
@@ -397678,7 +402165,7 @@
id: GO:0070773
name: protein-N-terminal glutamine amidohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-terminal L-glutaminyl-[protein] + H2O = N-terminal L-glutamyl-[protein] + NH3. This reaction is the deamidation of an N-terminal glutamine residue of a protein." [PMID:19560421, RHEA:50680]
+def: "Catalysis of the reaction: N-terminal L-glutaminyl-[protein] + H2O = N-terminal L-glutamyl-[protein] + NH4+. This reaction is the deamidation of an N-terminal glutamine residue of a protein." [PMID:19560421, RHEA:50680]
synonym: "NtQ-amidase activity" EXACT [PMID:19560421]
xref: EC:3.5.1.122
xref: RHEA:50680
@@ -397697,7 +402184,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: a phytoceramide + H2O = a fatty acid + phytosphingosine." [GOC:pde, PMID:11356846]
comment: The reason for obsoletion is that this term represents a specific substrate of GO:0017040 N-acylsphingosine amidohydrolase activity.
-xref: Reactome:R-HSA-428262 "ACER3 hydrolyzes phytoceramide"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28294" xsd:anyURI
is_obsolete: true
replaced_by: GO:0017040
@@ -400224,20 +404710,25 @@
synonym: "L-asparagine biosynthesis" EXACT [GOC:mah]
synonym: "L-asparagine formation" EXACT [GOC:mah]
synonym: "L-asparagine synthesis" EXACT [GOC:mah]
+xref: MetaCyc:ASPARAGINE-BIOSYNTHESIS
+xref: MetaCyc:ASPARAGINESYN-PWY
+is_a: GO:0006528 ! asparagine metabolic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
-is_a: GO:0070982 ! L-asparagine metabolic process
+property_value: skos:narrowMatch MetaCyc:ASPARAGINE-BIOSYNTHESIS
+property_value: skos:narrowMatch MetaCyc:ASPARAGINESYN-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: mah
creation_date: 2009-10-27T12:59:42Z
[Term]
id: GO:0070982
-name: L-asparagine metabolic process
+name: obsolete L-asparagine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-asparagine, (2S)-2-amino-3-carbamoylpropanoic acid." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways involving L-asparagine, (2S)-2-amino-3-carbamoylpropanoic acid." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "L-asparagine metabolism" EXACT [GOC:mah]
-is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
created_by: mah
creation_date: 2009-10-27T01:03:46Z
@@ -400337,10 +404828,32 @@
xref: EC:1.3.8.7
xref: MetaCyc:RXN-11734
xref: RHEA:14477
+xref: RHEA:43464
+xref: RHEA:47296
+xref: RHEA:48176
+xref: RHEA:48180
+xref: RHEA:48208
+xref: RHEA:82951
+xref: RHEA:84471
+xref: RHEA:84475
+xref: RHEA:84607
+xref: RHEA:84611
+xref: RHEA:84615
is_a: GO:0003995 ! acyl-CoA dehydrogenase activity
property_value: skos:exactMatch EC:1.3.8.7
property_value: skos:exactMatch MetaCyc:RXN-11734
property_value: skos:exactMatch RHEA:14477
+property_value: skos:narrowMatch RHEA:43464
+property_value: skos:narrowMatch RHEA:47296
+property_value: skos:narrowMatch RHEA:48176
+property_value: skos:narrowMatch RHEA:48180
+property_value: skos:narrowMatch RHEA:48208
+property_value: skos:narrowMatch RHEA:82951
+property_value: skos:narrowMatch RHEA:84471
+property_value: skos:narrowMatch RHEA:84475
+property_value: skos:narrowMatch RHEA:84607
+property_value: skos:narrowMatch RHEA:84611
+property_value: skos:narrowMatch RHEA:84615
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23273" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
created_by: mah
@@ -402931,7 +407444,7 @@
id: GO:0071229
name: cellular response to acid chemical
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of the dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:go_curators, GOC:mah, Wikipedia:Acid]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of the dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:curators, GOC:mah, Wikipedia:Acid]
comment: This term should be used to describe a response to a specific acid as a chemical. E.g., if a cell were responding to glutamate, then the response would be glutamate-specific; the cell is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0071468 'cellular response to acidic pH' instead.
subset: gocheck_do_not_annotate
synonym: "cellular response to acid" BROAD []
@@ -403369,9 +407882,10 @@
synonym: "L-methionine formation" EXACT [GOC:mah]
synonym: "L-methionine synthesis" EXACT [GOC:mah]
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
-is_a: GO:0006555 ! methionine metabolic process
+is_a: GO:0006555 ! L-methionine metabolic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31068" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: mah
creation_date: 2009-12-09T04:28:15Z
@@ -403379,12 +407893,26 @@
id: GO:0071266
name: 'de novo' L-methionine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components." [GOC:ecd]
+def: "The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components such as L-aspartate or L-homoserine. This process occurs in plants, bacteria, archae and fungi." [PMID:12818659, PMID:24939187]
synonym: "'de novo' L-methionine anabolism" EXACT [GOC:mah]
synonym: "'de novo' L-methionine biosynthesis" EXACT [GOC:mah]
synonym: "'de novo' L-methionine formation" EXACT [GOC:mah]
synonym: "'de novo' L-methionine synthesis" EXACT [GOC:mah]
+xref: MetaCyc:HOMOSER-METSYN-PWY
+xref: MetaCyc:HSERMETANA-PWY
+xref: MetaCyc:PWY-5345
+xref: MetaCyc:PWY-5347
+xref: MetaCyc:PWY-702
+xref: MetaCyc:PWY-7977
is_a: GO:0071265 ! L-methionine biosynthetic process
+property_value: skos:narrowMatch MetaCyc:HOMOSER-METSYN-PWY
+property_value: skos:narrowMatch MetaCyc:HSERMETANA-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5345
+property_value: skos:narrowMatch MetaCyc:PWY-5347
+property_value: skos:narrowMatch MetaCyc:PWY-702
+property_value: skos:narrowMatch MetaCyc:PWY-7977
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31318" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: mah
creation_date: 2009-12-09T04:34:41Z
@@ -403393,9 +407921,26 @@
name: L-methionine salvage
namespace: biological_process
def: "Any process that generates L-methionine from derivatives of it, without de novo synthesis." [GOC:ecd]
+comment: For the 'L-methionine cycle' (aka the 'S-adenosylmethionine cycle'), see GO:0033353.
+synonym: "L-methionine salvage cycle" NARROW []
+xref: MetaCyc:ADENOSYLHOMOCYSCAT-PWY
+xref: MetaCyc:PWY-4361
+xref: MetaCyc:PWY-7174
+xref: MetaCyc:PWY-7270
+xref: MetaCyc:PWY-7527
+xref: MetaCyc:PWY-7528
+xref: MetaCyc:PWY-8132
is_a: GO:0043102 ! amino acid salvage
is_a: GO:0071265 ! L-methionine biosynthetic process
+property_value: skos:narrowMatch MetaCyc:ADENOSYLHOMOCYSCAT-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-4361
+property_value: skos:narrowMatch MetaCyc:PWY-7174
+property_value: skos:narrowMatch MetaCyc:PWY-7270
+property_value: skos:narrowMatch MetaCyc:PWY-7527
+property_value: skos:narrowMatch MetaCyc:PWY-7528
+property_value: skos:narrowMatch MetaCyc:PWY-8132
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29900" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: mah
creation_date: 2009-12-09T04:36:49Z
@@ -403419,16 +407964,18 @@
id: GO:0071269
name: L-homocysteine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-homocysteine, the L-enantiomer of 2-amino-4-sulfanylbutanoic acid." [GOC:ecd, GOC:mah]
+def: "The chemical reactions and pathways resulting in the formation of L-homocysteine." [GOC:curators]
synonym: "L-homocysteine anabolism" EXACT [GOC:mah]
synonym: "L-homocysteine biosynthesis" EXACT [GOC:mah]
synonym: "L-homocysteine formation" EXACT [GOC:mah]
synonym: "L-homocysteine synthesis" EXACT [GOC:mah]
+xref: MetaCyc:PWY-5344
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
is_a: GO:0050667 ! homocysteine metabolic process
is_a: GO:0170034 ! L-amino acid biosynthetic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
created_by: mah
creation_date: 2009-12-09T05:36:37Z
@@ -405201,10 +409748,14 @@
name: rRNA (cytosine-N4-)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a cytidine in rRNA + S-adenosyl-L-methionine = an N(4)-methylcytidine in rRNA + H+ + S-adenosyl-L-homocysteine." [GOC:imk, PMID:19965768, RHEA:62520]
+xref: RHEA:42928
xref: RHEA:62520
+xref: RHEA:62524
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0016434 ! rRNA (cytosine) methyltransferase activity
property_value: skos:exactMatch RHEA:62520
+property_value: skos:narrowMatch RHEA:42928
+property_value: skos:narrowMatch RHEA:62524
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: mah
creation_date: 2009-12-15T03:46:52Z
@@ -405726,7 +410277,7 @@
id: GO:0071468
name: cellular response to acidic pH
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:go_curators, GOC:mah, Wikipedia:PH]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:curators, GOC:mah, Wikipedia:PH]
comment: This term should be used to annotate instances where a cell is responding to a chemical that is playing the role of an acid (e.g. proton donor) and therefore lowering the pH. If instead you wish to describe a response to a specific acid as a chemical, such as the anion portion of glutamate, please annotate to the appropriate child of GO:0071229 'cellular response to acid chemical'.
synonym: "cellular response to acidity" BROAD []
is_a: GO:0010447 ! response to acidic pH
@@ -405738,7 +410289,7 @@
id: GO:0071469
name: cellular response to alkaline pH
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH > 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:go_curators, GOC:mah, Wikipedia:PH]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH > 7. pH is a measure of the acidity or basicity of an aqueous solution." [GOC:curators, GOC:mah, Wikipedia:PH]
synonym: "cellular response to alkalinity" BROAD []
synonym: "cellular response to basic pH" EXACT [GOC:mah]
is_a: GO:0010446 ! response to alkaline pH
@@ -406389,7 +410940,7 @@
id: GO:0071522
name: ureidoglycine aminohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ureidoglycine + H2O = S-ureidoglycolate + NH3." [MetaCyc:URUR-RXN, PMID:19935661, PMID:20038185]
+def: "Catalysis of the reaction: (S)-2-ureidoglycine + H2O = (S)-ureidoglycolate + NH4+." [PMID:19935661, PMID:20038185, RHEA:25241]
xref: EC:3.5.3.26
xref: MetaCyc:URUR-RXN
xref: RHEA:25241
@@ -406414,15 +410965,17 @@
id: GO:0071524
name: pyrrolysine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of pyrrolysine, N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine." [GOC:dh, PMID:17204561]
+def: "The chemical reactions and pathways resulting in the formation of pyrrolysine." [GOC:curators, PMID:17204561]
synonym: "monomethylamine methyltransferase cofactor lysine adduct biosynthetic process" EXACT [CHEBI:21860]
synonym: "pyrrolysine anabolism" EXACT [GOC:mah]
synonym: "pyrrolysine biosynthesis" EXACT [GOC:mah]
synonym: "pyrrolysine formation" EXACT [GOC:mah]
synonym: "pyrrolysine synthesis" EXACT [GOC:mah]
+xref: MetaCyc:PWY-6994
is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0042398 ! modified amino acid biosynthetic process
is_a: GO:0170038 ! proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
created_by: mah
creation_date: 2010-01-07T02:40:24Z
@@ -407321,7 +411874,7 @@
id: GO:0071598
name: neuronal ribonucleoprotein granule
namespace: cellular_component
-def: "A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli." [GOC:BHF, GOC:go_curators, GOC:mah, PMID:19015237, PMID:20368989]
+def: "A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli." [GOC:BHF, GOC:curators, GOC:mah, PMID:19015237, PMID:20368989]
synonym: "neuronal RNA granule" NARROW []
synonym: "neuronal RNP granule" EXACT []
is_a: GO:0036464 ! cytoplasmic ribonucleoprotein granule
@@ -411418,6 +415971,7 @@
def: "Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:mah]
synonym: "oxidized flavin adenine dinucleotide binding" EXACT [GOC:mah]
synonym: "oxidized flavine-adenine dinucleotide binding" EXACT [GOC:mah]
+xref: Reactome:R-HSA-9854672 "FAD attaches to SDHA"
is_a: GO:0050660 ! flavin adenine dinucleotide binding
created_by: mah
creation_date: 2010-10-07T12:30:28Z
@@ -411904,6 +416458,7 @@
def: "The directed movement of phytochelatins into the vacuole. Phytochelatins are a group of peptides that bind metals (Cd, Zn, Cu, Pb, Hg) in thiolate coordination complexes." [GOC:mah, ISBN:0198506732]
synonym: "cadystin import into vacuole" RELATED [GOC:vw, Wikipedia:Phytochelatin#History]
synonym: "phytochelatin transport into vacuole" EXACT [GOC:vw]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0071994 ! phytochelatin transmembrane transport
created_by: mah
@@ -411915,6 +416470,7 @@
namespace: biological_process
def: "The directed movement of glutathione into the vacuole across the vacuolar membrane." [GOC:mah]
synonym: "glutathione transport into vacuole" EXACT [GOC:vw]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0034775 ! glutathione transmembrane transport
created_by: mah
@@ -415491,7 +420047,7 @@
def: "The directed movement of proteins from the plasma membrane across the periplasmic space to the outer membrane or cell wall." [GOC:mah, PMID:20378773]
synonym: "chaperone-mediated protein transport across periplasmic space" NARROW []
is_a: GO:0015031 ! protein transport
-relationship: has_part GO:0140597 ! protein carrier chaperone
+relationship: has_part GO:0140597 ! protein carrier activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15917" xsd:anyURI
created_by: mah
creation_date: 2010-10-28T04:24:59Z
@@ -415735,6 +420291,7 @@
name: rescue of stalled cytosolic ribosome
namespace: biological_process
def: "A process of cytosolic translational elongation that takes place when a cytosolic ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex." [GOC:jh2, GOC:mah, PMID:18557701, PMID:19170872, PMID:20117091, PMID:20185543]
+xref: Reactome:R-HSA-9948299 "Ribosome-associated quality control"
is_a: GO:0002182 ! cytoplasmic translational elongation
is_a: GO:0032790 ! ribosome disassembly
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22227" xsd:anyURI
@@ -417044,6 +421601,7 @@
synonym: "ammonia transport" BROAD []
synonym: "ammonium membrane transport" EXACT []
synonym: "ammonium transport" BROAD []
+xref: Reactome:R-HSA-444411 "Rhesus glycoproteins mediate ammonium transport"
is_a: GO:0055085 ! transmembrane transport
is_a: GO:0071705 ! nitrogen compound transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22228" xsd:anyURI
@@ -417802,7 +422360,7 @@
def: "A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids." [GOC:BHF, GOC:mah, PMID:16373184]
synonym: "cell membrane microparticle" EXACT [PMID:16373184]
is_a: GO:0110165 ! cellular anatomical structure
-relationship: part_of GO:0005615 ! extracellular space
+relationship: part_of GO:0005576 ! extracellular region
created_by: mah
creation_date: 2011-01-28T11:50:56Z
@@ -418007,9 +422565,25 @@
name: 17-beta-hydroxysteroid dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: a 17-beta-hydroxysteroid + NADP+ = a 17-oxosteroid + NADPH + H+." [GOC:kad, PMID:17074428]
+xref: RHEA:42120
+xref: RHEA:42156
+xref: RHEA:46628
+xref: RHEA:53480
+xref: RHEA:53484
+xref: RHEA:53488
xref: RHEA:69284
+xref: RHEA:85531
+xref: RHEA:85543
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch RHEA:69284
+property_value: skos:narrowMatch RHEA:42120
+property_value: skos:narrowMatch RHEA:42156
+property_value: skos:narrowMatch RHEA:46628
+property_value: skos:narrowMatch RHEA:53480
+property_value: skos:narrowMatch RHEA:53484
+property_value: skos:narrowMatch RHEA:53488
+property_value: skos:narrowMatch RHEA:85531
+property_value: skos:narrowMatch RHEA:85543
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21791" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: mah
@@ -418059,7 +422633,6 @@
namespace: molecular_function
def: "Binds to and modulates the activity of ATP-hydrolyzing DNA topoisomerase. DNA topoisomerase (ATP-hydrolyzing) regulator activity catalyzes a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [GOC:mah]
is_a: GO:0030234 ! enzyme regulator activity
-is_a: GO:0060590 ! ATPase regulator activity
relationship: regulates GO:0003918 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
created_by: mah
creation_date: 2011-02-09T05:31:50Z
@@ -418610,7 +423183,7 @@
name: osteoclast fusion
namespace: biological_process
def: "The plasma membrane fusion process that results in fusion of mononuclear osteoclasts to form a multinuclear osteoclast." [CL:0000092, CL:0000779, GOC:BHF, GOC:mah, PMID:12713016]
-is_a: GO:0000768 ! syncytium formation by plasma membrane fusion
+is_a: GO:0000768 ! syncytium formation by cell-cell fusion
relationship: part_of GO:0072674 ! multinuclear osteoclast differentiation
created_by: mah
creation_date: 2011-02-22T02:14:34Z
@@ -423306,12 +427879,14 @@
id: GO:0080002
name: UDP-glucose:4-aminobenzoate acylglucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-aminobenzoate + UDP-alpha-D-glucose = 1-O-(4-aminobenzoyl)-beta-D-glucose + UDP." [PMID:18385129]
+def: "Catalysis of the reaction: 4-aminobenzoate + UDP-alpha-D-glucose = 1-O-(4-aminobenzoyl)-beta-D-glucose + UDP." [PMID:18385129, RHEA:85851]
synonym: "UDP-glucose:p-aminobenzoate acylglucosyltransferase activity" RELATED []
synonym: "UDP-glucose:p-aminobenzoate glucosyltransferase activity" RELATED []
synonym: "UDP-glucose:pABA acylglucosyltransferase activity" RELATED []
xref: MetaCyc:RXN-6142
+xref: RHEA:85851
is_a: GO:0035251 ! UDP-glucosyltransferase activity
+property_value: skos:exactMatch RHEA:85851
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28273" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28775" xsd:anyURI
@@ -423441,10 +428016,14 @@
namespace: molecular_function
def: "Catalysis of the reaction: (2E)-geranyl diphosphate = diphosphate + sabinene." [PMID:12566586, PMID:9747540, RHEA:68636]
xref: MetaCyc:RXN-5103
+xref: RHEA:25508
+xref: RHEA:32547
xref: RHEA:68636
is_a: GO:0009975 ! cyclase activity
is_a: GO:0010333 ! terpene synthase activity
property_value: skos:exactMatch RHEA:68636
+property_value: skos:narrowMatch RHEA:25508
+property_value: skos:narrowMatch RHEA:32547
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28063" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -423493,10 +428072,18 @@
synonym: "fatty acyl-CoA reductase (alcohol-forming) activity" EXACT [GOC:mah]
synonym: "fatty-acyl-CoA reductase (alcohol-forming) activity" RELATED []
xref: MetaCyc:RXNQT-4192
+xref: RHEA:81735
+xref: RHEA:81739
xref: RHEA:81751
+xref: RHEA:81775
+xref: RHEA:81779
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch MetaCyc:RXNQT-4192
property_value: skos:exactMatch RHEA:81751
+property_value: skos:narrowMatch RHEA:81735
+property_value: skos:narrowMatch RHEA:81739
+property_value: skos:narrowMatch RHEA:81775
+property_value: skos:narrowMatch RHEA:81779
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24250" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29086" xsd:anyURI
@@ -423540,10 +428127,76 @@
xref: EC:4.2.1.119
xref: MetaCyc:RXN-7699
xref: RHEA:26526
+xref: RHEA:39303
+xref: RHEA:39343
+xref: RHEA:39351
+xref: RHEA:39363
+xref: RHEA:39375
+xref: RHEA:39387
+xref: RHEA:39399
+xref: RHEA:39411
+xref: RHEA:39423
+xref: RHEA:39439
+xref: RHEA:39475
+xref: RHEA:39487
+xref: RHEA:39499
+xref: RHEA:39511
+xref: RHEA:39523
+xref: RHEA:39535
+xref: RHEA:39547
+xref: RHEA:39559
+xref: RHEA:39579
+xref: RHEA:39591
+xref: RHEA:39603
+xref: RHEA:39615
+xref: RHEA:39627
+xref: RHEA:39639
+xref: RHEA:39687
+xref: RHEA:39699
+xref: RHEA:46720
+xref: RHEA:67216
+xref: RHEA:67228
+xref: RHEA:72575
+xref: RHEA:78863
+xref: RHEA:78867
+xref: RHEA:78931
is_a: GO:0018812 ! 3-hydroxyacyl-CoA dehydratase activity
property_value: skos:exactMatch EC:4.2.1.119
property_value: skos:exactMatch MetaCyc:RXN-7699
property_value: skos:exactMatch RHEA:26526
+property_value: skos:narrowMatch RHEA:39303
+property_value: skos:narrowMatch RHEA:39343
+property_value: skos:narrowMatch RHEA:39351
+property_value: skos:narrowMatch RHEA:39363
+property_value: skos:narrowMatch RHEA:39375
+property_value: skos:narrowMatch RHEA:39387
+property_value: skos:narrowMatch RHEA:39399
+property_value: skos:narrowMatch RHEA:39411
+property_value: skos:narrowMatch RHEA:39423
+property_value: skos:narrowMatch RHEA:39439
+property_value: skos:narrowMatch RHEA:39475
+property_value: skos:narrowMatch RHEA:39487
+property_value: skos:narrowMatch RHEA:39499
+property_value: skos:narrowMatch RHEA:39511
+property_value: skos:narrowMatch RHEA:39523
+property_value: skos:narrowMatch RHEA:39535
+property_value: skos:narrowMatch RHEA:39547
+property_value: skos:narrowMatch RHEA:39559
+property_value: skos:narrowMatch RHEA:39579
+property_value: skos:narrowMatch RHEA:39591
+property_value: skos:narrowMatch RHEA:39603
+property_value: skos:narrowMatch RHEA:39615
+property_value: skos:narrowMatch RHEA:39627
+property_value: skos:narrowMatch RHEA:39639
+property_value: skos:narrowMatch RHEA:39687
+property_value: skos:narrowMatch RHEA:39699
+property_value: skos:narrowMatch RHEA:46720
+property_value: skos:narrowMatch RHEA:67216
+property_value: skos:narrowMatch RHEA:67228
+property_value: skos:narrowMatch RHEA:72575
+property_value: skos:narrowMatch RHEA:78863
+property_value: skos:narrowMatch RHEA:78867
+property_value: skos:narrowMatch RHEA:78931
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24738" xsd:anyURI
[Term]
@@ -423923,10 +428576,11 @@
id: GO:0080061
name: indole-3-acetonitrile nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: indole-3-acetonitrile + 2 H2O = indole-3-acetic acid + NH3." [RHEA:45776]
+def: "Catalysis of the reaction: (indol-3-yl)acetonitrile + 2 H2O = (indol-3-yl)acetate + NH4+." [RHEA:45776]
xref: MetaCyc:RXN-1404
xref: RHEA:45776
is_a: GO:0000257 ! nitrilase activity
+property_value: skos:broadMatch EC:3.5.5.1
property_value: skos:exactMatch RHEA:45776
created_by: dhl
creation_date: 2009-04-13T03:30:42Z
@@ -424195,10 +428849,12 @@
name: regulation of primary metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694]
+subset: gocheck_do_not_annotate
is_a: GO:0019222 ! regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0044238 ! primary metabolic process
relationship: regulates GO:0044238 ! primary metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31498" xsd:anyURI
created_by: dhl
creation_date: 2009-04-22T04:30:52Z
@@ -424271,40 +428927,48 @@
[Term]
id: GO:0080097
-name: L-tryptophan:pyruvate aminotransferase activity
+name: L-tryptophan:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + pyruvate = 3-(indol-3-yl)pyruvate + L-alanine." [RHEA:27586]
+def: "Catalysis of the reaction: L-tryptophan + pyruvate = indole-3-pyruvate + L-alanine." [RHEA:27586]
+synonym: "L-tryptophan:pyruvate aminotransferase activity" EXACT []
xref: EC:2.6.1.99
xref: MetaCyc:RXN-10139
xref: RHEA:27586
-is_a: GO:0070529 ! L-tryptophan aminotransferase activity
+is_a: GO:0047635 ! L-alanine:oxo-acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.99
property_value: skos:exactMatch RHEA:27586
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: dhl
creation_date: 2009-04-23T03:45:23Z
[Term]
id: GO:0080098
-name: L-tyrosine-pyruvate transaminase activity
+name: L-tyrosine:pyruvate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine + pyruvate = (4-hydroxyphenyl)pyruvate + L-alanine." [MetaCyc:RXN3O-4157]
+def: "Catalysis of the reaction: L-tyrosine + pyruvate = 3-(4-hydroxyphenyl)pyruvate + L-alanine." [MetaCyc:RXN3O-4157]
synonym: "L-tyrosine aminotransferase activity" BROAD []
+synonym: "L-tyrosine-pyruvate transaminase activity" EXACT []
synonym: "L-tyrosine:pyruvate aminotransferase activity" EXACT []
xref: MetaCyc:RXN3O-4157
-is_a: GO:0008793 ! aromatic-amino-acid transaminase activity
+is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:broadMatch EC:2.6.1.58
+property_value: skos:exactMatch MetaCyc:RXN3O-4157
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: dhl
creation_date: 2009-04-23T03:47:53Z
[Term]
id: GO:0080099
-name: L-methionine:2-oxoglutarate aminotransferase activity
+name: L-methionine:2-oxoglutarate transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-methionine + 2-oxoglutarate = 4-methylthio-2-oxobutyrate + L-glutamate." [PMID:18394996]
-comment: This reaction falls within the larger set of reactions associated with EC:2.6.1.5 (See BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.6.1.5).
+def: "Catalysis of the reaction: L-methionine + 2-oxoglutarate = 4-methylsulfanyl-2-oxobutanoate + L-glutamate." [PMID:18394996, RHEA:25796]
+synonym: "L-methionine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "L-methionine:alpha-ketoglutarate aminotransferase activity" EXACT []
-is_a: GO:0010326 ! methionine-oxo-acid transaminase activity
+xref: MetaCyc:RXN-14147
+xref: RHEA:25796
+is_a: GO:0010326 ! L-methionine:oxo-acid transaminase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: dhl
creation_date: 2009-04-23T03:51:20Z
@@ -424576,6 +429240,7 @@
xref: MetaCyc:RXN-10435
xref: MetaCyc:RXN-10457
xref: MetaCyc:RXN-10459
+xref: RHEA:54812
xref: RHEA:55772
is_a: GO:0016881 ! acid-amino acid ligase activity
property_value: skos:exactMatch EC:6.3.2.52
@@ -424583,6 +429248,7 @@
property_value: skos:narrowMatch MetaCyc:RXN-10435
property_value: skos:narrowMatch MetaCyc:RXN-10457
property_value: skos:narrowMatch MetaCyc:RXN-10459
+property_value: skos:narrowMatch RHEA:54812
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26578" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dhl
@@ -424654,20 +429320,21 @@
[Term]
id: GO:0080130
-name: L-phenylalanine-2-oxoglutarate transaminase activity
+name: L-phenylalanine:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = 3-phenylpyruvate + L-glutamate." [PMID:18394996, RHEA:25152]
+synonym: "L-phenylalanine-2-oxoglutarate transaminase activity" EXACT []
synonym: "L-phenylalanine:2-oxoglutarate aminotransferase activity" EXACT []
synonym: "L-phenylalanine:alpha-ketoglutarate aminotransferase activity" EXACT []
xref: KEGG_REACTION:R00694
xref: MetaCyc:RXN-10814
xref: RHEA:25152
-is_a: GO:0008793 ! aromatic-amino-acid transaminase activity
+is_a: GO:0008793 ! aromatic-amino-acid:2-oxoglutarate transaminase activity
property_value: skos:broadMatch EC:2.6.1.5
-property_value: skos:broadMatch EC:2.6.1.57
property_value: skos:exactMatch RHEA:25152
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31139" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: dhl
creation_date: 2009-04-29T03:42:47Z
@@ -424847,8 +429514,6 @@
def: "Catalysis of the reaction: L-cysteine + H2O = hydrogen sulfide + pyruvate + NH4+ + H+." [PMID:19955263, RHEA:24931]
xref: EC:4.4.1.28
xref: MetaCyc:LCYSDESULF-RXN
-xref: Reactome:R-HSA-1614591 "Excess cysteine yields lanthionine and H2S"
-xref: Reactome:R-HSA-1614614 "Cysteine is degraded to serine and H2S"
xref: RHEA:24931
is_a: GO:0016846 ! carbon-sulfur lyase activity
property_value: skos:broadMatch EC:4.4.1.1
@@ -425037,6 +429702,7 @@
namespace: biological_process
def: "The directed movement of auxins from endoplasmic reticulum to cytosol." [PMID:19506555]
synonym: "intracellular auxin transport" BROAD []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0055085 ! transmembrane transport
is_a: GO:0060918 ! auxin transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22948" xsd:anyURI
@@ -425125,7 +429791,7 @@
id: GO:0080170
name: hydrogen peroxide transmembrane transport
namespace: biological_process
-def: "The process in which hydrogen peroxide is transported across a membrane." [GOC:tb]
+def: "The process in which H2O2 is transported across a membrane." [GOC:tb]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "hydrogen peroxide membrane transport" EXACT []
is_a: GO:0055085 ! transmembrane transport
@@ -425787,7 +430453,7 @@
comment: See also: haustorium ; GO:0085035 and extrahaustorial membrane ; GO:0085037.
is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0005576 ! extracellular region
-relationship: part_of GO:0043655 ! host extracellular space
+relationship: part_of GO:0043655 ! host extracellular region
created_by: jl
creation_date: 2010-07-27T03:58:20Z
@@ -427138,6 +431804,7 @@
name: L-aspartate transmembrane export from vacuole
namespace: biological_process
def: "The directed movement of L-aspartate out of the vacuole, across the vacuolar membrane." [PMID:21307582]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0034487 ! vacuolar amino acid transmembrane transport
is_a: GO:0070778 ! L-aspartate transmembrane transport
@@ -427155,8 +431822,8 @@
name: protein localization to outer membrane
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in, a specific location the cell outer membrane." [GOC:dos, PMID:12823819]
+is_a: GO:0071692 ! protein localization to extracellular region
is_a: GO:0072657 ! protein localization to membrane
-is_a: GO:1990778 ! protein localization to cell periphery
[Term]
id: GO:0089706
@@ -428639,6 +433306,7 @@
def: "The directed movement of cholesterol, cholest-5-en-3-beta-ol, or cholesterol-containing compounds, from the lysosome to the endoplasmic reticulum." [GOC:mah]
synonym: "lysosome to endoplasmic reticulum cholesterol transport" EXACT [GOC:mah]
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016192 ! vesicle-mediated transport
is_a: GO:0032367 ! intracellular cholesterol transport
relationship: occurs_in GO:0005737 ! cytoplasm
@@ -428671,11 +433339,10 @@
name: lysosomal glycocalyx
namespace: cellular_component
def: "The polysaccharide-based coating on the inner side of a lysosomal membrane. It may be involved in protecting the membrane from digestion by lysosomal enzymes." [GOC:ascb_2009, GOC:dph, GOC:krc, GOC:tb, PMID:10521503, PMID:22809326, PMID:29367433]
-is_a: GO:0030112 ! glycocalyx
-intersection_of: GO:0030112 ! glycocalyx
-intersection_of: part_of GO:0005764 ! lysosome
+is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0005764 ! lysosome
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19782" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: tb
creation_date: 2009-12-07T01:16:20Z
@@ -431571,32 +436238,27 @@
[Term]
id: GO:0090357
-name: regulation of L-tryptophan metabolic process
+name: obsolete 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]
+def: "OBSOLETE. 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]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
synonym: "regulation of tryptophan metabolic process" RELATED []
synonym: "regulation of tryptophan metabolism" EXACT [GOC:tb]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006568 ! L-tryptophan metabolic process
-relationship: regulates GO:0006568 ! L-tryptophan metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: tb
creation_date: 2010-06-29T02:38:48Z
[Term]
id: GO:0090358
-name: positive regulation of L-tryptophan metabolic process
+name: obsolete 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]
+def: "OBSOLETE. 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]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
synonym: "positive regulation of tryptophan metabolic process" RELATED []
synonym: "positive regulation of tryptophan metabolism" EXACT [GOC:tb]
-is_a: GO:0045764 ! positive regulation of amino acid metabolic process
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
-is_a: GO:0090357 ! regulation of L-tryptophan metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0006568 ! L-tryptophan metabolic process
-relationship: positively_regulates GO:0006568 ! L-tryptophan metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: tb
creation_date: 2010-06-29T02:38:48Z
@@ -431717,14 +436379,13 @@
[Term]
id: GO:0090368
-name: regulation of ornithine metabolic process
+name: obsolete regulation of ornithine metabolic process
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis." [GOC:dph, GOC:jp, GOC:tb]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006591 ! ornithine metabolic process
-relationship: regulates GO:0006591 ! ornithine metabolic process
+def: "OBSOLETE. Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis." [GOC:dph, GOC:jp, GOC:tb]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
+xref: Reactome:R-HSA-350562 "Regulation of ornithine decarboxylase (ODC)"
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: tb
creation_date: 2010-07-12T11:14:12Z
@@ -431794,6 +436455,7 @@
name: oligopeptide export from mitochondrion
namespace: biological_process
def: "The process in which an oligopeptide is transported out of the mitochondrial matrix. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages." [PMID:11251115]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0035672 ! oligopeptide transmembrane transport
created_by: tb
creation_date: 2010-08-27T04:38:18Z
@@ -431911,7 +436573,7 @@
id: GO:0090383
name: phagosome acidification
namespace: biological_process
-def: "Any process that reduces the pH of the phagosome, measured by the concentration of the hydrogen ion." [GOC:kmv, GOC:tb]
+def: "Any process that reduces the pH of the phagosome, corresponding to an increase in hydrogen ion concentration." [GOC:kmv, GOC:tb]
synonym: "phagosomal acidification" EXACT [GOC:kmv, GOC:tb]
is_a: GO:0051452 ! intracellular pH reduction
relationship: part_of GO:0090382 ! phagosome maturation
@@ -431992,7 +436654,7 @@
id: GO:0090390
name: phagosome acidification involved in apoptotic cell clearance
namespace: biological_process
-def: "Any process that reduces the pH of the phagosome, measured by the concentration of the hydrogen ion, and occurs as a part of apoptotic cell clearance." [GOC:kmv, GOC:tb]
+def: "Any process that reduces the pH of the phagosome, corresponding to an increase in hydrogen ion concentration, and occurs as a part of apoptotic cell clearance." [GOC:kmv, GOC:tb]
is_a: GO:0090383 ! phagosome acidification
intersection_of: GO:0090383 ! phagosome acidification
intersection_of: part_of GO:0090386 ! phagosome maturation involved in apoptotic cell clearance
@@ -432255,6 +436917,7 @@
name: molybdate ion export from vacuole
namespace: biological_process
def: "The directed movement of molybdate ions out of the vacuole." [GOC:tb]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015689 ! molybdate ion transport
is_a: GO:0034486 ! vacuolar transmembrane transport
created_by: tb
@@ -432280,7 +436943,7 @@
name: nicotinate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of nicotinate from one side of a membrane to the other." [GOC:tb]
-xref: Reactome:R-HSA-8869603 "SLC22A13 transports NCA from extracellular region to cytosol"
+xref: Reactome:R-HSA-8869603 "SLC22A13 exchanges extracellular NCA for cytosolic urate"
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
relationship: part_of GO:2001142 ! nicotinate transport
created_by: tb
@@ -432474,7 +437137,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: ATP + palmitic acid + CoA = AMP + diphosphate + palmitoyl-CoA." [GOC:al, PMID:18071249]
synonym: "palmitoyl-CoA synthetase activity" EXACT []
-xref: Reactome:R-HSA-434382 "ACSL3,4 ligates coenzyme A (CoA-SH) to palmitate yielding palmitoyl-coenzyme A in the pancreatic beta cell"
+xref: Reactome:R-HSA-434382 "ACSL3,4 ligates coenzyme A (CoA-SH) to a long chain fatty acid yielding fatty acyl-coenzyme A"
is_a: GO:0004467 ! long-chain fatty acid-CoA ligase activity
created_by: tb
creation_date: 2012-07-25T03:31:31Z
@@ -432724,6 +437387,7 @@
def: "The directed movement of ornithine into the vacuole across the vacuolar membrane." [GOC:tb]
synonym: "vacuolar ornithine import" RELATED [GOC:tb]
is_a: GO:0003333 ! amino acid transmembrane transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015822 ! ornithine transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
@@ -432941,10 +437605,11 @@
[Term]
id: GO:0090486
-name: small RNA 2'-O-methyltransferase activity
+name: small RNA 2'-O-ribose methyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the oxygen atom of a nucleoside residue in a small RNA molecule. Reaction: S-adenosyl-L-methionine + small RNA = S-adenosyl-L-homocysteine + small RNA containing a 3'-terminal 2'-O-methylnucleotide." [GOC:tb, GOC:vw, RHEA:37887]
synonym: "small RNA 2'-O-methyltransferase" EXACT []
+synonym: "small RNA 2'-O-methyltransferase activity" EXACT []
xref: EC:2.1.1.386
xref: RHEA:37887
is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
@@ -433644,7 +438309,7 @@
synonym: "phosphatidylcholine floppase activity (cytosolic to exoplasmic leaflet)" EXACT []
synonym: "phosphatidylcholine-translocating ATPase activity" BROAD []
xref: RHEA:38583
-is_a: GO:0008525 ! phosphatidylcholine transporter activity
+is_a: GO:0008525 ! phosphatidylcholine intramembrane carrier activity
is_a: GO:0140328 ! floppase activity
property_value: skos:broadMatch RHEA:66132
property_value: skos:exactMatch RHEA:38583
@@ -433678,7 +438343,6 @@
synonym: "phosphatidylserine floppase activity (cytosolic to exoplasmic leaflet)" EXACT []
synonym: "phosphatidylserine-translocating ATPase activity" BROAD []
xref: RHEA:38567
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0140328 ! floppase activity
property_value: skos:broadMatch RHEA:66132
property_value: skos:exactMatch RHEA:38567
@@ -433744,7 +438408,8 @@
name: protein-N(PI)-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase system transporter activity
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + N,N'-diacetylchitobiose(out) = protein histidine + N,N'-diacetylchitobiose phosphate(in)." [GOC:am, PMID:10913119]
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
created_by: tb
creation_date: 2014-04-08T14:55:02Z
@@ -433995,10 +438660,13 @@
[Term]
id: GO:0090590
-name: protein-N(PI)-phosphohistidine-D-glucosamine phosphotransferase system transporter activity
+name: obsolete protein-N(PI)-phosphohistidine-D-glucosamine phosphotransferase system transporter activity
namespace: molecular_function
-def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + D-glucosamine(out) = protein histidine + glucosamine-6-phosphate(in)." [PMID:8246840]
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+def: "OBSOLETE. Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + D-glucosamine(out) = protein histidine + glucosamine-6-phosphate(in)." [PMID:8246840]
+comment: This term was obsoleted because it represents a specific substrate of protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity ; GO:0022870 (see PMID:8246840).
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0022870
created_by: tb
creation_date: 2014-06-04T16:33:01Z
@@ -434007,7 +438675,8 @@
name: protein-N(PI)-phosphohistidine-N-acetyl-mannosamine phosphotransferase system transporter activity
namespace: molecular_function
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + N-acetyl-mannosamine(out) = protein histidine +N-acetyl- mannosamine-6-phosphate(in)." [PMID:9864311]
-is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
+is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
created_by: tb
creation_date: 2014-06-04T16:33:01Z
@@ -434048,7 +438717,7 @@
id: GO:0090595
name: L-lysine N6-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + L-lysine = CoA + H+ + N(6)-acetyl-L-lysine." [RHEA:69476]
+def: "Catalysis of the reaction: acetyl-CoA + L-lysine = CoA + H+ + N6-acetyl-L-lysine." [RHEA:69476]
synonym: "acetyl-CoA:L-lysine N6-acetyltransferase" EXACT []
xref: EC:2.3.1.306
xref: MetaCyc:LYSACET-RXN
@@ -434208,7 +438877,7 @@
id: GO:0090612
name: cAMP deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cyclic adenosine monophosphate + H2O = cyclic inosine monophosphate + NH3." [PMID:24074367, RHEA:22908]
+def: "Catalysis of the reaction: 3',5'-cyclic AMP + H2O + H+ = 3',5'-cyclic IMP + NH4+." [PMID:24074367, RHEA:22908]
synonym: "cyclic adenosine monophosphate deaminase activity" EXACT []
xref: EC:3.5.4.46
xref: RHEA:22908
@@ -434225,7 +438894,7 @@
id: GO:0090613
name: 5'-deoxyadenosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5'deoxyadenosine + H2O = 5'deoxyinosine + NH3." [PMID:23968233, RHEA:42892]
+def: "Catalysis of the reaction: 5'-deoxyadenosine + H2O + H+ = 5'-deoxyinosine + NH4+." [PMID:23968233, RHEA:42892]
xref: EC:3.5.4.41
xref: RHEA:42892
is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
@@ -434240,7 +438909,7 @@
id: GO:0090614
name: 5'-methylthioadenosine deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5'methyl thioadenosine + H2O = 5'methyl thioinosine + NH3." [PMID:23968233, RHEA:25025]
+def: "Catalysis of the reaction: S-methyl-5'-thioadenosine + H2O + H+ = S-methyl-5'-thioinosine + NH4+." [PMID:23968233, RHEA:25025]
xref: EC:3.5.4.31
xref: RHEA:25025
is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
@@ -434538,6 +439207,7 @@
comment: Microsporidian biology uses the term endospore differently than GO:0043593 endospore coat which is for a spore formed inside of another cell. Microsporidian endospore refers to the inner layer of the spore wall itself.
is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0031160 ! spore wall
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: tb
creation_date: 2015-05-04T14:17:06Z
@@ -434680,7 +439350,7 @@
namespace: molecular_function
def: "Binding to a junction formed at the point where double-stranded telomeric DNA becomes a single-stranded G-rich telomeric DNA 3' overhang." [GOC:BHF, GOC:BHF_telomere, GOC:bhm, GOC:nc, PMID:21852327]
is_a: GO:0000406 ! double-strand/single-strand DNA junction binding
-is_a: GO:0042162 ! telomeric DNA binding
+is_a: GO:0042162 ! telomeric repeat DNA binding
created_by: tb
creation_date: 2015-07-02T11:33:39Z
@@ -435468,6 +440138,7 @@
synonym: "Tenascin-W" NARROW []
synonym: "Tenascin-X" NARROW []
is_a: GO:0098637 ! protein complex involved in cell-matrix adhesion
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140149 ! non-collagenous component of interstitial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31064" xsd:anyURI
created_by: tb
@@ -436130,12 +440801,13 @@
[Term]
id: GO:0097052
-name: L-kynurenine metabolic process
+name: obsolete L-kynurenine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine)." [GOC:yaf]
+def: "OBSOLETE. The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine)." [GOC:yaf]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "L-kynurenine metabolism" EXACT []
-is_a: GO:0070189 ! kynurenine metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2011-05-24T03:28:44Z
@@ -436148,7 +440820,7 @@
synonym: "L-kynurenine catabolism" EXACT []
synonym: "L-kynurenine degradation" EXACT []
is_a: GO:0042182 ! ketone catabolic process
-is_a: GO:0097052 ! L-kynurenine metabolic process
+is_a: GO:0070189 ! kynurenine metabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
created_by: pr
@@ -436163,10 +440835,21 @@
synonym: "L-glutamate biosynthesis" EXACT []
synonym: "L-glutamate formation" EXACT []
synonym: "L-glutamate synthesis" EXACT []
+xref: MetaCyc:GLUGLNSYN-PWY
+xref: MetaCyc:GLUTAMATE-SYN2-PWY
+xref: MetaCyc:GLUTSYN-PWY
+xref: MetaCyc:GLUTSYNIII-PWY
+xref: MetaCyc:PWY-4341
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0009084 ! L-glutamine family amino acid biosynthetic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
property_value: skos:broadMatch MetaCyc:PWY-5505
+property_value: skos:narrowMatch MetaCyc:GLUGLNSYN-PWY
+property_value: skos:narrowMatch MetaCyc:GLUTAMATE-SYN2-PWY
+property_value: skos:narrowMatch MetaCyc:GLUTSYN-PWY
+property_value: skos:narrowMatch MetaCyc:GLUTSYNIII-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-4341
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: pr
creation_date: 2011-05-24T04:30:38Z
@@ -436216,8 +440899,7 @@
namespace: cellular_component
def: "A heterodimeric protein complex that is composed of cardiotrophin-like cytokine factor 1 (product of the CLCF1 gene) and cytokine receptor-like factor 1 (product of the CRLF gene) and is secreted into the extracellular space. The CRLF-CLCF1 complex is a ligand for the ciliary neurotrophic factor (CNTF) receptor complex." [GOC:BHF, PMID:10966616]
synonym: "CLF-CLC complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: pr
creation_date: 2011-05-26T10:37:55Z
@@ -436227,8 +440909,7 @@
namespace: cellular_component
def: "A protein complex that is composed of two soluble ciliary neurotrophic factor receptor alpha subunits (product of the CNTFR gene) and two molecules of cardiotrophin-like cytokine factor 1 (product of the CLCF1 gene). The complex is secreted into the extracellular space." [GOC:BHF, PMID:11285233]
synonym: "sCNTFR-CLC complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: pr
creation_date: 2011-05-26T10:43:22Z
@@ -437217,7 +441898,6 @@
comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "caspase activity" BROAD []
synonym: "metacaspase activity" NARROW [GOC:mtg_apoptosis]
-xref: Reactome:R-HSA-6800797 "The PIDDosome activates CASP2"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004197
@@ -437279,7 +441959,6 @@
namespace: molecular_function
def: "OBSOLETE. Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [GOC:sjw, PMID:7583672]
comment: The reason for obsoletion is that this term was an unnecessary grouping term.
-xref: Reactome:R-HSA-1497796 "BH2 binding can lead to eNOS uncoupling"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29143" xsd:anyURI
is_obsolete: true
created_by: pr
@@ -437647,6 +442326,7 @@
comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways.
synonym: "apoptotic signalling pathway" EXACT [GOC:mah]
synonym: "induction of apoptosis by extracellular signals" EXACT []
+xref: Reactome:R-HSA-111459 "Activation of caspases through apoptosome-mediated cleavage"
xref: Reactome:R-HSA-193681 "Ceramide signalling"
xref: Reactome:R-HSA-204998 "Cell death signalling via NRAGE, NRIF and NADE"
xref: Reactome:R-HSA-75157 "FasL/ CD95L signaling"
@@ -438450,7 +443130,6 @@
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: leukotriene A4 = eoxin A4." [GOC:mw, PMID:18184802, PMID:18647347]
comment: The reason for obsoletion is that this term is equivalent to leukotriene-C4 synthase activity.
-xref: Reactome:R-HSA-2162019 "LTA4 is converted to EXA4 by ALOX15"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29695" xsd:anyURI
is_obsolete: true
replaced_by: GO:0004464
@@ -438877,7 +443556,6 @@
comment: Components of the DISC (death-inducing signaling complex) may be annotated to this term. These include ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer), and signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. Note that GO:0097296 should only be used to annotate gene products directly involved in the initiation or start up of an inactive cysteine-type endopeptidase activity involved in the apoptotic signaling pathway (also known as an initiator caspase). If the evidence provided is not sufficient to account for direct activation of this enzymatic activity, consider using the more generic terms GO:2001269 positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway or GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process.\nThe reason for obsoletion is that this term represents a GO-CAM model.
synonym: "activation of cysteine-type endopeptidase activity involved in apoptotic signalling pathway" EXACT []
synonym: "activation of initiator caspase activity" NARROW []
-xref: Reactome:R-HSA-140534 "Caspase activation via Death Receptors in the presence of ligand"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28468" xsd:anyURI
is_obsolete: true
created_by: pr
@@ -439561,6 +444239,7 @@
synonym: "protein O-GlcNAc transferase activity" EXACT []
synonym: "UDP-N-acetyl-D-glucosamine:protein-O-beta-N-acetyl-D-glucosaminyl transferase" EXACT []
xref: EC:2.4.1.255
+xref: Reactome:R-HSA-8879117 "POMGNT2 transfers GlcNAc to Man-DAG1"
xref: Reactome:R-HSA-9687828 "O-GlcNAcylation of RIPK3 (TLR4 signaling)"
xref: RHEA:48904
xref: RHEA:48908
@@ -439996,6 +444675,7 @@
subset: goslim_synapse
synonym: "synaptic vesicle lumen pH reduction" EXACT []
synonym: "synaptic vesicle proton loading" EXACT syngo_official_label []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0070050 ! neuron cellular homeostasis
is_a: GO:1902600 ! proton transmembrane transport
@@ -441321,7 +446001,7 @@
id: GO:0097532
name: stress response to acid chemical
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis caused by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:aa, GOC:BHF, GOC:go_curators, GOC:rl, PMID:10615049, PMID:19170886, Wikipedia:Acid]
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis caused by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:aa, GOC:BHF, GOC:curators, GOC:rl, PMID:10615049, PMID:19170886, Wikipedia:Acid]
synonym: "response to acid stress" BROAD []
synonym: "stress response to acid" BROAD []
is_a: GO:0001101 ! response to acid chemical
@@ -441333,7 +446013,7 @@
id: GO:0097533
name: cellular stress response to acid chemical
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in cellular homeostasis caused by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:aa, GOC:BHF, GOC:go_curators, GOC:rl, PMID:10615049, PMID:19170886, Wikipedia:Acid]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in cellular homeostasis caused by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:aa, GOC:BHF, GOC:curators, GOC:rl, PMID:10615049, PMID:19170886, Wikipedia:Acid]
synonym: "cellular response to acid stress" BROAD []
synonym: "cellular stress response to acid" BROAD []
is_a: GO:0097532 ! stress response to acid chemical
@@ -443245,7 +447925,7 @@
id: GO:0097697
name: tRNA (5-carboxymethoxyuridine(34)-5-O)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-carboxymethoxyuridine34 in tRNA + S-adenosyl-L-methionine = 5-methoxycarbonylmethoxyuridine34 in tRNA + S-adenosyl-L-homocysteine." [PMID:26681692, RHEA:54080]
+def: "Catalysis of the reaction: 5-carboxymethoxyuridine34 in tRNA + S-adenosyl-L-methionine = 5-methoxycarbonylmethoxyuridine34 in tRNA + S-adenosyl-L-homocysteine. The methylation occurs on the modified base." [PMID:26681692, RHEA:54080]
synonym: "tRNA 5-carboxymethoxyuridine methyltransferase activity" RELATED []
xref: RHEA:54080
is_a: GO:0016300 ! tRNA (uridine) methyltransferase activity
@@ -444697,10 +449377,11 @@
id: GO:0098538
name: lumenal side of transport vesicle membrane
namespace: cellular_component
-def: "The side (leaflet) of the transport vesicle membrane that faces the lumen." [GOC:ab]
+def: "The leaflet of a transport vesicle membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab]
synonym: "internal side of transport vesicle membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0030658 ! transport vesicle membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-10-24T11:43:55Z
@@ -444708,10 +449389,11 @@
id: GO:0098539
name: cytoplasmic side of transport vesicle membrane
namespace: cellular_component
-def: "The side (leaflet) of the transport vesicle membrane that faces the cytoplasm." [GOC:ab]
+def: "The leaflet of the transport vesicle membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab]
synonym: "external side of transport vesicle membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0030658 ! transport vesicle membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-10-24T11:48:07Z
@@ -444719,10 +449401,11 @@
id: GO:0098540
name: lumenal side of trans-Golgi network transport vesicle membrane
namespace: cellular_component
-def: "The side (leaflet) of the trans-Golgi network transport vesicle membrane that faces the lumen." [GOC:ab]
+def: "The leaflet of a trans-Golgi network transport vesicle membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab]
synonym: "internal side of trans-Golgi network transport vesicle membrane" RELATED []
is_a: GO:0098538 ! lumenal side of transport vesicle membrane
relationship: part_of GO:0012510 ! trans-Golgi network transport vesicle membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-10-24T11:55:02Z
@@ -444730,10 +449413,11 @@
id: GO:0098541
name: cytoplasmic side of trans-Golgi network transport vesicle membrane
namespace: cellular_component
-def: "The side (leaflet) of the trans-Golgi network transport vesicle membrane that faces the cytoplasm." [GOC:ab]
+def: "The leaflet of the trans-Golgi network transport vesicle membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab]
synonym: "external side of trans-Golgi network transport vesicle membrane" EXACT []
is_a: GO:0098539 ! cytoplasmic side of transport vesicle membrane
relationship: part_of GO:0012510 ! trans-Golgi network transport vesicle membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-10-24T11:56:30Z
@@ -444793,9 +449477,10 @@
id: GO:0098547
name: lumenal side of Golgi membrane
namespace: cellular_component
-def: "The side of the Golgi membrane that faces the lumen." [GOC:ab, GOC:dos]
+def: "The leaflet of the Golgi membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0000139 ! Golgi membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T10:44:23Z
@@ -444803,9 +449488,10 @@
id: GO:0098548
name: cytoplasmic side of Golgi membrane
namespace: cellular_component
-def: "The side (leaflet) of the Golgi membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the Golgi membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0000139 ! Golgi membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T10:49:33Z
@@ -444820,27 +449506,29 @@
id: GO:0098550
name: lumenal side of early endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the early endosome membrane that faces the lumen." [GOC:lr]
+def: "The leaflet of the early endosome membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:lr]
synonym: "internal leaflet of early endosome membrane" EXACT [GOC:ab]
synonym: "internal side of early endosome membrane" EXACT []
is_a: GO:0098565 ! lumenal side of endosome membrane
relationship: part_of GO:0031901 ! early endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098551
name: lumenal side of late endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the late endosome membrane that faces the lumen." [GOC:lr]
+def: "The leaflet of the late endosomal membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:lr]
synonym: "internal leaflet of late endosome membrane" EXACT [GOC:ab]
synonym: "internal side of late endosome membrane" EXACT []
is_a: GO:0098565 ! lumenal side of endosome membrane
relationship: part_of GO:0031902 ! late endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098552
name: side of membrane
namespace: cellular_component
-def: "A cellular component consisting of one leaflet of a membrane bilayer and any proteins embedded or anchored in it or attached to its surface." [GOC:dos]
+def: "A cellular component consisting of one leaflet of a membrane bilayer and any protein embedded or anchored in it or attached to its surface." [GOC:dos]
is_a: GO:0110165 ! cellular anatomical structure
relationship: has_part GO:0097478 ! leaflet of membrane bilayer
relationship: part_of GO:0016020 ! membrane
@@ -444851,9 +449539,10 @@
id: GO:0098553
name: lumenal side of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the plasma membrane that faces the lumen." [GOC:ab, GOC:dos]
+def: "The leaflet of the endoplasmic reticulum membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:08:37Z
@@ -444861,9 +449550,10 @@
id: GO:0098554
name: cytoplasmic side of endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the plasma membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the endoplasmic reticulum membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:09:47Z
@@ -444871,9 +449561,10 @@
id: GO:0098555
name: lumenal side of rough endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the rough endoplasmic reticulum membrane that faces the lumen." [GOC:ab, GOC:dos]
+def: "The leaflet of the rough endoplasmic reticulum membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098553 ! lumenal side of endoplasmic reticulum membrane
relationship: part_of GO:0030867 ! rough endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:13:24Z
@@ -444881,9 +449572,10 @@
id: GO:0098556
name: cytoplasmic side of rough endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the rough endoplasmic reticulum membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the rough endoplasmic reticulum membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098554 ! cytoplasmic side of endoplasmic reticulum membrane
relationship: part_of GO:0030867 ! rough endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:15:44Z
@@ -444891,9 +449583,10 @@
id: GO:0098557
name: cytoplasmic side of smooth endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the smooth endoplasmic reticulum membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the smooth endoplasmic reticulum membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098554 ! cytoplasmic side of endoplasmic reticulum membrane
relationship: part_of GO:0030868 ! smooth endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:17:58Z
@@ -444901,9 +449594,10 @@
id: GO:0098558
name: lumenal side of smooth endoplasmic reticulum membrane
namespace: cellular_component
-def: "The side (leaflet) of the smooth endoplasmic reticulum membrane that faces the lumen." [GOC:ab, GOC:dos]
+def: "The leaflet of the smooth endoplasmic reticulum membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0098553 ! lumenal side of endoplasmic reticulum membrane
relationship: part_of GO:0030868 ! smooth endoplasmic reticulum membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-03T12:19:28Z
@@ -444911,23 +449605,25 @@
id: GO:0098559
name: cytoplasmic side of early endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the early endosome membrane that faces the cytoplasm." [GOC:lr]
+def: "The leaflet of the early endosome membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:lr]
comment: In GO, 'external side' still refers to part of the membrane and does not refer to components beyond (outside of) the membrane.
synonym: "external leaflet of early endosome membrane" EXACT [GOC:ab]
synonym: "external side of early endosome membrane" EXACT []
is_a: GO:0010009 ! cytoplasmic side of endosome membrane
relationship: part_of GO:0031901 ! early endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098560
name: cytoplasmic side of late endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the late endosome membrane that faces the cytoplasm." [GOC:lr]
+def: "The leaflet of the late endosome membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:lr]
comment: In GO, 'external side' still refers to part of the membrane and does not refer to components beyond (outside of) the membrane.
synonym: "external leaflet of late endosome membrane" EXACT [GOC:ab]
synonym: "external side of late endosome membrane" EXACT []
is_a: GO:0010009 ! cytoplasmic side of endosome membrane
relationship: part_of GO:0031902 ! late endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098561
@@ -444941,8 +449637,9 @@
id: GO:0098562
name: cytoplasmic side of membrane
namespace: cellular_component
-def: "The side of a membrane that faces the cytoplasm." [GOC:dos]
+def: "The leaflet of a membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098552 ! side of membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-12T11:21:30Z
@@ -444969,11 +449666,12 @@
id: GO:0098565
name: lumenal side of endosome membrane
namespace: cellular_component
-def: "The side (leaflet) of the endosome membrane that faces the lumen." [GOC:dos]
+def: "The leaflet of the endosome membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
synonym: "internal leaflet of endosome membrane" EXACT [GOC:ab]
synonym: "internal side of endosome membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0010008 ! endosome membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098566
@@ -444987,8 +449685,9 @@
id: GO:0098567
name: periplasmic side of plasma membrane
namespace: cellular_component
-def: "The side (leaflet) of a plasma membrane that faces the periplasm, and all proteins embedded in it or attached to its surface." [GOC:dos]
+def: "The leaflet of the plasma membrane that faces the periplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0009897 ! external side of plasma membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2013-12-19T09:31:30Z
@@ -444996,39 +449695,44 @@
id: GO:0098568
name: external side of mycolate outer membrane
namespace: cellular_component
-def: "The side (leaflet) of the mycolate outer membrane that faces the environment and any proteins embedded in it or loosely bound to its surface." [GOC:dos, PMID:18316738, PMID:18567661]
+def: "The leaflet of the mycolate outer membrane that faces the periplasm of the cell, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos, PMID:18316738, PMID:18567661]
is_a: GO:0031240 ! external side of cell outer membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098569
name: internal side of mycolate outer membrane
namespace: cellular_component
-def: "The side of the mycolate outer membrane that faces the cell wall peptidoglycan. It is rich in long-chain mycolic acids (hydroxylated branched-chain fatty acids) that are covalently linked to the cell wall peptidoglycan via an arabinogalactan network." [GOC:dos, PMID:18316738, PMID:18567661]
+def: "The leaflet of the mycolate outer membrane that faces the cell wall peptidoglycan, including any protein embedded in, attached to, or peripherally associated with it. It is rich in long-chain mycolic acids (hydroxylated branched-chain fatty acids) that are covalently linked to the cell wall peptidoglycan via an arabinogalactan network." [GOC:dos, PMID:18316738, PMID:18567661]
is_a: GO:0098552 ! side of membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098570
name: stromal side of plastid inner membrane
namespace: cellular_component
-def: "The side (leaflet) of the plastid inner membrane that faces the stroma, and any proteins embedded in it or loosely bound to its surface." [GOC:dos]
+def: "The leaflet of the plastid inner membrane that faces the stroma, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0009528 ! plastid inner membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098571
name: lumenal side of plastid thylakoid membrane
namespace: cellular_component
-def: "The side (leaflet) of the plastid thylakoid membrane that faces the lumen, and any proteins embedded in it or loosely bound to its surface." [GOC:dos]
+def: "The leaflet of a plastid thylakoid membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0055035 ! plastid thylakoid membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098572
name: stromal side of plastid thylakoid membrane
namespace: cellular_component
-def: "The side (leaflet) of the plastid thylakoid membrane that faces the stroma, and any proteins embedded in it or loosely bound to its surface." [GOC:dos]
+def: "The leaflet of the plastid thylakoid membrane that faces the stroma, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098552 ! side of membrane
relationship: part_of GO:0055035 ! plastid thylakoid membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098573
@@ -445045,28 +449749,31 @@
id: GO:0098574
name: cytoplasmic side of lysosomal membrane
namespace: cellular_component
-def: "The side (leaflet) of the lysosomal membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the lysosomal membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
synonym: "external leaflet of lysosomal membrane" EXACT [GOC:dos]
synonym: "external side of lysosomal membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0005765 ! lysosomal membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098575
name: lumenal side of lysosomal membrane
namespace: cellular_component
-def: "The side (leaflet) of the lysosomal membrane that faces the lumen." [GOC:dos]
+def: "The leaflet of the lysosomal membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
synonym: "internal leaflet of lysosomal membrane" EXACT [GOC:ab]
synonym: "internal side of lysosomal membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0005765 ! lysosomal membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098576
name: lumenal side of membrane
namespace: cellular_component
-def: "Any side (leaflet) of a membrane that faces the lumen of an organelle." [GOC:dos]
+def: "The leaflet of an organelle membrane that faces the lumen, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098552 ! side of membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0098577
@@ -445191,9 +449898,10 @@
id: GO:0098591
name: external side of apical plasma membrane
namespace: cellular_component
-def: "The leaflet the apical region of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:ab, GOC:dos]
+def: "The leaflet the apical region of the plasma membrane that faces the extracellular side of the cell, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0009897 ! external side of plasma membrane
relationship: part_of GO:0016324 ! apical plasma membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2014-03-06T12:04:33Z
@@ -445201,9 +449909,10 @@
id: GO:0098592
name: cytoplasmic side of apical plasma membrane
namespace: cellular_component
-def: "The side (leaflet) of the apical region of the plasma membrane that faces the cytoplasm." [GOC:ab, GOC:dos]
+def: "The leaflet of the apical region of the plasma membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:ab, GOC:dos]
is_a: GO:0009898 ! cytoplasmic side of plasma membrane
relationship: part_of GO:0016324 ! apical plasma membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: dos
creation_date: 2014-03-06T12:07:32Z
@@ -445232,7 +449941,9 @@
name: perivitelline space
namespace: cellular_component
def: "The space between the membrane of an oocyte and a surrounding membranous structure (zona pellucida or perivitelline membrane)." [GOC:dos]
-is_a: GO:0005576 ! extracellular region
+is_a: GO:0110165 ! cellular anatomical structure
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: dos
creation_date: 2014-04-08T16:07:31Z
@@ -445352,12 +450063,13 @@
[Term]
id: GO:0098607
-name: methylselenocysteine deselenhydrase activity
+name: obsolete methylselenocysteine deselenhydrase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Se-Methyl-L-selenocysteine + H2O = pyruvic acid + NH3 + Methaneselenol." [PMID:17451884, PMID:20383543]
+def: "OBSOLETE. Catalysis of the reaction: Se-Methyl-L-selenocysteine + H2O = pyruvic acid + NH3 + Methaneselenol." [PMID:17451884, PMID:20383543]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: Reactome:R-HSA-2408539 "MeSec is hydrolysed to MeSeH by PXLP-K212-CTH"
-is_a: GO:0016846 ! carbon-sulfur lyase activity
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30815" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
created_by: dos
creation_date: 2014-04-16T11:24:12Z
@@ -445692,8 +450404,10 @@
namespace: cellular_component
def: "A collagen trimer that forms networks." [PMID:21421911]
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
intersection_of: GO:0005581 ! collagen trimer
intersection_of: part_of GO:0098645 ! complex of network-forming collagens
+relationship: part_of GO:0031012 ! extracellular matrix
relationship: part_of GO:0098645 ! complex of network-forming collagens
[Term]
@@ -445717,7 +450431,7 @@
synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911]
is_a: GO:0099080 ! supramolecular complex
relationship: has_part GO:0005581 ! collagen trimer
-relationship: part_of GO:0031012 ! extracellular matrix
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31491" xsd:anyURI
[Term]
id: GO:0098645
@@ -445730,14 +450444,18 @@
[Term]
id: GO:0098646
-name: interstitial hexagonal collagen network
+name: hexagonal collagen network
namespace: cellular_component
-def: "A hexagonal shaped collagen network formed by collagen type X trimer, mostly found in the cartilage hyaline matrix, which located in the interstitial area." [PMID:21421911, PMID:34948124]
+def: "A hexagonal-shaped collagen network formed by collagen type X trimer or collagen type VIII trimers. Collagen type X trimers are mostly found in the cartilage hyaline matrix, which is located in the interstitial area. Note that collagen type VIII has been found in the basement membrane, but the localization is not definitive." [PMID:21421911, PMID:3047147, PMID:31387942, PMID:34948124]
+synonym: "basement membrane hexagonal collagen network" NARROW []
synonym: "collagen hexagonal network" EXACT [PMID:21421911]
+synonym: "hexagonal collagen network of basement membrane" NARROW []
+synonym: "interstitial hexagonal collagen network" NARROW []
is_a: GO:0098645 ! complex of network-forming collagens
relationship: part_of GO:0140152 ! collagenous component of interstitial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29415" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30146" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31494" xsd:anyURI
[Term]
id: GO:0098647
@@ -445933,7 +450651,7 @@
synonym: "5-HT receptor complex" EXACT []
synonym: "5-hydroxytryptamine receptor complex" EXACT []
synonym: "5HT receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: dos
creation_date: 2016-12-21T12:24:56Z
@@ -445943,7 +450661,7 @@
namespace: cellular_component
def: "A protein complex that is capable of G protein-coupled serotonin receptor activity." [GO_REF:0000088, GOC:bhm, GOC:TermGenie]
synonym: "G-protein coupled serotonin receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12942" xsd:anyURI
created_by: dos
creation_date: 2016-12-21T12:28:12Z
@@ -446331,6 +451049,7 @@
synonym: "neurotransmitter uptake into synaptic vesicle" EXACT [PMID:15217342]
synonym: "synaptic vesicle neurotransmitter loading" EXACT syngo_official_label []
is_a: GO:0006836 ! neurotransmitter transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0051649 ! establishment of localization in cell
relationship: part_of GO:0099504 ! synaptic vesicle cycle
@@ -446759,6 +451478,7 @@
name: 1-phosphatidylinositol 4-kinase activator activity
namespace: molecular_function
def: "Binds to and increases the activity of 1-phosphatidylinositol 4-kinase." [PMID:21288895]
+xref: Reactome:R-HSA-1676152 "PI4KB binds to ARF1/3:GTP at the Golgi membrane"
is_a: GO:0019209 ! kinase activator activity
relationship: positively_regulates GO:0004430 ! 1-phosphatidylinositol 4-kinase activity
@@ -447296,7 +452016,7 @@
def: "Any protein complex that is part of the plasma membrane and which functions as a signaling receptor." [GOC:dos]
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
is_a: GO:0098797 ! plasma membrane protein complex
[Term]
@@ -448131,6 +452851,7 @@
def: "The directed movement of neurotransmitter receptor from the postsynaptic endosome to the postsynaptic membrane in transport vesicles." [GOC:dos]
subset: goslim_synapse
synonym: "postsynaptic neurotransmitter receptor endosomal trafficking" BROAD []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0098969 ! neurotransmitter receptor transport to postsynaptic membrane
is_a: GO:0099639 ! neurotransmitter receptor transport, endosome to plasma membrane
@@ -448266,7 +452987,7 @@
id: GO:0098900
name: regulation of action potential
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:dos, GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8]
+def: "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:curators, GOC:dos, GOC:dph, GOC:tb, ISBN:978-0-07-139011-8]
comment: The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term.
is_a: GO:0042391 ! regulation of membrane potential
is_a: GO:0050789 ! regulation of biological process
@@ -448578,6 +453299,7 @@
name: vesicle-mediated transport between endosomal compartments
namespace: biological_process
def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles between endosomal compartments, e.g, between early endosome and sorting endosome." [GOC:dos, PMID:10930469]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016197 ! endosomal transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26386" xsd:anyURI
@@ -450029,6 +454751,7 @@
synonym: "mitochondrion to lysosome transport" EXACT []
is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0099075 ! mitochondrion-derived vesicle mediated transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26246" xsd:anyURI
@@ -450046,6 +454769,7 @@
namespace: biological_process
def: "Vesicle-mediated transport of cargo from the mitochondrion to the peroxisome, mediated by a mitochondrion-derived vesicle." [GOC:bc, GOC:pad, GOC:PARL-UCL, PMID:20619655]
synonym: "mitochondrion to peroxisome transport" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0099075 ! mitochondrion-derived vesicle mediated transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26246" xsd:anyURI
@@ -450289,6 +455013,7 @@
name: potassium channel activator activity
namespace: molecular_function
def: "Binds to and increases the activity of a potassium channel, resulting in its opening." [GOC:dos]
+xref: Reactome:R-HSA-400063 "Low conductance potassium channels in pancreatic beta cells open in response to epinephrine"
is_a: GO:0015459 ! potassium channel regulator activity
is_a: GO:0099103 ! channel activator activity
relationship: positively_regulates GO:0005267 ! potassium channel activity
@@ -450510,8 +455235,7 @@
synonym: "TGFB dimer" EXACT []
synonym: "TGFbeta complex" EXACT []
synonym: "TGFbeta dimer" EXACT []
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005576 ! extracellular region
+is_a: GO:0140392 ! extracellular protein-containing complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31130" xsd:anyURI
created_by: bhm
@@ -451113,6 +455837,7 @@
subset: goslim_synapse
synonym: "zinc import into synaptic vesicle" EXACT []
synonym: "Zn2+ import into synaptic vesicle" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0062111 ! zinc ion import into organelle
[Term]
@@ -451784,7 +456509,9 @@
def: "The extracellular region immediately adjacent to to a synapse." [GOC:dos]
subset: goslim_synapse
synonym: "extrasynaptic space" EXACT syngo_official_label []
-is_a: GO:0005576 ! extracellular region
+is_a: GO:0110165 ! cellular anatomical structure
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
[Term]
id: GO:0099545
@@ -452296,6 +457023,10 @@
name: ligand-gated calcium channel activity
namespace: molecular_function
def: "Enables the transmembrane transfer of a calcium ions by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:dos]
+xref: Reactome:R-HSA-1168376 "STIM1 oligomerizes"
+xref: Reactome:R-HSA-169680 "IP3 binds to the IP3 receptor, opening the endoplasmic reticulum Ca2+ channel"
+xref: Reactome:R-HSA-169683 "IP3R:I(1,4,5)P3 tetramer transports Ca2+ from ER lumen to cytosol"
+xref: Reactome:R-HSA-4420052 "Decreasing cGMP concentration promotes intracellular Ca2+ release in response to WNT"
is_a: GO:0005262 ! calcium channel activity
is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity
relationship: part_of GO:0019722 ! calcium-mediated signaling
@@ -452371,7 +457102,8 @@
name: protein localization to cell wall
namespace: biological_process
def: "The process of directing proteins towards the cell-wall." [ISBN:0716731363]
-is_a: GO:1990778 ! protein localization to cell periphery
+is_a: GO:0008104 ! intracellular protein localization
+is_a: GO:0071692 ! protein localization to extracellular region
[Term]
id: GO:0099614
@@ -452379,7 +457111,8 @@
namespace: biological_process
def: "A process in which a protein is transported, tethered to or otherwise maintained in a spore cell wall." [GOC:dos]
synonym: "protein targeting to spore cell wall" RELATED []
-is_a: GO:1990778 ! protein localization to cell periphery
+is_a: GO:0008104 ! intracellular protein localization
+is_a: GO:0071692 ! protein localization to extracellular region
[Term]
id: GO:0099615
@@ -452412,9 +457145,10 @@
id: GO:0099617
name: matrix side of mitochondrial inner membrane
namespace: cellular_component
-def: "The side (leaflet) of the mitochondrial inner membrane that faces the matrix." [GOC:dos]
+def: "The leaflet of a mitochondrial inner membrane that faces the matrix, including any protein embedded in, attached to, or peripherally associated with it." [GOC:dos]
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0005743 ! mitochondrial inner membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
[Term]
id: GO:0099618
@@ -452449,11 +457183,12 @@
[Term]
id: GO:0099620
-name: UDP-4-amino-4-deoxy-L-arabinose aminotransferase activity
+name: UDP-4-amino-4-deoxy-L-arabinose:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo-pentopyranos-4-ulose + L-glutamate." [PMID:12429098, PMID:12704196, RHEA:24710]
synonym: "UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) aminotransferase" EXACT []
synonym: "UDP-4-amino-4-deoxy-beta-L-arabinose:2-oxoglutarate aminotransferase" EXACT []
+synonym: "UDP-4-amino-4-deoxy-L-arabinose aminotransferase" BROAD []
synonym: "UDP-4-amino-4-deoxy-L-arabinose---oxoglutarate aminotransferase" EXACT []
synonym: "UDP-Ara4O aminotransferase" EXACT []
synonym: "UDP-L-Ara4N transaminase" EXACT []
@@ -452463,6 +457198,7 @@
property_value: skos:exactMatch EC:2.6.1.87
property_value: skos:exactMatch RHEA:24710
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0099621
@@ -453523,6 +458259,7 @@
comment: There are two main classes of deubiquitinating enzymes: cysteine proteases (i.e., thiol dependent) and metalloproteases.
synonym: "ubiquitinyl hydrolase activity" EXACT []
xref: Reactome:R-HSA-9674127 "USP30 deubiquitinates ATM dimer:Ub-p-PEX5"
+xref: Reactome:R-HSA-9929353 "Deubiquitination of CD274"
is_a: GO:0019783 ! ubiquitin-like protein peptidase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17398" xsd:anyURI
created_by: mec
@@ -453917,11 +458654,13 @@
synonym: "D-lactate dehydrogenase activity" BROAD []
xref: EC:1.1.5.12
xref: MetaCyc:DLACTDEHYDROGFAD-RXN
+xref: RHEA:29079
xref: RHEA:51468
is_a: GO:0047809 ! D-lactate dehydrogenase activity
is_a: GO:1990464 ! (2R)-hydroxyacid dehydrogenase (quinone) activity
property_value: skos:exactMatch EC:1.1.5.12
property_value: skos:exactMatch RHEA:51468
+property_value: skos:narrowMatch RHEA:29079
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30138" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -453956,10 +458695,24 @@
synonym: "cytochrome P450 fatty acid omega-hydroxylase activity" RELATED []
xref: EC:1.14.14.80
xref: MetaCyc:RXN-16394
+xref: RHEA:40199
+xref: RHEA:40203
+xref: RHEA:41728
+xref: RHEA:46356
+xref: RHEA:48664
xref: RHEA:56748
+xref: RHEA:60940
+xref: RHEA:78611
is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
property_value: skos:exactMatch EC:1.14.14.80
property_value: skos:exactMatch RHEA:56748
+property_value: skos:narrowMatch RHEA:40199
+property_value: skos:narrowMatch RHEA:40203
+property_value: skos:narrowMatch RHEA:41728
+property_value: skos:narrowMatch RHEA:46356
+property_value: skos:narrowMatch RHEA:48664
+property_value: skos:narrowMatch RHEA:60940
+property_value: skos:narrowMatch RHEA:78611
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14194" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19899" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -453989,19 +458742,22 @@
[Term]
id: GO:0102037
-name: 4-nitrotoluene monooxygenase activity
+name: obsolete 4-nitrotoluene monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + 4-nitrotoluene + NADH + O2 = 4-nitrobenzyl alcohol + NAD+ + H2O." [GOC:pz]
-xref: MetaCyc:R361-RXN
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + 4-nitrotoluene + NADH + O2 = 4-nitrobenzyl alcohol + NAD+ + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102038
-name: 4-nitrobenzyl alcohol oxidase activity
+name: obsolete 4-nitrobenzyl alcohol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-nitrobenzyl alcohol + O2 = 4-nitrobenzaldehyde + hydrogen peroxide." [GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: 4-nitrobenzyl alcohol + O2 = 4-nitrobenzaldehyde + hydrogen peroxide." [GOC:pz]
+comment: This term was obsoleted because there is no evidence that this reaction exists.
xref: MetaCyc:R362-RXN
-is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31530" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102039
@@ -454070,11 +458826,12 @@
[Term]
id: GO:0102044
-name: 3-chlorobenzoate-4,5-oxygenase activity
+name: obsolete 3-chlorobenzoate-4,5-oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-chlorobenzoate + O2 + a reduced electron acceptor = 3-chlorobenzoate-cis-4,5-diol + an oxidized electron acceptor." [GOC:pz]
-xref: MetaCyc:RXN-10421
-is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
+def: "OBSOLETE. Catalysis of the reaction: 3-chlorobenzoate + O2 + a reduced electron acceptor = 3-chlorobenzoate-cis-4,5-diol + an oxidized electron acceptor." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102045
@@ -454543,9 +459300,15 @@
synonym: "phosphatidylinositol-5-phosphate 5-phosphatase activity" EXACT []
xref: MetaCyc:RXN-10962
xref: RHEA:41147
+xref: RHEA:42308
+xref: RHEA:42320
+xref: RHEA:42584
is_a: GO:0034595 ! phosphatidylinositol phosphate 5-phosphatase activity
is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
property_value: skos:exactMatch RHEA:41147
+property_value: skos:narrowMatch RHEA:42308
+property_value: skos:narrowMatch RHEA:42320
+property_value: skos:narrowMatch RHEA:42584
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24252" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30249" xsd:anyURI
@@ -454725,11 +459488,12 @@
[Term]
id: GO:0102115
-name: peptidoglycan asparagine synthase activity
+name: obsolete peptidoglycan asparagine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-isoglutaminyl-N-(beta-D-asparatyl)-L-lysyl-D-alanyl-D-alanine + ammonium + ATP = H+ + ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-isoglutaminyl-N-(beta-D-asparaginyl)-L-lysyl-D-alanyl-D-alanine + AMP + diphosphoric acid." [EC:6.3.1.-, GOC:pz]
-xref: MetaCyc:RXN-11338
-is_a: GO:0016880 ! acid-ammonia (or amide) ligase activity
+def: "OBSOLETE. Catalysis of the reaction: ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-isoglutaminyl-N-(beta-D-asparatyl)-L-lysyl-D-alanyl-D-alanine + ammonium + ATP = H+ + ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-isoglutaminyl-N-(beta-D-asparaginyl)-L-lysyl-D-alanyl-D-alanine + AMP + diphosphoric acid." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102116
@@ -454827,11 +459591,12 @@
[Term]
id: GO:0102126
-name: coniferyl aldehyde 5-hydroxylase activity
+name: obsolete coniferyl aldehyde 5-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + coniferyl aldehyde + NADPH + O2 = 5-hydroxy-coniferaldehyde + NADP + H2O." [GOC:pz]
-xref: MetaCyc:RXN-1142
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + coniferyl aldehyde + NADPH + O2 = 5-hydroxy-coniferaldehyde + NADP + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102127
@@ -454900,19 +459665,21 @@
[Term]
id: GO:0102134
-name: (22S)-22-hydroxy-campesterol C-23 hydroxylase activity
+name: obsolete (22S)-22-hydroxy-campesterol C-23 hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + (22S)-22-hydroxycampesterol + NADPH + O2 = (22R,23R)-22,23-dihydroxycampesterol + NADP + H2O." [GOC:pz]
-xref: MetaCyc:RXN-11529
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + (22S)-22-hydroxycampesterol + NADPH + O2 = (22R,23R)-22,23-dihydroxycampesterol + NADP + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102135
-name: (22S)-22-hydroxy-campest-4-en-3-one C-23 hydroxylase activity
+name: obsolete (22S)-22-hydroxy-campest-4-en-3-one C-23 hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + (22S)-22-hydroxycampest-4-en-3-one + NADPH + O2 = (22R,23R)-22,23-dihydroxy-campest-4-en-3-one + NADP + H2O." [GOC:pz]
-xref: MetaCyc:RXN-11530
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + (22S)-22-hydroxycampest-4-en-3-one + NADPH + O2 = (22R,23R)-22,23-dihydroxy-campest-4-en-3-one + NADP + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102136
@@ -455065,7 +459832,7 @@
id: GO:0102149
name: farnesylcysteine lyase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-[(2E,6E)-farnesyl]-L-cysteine + O2 + H2O = (2-trans,6-trans)-farnesal + L-cysteine + hydrogen peroxide." [EC:1.8.3.6, GOC:pz]
+def: "Catalysis of the reaction: S-[(2E,6E)-farnesyl]-L-cysteine + O2 + H2O = (2-trans,6-trans)-farnesal + L-cysteine + H2O2." [EC:1.8.3.6, GOC:pz]
xref: EC:1.8.3.6
xref: MetaCyc:RXN-11623
xref: RHEA:30231
@@ -455151,10 +459918,24 @@
synonym: "very-long-chain 3-hydroxyacyl-CoA dehydratase activity" EXACT []
xref: EC:4.2.1.134
xref: MetaCyc:RXN-11750
+xref: RHEA:39199
+xref: RHEA:39211
+xref: RHEA:39223
+xref: RHEA:39235
+xref: RHEA:39271
xref: RHEA:45812
+xref: RHEA:79187
+xref: RHEA:83119
is_a: GO:0080023 ! (2E)-enoyl-CoA hydratase activity
property_value: skos:exactMatch EC:4.2.1.134
property_value: skos:exactMatch RHEA:45812
+property_value: skos:narrowMatch RHEA:39199
+property_value: skos:narrowMatch RHEA:39211
+property_value: skos:narrowMatch RHEA:39223
+property_value: skos:narrowMatch RHEA:39235
+property_value: skos:narrowMatch RHEA:39271
+property_value: skos:narrowMatch RHEA:79187
+property_value: skos:narrowMatch RHEA:83119
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24738" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25805" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -455361,10 +460142,16 @@
def: "Catalysis of the reaction: a 3-beta-hydroxysteroid-4-alpha-carboxylate + NAD+ = a 3-oxosteroid + CO2 + NADH." [RHEA:34775]
xref: EC:1.1.1.418
xref: MetaCyc:RXN-11928
+xref: RHEA:20669
xref: RHEA:34775
+xref: RHEA:59016
+xref: RHEA:60084
is_a: GO:0000252 ! 3-beta-hydroxysteroid dehydrogenase [NAD(P)+]/C4-decarboxylase activity
property_value: skos:exactMatch EC:1.1.1.418
property_value: skos:exactMatch RHEA:34775
+property_value: skos:narrowMatch RHEA:20669
+property_value: skos:narrowMatch RHEA:59016
+property_value: skos:narrowMatch RHEA:60084
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29311" xsd:anyURI
[Term]
@@ -455694,10 +460481,20 @@
def: "Catalysis of the reaction: a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L-methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + H+ + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:31411]
xref: EC:2.1.1.222
xref: MetaCyc:RXN-12160
+xref: RHEA:27770
xref: RHEA:31411
+xref: RHEA:44592
+xref: RHEA:44608
+xref: RHEA:44612
+xref: RHEA:50224
is_a: GO:0008168 ! methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.222
property_value: skos:exactMatch RHEA:31411
+property_value: skos:narrowMatch RHEA:27770
+property_value: skos:narrowMatch RHEA:44592
+property_value: skos:narrowMatch RHEA:44608
+property_value: skos:narrowMatch RHEA:44612
+property_value: skos:narrowMatch RHEA:50224
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28942" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -455923,11 +460720,12 @@
[Term]
id: GO:0102235
-name: 1-penten-3-one reductase activity
+name: obsolete 1-penten-3-one reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-penten-3-one + NADPH + H+ = 1-pentan-3-one + NADP." [GOC:pz]
-xref: MetaCyc:RXN-12295
-is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: 1-penten-3-one + NADPH + H+ = 1-pentan-3-one + NADP." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102236
@@ -456060,11 +460858,12 @@
[Term]
id: GO:0102249
-name: phosphatidylcholine:diacylglycerol cholinephosphotransferase activity
+name: obsolete phosphatidylcholine:diacylglycerol cholinephosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a phosphatidylcholine + a 1,2-diacyl-sn-glycerol = a 1,2-diacyl-sn-glycerol + a phosphatidylcholine." [GOC:pz, MetaCyc:RXN-12386]
-xref: MetaCyc:RXN-12386
-is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
+def: "OBSOLETE. Catalysis of the reaction: a phosphatidylcholine + a 1,2-diacyl-sn-glycerol = a 1,2-diacyl-sn-glycerol + a phosphatidylcholine." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102250
@@ -456723,7 +461522,7 @@
id: GO:0102317
name: 4-methylaminobutyrate oxidase (demethylating) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(methylamino)butyric acid + O2 + H2O = gamma-aminobutyric acid + formaldehyde + hydrogen peroxide." [EC:1.5.3.19, GOC:pz]
+def: "Catalysis of the reaction: 4-(methylamino)butanoate + O2 + H2O = 4-aminobutanoate + formaldehyde + H2O2." [RHEA:33907]
xref: EC:1.5.3.19
xref: MetaCyc:RXN-13067
xref: RHEA:33907
@@ -457134,7 +461933,9 @@
namespace: molecular_function
def: "Catalysis of the reaction: mithramycin DK + NADPH + H+ = iso-mithramycin + NADP+. Note that iso-mithramycin (iso-MTM) is a C2-epimer of mithramycin. This intermediate appears to be biologically important because it is non-toxic, then exported out of the cell and finally spontaneously epimerized into the toxic mithramycin. This could represent a self-resistance mechanism against MTM toxicity." [PMID:31702856]
xref: MetaCyc:RXN-13385
+xref: RHEA:85451
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+property_value: skos:exactMatch RHEA:85451
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30329" xsd:anyURI
@@ -457249,11 +462050,12 @@
[Term]
id: GO:0102369
-name: 11alpha-30-dihydroxy beta-amyrin dehydrogenase activity
+name: obsolete 11alpha-30-dihydroxy beta-amyrin dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 11alpha,30-dihydroxy-beta-amyrin + NADPH + O2 + H+ = 30-hydroxy-11-oxo-beta-amyrin + NADP + 2 H2O." [GOC:pz]
-xref: MetaCyc:RXN-13491
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+def: "OBSOLETE. Catalysis of the reaction: 11alpha,30-dihydroxy-beta-amyrin + NADPH + O2 + H+ = 30-hydroxy-11-oxo-beta-amyrin + NADP + 2 H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102370
@@ -457984,10 +462786,16 @@
def: "Catalysis of the reaction: a (2S)-2-hydroxycarboxylate + NAD+ = a 2-oxocarboxylate + NADH + H+." [RHEA:34555]
xref: EC:1.1.1.337
xref: MetaCyc:RXN-13927
+xref: RHEA:10176
+xref: RHEA:15533
xref: RHEA:34555
+xref: RHEA:36371
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.337
property_value: skos:exactMatch RHEA:34555
+property_value: skos:narrowMatch RHEA:10176
+property_value: skos:narrowMatch RHEA:15533
+property_value: skos:narrowMatch RHEA:36371
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -458174,13 +462982,14 @@
[Term]
id: GO:0102459
-name: 8-oxo-dADP diphosphate phosphatase activity
+name: obsolete 8-oxo-dADP diphosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8-oxo-dADP + H2O = 8-oxo-dAMP + hydrogenphosphate + H+." [GOC:pz]
+def: "OBSOLETE. Catalysis of the reaction: 8-oxo-dADP + H2O = 8-oxo-dAMP + hydrogenphosphate + H+." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
synonym: "8-oxo-deoxyadenine diphosphate phosphatase activity" EXACT []
-xref: MetaCyc:RXN-14005
-is_a: GO:0017110 ! nucleoside diphosphate phosphatase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23401" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102460
@@ -458228,11 +463037,12 @@
[Term]
id: GO:0102465
-name: zeaxanthin 2,2'-beta-hydroxylase activity
+name: obsolete zeaxanthin 2,2'-beta-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: zeaxanthin + 2 NADH + 2 H+ + 2 O2 = nostoxanthin + 2 NAD + 2 H2O." [GOC:pz]
-xref: MetaCyc:RXN-14018
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: zeaxanthin + 2 NADH + 2 H+ + 2 O2 = nostoxanthin + 2 NAD + 2 H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102466
@@ -459982,11 +464792,12 @@
[Term]
id: GO:0102641
-name: (R)-lactaldehyde dehydrogenase activity
+name: obsolete (R)-lactaldehyde dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-propane-1,2-diol + NADP = (R)-lactaldehyde + NADPH + H+." [GOC:pz]
-xref: MetaCyc:RXN-15743
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: (R)-propane-1,2-diol + NADP = (R)-lactaldehyde + NADPH + H+." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102643
@@ -460274,11 +465085,25 @@
synonym: "fatty acid alpha-oxygenase activity" BROAD []
xref: EC:1.13.11.92
xref: MetaCyc:RXN-4121
+xref: RHEA:16329
xref: RHEA:63508
+xref: RHEA:63836
+xref: RHEA:63852
+xref: RHEA:63856
+xref: RHEA:63860
+xref: RHEA:63864
+xref: RHEA:63868
is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
property_value: skos:exactMatch EC:1.13.11.92
property_value: skos:exactMatch MetaCyc:RXN-4121
property_value: skos:exactMatch RHEA:63508
+property_value: skos:narrowMatch RHEA:16329
+property_value: skos:narrowMatch RHEA:63836
+property_value: skos:narrowMatch RHEA:63852
+property_value: skos:narrowMatch RHEA:63856
+property_value: skos:narrowMatch RHEA:63860
+property_value: skos:narrowMatch RHEA:63864
+property_value: skos:narrowMatch RHEA:63868
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
[Term]
@@ -460288,9 +465113,13 @@
def: "Catalysis of the reaction: a fatty aldehyde + H2O + NAD+ = a fatty acid + 2 H+ + NADH." [RHEA:49832]
synonym: "fatty aldehyde dehydrogenase activity" EXACT []
xref: MetaCyc:RXN-4142
+xref: RHEA:44008
xref: RHEA:49832
+xref: RHEA:69771
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch RHEA:49832
+property_value: skos:narrowMatch RHEA:44008
+property_value: skos:narrowMatch RHEA:69771
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28142" xsd:anyURI
[Term]
@@ -461163,9 +465992,11 @@
xref: EC:1.3.1.93
xref: MetaCyc:RXN-7711
xref: RHEA:14473
+xref: RHEA:85835
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.93
property_value: skos:exactMatch RHEA:14473
+property_value: skos:narrowMatch RHEA:85835
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25304" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25805" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -461203,11 +466034,12 @@
[Term]
id: GO:0102762
-name: eriodictyol 4'-O-methyltransferase activity
+name: obsolete eriodictyol 4'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine = H+ + hesperetin(1-) + S-adenosyl-L-homocysteine." [GOC:pz, MetaCyc:RXN-7754]
-xref: MetaCyc:RXN-7754
-is_a: GO:0008168 ! methyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: eriodictyol + S-adenosyl-L-methionine = H+ + hesperetin(1-) + S-adenosyl-L-homocysteine." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102763
@@ -461216,8 +466048,10 @@
def: "Catalysis of the reaction: a ribonucleoside 5'-triphosphate + phytyl phosphate = a ribonucleoside 5'-diphosphate + phytyl diphosphate." [RHEA:38099]
xref: MetaCyc:RXN-7763
xref: RHEA:38099
+xref: RHEA:49276
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
property_value: skos:exactMatch RHEA:38099
+property_value: skos:narrowMatch RHEA:49276
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -461264,9 +466098,11 @@
xref: EC:2.1.1.231
xref: MetaCyc:RXN-12719
xref: RHEA:31743
+xref: RHEA:74723
is_a: GO:0008168 ! methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.231
property_value: skos:exactMatch RHEA:31743
+property_value: skos:narrowMatch RHEA:74723
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -461324,10 +466160,17 @@
synonym: "sphingolipid long-chain base 4-hydroxylase activity" RELATED []
xref: EC:1.14.18.5
xref: MetaCyc:RXN-14250
+xref: Reactome:R-HSA-428260 "DEGS2 oxygenates dihydroceramide"
+xref: RHEA:46364
+xref: RHEA:55476
xref: RHEA:55808
+xref: RHEA:81475
is_a: GO:0016716 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.18.5
property_value: skos:exactMatch RHEA:55808
+property_value: skos:narrowMatch RHEA:46364
+property_value: skos:narrowMatch RHEA:55476
+property_value: skos:narrowMatch RHEA:81475
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25981" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -461382,7 +466225,7 @@
id: GO:0102778
name: delta9-tetrahydrocannabinolate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cannabigerolate + O2 = delta(9)-tetrahydrocannabinolic acid + hydrogen peroxide." [GOC:pz, RHEA:34135]
+def: "Catalysis of the reaction: cannabigerolate + O2 = delta(9)-tetrahydrocannabinolic acid + H2O2." [RHEA:34135]
xref: EC:1.21.3.7
xref: MetaCyc:RXN-7854
xref: RHEA:34135
@@ -461395,7 +466238,7 @@
id: GO:0102779
name: cannabidiolate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cannabigerolate + O2 = cannabidiolate + hydrogen peroxide." [GOC:pz, RHEA:34411]
+def: "Catalysis of the reaction: cannabigerolate + O2 = cannabidiolate + H2O2." [RHEA:34411]
xref: EC:1.21.3.8
xref: MetaCyc:RXN-7855
xref: RHEA:34411
@@ -461792,12 +466635,13 @@
[Term]
id: GO:0102818
-name: lycopene cleavage oxygenase activity
+name: obsolete lycopene cleavage oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: lycopene + 2 O2 = 2 sulcatone + bixin aldehyde." [GOC:pz, MetaCyc:RXN-8236]
-xref: MetaCyc:RXN-8236
-is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases)
+def: "OBSOLETE. Catalysis of the reaction: lycopene + 2 O2 = 2 sulcatone + bixin aldehyde." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28942" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102819
@@ -461835,12 +466679,16 @@
synonym: "quercetin 3'-O-methyltransferase activity" NARROW []
xref: EC:2.1.1.42
xref: MetaCyc:RXN-8262
+xref: RHEA:14589
xref: RHEA:55332
+xref: RHEA:60944
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:broadMatch EC:2.1.1.267
property_value: skos:exactMatch EC:2.1.1.42
property_value: skos:exactMatch RHEA:55332
+property_value: skos:narrowMatch RHEA:14589
+property_value: skos:narrowMatch RHEA:60944
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -462214,6 +467062,8 @@
xref: MetaCyc:RXN-8331
xref: MetaCyc:RXN-8361
xref: RHEA:46404
+xref: RHEA:66504
+xref: RHEA:66508
is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water
property_value: skos:exactMatch EC:1.14.19.25
property_value: skos:exactMatch MetaCyc:RXN-16046
@@ -462224,6 +467074,8 @@
property_value: skos:narrowMatch MetaCyc:RXN-8329
property_value: skos:narrowMatch MetaCyc:RXN-8331
property_value: skos:narrowMatch MetaCyc:RXN-8361
+property_value: skos:narrowMatch RHEA:66504
+property_value: skos:narrowMatch RHEA:66508
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -462992,9 +467844,10 @@
[Term]
id: GO:0102933
-name: GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity
+name: GDP-perosamine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-4-amino-4,6-dideoxy-alpha-D-mannose + 2-oxoglutarate = GDP-4-dehydro-6-deoxy-alpha-D-mannose + L-glutamate." [GOC:pz, RHEA:36779]
+def: "Catalysis of the reaction: GDP-alpha-D-perosamine + 2-oxoglutarate = GDP-4-dehydro-alpha-D-rhamnose + L-glutamate." [RHEA:36779]
+synonym: "GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity" EXACT []
xref: EC:2.6.1.102
xref: MetaCyc:RXN-8953
xref: RHEA:36779
@@ -463002,6 +467855,7 @@
property_value: skos:exactMatch EC:2.6.1.102
property_value: skos:exactMatch RHEA:36779
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
[Term]
id: GO:0102934
@@ -463036,11 +467890,12 @@
[Term]
id: GO:0102937
-name: 16-alpha-hydroxygypsogenate-UDP-glucosyltransferase activity
+name: obsolete 16-alpha-hydroxygypsogenate-UDP-glucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: UDP-alpha-D-glucose + 16-alpha-hydroxygypsogenate = 16-alpha-hydroxygypsogenate-28-beta-D-glucoside + UDP." [GOC:pz]
-xref: MetaCyc:RXN-9014
-is_a: GO:0016758 ! hexosyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: UDP-alpha-D-glucose + 16-alpha-hydroxygypsogenate = 16-alpha-hydroxygypsogenate-28-beta-D-glucoside + UDP." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102938
@@ -463129,11 +467984,12 @@
[Term]
id: GO:0102947
-name: (+)-delta-cadinene-8-hydroxylase activity
+name: obsolete (+)-delta-cadinene-8-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + (+)-delta-cadinene + NADPH + O2 = 8-hydroxy-(+)-delta-cadinene + NADP + H2O." [GOC:pz]
-xref: MetaCyc:RXN-9045
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + (+)-delta-cadinene + NADPH + O2 = 8-hydroxy-(+)-delta-cadinene + NADP + H2O." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102948
@@ -463181,11 +468037,12 @@
[Term]
id: GO:0102953
-name: hypoglycin A gamma-glutamyl transpeptidase activity
+name: obsolete hypoglycin A gamma-glutamyl transpeptidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: glutathionate + hypoglycin A = L-cysteinylglycine + hypoglycin B." [GOC:pz]
-xref: MetaCyc:RXN-9157
-is_a: GO:0016755 ! aminoacyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: glutathionate + hypoglycin A = L-cysteinylglycine + hypoglycin B." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0102954
@@ -463267,10 +468124,24 @@
synonym: "alcohol-forming fatty acyl-CoA reductase activity" BROAD []
xref: EC:1.2.1.84
xref: MetaCyc:RXN-9344
+xref: RHEA:36315
+xref: RHEA:36319
xref: RHEA:52716
+xref: RHEA:81727
+xref: RHEA:81731
+xref: RHEA:81763
+xref: RHEA:81767
+xref: RHEA:81771
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.2.1.84
property_value: skos:exactMatch RHEA:52716
+property_value: skos:narrowMatch RHEA:36315
+property_value: skos:narrowMatch RHEA:36319
+property_value: skos:narrowMatch RHEA:81727
+property_value: skos:narrowMatch RHEA:81731
+property_value: skos:narrowMatch RHEA:81763
+property_value: skos:narrowMatch RHEA:81767
+property_value: skos:narrowMatch RHEA:81771
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24250" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -463526,18 +468397,17 @@
name: trehalose synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: an NDP-alpha-D-glucose + D-glucose = a ribonucleoside 5'-diphosphate + alpha,alpha-trehalose + H+." [RHEA:47416]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
xref: EC:2.4.1.245
xref: MetaCyc:RXN-9603
+xref: RHEA:25408
xref: RHEA:47416
is_a: GO:0016758 ! hexosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.245
property_value: skos:exactMatch MetaCyc:RXN-9603
property_value: skos:exactMatch RHEA:47416
-property_value: skos:relatedMatch MetaCyc:PWY-2622
-property_value: skos:relatedMatch MetaCyc:PWY-5983
-property_value: skos:relatedMatch MetaCyc:PWY-5985
+property_value: skos:narrowMatch RHEA:25408
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
[Term]
id: GO:0102987
@@ -463753,11 +468623,12 @@
[Term]
id: GO:0103004
-name: 9,10-epoxystearate hydroxylase activity
+name: obsolete 9,10-epoxystearate hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + 9,10-epoxystearate + O2 + NADPH = 9,10-epoxy-18-hydroxystearate + H2O + NADP." [GOC:pz]
-xref: MetaCyc:RXN-9805
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + 9,10-epoxystearate + O2 + NADPH = 9,10-epoxy-18-hydroxystearate + H2O + NADP." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0103005
@@ -463770,11 +468641,12 @@
[Term]
id: GO:0103006
-name: 9,10-dihydroxystearate hydroxylase activity
+name: obsolete 9,10-dihydroxystearate hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + (9R,10S)-dihydroxystearate + O2 + NADPH = 9,10,18-trihydroxystearate + H2O + NADP." [GOC:pz]
-xref: MetaCyc:RXN-9807
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+def: "OBSOLETE. Catalysis of the reaction: H+ + (9R,10S)-dihydroxystearate + O2 + NADPH = 9,10,18-trihydroxystearate + H2O + NADP." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0103007
@@ -463978,11 +468850,12 @@
[Term]
id: GO:0103033
-name: beta-galactosidase activity (lactose isomerization)
+name: obsolete beta-galactosidase activity (lactose isomerization)
namespace: molecular_function
-def: "Catalysis of the reaction: alpha-lactose = beta-(1->6)-galactobiose." [EC:5.4.1.-, GOC:pz]
-xref: MetaCyc:RXN0-5363
-is_a: GO:0016867 ! intramolecular acyltransferase activity
+def: "OBSOLETE. Catalysis of the reaction: alpha-lactose = beta-(1->6)-galactobiose." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0103035
@@ -464000,8 +468873,14 @@
def: "Catalysis of the reaction: a menaquinone + NADH + H+ = a menaquinol + NAD+." [RHEA:29235]
synonym: "NADH:menaquinone oxidoreductase activity" EXACT []
xref: RHEA:29235
+xref: RHEA:29243
+xref: RHEA:30507
+xref: RHEA:35559
is_a: GO:0050136 ! NADH dehydrogenase (quinone) (non-electrogenic) activity
property_value: skos:exactMatch RHEA:29235
+property_value: skos:narrowMatch RHEA:29243
+property_value: skos:narrowMatch RHEA:30507
+property_value: skos:narrowMatch RHEA:35559
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -464268,14 +469147,14 @@
[Term]
id: GO:0103068
-name: leukotriene C4 gamma-glutamyl transferase activity
+name: obsolete leukotriene C4 gamma-glutamyl transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: leukotriene C4 + a standard alpha amino acid = leukotriene D4 + an (gamma-L-glutamyl)-L-amino acid." [GOC:pz, PMID:1676842, PMID:9139674]
+def: "OBSOLETE. Catalysis of the reaction: leukotriene C4 + a standard alpha amino acid = leukotriene D4 + an (gamma-L-glutamyl)-L-amino acid." [GOC:pz, PMID:1676842, PMID:9139674]
xref: EC:2.3.2.2
-xref: MetaCyc:RXN66-336
-is_a: GO:0016755 ! aminoacyltransferase activity
property_value: skos:exactMatch EC:2.3.2.2
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31373" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0103069
@@ -464621,19 +469500,18 @@
[Term]
id: GO:0103111
-name: protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity
+name: obsolete protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N(pros)-phospho-L-histidyl-[protein] + N-acetyl-D-glucosamine(out) = L-histidyl-[protein] + N-acetyl-D-glucosamine 6-phosphate(in)." [RHEA:49240]
+def: "OBSOLETE. Catalysis of the reaction: N(pros)-phospho-L-histidyl-[protein] + N-acetyl-D-glucosamine(out) = L-histidyl-[protein] + N-acetyl-D-glucosamine 6-phosphate(in)." [RHEA:49240]
+comment: This term was obsoleted because it represents the same reaction as [protein-N(PI)-phosphohistidine-N-acetylglucosamine phosphotransferase system transporter activity ; GO:0022880.
synonym: "D-glucosamine PTS permease activity" EXACT []
synonym: "N-acetyl-D-glucosamine PTS permease activity" EXACT [EC:2.7.1.193]
-xref: EC:2.7.1.193
-xref: RHEA:49240
-is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
-property_value: skos:exactMatch EC:2.7.1.193
-property_value: skos:exactMatch RHEA:49240
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27694" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0022880
[Term]
id: GO:0103113
@@ -464669,10 +469547,12 @@
def: "Catalysis of the reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-alpha-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + acetate." [GOC:pz, RHEA:67816]
xref: EC:3.5.1.108
xref: MetaCyc:UDPACYLGLCNACDEACETYL-RXN
+xref: RHEA:25209
xref: RHEA:67816
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
property_value: skos:exactMatch EC:3.5.1.108
property_value: skos:exactMatch RHEA:67816
+property_value: skos:narrowMatch RHEA:25209
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -464685,10 +469565,12 @@
synonym: "UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase activity" RELATED []
xref: EC:2.3.1.191
xref: MetaCyc:RXN-22482
+xref: RHEA:17817
xref: RHEA:53836
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.191
property_value: skos:exactMatch RHEA:53836
+property_value: skos:narrowMatch RHEA:17817
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30153" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -465079,10 +469961,16 @@
synonym: "tRNA-pseudouridine synthase activity" EXACT []
synonym: "tRNA-uridine isomerase activity" EXACT []
synonym: "tRNA-uridine uracilmutase activity" EXACT []
+xref: RHEA:42964
xref: RHEA:54572
+xref: RHEA:57876
+xref: RHEA:60556
is_a: GO:0009982 ! pseudouridine synthase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
property_value: skos:exactMatch RHEA:54572
+property_value: skos:narrowMatch RHEA:42964
+property_value: skos:narrowMatch RHEA:57876
+property_value: skos:narrowMatch RHEA:60556
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26797" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -465234,15 +470122,13 @@
[Term]
id: GO:0106045
-name: guanine deglycation, methylglyoxal removal
+name: obsolete guanine deglycation, methylglyoxal removal
namespace: biological_process
-def: "The removal of methylglyoxal from a glycated guanine, to form lactate and a deglycated guanine." [PMID:28596309]
-is_a: GO:0009438 ! methylglyoxal metabolic process
-is_a: GO:0051595 ! response to methylglyoxal
-is_a: GO:0106044 ! guanine deglycation
-is_a: GO:0140041 ! cellular detoxification of methylglyoxal
-created_by: hjd
-creation_date: 2017-08-01T18:17:28Z
+def: "OBSOLETE. The removal of methylglyoxal from a glycated guanine, to form lactate and a deglycated guanine." [PMID:28596309]
+comment: The reason for obsoletion is that this term represents a molecular function rather than a biological process.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31367" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0036524
[Term]
id: GO:0106046
@@ -465289,14 +470175,17 @@
[Term]
id: GO:0106050
-name: tRNA 2'-O-methyltransferase activity
+name: obsolete tRNA 2'-O-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing a 2'-O-nucleotide." [PMID:17242307]
+def: "OBSOLETE. Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing a 2'-O-nucleotide." [PMID:17242307]
+comment: This term was obsoleted because it is an unnecessray grouping term.
xref: Reactome:R-HSA-6788668 "TRMT13 2'-O-methylates adenosine-4 in tRNA"
xref: Reactome:R-HSA-6788684 "TRMT13 2'-O-methylates cytidine-4 in tRNA"
xref: Reactome:R-HSA-9024159 "FTSJ1 2'-O-methylates cytidine-32 in tRNA(Phe)"
-is_a: GO:0008175 ! tRNA methyltransferase activity
-is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31519" xsd:anyURI
+is_obsolete: true
+consider: GO:0106339
+consider: GO:0106340
created_by: hjd
creation_date: 2017-08-11T20:30:31Z
@@ -465368,10 +470257,11 @@
[Term]
id: GO:0106059
-name: tRNA (cytidine(56)-2'-O)-methyltransferase activity
+name: tRNA (cytidine(56)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + cytidine56 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylcytidine56 in tRNA." [RHEA:42968]
synonym: "tRNA (cytidine 56-2'-O)-methyltransferase activity" EXACT []
+synonym: "tRNA (cytidine(56)-2'-O)-methyltransferase activity" EXACT []
xref: EC:2.1.1.206
xref: MetaCyc:RXN-11869
xref: RHEA:42968
@@ -466399,11 +471289,17 @@
xref: EC:1.14.11.73
xref: Reactome:R-HSA-9629869 "KDM8:Fe2+ hydroxylates an arginine residue of RPS6"
xref: Reactome:R-HSA-9629888 "KDM8:Fe2+ hydroxylates an arginine residue of RCCD1"
+xref: RHEA:41556
xref: RHEA:56744
+xref: RHEA:57160
+xref: RHEA:57164
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:1.14.11.73
property_value: skos:exactMatch RHEA:56744
+property_value: skos:narrowMatch RHEA:41556
+property_value: skos:narrowMatch RHEA:57160
+property_value: skos:narrowMatch RHEA:57164
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16689" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -466459,13 +471355,16 @@
[Term]
id: GO:0106162
-name: mRNA N-acetyltransferase activity
+name: mRNA cytidine N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a cytidine in mRNA + acetyl-CoA + ATP + H2O = ADP + an N(4)-acetylcytidine in mRNA + CoA + H+ + phosphate." [GOC:sp, PMID:30449621, RHEA:58480]
+synonym: "mRNA N-acetyltransferase activity" BROAD []
xref: RHEA:58480
is_a: GO:0008080 ! N-acetyltransferase activity
+is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
property_value: skos:exactMatch RHEA:58480
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: terms:contributor "https://github.com/geneontology/go-ontology/issues/16755" xsd:anyURI
created_by: hjd
creation_date: 2018-12-18T19:19:06Z
@@ -466681,9 +471580,10 @@
id: GO:0106186
name: cytoplasmic side of plasma membrane, cell tip
namespace: cellular_component
-def: "The leaflet the plasma membrane at the cell tip that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface." [GOC:vw, PMID:28292899]
+def: "The leaflet the plasma membrane at the cell tip that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [GOC:vw, PMID:28292899]
is_a: GO:0009898 ! cytoplasmic side of plasma membrane
relationship: part_of GO:0031520 ! plasma membrane of cell tip
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: hjd
creation_date: 2019-05-01T17:48:02Z
@@ -467053,6 +471953,7 @@
name: peptide glutaryltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: glutaryl-CoA + L-lysyl-[protein] = CoA + H+ + N6-glutaryl-L-lysyl-[protein]." [GOC:sp, PMID:31542297]
+xref: Reactome:R-HSA-9858590 "DLST transfers glutaryl to CoA"
xref: RHEA:18009
is_a: GO:0016410 ! N-acyltransferase activity
property_value: skos:exactMatch RHEA:18009
@@ -467135,9 +472036,11 @@
name: ceramide-1-phosphate phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: ceramide-1-phosphate + H2O = ceramide+ phosphate." [GOC:lb, PMID:10359651]
+xref: RHEA:33743
xref: RHEA:50888
is_a: GO:0042577 ! lipid phosphatase activity
property_value: skos:exactMatch RHEA:50888
+property_value: skos:narrowMatch RHEA:33743
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2019-11-21T20:40:39Z
@@ -467357,10 +472260,30 @@
namespace: molecular_function
def: "A hydroperoxy icosatetraenoate = a hydroxy epoxy icosatrienoate." [PMID:12881489, RHEA:55560]
xref: EC:5.4.4.7
+xref: Reactome:R-HSA-2161794 "Arachidonate is converted to HXA3/B3 by ALOX12"
+xref: Reactome:R-HSA-8942208 "ALOXE3 isomerises 12R-HpETE to HXA3"
+xref: RHEA:37931
+xref: RHEA:37939
+xref: RHEA:37951
+xref: RHEA:37955
+xref: RHEA:37959
+xref: RHEA:41251
+xref: RHEA:50216
+xref: RHEA:53400
+xref: RHEA:53404
xref: RHEA:55560
is_a: GO:0050486 ! intramolecular hydroxytransferase activity
property_value: skos:exactMatch EC:5.4.4.7
property_value: skos:exactMatch RHEA:55560
+property_value: skos:narrowMatch RHEA:37931
+property_value: skos:narrowMatch RHEA:37939
+property_value: skos:narrowMatch RHEA:37951
+property_value: skos:narrowMatch RHEA:37955
+property_value: skos:narrowMatch RHEA:37959
+property_value: skos:narrowMatch RHEA:41251
+property_value: skos:narrowMatch RHEA:50216
+property_value: skos:narrowMatch RHEA:53400
+property_value: skos:narrowMatch RHEA:53404
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2020-03-20T14:00:30Z
@@ -467371,10 +472294,24 @@
namespace: molecular_function
def: "A hydroperoxy icosatetraenoate = an oxoicosatetraenoate + H2O." [PMID:12881489, RHEA:55556]
xref: EC:4.2.1.152
+xref: RHEA:37927
+xref: RHEA:37935
+xref: RHEA:37943
+xref: RHEA:37947
+xref: RHEA:48632
+xref: RHEA:48636
+xref: RHEA:50152
xref: RHEA:55556
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.152
property_value: skos:exactMatch RHEA:55556
+property_value: skos:narrowMatch RHEA:37927
+property_value: skos:narrowMatch RHEA:37935
+property_value: skos:narrowMatch RHEA:37943
+property_value: skos:narrowMatch RHEA:37947
+property_value: skos:narrowMatch RHEA:48632
+property_value: skos:narrowMatch RHEA:48636
+property_value: skos:narrowMatch RHEA:50152
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2020-03-20T14:40:16Z
@@ -467442,9 +472379,37 @@
def: "Catalysis of the reaction: a 1-acyl-sn-glycero-3-phosphoethanolamine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CoA." [PMID:18287005, RHEA:32995]
xref: EC:2.3.1.n7
xref: RHEA:32995
+xref: RHEA:36015
+xref: RHEA:36019
+xref: RHEA:36023
+xref: RHEA:37495
+xref: RHEA:37499
+xref: RHEA:37503
+xref: RHEA:37523
+xref: RHEA:37575
+xref: RHEA:37579
+xref: RHEA:37727
+xref: RHEA:37731
+xref: RHEA:37767
+xref: RHEA:37771
+xref: RHEA:37775
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.n7
property_value: skos:exactMatch RHEA:32995
+property_value: skos:narrowMatch RHEA:36015
+property_value: skos:narrowMatch RHEA:36019
+property_value: skos:narrowMatch RHEA:36023
+property_value: skos:narrowMatch RHEA:37495
+property_value: skos:narrowMatch RHEA:37499
+property_value: skos:narrowMatch RHEA:37503
+property_value: skos:narrowMatch RHEA:37523
+property_value: skos:narrowMatch RHEA:37575
+property_value: skos:narrowMatch RHEA:37579
+property_value: skos:narrowMatch RHEA:37727
+property_value: skos:narrowMatch RHEA:37731
+property_value: skos:narrowMatch RHEA:37767
+property_value: skos:narrowMatch RHEA:37771
+property_value: skos:narrowMatch RHEA:37775
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27226" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -467457,9 +472422,27 @@
def: "Catalysis of the reaction:a 1-acyl-sn-glycero-3-phospho-L-serine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-L-serine + CoA." [PMID:18287005, RHEA:33191]
xref: EC:2.3.1.n6
xref: RHEA:33191
+xref: RHEA:37399
+xref: RHEA:37403
+xref: RHEA:37415
+xref: RHEA:37531
+xref: RHEA:37539
+xref: RHEA:37567
+xref: RHEA:37571
+xref: RHEA:37735
+xref: RHEA:37739
is_a: GO:0008374 ! O-acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.n6
property_value: skos:exactMatch RHEA:33191
+property_value: skos:narrowMatch RHEA:37399
+property_value: skos:narrowMatch RHEA:37403
+property_value: skos:narrowMatch RHEA:37415
+property_value: skos:narrowMatch RHEA:37531
+property_value: skos:narrowMatch RHEA:37539
+property_value: skos:narrowMatch RHEA:37567
+property_value: skos:narrowMatch RHEA:37571
+property_value: skos:narrowMatch RHEA:37735
+property_value: skos:narrowMatch RHEA:37739
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27226" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -467888,9 +472871,13 @@
namespace: molecular_function
def: "Catalysis of an NADPH- and oxygen-dependent reaction that converts arachidonic acid to cis-8,9-epoxyeicosatrienoic acid." [PMID:10491410, PMID:8246128, RHEA:64984]
synonym: "arachidonic acid 8,9-epoxygenase activity" EXACT []
+xref: RHEA:49884
+xref: RHEA:49928
xref: RHEA:64984
is_a: GO:0008392 ! arachidonate epoxygenase activity
property_value: skos:exactMatch RHEA:64984
+property_value: skos:narrowMatch RHEA:49884
+property_value: skos:narrowMatch RHEA:49928
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -467964,9 +472951,14 @@
xref: Reactome:R-HSA-9841265 "p-S473-AKT1 phosphorylates ESR1 on serine-167"
xref: Reactome:R-HSA-9860792 "Phospho-AKT1 phosphorylates NOS3 (eNOS) on serine-1177"
xref: Reactome:R-HSA-9860808 "p-T816-PKN2 phosphorylates NOS3 (eNOS) on serine-1179"
+xref: Reactome:R-HSA-9948087 "CAMK2 complex phosphorylates VIM:NS4A"
+xref: RHEA:15881
xref: RHEA:17989
+xref: RHEA:46600
is_a: GO:0004672 ! protein kinase activity
property_value: skos:exactMatch RHEA:17989
+property_value: skos:narrowMatch RHEA:15881
+property_value: skos:narrowMatch RHEA:46600
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20114" xsd:anyURI
created_by: hjd
creation_date: 2020-09-22T20:01:17Z
@@ -468182,7 +473174,7 @@
id: GO:0106329
name: L-phenylalaine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + L-phenylalanine + O2 = 3-phenylpyruvate + H2O2 + NH4(+)." [RHEA:61240]
+def: "Catalysis of the reaction: H2O + L-phenylalanine + O2 = 3-phenylpyruvate + H2O2 + NH4+." [RHEA:61240]
xref: RHEA:61240
is_a: GO:0001716 ! L-amino-acid oxidase activity
property_value: skos:exactMatch RHEA:61240
@@ -468256,7 +473248,7 @@
id: GO:0106335
name: tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-(carboxymethyl)uridine34 in tRNA + S-adenosyl-L-methionine = 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA + S-adenosyl-L-homocysteine." [PMID:20123966, RHEA:43208]
+def: "Catalysis of the reaction: 5-(carboxymethyl)uridine34 in tRNA + S-adenosyl-L-methionine = 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA + S-adenosyl-L-homocysteine. The methylation occurs on the modified base." [PMID:20123966, RHEA:43208]
xref: EC:2.1.1.229
xref: RHEA:43208
is_a: GO:0016300 ! tRNA (uridine) methyltransferase activity
@@ -468280,10 +473272,11 @@
[Term]
id: GO:0106339
-name: tRNA (cytidine(32)-2'-O)-methyltransferase activity
+name: tRNA (cytidine(32)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: cytidine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32) in tRNA + S-adenosyl-L-homocysteine + H+." [PMID:25404562, RHEA:42932]
synonym: "tRNA (cytidine 32-2'-O)-methyltransferase activity" EXACT []
+synonym: "tRNA (cytidine(32)-2'-O)-methyltransferase activity" EXACT []
xref: MetaCyc:RXN-11866
xref: RHEA:42932
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
@@ -468302,12 +473295,15 @@
[Term]
id: GO:0106340
-name: tRNA (guanosine(34)-2'-O)-methyltransferase activity
+name: tRNA (guanosine(34)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanosine(34) in tRNA + S-adenosyl-L-methionine = 2'-O-methylguanosine(34) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:31943105]
+def: "Catalysis of the reaction: guanosine(34) in tRNA + S-adenosyl-L-methionine = 2'-O-methylguanosine(34) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:31943105, RHEA:85171]
+synonym: "tRNA (guanosine(34)-2'-O)-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-9024161 "FTSJ1 2'-O-methylates guanosine-34 in tRNA(Phe)"
+xref: RHEA:85171
is_a: GO:0016423 ! tRNA (guanine) methyltransferase activity
property_value: skos:broadMatch EC:2.1.1.205
+property_value: skos:exactMatch RHEA:85171
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25257" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26085" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26086" xsd:anyURI
@@ -468324,10 +473320,16 @@
xref: EC:2.3.1.296
xref: MetaCyc:RXN-20362
xref: RHEA:61528
+xref: RHEA:65692
+xref: RHEA:78115
+xref: RHEA:78119
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.296
property_value: skos:exactMatch MetaCyc:RXN-20362
property_value: skos:exactMatch RHEA:61528
+property_value: skos:narrowMatch RHEA:65692
+property_value: skos:narrowMatch RHEA:78115
+property_value: skos:narrowMatch RHEA:78119
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30910" xsd:anyURI
created_by: hjd
creation_date: 2020-11-17T17:12:43Z
@@ -468389,9 +473391,10 @@
[Term]
id: GO:0106347
-name: U2 snRNA 2'-O-methyladenosine m6 methyltransferase activity
+name: U2 snRNA (2'-O-methyladenosine-N6)-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 2'-O-methyladenosine in U2 snRNA + S-adenosyl-L-methionine = an N6-methyl-2'-O-methyladenosine in U2 snRNA + S-adenosyl-L-homocysteine + H+." [PMID:31913360, RHEA:62672]
+def: "Catalysis of the reaction: a 2'-O-methyladenosine in U2 snRNA + S-adenosyl-L-methionine = an N6-methyl-2'-O-methyladenosine in U2 snRNA + S-adenosyl-L-homocysteine + H+; methylates the 6th position of adenine residues with a pre-deposited 2'-O-methylation." [PMID:31913360, RHEA:62672]
+synonym: "U2 snRNA (2'-O-methyladenosine) m6 methyltransferase activity" EXACT []
xref: RHEA:62672
is_a: GO:0106346 ! snRNA methyltransferase activity
property_value: skos:exactMatch RHEA:62672
@@ -468401,9 +473404,11 @@
[Term]
id: GO:0106348
-name: U2 snRNA adenosine m6 methyltransferase activity
+name: U2 snRNA (adenine-N6)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a adenosine in U2 snRNA + S-adenosyl-L-methionine = an N6-methyl-adenosine in U2 snRNA + S-adenosyl-L-homocysteine + H+." [PMID:32637152]
+synonym: "U2 snRNA adenosine m6 methyltransferase activity" EXACT []
+synonym: "U2 snRNA adenosine N6 methyltransferase activity" EXACT []
is_a: GO:0106346 ! snRNA methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27392" xsd:anyURI
created_by: hjd
@@ -468580,11 +473585,21 @@
synonym: "4-hydroxy-3-all-trans-hexaprenylbenzoate oxygenase activity" NARROW []
xref: EC:1.14.15.45
xref: MetaCyc:RXN3O-58
+xref: RHEA:20361
xref: RHEA:81195
+xref: RHEA:81247
+xref: RHEA:81251
+xref: RHEA:81255
+xref: RHEA:81259
is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.15.45
property_value: skos:exactMatch RHEA:81195
property_value: skos:narrowMatch MetaCyc:RXN3O-58
+property_value: skos:narrowMatch RHEA:20361
+property_value: skos:narrowMatch RHEA:81247
+property_value: skos:narrowMatch RHEA:81251
+property_value: skos:narrowMatch RHEA:81255
+property_value: skos:narrowMatch RHEA:81259
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27952" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29459" xsd:anyURI
created_by: hjd
@@ -468623,9 +473638,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dGTP = a 2'-deoxyribonucleoside 5'-diphosphate + dGDP." [PMID:20497505, RHEA:62128]
xref: RHEA:62128
+xref: RHEA:62144
+xref: RHEA:62148
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch RHEA:62128
+property_value: skos:narrowMatch RHEA:62144
+property_value: skos:narrowMatch RHEA:62148
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2021-03-11T20:06:53Z
@@ -468636,9 +473655,11 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dTTP = a 2'-deoxyribonucleoside 5'-diphosphate + dTDP." [PMID:20497505, RHEA:62132]
xref: RHEA:62132
+xref: RHEA:62152
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch RHEA:62132
+property_value: skos:narrowMatch RHEA:62152
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2021-03-11T20:09:34Z
@@ -468649,9 +473670,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + GTP = a 2'-deoxyribonucleoside 5'-diphosphate + GDP." [PMID:20497505, RHEA:62124]
xref: RHEA:62124
+xref: RHEA:62136
+xref: RHEA:62140
is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
is_a: GO:0019205 ! nucleobase-containing compound kinase activity
property_value: skos:exactMatch RHEA:62124
+property_value: skos:narrowMatch RHEA:62136
+property_value: skos:narrowMatch RHEA:62140
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2021-03-11T20:12:21Z
@@ -468712,8 +473737,14 @@
namespace: molecular_function
def: "Catalysis of the reaction: dNTP + H2O = 2'-deoxynucleoside + H+ + triphosphate." [RHEA:46148]
xref: RHEA:46148
+xref: RHEA:67648
+xref: RHEA:80079
+xref: RHEA:80083
is_a: GO:0016793 ! triphosphoric monoester hydrolase activity
property_value: skos:exactMatch RHEA:46148
+property_value: skos:narrowMatch RHEA:67648
+property_value: skos:narrowMatch RHEA:80079
+property_value: skos:narrowMatch RHEA:80083
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2021-04-15T20:44:33Z
@@ -468832,9 +473863,21 @@
xref: EC:1.1.1.n12
xref: MetaCyc:RXN66-485
xref: RHEA:32711
+xref: RHEA:67220
+xref: RHEA:67232
+xref: RHEA:78871
+xref: RHEA:78875
+xref: RHEA:78879
+xref: RHEA:78935
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.n12
property_value: skos:exactMatch RHEA:32711
+property_value: skos:narrowMatch RHEA:67220
+property_value: skos:narrowMatch RHEA:67232
+property_value: skos:narrowMatch RHEA:78871
+property_value: skos:narrowMatch RHEA:78875
+property_value: skos:narrowMatch RHEA:78879
+property_value: skos:narrowMatch RHEA:78935
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30577" xsd:anyURI
created_by: hjd
@@ -468857,11 +473900,15 @@
def: "Catalysis of the reaction: N1-methylpseudouridine in small subunit rRNA + S-adenosyl-L-methionine = H+ + N1-methyl-N3-[(3S)-3-amino-3-carboxypropyl]pseudouridine in small subunit rRNA + S-methyl-5'-thioadenosine." [PMID:27084949, RHEA:63296]
synonym: "18S rRNA aminocarboxypropyltransferase activity" NARROW []
xref: EC:2.5.1.157
+xref: RHEA:63292
xref: RHEA:63296
+xref: RHEA:63300
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
is_a: GO:0140102 ! catalytic activity, acting on a rRNA
property_value: skos:exactMatch EC:2.5.1.157
property_value: skos:exactMatch RHEA:63296
+property_value: skos:narrowMatch RHEA:63292
+property_value: skos:narrowMatch RHEA:63300
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29843" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -469317,11 +474364,15 @@
namespace: molecular_function
def: "(S)-dihydroorotate + a quinone = orotate + a quinol." [RHEA:30187]
xref: EC:1.3.5.2
+xref: RHEA:28691
+xref: RHEA:29195
xref: RHEA:30187
is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
property_value: skos:exactMatch EC:1.3.5.2
property_value: skos:exactMatch RHEA:30187
+property_value: skos:narrowMatch RHEA:28691
+property_value: skos:narrowMatch RHEA:29195
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23786" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -469402,9 +474453,19 @@
xref: Reactome:R-HSA-9727567 "CES1 hydrolyses sacubitril to sacubitrilat"
xref: Reactome:R-HSA-9749647 "CES2 hydrolyzes ASA-"
xref: RHEA:21164
+xref: RHEA:31779
+xref: RHEA:38555
+xref: RHEA:50148
+xref: RHEA:59388
+xref: RHEA:63052
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.1
property_value: skos:exactMatch RHEA:21164
+property_value: skos:narrowMatch RHEA:31779
+property_value: skos:narrowMatch RHEA:38555
+property_value: skos:narrowMatch RHEA:50148
+property_value: skos:narrowMatch RHEA:59388
+property_value: skos:narrowMatch RHEA:63052
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21843" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -469418,9 +474479,11 @@
synonym: "eukaryotic sulfide quinone oxidoreductase" RELATED []
xref: EC:1.8.5.8
xref: RHEA:55156
+xref: RHEA:62608
is_a: GO:0016672 ! oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.8.5.8
property_value: skos:exactMatch RHEA:55156
+property_value: skos:narrowMatch RHEA:62608
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23325" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -469432,8 +474495,10 @@
namespace: molecular_function
def: "Catalytic reaction: ATP + L-glutamate + L-glutamyl-[protein] = ADP + H+ + L-gamma-glutamyl-L-glutamyl-[protein] + phosphate." [PMID:32747782, RHEA:60144]
xref: RHEA:60144
+xref: RHEA:69192
is_a: GO:0070739 ! protein-glutamic acid ligase activity
property_value: skos:exactMatch RHEA:60144
+property_value: skos:narrowMatch RHEA:69192
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21309" xsd:anyURI
created_by: hjd
creation_date: 2022-10-21T21:11:47Z
@@ -469444,8 +474509,10 @@
namespace: molecular_function
def: "Catalytic reaction :(L-glutamyl)n-L-gamma-glutamyl-L-glutamyl-[protein] + ATP + L-glutamate = (L-glutamyl)n+1-L-gamma-glutamyl-L-glutamyl-[protein] + ADP + H+ + phosphate." [PMID:32747782, RHEA:60148]
xref: RHEA:60148
+xref: RHEA:69208
is_a: GO:0070739 ! protein-glutamic acid ligase activity
property_value: skos:exactMatch RHEA:60148
+property_value: skos:narrowMatch RHEA:69208
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21309" xsd:anyURI
created_by: hjd
creation_date: 2022-10-21T21:15:15Z
@@ -469851,11 +474918,14 @@
[Term]
id: GO:0110035
-name: rDNA spacer replication fork barrier binding, bending
+name: obsolete rDNA spacer replication fork barrier binding, bending
namespace: molecular_function
-def: "The activity of binding selectively, and in a sequence-specific manner, a replication fork barrier found in rDNA spacers, and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:al, GOC:vw, PMID:27035982]
-is_a: GO:0043110 ! rDNA spacer replication fork barrier binding
-is_a: GO:0044374 ! sequence-specific DNA binding, bending
+def: "OBSOLETE. The activity of binding selectively, and in a sequence-specific manner, a replication fork barrier found in rDNA spacers, and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:al, GOC:vw, PMID:27035982]
+comment: This term was obsoleted because it is precomposed.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31529" xsd:anyURI
+is_obsolete: true
+consider: GO:0008301
+consider: GO:0043110
created_by: kmv
creation_date: 2017-07-17T21:09:50Z
@@ -471040,6 +476110,7 @@
name: L-glutamate import into mitochondrion
namespace: biological_process
def: "The process in which L-glutamate is transported from the cytosol into the mitochondrial matrix." [GOC:vw, PMID:30297026]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015813 ! L-glutamate transmembrane transport
created_by: kmv
creation_date: 2019-04-24T19:13:46Z
@@ -471244,8 +476315,7 @@
name: reelin complex
namespace: cellular_component
def: "An extracellular complex that binds lipoprotein receptors VLDLR and APOER2, cadherin-related neuronal receptors (CNRs) or alpha3beta1 integrin and induces various downstream, reelin-dependent, phosphorylation cascades. It ultimately affects polarization, differentiation, neuronal migration and layer formation in the embryonic brain and neuron growth, maturation, and synaptic activity in the postnatal and adult brain." [GOC:bhm, PMID:21844191, PMID:28887403]
-is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0005615 ! extracellular space
+is_a: GO:0140392 ! extracellular protein-containing complex
created_by: kmv
creation_date: 2019-07-15T15:10:58Z
@@ -471502,13 +476572,19 @@
namespace: molecular_function
def: "Removes a lipid from a membrane or a monolayer lipid particle, transports it through the aqueous phase while protected in a hydrophobic pocket, and brings it to an acceptor membrane or lipid particle. This results in intermembrane transfer of lipids." [GOC:krc, PMID:20823909, PMID:24220498, PMID:25797198]
synonym: "intermembrane lipid transfer activity" EXACT []
-synonym: "lipid carrier activity" EXACT []
+synonym: "lipid carrier activity" BROAD []
+xref: Reactome:R-HSA-8856630 "CIDEA:CIDEC binds lipid droplets"
+xref: Reactome:R-HSA-8858270 "HILPDA binds lipid droplets"
+xref: Reactome:R-HSA-8862380 "HSD17B13 binds lipid droplets"
+xref: Reactome:R-HSA-8874705 "TTPA transports alpha-TOH from lysosomal membrane to plasma membrane"
xref: Reactome:R-HSA-9856502 "mito-STARD7 transports Q10 to outer mitochondrial membrane"
xref: Reactome:R-HSA-9856510 "STARD7 transports Q10 to plasma membrane"
-is_a: GO:0005319 ! lipid transporter activity
+is_a: GO:0005215 ! transporter activity
+is_a: GO:0005319 ! lipid carrier activity
relationship: part_of GO:0120009 ! intermembrane lipid transfer
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12329" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17648" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
created_by: krc
creation_date: 2017-03-17T03:17:29Z
@@ -471519,9 +476595,9 @@
def: "Removes a phospholipid from a membrane or a monolayer lipid particle, transports it through the aqueous phase while protected in a hydrophobic pocket, and brings it to an acceptor membrane or lipid particle." [GOC:krc, PMID:20823909, PMID:24220498, PMID:25797198]
synonym: "intermembrane phospholipid transfer activity" NARROW []
synonym: "phospholipid carrier activity" EXACT []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0120013 ! lipid transfer activity
relationship: has_part GO:0005543 ! phospholipid binding
+relationship: part_of GO:0015914 ! phospholipid transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12329" xsd:anyURI
created_by: krc
creation_date: 2017-03-17T03:34:17Z
@@ -471550,7 +476626,6 @@
def: "Removes a sphingolipid from a membrane or a monolayer lipid particle, transports it through the aqueous phase while protected in a hydrophobic pocket, and brings it to an acceptor membrane or lipid particle." [GOC:krc, PMID:20823909, PMID:24220498, PMID:25797198]
synonym: "intermembrane sphingolipid transfer activity" NARROW []
synonym: "sphingolipid carrier activity" NARROW []
-is_a: GO:0046624 ! sphingolipid transporter activity
is_a: GO:0120013 ! lipid transfer activity
relationship: has_part GO:0046625 ! sphingolipid binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12329" xsd:anyURI
@@ -471566,6 +476641,7 @@
synonym: "ceramide carrier activity" EXACT []
synonym: "ceramide transporter activity" BROAD []
synonym: "intermembrane ceramide transfer activity" NARROW []
+xref: Reactome:R-HSA-9956909 "CERT1-2 transfers CERA from the ER membrane to the Golgi membrane"
is_a: GO:0120016 ! sphingolipid transfer activity
relationship: has_part GO:0097001 ! ceramide binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12329" xsd:anyURI
@@ -471582,7 +476658,7 @@
xref: Reactome:R-HSA-1483087 "PI is exchanged with PC by PITPNB"
xref: Reactome:R-HSA-1483211 "PC:PITPNB is transported from the Golgi membrane to the ER membrane"
xref: Reactome:R-HSA-1483219 "PC is exchanged with PI by PITPNB"
-is_a: GO:0008525 ! phosphatidylcholine transporter activity
+xref: Reactome:R-HSA-9956308 "STARD7 transports PC from ER membrane to mitochondrial outer membrane"
is_a: GO:0120014 ! phospholipid transfer activity
relationship: has_part GO:0031210 ! phosphatidylcholine binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/12329" xsd:anyURI
@@ -471923,9 +476999,10 @@
[Term]
id: GO:0120048
-name: U6 snRNA (adenine-(43)-N(6))-methyltransferase activity
+name: U6 snRNA (adenine(43)-N6)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: adenosine in U6 snRNA + S-adenosyl-L-methionine = H+ + N(6)-methyladenosine in U6 snRNA + S-adenosyl-L-homocysteine." [PMID:28525753, PMID:32266935, RHEA:52808]
+synonym: "U6 snRNA m(6)A methyltransferase activity" EXACT []
xref: EC:2.1.1.346
xref: MetaCyc:RXN-18779
xref: RHEA:52808
@@ -471953,6 +477030,7 @@
name: ribitol beta-1,4-xylosyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-D-xylose + D-ribitol 5-phosphate-R = UDP + beta1,4-xylosyl-D-ribitol 5-phosphate-R." [PMID:27733679]
+xref: Reactome:R-HSA-9940805 "RXYLT1 transfers initial Xyl to matriglycan chain"
is_a: GO:0035252 ! UDP-xylosyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13641" xsd:anyURI
created_by: krc
@@ -472440,9 +477518,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: 3-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O. (2E)-butenoyl-CoA is also known as crotonoyl-CoA." [PMID:28803779, RHEA:45584]
synonym: "crotonyl-CoA hydratase activity" EXACT []
+xref: RHEA:17849
+xref: RHEA:26558
xref: RHEA:45584
is_a: GO:0018812 ! 3-hydroxyacyl-CoA dehydratase activity
property_value: skos:exactMatch RHEA:45584
+property_value: skos:narrowMatch RHEA:17849
+property_value: skos:narrowMatch RHEA:26558
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14109" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29789" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -473214,10 +478296,12 @@
name: rRNA pseudouridine synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: a uridine in rRNA = a pseudouridine in rRNA. Conversion of uridine in an rRNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5." [PMID:28432181, RHEA:54568]
+xref: RHEA:47036
xref: RHEA:54568
is_a: GO:0009982 ! pseudouridine synthase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
property_value: skos:exactMatch RHEA:54568
+property_value: skos:narrowMatch RHEA:47036
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15632" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26618" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -474020,13 +479104,13 @@
id: GO:0120216
name: matrilin complex
namespace: cellular_component
-def: "A cartilage extracellular matrix complex that mediates interactions between major components of the extracellular matrix such as collagens and proteoglycans and contributes to their fibrillar network. Exists as an obligate homotrimer." [PMID:10367731, PMID:15075323, PMID:15094109, PMID:9699631]
+def: "A cartilage extracellular matrix complex that mediates interactions between major components of the extracellular matrix such as collagens and proteoglycans and contributes to their fibrillar network. Exists as an obligate homotrimer." [PMID:10367731, PMID:15075323, PMID:29310791, PMID:9699631]
synonym: "matrilin family complex" RELATED [GOC:bhm]
synonym: "matrilin-1 complex" NARROW [GOC:bhm]
synonym: "matrilin-2 complex" NARROW [GOC:bhm]
synonym: "matrilin-3 complex" NARROW [GOC:bhm]
synonym: "matrilin-4 complex" NARROW [GOC:bhm]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140149 ! non-collagenous component of interstitial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17598" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31067" xsd:anyURI
@@ -474226,10 +479310,12 @@
synonym: "prenylated FMNH2 biosynthetic process" EXACT []
synonym: "prenylated FMNH2 formation" EXACT []
synonym: "prenylated FMNH2 synthesis" EXACT []
+xref: MetaCyc:PWY0-1597
is_a: GO:0009156 ! ribonucleoside monophosphate biosynthetic process
is_a: GO:0009260 ! ribonucleotide biosynthetic process
is_a: GO:0042727 ! flavin-containing compound biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19244" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: krc
creation_date: 2020-06-30T19:09:11Z
@@ -474253,9 +479339,9 @@
synonym: "auditory hair cell glycocalyx" BROAD []
synonym: "stereocilium glycocalyx" EXACT []
is_a: GO:0030112 ! glycocalyx
-relationship: part_of GO:0032420 ! stereocilium
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19780" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19782" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: krc
creation_date: 2020-07-15T00:56:35Z
@@ -474320,6 +479406,7 @@
def: "The carbohydrate rich layer at the outermost periphery of a sperm cell." [GOC:krc]
is_a: GO:0030112 ! glycocalyx
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19782" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: krc
creation_date: 2020-07-27T21:42:50Z
@@ -474341,6 +479428,7 @@
def: "The carbohydrate rich layer at the outermost periphery of a platelet." [GOC:krc, PMID:24967889]
is_a: GO:0030112 ! glycocalyx
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19782" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: krc
creation_date: 2020-07-27T22:44:42Z
@@ -474366,10 +479454,11 @@
id: GO:0120242
name: 2-iminobutanoate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-iminobutanoate + H2O = 2-oxobutanoate + NH4(+)." [RHEA:39975]
+def: "Catalysis of the reaction: 2-iminobutanoate + H2O = 2-oxobutanoate + NH4+." [RHEA:39975]
synonym: "2-iminobutanoate/2-iminopropanoate deaminase" BROAD [EC:3.5.99.10]
xref: KEGG_REACTION:R11098
xref: MetaCyc:RXN-15123
+xref: Reactome:R-HSA-9014641 "HRSP12 deaminates 2-iminobutanoate to 2OBUTA"
xref: RHEA:39975
is_a: GO:0120241 ! 2-iminobutanoate/2-iminopropanoate deaminase activity
property_value: skos:exactMatch RHEA:39975
@@ -474382,7 +479471,7 @@
id: GO:0120243
name: 2-iminopropanoate deaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-iminopropanoate + H2O = NH4(+) + pyruvate." [RHEA:40671]
+def: "Catalysis of the reaction: 2-iminopropanoate + H2O = NH4+ + pyruvate." [RHEA:40671]
synonym: "2-iminobutanoate/2-iminopropanoate deaminase" BROAD [EC:3.5.99.10]
xref: KEGG_REACTION:R11099
xref: MetaCyc:RXN-15127
@@ -474491,9 +479580,11 @@
def: "Catalysis of the reaction: an omega-methyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, RHEA:39023]
synonym: "omega-hydroxylase activity" BROAD [EC:1.14.15.3]
xref: RHEA:39023
+xref: RHEA:40079
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: skos:broadMatch EC:1.14.15.3
property_value: skos:exactMatch RHEA:39023
+property_value: skos:narrowMatch RHEA:40079
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19899" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24664" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27756" xsd:anyURI
@@ -475114,7 +480205,7 @@
id: GO:0120294
name: peptide serotonyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutaminyl-[protein] + serotonin = 5-serotonyl-L-glutamyl-[protein] + NH4(+)." [GOC:sp, PMID:14697203]
+def: "Catalysis of the reaction: L-glutaminyl-[protein] + serotonin = 5-serotonyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:14697203]
xref: RHEA:66552
is_a: GO:0016410 ! N-acyltransferase activity
property_value: skos:exactMatch RHEA:66552
@@ -475127,7 +480218,7 @@
id: GO:0120295
name: histone serotonyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-glutaminyl-[histone] + serotonin = 5-serotonyl-L-glutamyl-[histone] + NH4(+)." [GOC:sp, PMID:30867594]
+def: "Catalysis of the reaction: L-glutaminyl-[histone] + serotonin = 5-serotonyl-L-glutamyl-[histone] + NH4+." [GOC:sp, PMID:30867594]
is_a: GO:0120294 ! peptide serotonyltransferase activity
is_a: GO:0140993 ! histone modifying activity
property_value: skos:broadMatch RHEA:66552
@@ -475140,7 +480231,7 @@
id: GO:0120296
name: peptide dopaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dopamine + L-glutaminyl-[protein] = 5-dopaminyl-L-glutamyl-[protein] + NH4(+)." [GOC:sp, PMID:22858378, PMID:32273471]
+def: "Catalysis of the reaction: dopamine + L-glutaminyl-[protein] = 5-dopaminyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:22858378, PMID:32273471]
xref: RHEA:66556
is_a: GO:0016410 ! N-acyltransferase activity
property_value: skos:exactMatch RHEA:66556
@@ -475153,7 +480244,7 @@
id: GO:0120297
name: histone dopaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dopamine + L-glutaminyl-[histone] = 5-dopaminyl-L-glutamyl-[histone] + NH4(+)." [GOC:sp, PMID:32273471]
+def: "Catalysis of the reaction: dopamine + L-glutaminyl-[histone] = 5-dopaminyl-L-glutamyl-[histone] + NH4+." [GOC:sp, PMID:32273471]
is_a: GO:0120296 ! peptide dopaminyltransferase activity
is_a: GO:0140993 ! histone modifying activity
property_value: skos:broadMatch RHEA:66556
@@ -475166,7 +480257,7 @@
id: GO:0120298
name: peptide noradrenalinyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-noradrenaline + L-glutaminyl-[protein] = 5-(R)-noradrenalinyl-L-glutamyl-[protein] + NH4(+)." [GOC:sp, PMID:22858378]
+def: "Catalysis of the reaction: (R)-noradrenaline + L-glutaminyl-[protein] = 5-(R)-noradrenalinyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:22858378]
xref: RHEA:66560
is_a: GO:0016410 ! N-acyltransferase activity
property_value: skos:exactMatch RHEA:66560
@@ -475455,9 +480546,13 @@
def: "Catalysis of the reaction: an (omega-1)-ethyl long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an (omega-1)-hydroxy-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase. A long-chain fatty acid has an aliphatic tail containing 13 to 22 carbons." [GOC:nhn, PMID:18577768, PMID:22772592, PMID:24242247, RHEA:60936]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
synonym: "cytochrome P450 fatty acid omega-1 hydroxylase activity" RELATED []
+xref: RHEA:60928
+xref: RHEA:60932
xref: RHEA:60936
is_a: GO:0120502 ! fatty acid omega-1 hydroxylase activity
property_value: skos:exactMatch RHEA:60936
+property_value: skos:narrowMatch RHEA:60928
+property_value: skos:narrowMatch RHEA:60932
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21648" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: krc
@@ -475769,10 +480864,14 @@
namespace: molecular_function
def: "Catalysis of the reaction: L-methionyl-[F-actin] + NADPH + O2 + H+ = L-methionyl-(R)-S-oxide-[F-actin] + NADP+ + H2O." [RHEA:51308]
xref: EC:1.14.13.225
+xref: RHEA:24722
+xref: RHEA:49676
xref: RHEA:51308
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.13.225
property_value: skos:exactMatch RHEA:51308
+property_value: skos:narrowMatch RHEA:24722
+property_value: skos:narrowMatch RHEA:49676
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27530" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -475783,9 +480882,13 @@
name: fatty acid omega-1 hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: an (omega-1)-ethyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an (omega-1)-hydroxy fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [RHEA:44548]
+xref: RHEA:39751
+xref: RHEA:39759
xref: RHEA:44548
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: skos:exactMatch RHEA:44548
+property_value: skos:narrowMatch RHEA:39751
+property_value: skos:narrowMatch RHEA:39759
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24661" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -475959,10 +481062,12 @@
def: "Catalysis of the reaction: a fatty acid + ATP + CoA = a fatty acyl-CoA + AMP + diphosphate." [RHEA:38883]
xref: MetaCyc:BUTYRATE--COA-LIGASE-RXN
xref: RHEA:38883
+xref: RHEA:44004
is_a: GO:0015645 ! fatty acid ligase activity
is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch MetaCyc:BUTYRATE--COA-LIGASE-RXN
property_value: skos:exactMatch RHEA:38883
+property_value: skos:narrowMatch RHEA:44004
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
created_by: sjm
creation_date: 2024-06-25T12:17:07Z
@@ -475974,10 +481079,16 @@
def: "Catalysis of the reaction: a diacylglycerol + H2O = a fatty acid + a monoacylglycerol + H+." [RHEA:32731]
xref: MetaCyc:RXN-19279
xref: RHEA:32731
+xref: RHEA:44444
+xref: RHEA:47868
+xref: RHEA:78019
is_a: GO:0016298 ! lipase activity
property_value: skos:broadMatch EC:3.1.1.79
property_value: skos:exactMatch MetaCyc:RXN-19279
property_value: skos:exactMatch RHEA:32731
+property_value: skos:narrowMatch RHEA:44444
+property_value: skos:narrowMatch RHEA:47868
+property_value: skos:narrowMatch RHEA:78019
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
created_by: sjm
creation_date: 2024-06-28T12:36:24Z
@@ -476003,6 +481114,21 @@
xref: EC:2.3.1.256
xref: EC:2.3.1.258
xref: EC:2.3.1.259
+xref: RHEA:50480
+xref: RHEA:50484
+xref: RHEA:50488
+xref: RHEA:50492
+xref: RHEA:50520
+xref: RHEA:50524
+xref: RHEA:50528
+xref: RHEA:50532
+xref: RHEA:50560
+xref: RHEA:50564
+xref: RHEA:50568
+xref: RHEA:50572
+xref: RHEA:50576
+xref: RHEA:50580
+xref: RHEA:50604
xref: RHEA:75239
is_a: GO:0004596 ! protein-N-terminal amino-acid acetyltransferase activity
property_value: skos:exactMatch RHEA:75239
@@ -476010,6 +481136,21 @@
property_value: skos:narrowMatch EC:2.3.1.256
property_value: skos:narrowMatch EC:2.3.1.258
property_value: skos:narrowMatch EC:2.3.1.259
+property_value: skos:narrowMatch RHEA:50480
+property_value: skos:narrowMatch RHEA:50484
+property_value: skos:narrowMatch RHEA:50488
+property_value: skos:narrowMatch RHEA:50492
+property_value: skos:narrowMatch RHEA:50520
+property_value: skos:narrowMatch RHEA:50524
+property_value: skos:narrowMatch RHEA:50528
+property_value: skos:narrowMatch RHEA:50532
+property_value: skos:narrowMatch RHEA:50560
+property_value: skos:narrowMatch RHEA:50564
+property_value: skos:narrowMatch RHEA:50568
+property_value: skos:narrowMatch RHEA:50572
+property_value: skos:narrowMatch RHEA:50576
+property_value: skos:narrowMatch RHEA:50580
+property_value: skos:narrowMatch RHEA:50604
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27532" xsd:anyURI
created_by: sjm
creation_date: 2024-07-10T12:16:39Z
@@ -476038,9 +481179,13 @@
name: free fatty acid 2-hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: a 1,2-saturated fatty acid + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = a (R)-2-hydroxy fatty acid + 2 Fe(III)-[cytochrome b5] + H2O. Note that the substrate is a free fatty acid, not a fatty acyl chain within a sphingolipid." [GOC:sjm, RHEA:38855]
+xref: RHEA:38551
+xref: RHEA:38559
xref: RHEA:38855
is_a: GO:0080132 ! fatty acid 2-hydroxylase activity
property_value: skos:exactMatch RHEA:38855
+property_value: skos:narrowMatch RHEA:38551
+property_value: skos:narrowMatch RHEA:38559
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27541" xsd:anyURI
created_by: sjm
creation_date: 2024-07-12T08:40:48Z
@@ -476052,10 +481197,12 @@
def: "Catalysis of the reaction: an N-(1,2 saturated acyl)-(4R)-hydroxysphinganine + 2 Fe(II)-[cytochrome b5] + 2 H+ + O2 = an N-(2R-hydroxyacyl)-4R-hydroxysphinganine + 2 Fe(III)-[cytochrome b5] + H2O." [RHEA:46520]
xref: MetaCyc:RXN3O-4042
xref: RHEA:46520
+xref: RHEA:64532
is_a: GO:0080132 ! fatty acid 2-hydroxylase activity
property_value: skos:broadMatch EC:1.14.18.6
property_value: skos:exactMatch MetaCyc:RXN3O-4042
property_value: skos:exactMatch RHEA:46520
+property_value: skos:narrowMatch RHEA:64532
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27541" xsd:anyURI
created_by: sjm
creation_date: 2024-07-12T08:47:01Z
@@ -476066,9 +481213,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: a short-chain 2,3-saturated fatty acyl-CoA + O2 = a short-chain (2E)-enoyl-CoA + H2O2." [RHEA:78859]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+xref: RHEA:41964
+xref: RHEA:66200
xref: RHEA:78859
is_a: GO:0003997 ! acyl-CoA oxidase activity
property_value: skos:exactMatch RHEA:78859
+property_value: skos:narrowMatch RHEA:41964
+property_value: skos:narrowMatch RHEA:66200
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28733" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -476080,9 +481231,21 @@
namespace: molecular_function
def: "Catalysis of the reaction: a medium-chain 2,3-saturated fatty acyl-CoA + O2 = a medium-chain (2E)-enoyl-CoA + H2O2." [RHEA:78855]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+xref: RHEA:38987
+xref: RHEA:40171
+xref: RHEA:40175
+xref: RHEA:40179
+xref: RHEA:40311
+xref: RHEA:66204
xref: RHEA:78855
is_a: GO:0003997 ! acyl-CoA oxidase activity
property_value: skos:exactMatch RHEA:78855
+property_value: skos:narrowMatch RHEA:38987
+property_value: skos:narrowMatch RHEA:40171
+property_value: skos:narrowMatch RHEA:40175
+property_value: skos:narrowMatch RHEA:40179
+property_value: skos:narrowMatch RHEA:40311
+property_value: skos:narrowMatch RHEA:66204
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28733" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -476094,9 +481257,23 @@
namespace: molecular_function
def: "Catalysis of the reaction: a long-chain 2,3-saturated fatty acyl-CoA + O2 = a long-chain (2E)-enoyl-CoA + H2O2." [RHEA:78851]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+xref: RHEA:38971
+xref: RHEA:40167
+xref: RHEA:40183
+xref: RHEA:69643
+xref: RHEA:78571
+xref: RHEA:78587
xref: RHEA:78851
+xref: RHEA:83059
is_a: GO:0003997 ! acyl-CoA oxidase activity
property_value: skos:exactMatch RHEA:78851
+property_value: skos:narrowMatch RHEA:38971
+property_value: skos:narrowMatch RHEA:40167
+property_value: skos:narrowMatch RHEA:40183
+property_value: skos:narrowMatch RHEA:69643
+property_value: skos:narrowMatch RHEA:78571
+property_value: skos:narrowMatch RHEA:78587
+property_value: skos:narrowMatch RHEA:83059
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28733" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -476107,7 +481284,6 @@
name: choline trimethylamine lyase activity
namespace: molecular_function
def: "Catalysis of the reaction: choline = acetaldehyde + trimethylamine." [RHEA:35095]
-comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
xref: EC:4.3.99.4
xref: KEGG_REACTION:R10285
xref: MetaCyc:RXN-13946
@@ -476117,8 +481293,8 @@
property_value: skos:exactMatch KEGG_REACTION:R10285
property_value: skos:exactMatch MetaCyc:RXN-13946
property_value: skos:exactMatch RHEA:35095
-property_value: skos:relatedMatch MetaCyc:PWY-7167
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28808" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
created_by: sjm
creation_date: 2024-08-30T13:13:55Z
@@ -476130,12 +481306,22 @@
xref: EC:1.14.14.42
xref: KEGG_REACTION:R11646
xref: MetaCyc:RXN-18175
+xref: RHEA:32719
+xref: RHEA:32723
+xref: RHEA:33243
+xref: RHEA:33291
+xref: RHEA:33295
xref: RHEA:51972
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: skos:exactMatch EC:1.14.14.42
property_value: skos:exactMatch KEGG_REACTION:R11646
property_value: skos:exactMatch MetaCyc:RXN-18175
property_value: skos:exactMatch RHEA:51972
+property_value: skos:narrowMatch RHEA:32719
+property_value: skos:narrowMatch RHEA:32723
+property_value: skos:narrowMatch RHEA:33243
+property_value: skos:narrowMatch RHEA:33291
+property_value: skos:narrowMatch RHEA:33295
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
created_by: sjm
creation_date: 2024-09-05T07:47:05Z
@@ -476228,6 +481414,7 @@
synonym: "Glycosaminoglycan biosynthesis, linkage tetrasaccharide" EXACT []
synonym: "glycosaminoglycan-protein linkage region biosynthesis" EXACT [MetaCyc:PWY-6557]
xref: MetaCyc:PWY-6557
+xref: Reactome:R-HSA-1971475 "Glycosaminoglycan-protein linkage region biosynthesis"
is_a: GO:0180064 ! protein O-linked glycosylation via xylose
relationship: part_of GO:0015012 ! heparan sulfate proteoglycan biosynthetic process
relationship: part_of GO:0030210 ! heparin proteoglycan biosynthetic process
@@ -476302,10 +481489,20 @@
def: "Catalysis of the reaction: 2-methoxy-6-(all-trans-polyprenyl)phenol + 2 reduced [2Fe-2S]-[ferredoxin] + O2 + 2 H+ = 2-methoxy-6-(all-trans-polyprenyl)benzene-1,4-diol + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O." [PMID:38425362, RHEA:81183]
xref: EC:1.14.15.46
xref: RHEA:81183
+xref: RHEA:81279
+xref: RHEA:81283
+xref: RHEA:81287
+xref: RHEA:81291
+xref: RHEA:81295
is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
relationship: part_of GO:0006744 ! ubiquinone biosynthetic process
property_value: skos:exactMatch EC:1.14.15.46
property_value: skos:exactMatch RHEA:81183
+property_value: skos:narrowMatch RHEA:81279
+property_value: skos:narrowMatch RHEA:81283
+property_value: skos:narrowMatch RHEA:81287
+property_value: skos:narrowMatch RHEA:81291
+property_value: skos:narrowMatch RHEA:81295
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29459" xsd:anyURI
created_by: sjm
creation_date: 2024-12-18T09:30:52Z
@@ -476316,11 +481513,22 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 4-hydroxy-3-methoxy-5-(all-trans-polyprenyl)benzoate + H+ = a 2-methoxy-6-(all-trans-polyprenyl)phenol + CO2." [PMID:38295803, PMID:38425362, RHEA:81179]
xref: EC:4.1.1.130
+xref: Reactome:R-HSA-2162195 "COQ4 decarboxylates MHDB"
+xref: RHEA:44768
xref: RHEA:81179
+xref: RHEA:81263
+xref: RHEA:81267
+xref: RHEA:81271
+xref: RHEA:81275
is_a: GO:0016831 ! carboxy-lyase activity
relationship: part_of GO:0006744 ! ubiquinone biosynthetic process
property_value: skos:exactMatch EC:4.1.1.130
property_value: skos:exactMatch RHEA:81179
+property_value: skos:narrowMatch RHEA:44768
+property_value: skos:narrowMatch RHEA:81263
+property_value: skos:narrowMatch RHEA:81267
+property_value: skos:narrowMatch RHEA:81271
+property_value: skos:narrowMatch RHEA:81275
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29459" xsd:anyURI
created_by: sjm
creation_date: 2024-12-18T09:36:09Z
@@ -476423,6 +481631,7 @@
def: "Catalysis of the reaction: Fe(II)-heme o + 2 acceptor + H2O = Fe(II)-heme a + 2 acceptor-H2. The conversion of heme o to heme a occcurs by two successive hydroxylations of the methyl group at C8 using water as the oxygen source. The first hydroxylation forms heme i, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of heme A." [PMID:30397130, RHEA:63388]
xref: EC:1.17.99.9
xref: MetaCyc:RXN-18399
+xref: Reactome:R-HSA-2995334 "COX15 transforms heme O to heme A"
xref: RHEA:63388
is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
property_value: skos:exactMatch EC:1.17.99.9
@@ -476468,11 +481677,12 @@
synonym: "cap2-MTase activity" EXACT [EC:2.1.1.296]
synonym: "mRNA (nucleoside-2'-O-)-methyltransferase activity" RELATED [EC:2.1.1.296]
xref: EC:2.1.1.296
-xref: MetaCyc:RXN-14928 {xref="skos:narrowMatch"}
+xref: MetaCyc:RXN-14928
xref: RHEA:67024
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.296
+property_value: skos:narrowMatch MetaCyc:RXN-14928
property_value: skos:narrowMatch RHEA:67024
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27387" xsd:anyURI
created_by: sjm
@@ -476527,15 +481737,17 @@
[Term]
id: GO:0120554
-name: 2-aminobutanoate transaminase activity
+name: (2S)-2-aminobutanoate:2-oxoglutarate transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: (2S)-2-aminobutanoate + 2-oxoglutarate = 2-oxobutanoate + L-glutamate." [PMID:27827456, RHEA:70223]
+synonym: "2-aminobutanoate transaminase activity" EXACT []
xref: MetaCyc:RXN-20408
xref: RHEA:70223
is_a: GO:0008483 ! transaminase activity
property_value: skos:exactMatch MetaCyc:RXN-20408
property_value: skos:exactMatch RHEA:70223
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30260" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
created_by: sjm
creation_date: 2025-05-15T14:38:07Z
@@ -476609,9 +481821,11 @@
synonym: "phosphatidylserine-specific phospholipase A1" RELATED [EC:3.1.1.111]
xref: MetaCyc:RXN-20544
xref: RHEA:32979
+xref: RHEA:51184
is_a: GO:0120558 ! lysophospholipase A1 activity
property_value: skos:broadMatch EC:3.1.1.111
property_value: skos:exactMatch RHEA:32979
+property_value: skos:narrowMatch RHEA:51184
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30258" xsd:anyURI
created_by: sjm
creation_date: 2025-05-23T13:15:28Z
@@ -476623,8 +481837,10 @@
def: "Catalysis of the reaction: a 1-acyl-sn-glycero-3-phospho-(1D-myo-inositol) + H2O = sn-glycero-3-phospho-1D-myo-inositol + a fatty acid + H+." [RHEA:32987]
synonym: "phosphatidylinositol lysophospholipase A1-type activity" EXACT []
xref: RHEA:32987
+xref: RHEA:44588
is_a: GO:0120558 ! lysophospholipase A1 activity
property_value: skos:exactMatch RHEA:32987
+property_value: skos:narrowMatch RHEA:44588
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30258" xsd:anyURI
created_by: sjm
creation_date: 2025-05-23T13:15:46Z
@@ -476774,6 +481990,74 @@
creation_date: 2026-01-20T09:45:52Z
[Term]
+id: GO:0120573
+name: FAHFA hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the hydrolysis of the ester bond in a fatty acid ester of a hydroxy fatty acid (FAHFA), yielding a free fatty acid and a hydroxy fatty acid. FAHFAs are a class of endogenous bioactive signaling lipids in which a fatty acid is esterified to a hydroxyl group on a second fatty acid backbone." [PMID:27018888, PMID:32152231]
+synonym: "fatty-acid ester of hydroxy-fatty-acid hydrolase activity" EXACT []
+xref: RHEA:52048
+xref: RHEA:52052
+xref: RHEA:52056
+xref: RHEA:52060
+xref: RHEA:52064
+xref: RHEA:52068
+xref: RHEA:52072
+xref: RHEA:52076
+xref: RHEA:52080
+xref: RHEA:52084
+xref: RHEA:52092
+xref: RHEA:52096
+is_a: GO:0052689 ! carboxylic ester hydrolase activity
+property_value: skos:narrowMatch RHEA:52048
+property_value: skos:narrowMatch RHEA:52052
+property_value: skos:narrowMatch RHEA:52056
+property_value: skos:narrowMatch RHEA:52060
+property_value: skos:narrowMatch RHEA:52064
+property_value: skos:narrowMatch RHEA:52068
+property_value: skos:narrowMatch RHEA:52072
+property_value: skos:narrowMatch RHEA:52076
+property_value: skos:narrowMatch RHEA:52080
+property_value: skos:narrowMatch RHEA:52084
+property_value: skos:narrowMatch RHEA:52092
+property_value: skos:narrowMatch RHEA:52096
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31722" xsd:anyURI
+created_by: sjm
+creation_date: 2026-03-13T16:05:52Z
+
+[Term]
+id: GO:0120574
+name: GPI anchor remodelling
+namespace: biological_process
+def: "Any process leading to the modification of the GPI-anchor after its transfer and attachment to a protein." [PMID:32156170]
+xref: MetaCyc:PWY-8602
+xref: MetaCyc:PWY-8603
+is_a: GO:0051604 ! protein maturation
+relationship: part_of GO:0180046 ! GPI anchored protein biosynthesis
+property_value: skos:narrowMatch MetaCyc:PWY-8602
+property_value: skos:narrowMatch MetaCyc:PWY-8603
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30568" xsd:anyURI
+created_by: sjm
+creation_date: 2026-03-23T16:23:47Z
+
+[Term]
+id: GO:0120575
+name: L-dopa catabolic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of L-dopa." [MetaCyc:PWY-6334, MetaCyc:PWY-8110]
+xref: MetaCyc:PWY-6334
+xref: MetaCyc:PWY-8110
+is_a: GO:0009074 ! aromatic amino acid family catabolic process
+is_a: GO:0042219 ! modified amino acid catabolic process
+is_a: GO:0170035 ! L-amino acid catabolic process
+is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+is_a: GO:1903184 ! L-dopa metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-6334
+property_value: skos:narrowMatch MetaCyc:PWY-8110
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+created_by: sjm
+creation_date: 2026-03-24T16:54:04Z
+
+[Term]
id: GO:0140001
name: morula formation
namespace: biological_process
@@ -477576,7 +482860,7 @@
id: GO:0140070
name: hydrogen peroxide channel activity
namespace: molecular_function
-def: "Enables the energy-independent facilitated diffusion of hydrogen peroxide through a transmembrane aqueous pore or channel." [PMID:23541115, PMID:27256569]
+def: "Enables the energy-independent facilitated diffusion of H2O2 through a transmembrane aqueous pore or channel." [PMID:23541115, PMID:27256569]
synonym: "hydrogen peroxide transmembrane transporter activity" RELATED []
is_a: GO:0015267 ! channel activity
relationship: part_of GO:0080170 ! hydrogen peroxide transmembrane transport
@@ -477757,11 +483041,12 @@
id: GO:0140085
name: L-amino-acid N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + a L-amino acid = CoA + an N-acetyl-L-amino-acid. In some cases acetyl phosphate can be used as a donor." [GOC:pg, RHEA:83863]
+def: "Catalysis of the reaction: acetyl-CoA + a L-amino acid = CoA + an N-acetyl-L-amino-acid. In some cases other acetyl containing molecules can be used as donor." [GOC:pg, RHEA:83863]
xref: RHEA:83863
-is_a: GO:0008080 ! N-acetyltransferase activity
-property_value: skos:exactMatch RHEA:83863
+is_a: GO:0140379 ! amino acid acyltransferase activity
+property_value: skos:narrowMatch RHEA:83863
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29604" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
created_by: pg
creation_date: 2025-01-24T10:40:36Z
@@ -477985,10 +483270,23 @@
subset: goslim_prokaryote
subset: goslim_prokaryote_ribbon
xref: Reactome:R-HSA-1449687 "Corticosteroids bind to CBG in blood"
+xref: Reactome:R-HSA-196126 "STAR mediates CHOL translocation from cytosol to mitochondrial intermembrane space"
+xref: Reactome:R-HSA-209738 "VD3 binds GC"
+xref: Reactome:R-HSA-209944 "25(OH)D binds GC"
+xref: Reactome:R-HSA-2395764 "atREs binds to nascent CM"
+xref: Reactome:R-HSA-2399913 "atRAL binds to RBP2"
+xref: Reactome:R-HSA-2404142 "atROL binds RBP1"
+xref: Reactome:R-HSA-2855259 "atROL binds RBP1 (parenchymal cell)"
xref: Reactome:R-HSA-3149494 "MMACHC:cob(II)alamin binds MMADHC"
xref: Reactome:R-HSA-3149563 "MMADHC targets transport of cytosolic cob(II)alamin to mitochondria"
xref: Reactome:R-HSA-3159259 "MMAA:MUT binds AdoCbl"
xref: Reactome:R-HSA-3204318 "cob(II)alamin is transferred from MMACHC:MMADHC:cob(II)alamin to MTRR:MTR"
+xref: Reactome:R-HSA-5246478 "APOM binds retinoids"
+xref: Reactome:R-HSA-8870499 "PLEKHA3,8 bind PI4P, ARF1"
+xref: Reactome:R-HSA-8932980 "SERINC3,5,(1,2,4) transport L-Ser from cytosol to plasma membrane"
+xref: Reactome:R-HSA-8963851 "VD3 dissociates from GC"
+xref: Reactome:R-HSA-9661432 "BIL binds ALB"
+xref: Reactome:R-HSA-9663511 "BIL binds GSTA1, FABP1"
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
@@ -478490,6 +483788,7 @@
name: copper ion export from vacuole
namespace: biological_process
def: "The directed movement of copper ions out of the vacuole across the vacuolar membrane." [GOC:vw, PMID:12244050]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0035434 ! copper ion transmembrane transport
created_by: pg
@@ -478500,6 +483799,7 @@
name: calcium ion import into vacuole
namespace: biological_process
def: "The directed movement of calcium cations into the vacuole across the vacuolar membrane." [GOC:vw, PMID:8628289]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0070588 ! calcium ion transmembrane transport
created_by: pg
@@ -478510,6 +483810,7 @@
name: zinc ion export from vacuole
namespace: biological_process
def: "The directed movement of zinc ions from inside the vacuole across the vacuolar membrane and into the cytosol." [GOC:vw, PMC:PMC203372]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0071577 ! zinc ion transmembrane transport
created_by: pg
@@ -478599,12 +483900,14 @@
[Term]
id: GO:0140155
-name: hexagonal collagen network of basement membrane
+name: obsolete hexagonal collagen network of basement membrane
namespace: cellular_component
-def: "Supramolecular structure formed by trimers of collagen VIII and found in the basement membrane." [PMID:21421911, PMID:2376131, PMID:3047147, PMID:31387942]
-is_a: GO:0098645 ! complex of network-forming collagens
-relationship: part_of GO:0140143 ! collagenous component of basement membrane
+def: "OBSOLETE. Supramolecular structure formed by trimers of collagen VIII and found in the basement membrane." [PMID:21421911, PMID:2376131, PMID:3047147, PMID:31387942]
+comment: This term was obsoleted because it is an uncessary grouping term. There is not sufficient evidence to show that collagen VIII is only located in the basement membrane in all organs and species.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29402" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31492" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0098646
created_by: pg
creation_date: 2025-03-26T06:55:36Z
@@ -478614,6 +483917,7 @@
namespace: cellular_component
def: "Collagen that contains multiple triple-helix domains with interruptions." [PMID:21421911, PMID:27746220, PMID:31479735, PMID:33543021]
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140143 ! collagenous component of basement membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29469" xsd:anyURI
created_by: pg
@@ -478687,11 +483991,12 @@
[Term]
id: GO:0140164
-name: Golgi transport complex binding
+name: COG complex binding
namespace: molecular_function
def: "Binding to a Golgi transport complex, a multisubunit tethering complex of the CATCHR family." [GOC:ha, PMID:28100664]
-synonym: "COG complex binding" EXACT []
+synonym: "Golgi transport complex binding" EXACT []
is_a: GO:0044877 ! protein-containing complex binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31397" xsd:anyURI
created_by: pg
creation_date: 2018-02-08T11:49:38Z
@@ -478822,9 +484127,25 @@
name: (2R)-2-hydroxycarboxylate dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the activity: a (2R)-2-hydroxycarboxylate + FAD + H+ = a 2-oxocarboxylate + FADH2." [PMID:37863926, RHEA:82511]
+xref: RHEA:82483
+xref: RHEA:82487
+xref: RHEA:82491
+xref: RHEA:82495
+xref: RHEA:82499
+xref: RHEA:82503
+xref: RHEA:82507
xref: RHEA:82511
+xref: RHEA:84927
is_a: GO:0033719 ! (2R)-oxo-acid reductase activity
property_value: skos:exactMatch RHEA:82511
+property_value: skos:narrowMatch RHEA:82483
+property_value: skos:narrowMatch RHEA:82487
+property_value: skos:narrowMatch RHEA:82491
+property_value: skos:narrowMatch RHEA:82495
+property_value: skos:narrowMatch RHEA:82499
+property_value: skos:narrowMatch RHEA:82503
+property_value: skos:narrowMatch RHEA:82507
+property_value: skos:narrowMatch RHEA:84927
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30138" xsd:anyURI
created_by: pg
creation_date: 2025-05-20T06:45:42Z
@@ -478837,10 +484158,18 @@
xref: EC:1.1.1.345
xref: RHEA:10052
xref: RHEA:35643
+xref: RHEA:57408
+xref: RHEA:70327
+xref: RHEA:86067
+xref: RHEA:86071
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.345
property_value: skos:exactMatch RHEA:35643
property_value: skos:narrowMatch RHEA:10052
+property_value: skos:narrowMatch RHEA:57408
+property_value: skos:narrowMatch RHEA:70327
+property_value: skos:narrowMatch RHEA:86067
+property_value: skos:narrowMatch RHEA:86071
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30138" xsd:anyURI
created_by: pg
creation_date: 2025-05-20T08:52:20Z
@@ -478850,10 +484179,8 @@
name: positive regulation of pyruvate decarboxylation to acetyl-CoA
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions." [PMID:15855260]
-is_a: GO:0009891 ! positive regulation of biosynthetic process
is_a: GO:0010510 ! regulation of pyruvate decarboxylation to acetyl-CoA
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
+is_a: GO:0140390 ! positive regulation of acetyl-CoA biosynthesis
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0006086 ! pyruvate decarboxylation to acetyl-CoA
relationship: positively_regulates GO:0006086 ! pyruvate decarboxylation to acetyl-CoA
@@ -478865,7 +484192,7 @@
id: GO:0140177
name: membrane-membrane adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:curator]
+def: "The binding activity of a molecule that brings together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:curators]
is_a: GO:0060090 ! molecular adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24964" xsd:anyURI
created_by: pg
@@ -478875,10 +484202,11 @@
id: GO:0140178
name: lumenal side of cis-Golgi network membrane
namespace: cellular_component
-def: "The membrane leaflet of the cis-Golgi network directly contacts the Golgi lumen and may be involved in glycosylation, cargo sorting, or interactions with resident Golgi proteins." [PMID:1747103, PMID:29802621, PMID:34080016]
+def: "The leaflet of the cis-Golgi network membrane directly contacts the Golgi lumen, including any protein embedded in, attached to, or peripherally associated with it. This is the site where glycosylation, cargo sorting, or interactions with resident Golgi proteins occur." [PMID:1747103, PMID:29802621, PMID:34080016]
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0033106 ! cis-Golgi network membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30389" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: pg
creation_date: 2025-06-05T08:47:14Z
@@ -478886,10 +484214,11 @@
id: GO:0140179
name: cytoplasmic side of cis-Golgi network membrane
namespace: cellular_component
-def: "The leaflet of the membrane bilayer of the cis-Golgi network faces the cytoplasm and is where interactions with cytosolic proteins occur, including those for vesicle tethering, fusion, and Golgi-associated trafficking activities." [PMID:1747103, PMID:23913272, PMID:34080016, PMID:34597626]
+def: "The leaflet of the cis-Golgi network membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it. This is the site of interactions with cytosolic proteins, including those for vesicle tethering, fusion, and Golgi-associated trafficking activities." [PMID:1747103, PMID:23913272, PMID:34080016, PMID:34597626]
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0033106 ! cis-Golgi network membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: pg
creation_date: 2025-06-05T08:50:47Z
@@ -478898,8 +484227,9 @@
name: centriole scaffold activity
namespace: molecular_function
def: "The binding activity of a protein that contributes to the stable formation of a centriole by forming persistent structures, or templates, upon which other centriolar proteins assemble." [PMID:29784964, PMID:32956907, PMID:34702818]
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
+is_a: GO:0140378 ! protein complex scaffold activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30443" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31499" xsd:anyURI
created_by: pg
creation_date: 2025-06-11T13:59:35Z
@@ -478970,9 +484300,19 @@
def: "Catalysis of the reaction: an acyl-CoA + L-lysyl-[protein] = N6-acyl-L-lysyl-[protein] + CoA + H+." [RHEA:53916]
synonym: "protein acyltransferase activity" EXACT []
xref: RHEA:53916
+xref: RHEA:59764
+xref: RHEA:59796
+xref: RHEA:59800
+xref: RHEA:83531
+xref: RHEA:85279
is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:53916
+property_value: skos:narrowMatch RHEA:59764
+property_value: skos:narrowMatch RHEA:59796
+property_value: skos:narrowMatch RHEA:59800
+property_value: skos:narrowMatch RHEA:83531
+property_value: skos:narrowMatch RHEA:85279
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
creation_date: 2025-07-22T09:31:41Z
@@ -479250,6 +484590,8 @@
name: folic acid:proton symporter activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: folic acid(out) + H+(out) = folic acid(in) + H+(in). The main folic acid symporter is the Proton-Coupled Folate Transporter (PCFT/SLC46A1), which has similar affinity for transport of reduced folates (5-methyl THF, 5-formyl THF) and folic acid." [PMID:24745983]
+xref: Reactome:R-HSA-200646 "Cytosolic folate export across the plasma membrane"
+xref: Reactome:R-HSA-200729 "SLC46A1 transports FOLA from extracellular region to cytosol"
xref: TC:2.A.1.50.1
is_a: GO:0008517 ! folic acid transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
@@ -479816,8 +485158,8 @@
def: "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." [Wikipedia:Cell_fusion]
synonym: "cell cell fusion" EXACT []
synonym: "cell fusion" BROAD []
+synonym: "plasma membrane fusion" EXACT []
is_a: GO:0009987 ! cellular process
-relationship: has_part GO:0045026 ! plasma membrane fusion
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI
created_by: pg
creation_date: 2018-08-13T18:38:18Z
@@ -480414,6 +485756,7 @@
synonym: "small molecular sensor activity" EXACT []
synonym: "small molecule sensing activity" EXACT []
synonym: "small molecule sensor activity" NARROW []
+xref: Reactome:R-HSA-9854368 "ROS,RNS oxidize ACO2:4Fe-4S"
is_a: GO:0098772 ! molecular function regulator activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28772" xsd:anyURI
created_by: pg
@@ -480451,15 +485794,18 @@
[Term]
id: GO:0140303
-name: intramembrane lipid transporter activity
+name: intramembrane lipid carrier activity
namespace: molecular_function
def: "Enables the transport of a lipid from a region of a membrane to a different region on the same membrane." [PMID:16828084]
synonym: "flippase activity" RELATED []
+synonym: "intramembrane lipid transporter activity" BROAD []
synonym: "translocase activity" BROAD []
-is_a: GO:0005319 ! lipid transporter activity
+is_a: GO:0005215 ! transporter activity
+is_a: GO:0005319 ! lipid carrier activity
relationship: part_of GO:0034204 ! lipid translocation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17648" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19477" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31454" xsd:anyURI
created_by: pg
creation_date: 2019-03-01T20:14:09Z
@@ -480527,13 +485873,16 @@
[Term]
id: GO:0140309
-name: unfolded protein carrier activity
+name: unfolded protein holdase activity
namespace: molecular_function
-def: "A protein carrier activity that binds to a protein in an unfolded state and escorts it between two different cellular components. The unfolded protein carrier prevents aggregation of the target protein." [PMID:39488384]
-synonym: "holdase" BROAD []
+def: "A protein carrier activity that binds to a protein in an unfolded state and escorts it to an acceptor molecule or to a specific location. The unfolded protein carrier prevents aggregation of the target protein while it's being delivers to its final destination." [PMID:39488384]
+comment: Note that an holdase binds an unfolded protein and keeps it unfolded, unlike a protein folding chaperone, which binds an unfolded protein to fold it.
+synonym: "holdase" EXACT []
synonym: "holdase-carrier chaperone" EXACT []
-is_a: GO:0140597 ! protein carrier chaperone
+synonym: "unfolded protein carrier activity" EXACT []
+is_a: GO:0140597 ! protein carrier activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30552" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31601" xsd:anyURI
created_by: pg
creation_date: 2025-11-03T13:14:32Z
@@ -480556,6 +485905,7 @@
name: protein sequestering activity
namespace: molecular_function
def: "Binding to a protein to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active." [PMID:1493333]
+xref: Reactome:R-HSA-1678694 "Heparanase 2 (HPSE2) binds heparan sulfate proteoglycans"
is_a: GO:0140313 ! molecular sequestering activity
intersection_of: GO:0140313 ! molecular sequestering activity
intersection_of: has_part GO:0005515 ! protein binding
@@ -480593,6 +485943,7 @@
subset: goslim_prokaryote_ribbon
xref: Reactome:R-HSA-203553 "eNOS binds NOSIP"
xref: Reactome:R-HSA-203680 "eNOS:NOSIP translocation from caveolae to intracellular compartments"
+xref: Reactome:R-HSA-2404134 "RBP4:atROL binds TTR"
xref: Reactome:R-HSA-3245898 "TCN1 binds correnoids in the circulation"
is_a: GO:0003674 ! molecular_function
created_by: pg
@@ -480726,7 +486077,11 @@
name: lysophospholipase C activity
namespace: molecular_function
def: "Hydrolysis of a lysoglycerophospholipid at the first phosphodiester bond between the phosphate and glycerol." [PMID:32917725]
+xref: RHEA:86375
+xref: RHEA:86379
is_a: GO:0004629 ! C-type glycerophospholipase activity
+property_value: skos:narrowMatch RHEA:86375
+property_value: skos:narrowMatch RHEA:86379
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30949" xsd:anyURI
created_by: pg
creation_date: 2025-11-10T12:35:51Z
@@ -480747,12 +486102,13 @@
[Term]
id: GO:0140326
-name: ATPase-coupled intramembrane lipid transporter activity
+name: ATPase-coupled intramembrane lipid carrier activity
namespace: molecular_function
alt_id: GO:0004012
alt_id: GO:0008557
def: "Catalysis of the movement of lipids from one membrane leaflet to the other, driven by ATP hydrolysis. This includes flippases and floppases." [PMID:16828084]
synonym: "aminophospholipid-transporting ATPase" RELATED []
+synonym: "ATPase-coupled intramembrane lipid transporter activity" BROAD []
synonym: "ATPase-coupled phospholipid transporter activity" RELATED []
synonym: "ATPase-dependent phospholipid transporter activity" RELATED []
synonym: "phospholipid flippase activity" NARROW []
@@ -480763,7 +486119,7 @@
xref: MetaCyc:3.6.3.1-RXN
xref: Reactome:R-HSA-939763 "P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane"
xref: Reactome:R-HSA-947591 "P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane"
-is_a: GO:0140303 ! intramembrane lipid transporter activity
+is_a: GO:0140303 ! intramembrane lipid carrier activity
is_a: GO:0140657 ! ATP-dependent activity
property_value: skos:broadMatch RHEA:66132
property_value: skos:exactMatch EC:7.6.2.1
@@ -480781,7 +486137,7 @@
def: "Catalysis of the movement of lipids from the exoplasmic to the cytosolic leaflet of a membrane, using energy from the hydrolysis of ATP." [PMID:20043909, PMID:25284293, Wikipedia:Flippase]
comment: Nomenclature note. Flippases and floppases are ATP-dependent transbilayer lipid translocators. According to an extensively used, though not universal, nomenclature, they catalyze lipid transfer towards the inward monolayer (flippases) or towards the outward monolayer (floppases). Scramblases are ATP-independent, non-selective, inducing non-specific transbilayer movements across the membrane. The direction of the translocation should be taken into account for annotation (from the exoplasmic to the cytosolic leaflet of a membrane).
synonym: "flippase activity (exoplasmic to cytosolic leaflet)" EXACT []
-is_a: GO:0140326 ! ATPase-coupled intramembrane lipid transporter activity
+is_a: GO:0140326 ! ATPase-coupled intramembrane lipid carrier activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
creation_date: 2019-04-29T12:51:21Z
@@ -480793,7 +486149,7 @@
def: "Catalysis of the movement of a lipid from the cytosolic to the exoplasmic leaflet of a membrane, using energy from the hydrolysis of ATP." [PMID:20043909, PMID:25284293, Wikipedia:Flippase]
comment: Nomenclature note. Flippases and floppases are ATP-dependent transbilayer lipid translocators. According to an extensively used, though not universal, nomenclature, they catalyze lipid transfer towards the inward monolayer (flippases) or towards the outward monolayer (floppases). Scramblases are ATP-independent, non-selective, inducing non-specific transbilayer movements across the membrane. The direction of the translocation should be taken into account for annotation (from the cytosolic to the exoplasmic leaflet of a membrane).
synonym: "floppase activity (cytosolic to exoplasmic leaflet)" EXACT []
-is_a: GO:0140326 ! ATPase-coupled intramembrane lipid transporter activity
+is_a: GO:0140326 ! ATPase-coupled intramembrane lipid carrier activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
creation_date: 2019-04-29T12:58:53Z
@@ -480849,7 +486205,6 @@
namespace: molecular_function
def: "Catalysis of the movement of a glycerophospholipid from the exoplasmic to the cytosolic leaflet of a membrane, using energy from the hydrolysis of ATP." [PMID:26212235]
synonym: "glycerophospholipid flippase activity (exoplasmic to cytosolic leaflet)" EXACT []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0140327 ! flippase activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
@@ -480874,7 +486229,9 @@
synonym: "glycoprotein phospholipase C activity" EXACT []
synonym: "glycosylphosphatidyl inositol-anchor protein phospholipase C activity" EXACT []
synonym: "GPI-PLC activity" EXACT []
+xref: RHEA:86259
is_a: GO:0004629 ! C-type glycerophospholipase activity
+property_value: skos:narrowMatch RHEA:86259
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28868" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31078" xsd:anyURI
created_by: pg
@@ -480945,7 +486302,6 @@
namespace: molecular_function
def: "Catalysis of the movement of phosphatidylethanolamine from the cytosolic to the exoplasmic leaflet of a membrane, using energy from the hydrolysis of ATP." [PMID:10029989]
synonym: "phosphatidylethanolamine floppase activity (cytosolic to exoplasmic leaflet)" EXACT []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0140328 ! floppase activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
@@ -480987,7 +486343,7 @@
namespace: molecular_function
def: "Catalysis of the movement of phosphatidylcholine from the exoplasmic to the cytosolic leaflet of a membrane, using energy from the hydrolysis of ATP." [PMID:11870854]
synonym: "phosphatidylcholine flippase activity (exoplasmic to cytosolic leaflet)" EXACT []
-is_a: GO:0008525 ! phosphatidylcholine transporter activity
+is_a: GO:0008525 ! phosphatidylcholine intramembrane carrier activity
is_a: GO:0140333 ! glycerophospholipid flippase activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
@@ -481039,7 +486395,9 @@
def: "A supramolecular network that forms mainly through linkages of the short laminin arms between the N-terminal regions of one alpha, one beta, and one gamma chain. The laminin network associates with the collagen network to create the stable, sheet-like structure of the basement membrane ECM." [PMID:1577869, PMID:21421915, PMID:23263632, PMID:28187500]
synonym: "laminin complex" BROAD []
is_a: GO:0099080 ! supramolecular complex
+relationship: part_of GO:0140144 ! non-collagenous component of basement membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31053" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31490" xsd:anyURI
created_by: pg
creation_date: 2025-12-01T12:38:57Z
@@ -481063,7 +486421,7 @@
synonym: "glucosylceramide flippase activity" NARROW []
synonym: "glycoceramide flippase activity" EXACT []
synonym: "glycosylceramide flippase activity (exoplasmic to cytosolic leaflet)" EXACT []
-is_a: GO:0046624 ! sphingolipid transporter activity
+is_a: GO:0046624 ! sphingolipid intramembrane carrier activity
is_a: GO:0140327 ! flippase activity
property_value: skos:broadMatch RHEA:66132
created_by: pg
@@ -481136,6 +486494,7 @@
name: heme export from vacuole to cytoplasm
namespace: biological_process
def: "The directed movement of heme from inside the vacuole across the vacuolar membrane and into the cytosol." [PMID:28193844]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0035351 ! heme transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17407" xsd:anyURI
@@ -481224,7 +486583,7 @@
namespace: cellular_component
def: "A ribonucleoprotein granule located in the cytoplasm and the nucleus. GW-bodies minimally contain the Argonaute2 (Ago2) and TNRC6B proteins, together with specific target RNAs." [PMID:16418578, PMID:26930655, PMID:29576456]
synonym: "GW-body" EXACT []
-is_a: GO:0036464 ! cytoplasmic ribonucleoprotein granule
+is_a: GO:0035770 ! ribonucleoprotein granule
created_by: pg
creation_date: 2019-07-25T19:26:48Z
@@ -481264,7 +486623,7 @@
def: "A receptor complex that recognizes, binds and sequesters a specific receptor ligand to prevent it from binding to its regular receptor. May be soluble or membrane bound." [GOC:bhm, PMID:30621730, PMID:9168977]
synonym: "osteoclastogenesis inhibitory factor" NARROW []
synonym: "osteoprotegerin complex" NARROW []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: pg
creation_date: 2019-09-13T16:39:24Z
@@ -481297,8 +486656,10 @@
name: ornithine lipid biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of ornithine lipids, any of a class of phosphorus-free bacterial membrane lipids with an L-ornithine-derived head group." [PMID:22724388]
+xref: MetaCyc:PWY-6818
is_a: GO:0008652 ! amino acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31271" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
created_by: pg
creation_date: 2026-01-20T12:30:41Z
@@ -481368,6 +486729,29 @@
creation_date: 2026-01-21T10:01:05Z
[Term]
+id: GO:0140378
+name: protein complex scaffold activity
+namespace: molecular_function
+def: "A structural molecule activity of a protein-containing complex component that serves to hold the complex together. Protein complex scaffolds are integral members of complexes." [PMID:41298522]
+synonym: "protein-complex scaffolding activity" EXACT []
+synonym: "protein-containing complex scaffold activity" EXACT []
+is_a: GO:0005198 ! structural molecule activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31444" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-02T08:05:02Z
+
+[Term]
+id: GO:0140379
+name: amino acid acyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the transfer of an acyl group to an acceptor group on a free amino acid, usually using acetyl-CoA as donor." [GOC:curators]
+synonym: "amino acid N-acetyltransferase activity" NARROW []
+is_a: GO:0016746 ! acyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-02T11:14:33Z
+
+[Term]
id: GO:0140380
name: psilocybin biosynthetic process
namespace: biological_process
@@ -481443,6 +486827,123 @@
creation_date: 2019-11-20T13:25:55Z
[Term]
+id: GO:0140385
+name: amino acid transaminase activity
+namespace: molecular_function
+def: "Transfer of an amino group from an amino acid to an acceptor, usually a 2-oxo acid." [GOC:curators]
+is_a: GO:0008483 ! transaminase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31140" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-02T13:30:09Z
+
+[Term]
+id: GO:0140386
+name: tRNA (cytidine(4)/adenine(4)-2'-O-ribose)-methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: cytidine(4) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(4) in tRNA + S-adenosyl-L-homocysteine + H+. Acts on cytidine(4) on tRNAPro and tRNAGly(GCC), and on adenosine(4) in tRNAHis." [EC:2.1.1.225, PMID:17242307]
+xref: EC:2.1.1.225
+xref: RHEA:32767
+xref: RHEA:43192
+xref: RHEA:43196
+is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity
+is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
+property_value: skos:exactMatch EC:2.1.1.225
+property_value: skos:narrowMatch RHEA:32767
+property_value: skos:narrowMatch RHEA:43192
+property_value: skos:narrowMatch RHEA:43196
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31521" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-06T12:44:45Z
+
+[Term]
+id: GO:0140387
+name: negative regulation of L-glutamate biosynthetic process
+namespace: biological_process
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of L-glutamate biosynthetic process." [PMID:16899818, PMID:29649217]
+synonym: "negative regulation of glutamate biosynthetic process" BROAD []
+synonym: "negative regulation of L-glutamate biosynthesis" BROAD []
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
+is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: negatively_regulates GO:0097054 ! L-glutamate biosynthetic process
+relationship: negatively_regulates GO:0097054 ! L-glutamate biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31582" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-17T08:55:47Z
+
+[Term]
+id: GO:0140388
+name: protein translocation chaperone activity
+namespace: molecular_function
+def: "Binding to the exposed unfolded portion of a polypeptide as it emerges from a membrane translocation channel/pore to drive its unidirectional transport across a membrane. Iterative cycles of ATP-dependent binding/rebinding by the chaperone prevents back sliding and drive vectorial transport." [PMID:11733493]
+synonym: "import motor chaperone activity" RELATED []
+synonym: "translocation ratchet activity" RELATED []
+is_a: GO:0140597 ! protein carrier activity
+is_a: GO:0140657 ! ATP-dependent activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31580" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-18T12:58:22Z
+
+[Term]
+id: GO:0140389
+name: pattern recognition receptor complex
+namespace: cellular_component
+def: "A signaling receptor complex that combines with a pathogen-associated molecular pattern (PAMP), a structure conserved among pathogenic organisms, to initiate an innate immune response." [PMID:22654057, PMID:28302675, PMID:41719893]
+synonym: "PAMP receptor complex" EXACT []
+is_a: GO:0043235 ! signaling receptor complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31605" xsd:anyURI
+created_by: pg
+creation_date: 2026-02-27T15:46:56Z
+
+[Term]
+id: GO:0140390
+name: positive regulation of acetyl-CoA biosynthesis
+namespace: biological_process
+def: "Any process that increases the rate, frequency, or extent of acetyl-CoA biosynthetic process." [PMID:41730913]
+is_a: GO:0009891 ! positive regulation of biosynthetic process
+is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0050812 ! regulation of acyl-CoA biosynthetic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: positively_regulates GO:0006085 ! acetyl-CoA biosynthetic process
+relationship: positively_regulates GO:0006085 ! acetyl-CoA biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31614" xsd:anyURI
+created_by: pg
+creation_date: 2026-03-04T08:21:53Z
+
+[Term]
+id: GO:0140391
+name: negative regulation of acetyl-CoA biosynthesis
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of acetyl-CoA biosynthetic process." [PMID:39019872]
+is_a: GO:0009890 ! negative regulation of biosynthetic process
+is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
+is_a: GO:0045936 ! negative regulation of phosphate metabolic process
+is_a: GO:0050812 ! regulation of acyl-CoA biosynthetic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: negatively_regulates GO:0006085 ! acetyl-CoA biosynthetic process
+relationship: negatively_regulates GO:0006085 ! acetyl-CoA biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31614" xsd:anyURI
+created_by: pg
+creation_date: 2026-03-04T08:22:01Z
+
+[Term]
+id: GO:0140392
+name: extracellular protein-containing complex
+namespace: cellular_component
+def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together outside a cell." [GOC:curators]
+subset: gocheck_do_not_annotate
+synonym: "extracellular protein complex" BROAD []
+is_a: GO:0032991 ! protein-containing complex
+intersection_of: GO:0032991 ! protein-containing complex
+intersection_of: part_of GO:0005576 ! extracellular region
+relationship: part_of GO:0005576 ! extracellular region
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31673" xsd:anyURI
+created_by: pg
+creation_date: 2020-09-09T05:12:38Z
+
+[Term]
id: GO:0140393
name: norsolorinic acid ketoreductase activity
namespace: molecular_function
@@ -481561,6 +487062,16 @@
creation_date: 2019-11-29T11:06:07Z
[Term]
+id: GO:0140400
+name: embryonic sheath
+namespace: cellular_component
+def: "A specialized, transient apical extracellular matrix (aECM) that overlays the apical surface of the embryonic epidermis in Caenorhabditis elegans. It is secreted just prior to the start of embryonic elongation and acts as a mechanical scaffold to maintain embryonic integrity, distribute actomyosin-dependent stress, and anchor developing muscles." [PMID:22278925, PMID:25798732, PMID:28526752, PMID:33036165]
+is_a: GO:0140047 ! specialized extracellular matrix
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31680" xsd:anyURI
+created_by: pg
+creation_date: 2026-03-06T09:07:34Z
+
+[Term]
id: GO:0140403
name: effector-mediated suppression of host innate immune response
namespace: biological_process
@@ -482196,11 +487707,13 @@
[Term]
id: GO:0140462
-name: pericentric heterochromatin organization
+name: obsolete pericentric heterochromatin organization
namespace: biological_process
-def: "The organization of chromatin into heterochromatin at the pericentric region of a chromosome." [PMID:26744419]
-is_a: GO:0031507 ! heterochromatin formation
+def: "OBSOLETE. The organization of chromatin into heterochromatin at the pericentric region of a chromosome." [PMID:26744419]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19396" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31331" xsd:anyURI
+is_obsolete: true
created_by: pg
creation_date: 2020-05-06T07:47:09Z
@@ -482240,6 +487753,7 @@
name: iron-sulfur cluster export from the mitochondrion
namespace: biological_process
def: "The directed movement of iron sulfur clusters from inside the mitochondrion into the cytosol by crossing the inner mitochondrial membrane." [PMID:31040179]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:1902497 ! iron-sulfur cluster transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19504" xsd:anyURI
created_by: pg
@@ -483074,6 +488588,7 @@
name: defense response to symbiont
namespace: biological_process
def: "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." [GOC:pg]
+xref: Reactome:R-HSA-9953170 "GBP-mediated host defense"
is_a: GO:0098542 ! defense response to other organism
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20261" xsd:anyURI
created_by: pg
@@ -483228,13 +488743,15 @@
name: membrane protein dislocase activity
namespace: molecular_function
def: "The activity of removing a protein from a membrane, by binding to a transmembrane helical fragment of a tail-anchored protein and releasing it from the the hydrophobic region of one or both lipid bilayers. The reaction is driven by ATP hydrolysis." [PMID:24821790, PMID:28712723, PMID:32973005]
-synonym: "transmembrane helix dislocase\ntransmembrane protein dislocase activity" RELATED []
+synonym: "transmembrane helix dislocase" RELATED []
+synonym: "transmembrane protein dislocase activity" RELATED []
xref: RHEA:66168
-is_a: GO:0140318 ! protein transporter activity
+is_a: GO:0140597 ! protein carrier activity
is_a: GO:0140657 ! ATP-dependent activity
property_value: skos:narrowMatch RHEA:66168
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20237" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22209" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30369" xsd:anyURI
created_by: pg
creation_date: 2020-12-15T07:13:21Z
@@ -483366,6 +488883,10 @@
comment: Note that this enzyme transports Cu(+) or Ag(+), and cannot transport the divalent ions, contrary to EC:7.2.2.9, which mainly transports the divalent copper ion (source: EC:7.2.2.8).
xref: EC:7.2.2.8
xref: MetaCyc:RXN-14455
+xref: Reactome:R-HSA-3697838 "ATP7A transfers Cu from ATOX1 to SOD3"
+xref: Reactome:R-HSA-6803545 "ATP7A transports cytosolic Cu2+ to phagosomal lumen"
+xref: Reactome:R-HSA-936802 "ATP7A transports cytosolic Cu1+ to extracellular region"
+xref: Reactome:R-HSA-936895 "ATP7B transports cytosolic Cu1+ to Golgi lumen"
xref: RHEA:25792
is_a: GO:0005375 ! copper ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
@@ -483549,16 +489070,16 @@
[Term]
id: GO:0140597
-name: protein carrier chaperone
+name: protein carrier activity
namespace: molecular_function
-def: "Binding to and carrying a protein between two different cellular components by moving along with the target protein." [PMID:7628437]
-synonym: "protein carrier activity" EXACT []
+def: "Binding to and carrying a protein to an acceptor molecule or to a specific location by moving along with the target protein." [PMID:7628437]
+synonym: "protein carrier chaperone" EXACT []
synonym: "protein chaperone" BROAD []
is_a: GO:0140104 ! molecular carrier activity
-relationship: has_part GO:0005515 ! protein binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15917" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22127" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22356" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31601" xsd:anyURI
created_by: pg
creation_date: 2021-02-10T06:16:16Z
@@ -483567,7 +489088,7 @@
name: lipoprotein carrier activity
namespace: molecular_function
def: "Binding to and carrying a lipoprotein between two different cellular locations by moving along with the target lipoprotein." [PMID:7628437]
-is_a: GO:0140597 ! protein carrier chaperone
+is_a: GO:0140597 ! protein carrier activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15917" xsd:anyURI
created_by: pg
creation_date: 2021-02-10T06:16:26Z
@@ -483732,6 +489253,8 @@
synonym: "monoiodotyrosine deiodinase activity" RELATED []
synonym: "tyrosine iodinase activity" RELATED []
xref: EC:1.21.1.1
+xref: Reactome:R-HSA-209921 "Monoiodinated tyrosine can be deiodinated"
+xref: Reactome:R-HSA-209960 "Diiodinated tyrosine can be deiodinated"
xref: RHEA:32479
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
property_value: skos:exactMatch EC:1.21.1.1
@@ -483984,6 +489507,7 @@
name: copper import into the mitochondrion
namespace: biological_process
def: "The process in which copper is transported from the cytosol into the mitochondrial matrix." [PMID:32979421]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0035434 ! copper ion transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21294" xsd:anyURI
created_by: pg
@@ -484551,6 +490075,7 @@
namespace: molecular_function
def: "A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators]
comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
+xref: Reactome:R-HSA-8866941 "MID1IP1 binds THRSP"
is_a: GO:0098772 ! molecular function regulator activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21782" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25165" xsd:anyURI
@@ -484741,9 +490266,13 @@
namespace: molecular_function
def: "Catalysis of the reaction: an omega-methyl-very-long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an omega-hydroxy-very-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase]. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons." [PMID:16547005, RHEA:67952]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+xref: RHEA:39719
+xref: RHEA:40083
xref: RHEA:67952
is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
property_value: skos:exactMatch RHEA:67952
+property_value: skos:narrowMatch RHEA:39719
+property_value: skos:narrowMatch RHEA:40083
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21925" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -484996,7 +490525,7 @@
synonym: "histone carrier activity" EXACT []
synonym: "nucleosome remodeling activity" RELATED []
xref: Reactome:R-HSA-9822185 "HIRA and NPM2 assemble H3.3-containing nucleosomes on paternal DNA"
-is_a: GO:0140597 ! protein carrier chaperone
+is_a: GO:0140597 ! protein carrier activity
relationship: has_part GO:0042393 ! histone binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22126" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22129" xsd:anyURI
@@ -485352,8 +490881,9 @@
id: GO:0140740
name: ADP-riboxanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginyl-[protein] + NAD+ = ADP-riboxanated L-argininyl-[protein] + H+ + NH4(+) + nicotinamide." [PMID:34671164, RHEA:69500]
+def: "Catalysis of the reaction: L-arginyl-[protein] + NAD+ = ADP-riboxanated L-argininyl-[protein] + H+ + NH4+ + nicotinamide." [PMID:34671164, RHEA:69500]
comment: Note that this activity has two steps: a transfer of an ADP-ribose group, followed by the elimination of an ammonia group.
+xref: Reactome:R-HSA-9956624 "OspC3 ADP-riboxanates CASP4"
xref: RHEA:69500
xref: RHEA:75883
xref: RHEA:75887
@@ -485588,14 +491118,16 @@
id: GO:0140759
name: histone H3K56 methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 56) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 56). This reaction is the addition of a methyl group to the lysine residue at position 56 of the histone H3 protein." [PMID:23451023, PMID:28743002]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 56) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 56). This reaction is the addition of a methyl group to the lysine residue at position 56 of the histone H3 protein." [PMID:23451023, PMID:28743002, RHEA:85519]
comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
synonym: "histone H3K56 methylase activity" EXACT []
synonym: "histone lysine N-methyltransferase activity (H3-K56 specific)" EXACT []
synonym: "histone methyltransferase activity (H3-K56 specific)" EXACT []
synonym: "histone-H3K56 methyltransferase activity" EXACT []
+xref: RHEA:85519
is_a: GO:0016279 ! protein-lysine N-methyltransferase activity
is_a: GO:0140938 ! histone H3 methyltransferase activity
+property_value: skos:exactMatch RHEA:85519
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22757" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24337" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI
@@ -485615,8 +491147,12 @@
synonym: "histone H3-tri/dimethyl-lysine-56 demethylase activity" EXACT []
synonym: "histone H3K56me2 demethylase activity" RELATED []
synonym: "histone H3K56me3 demethylase activity" RELATED []
+xref: RHEA:85927
+xref: RHEA:85931
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0141052 ! histone H3 demethylase activity
+property_value: skos:narrowMatch RHEA:85927
+property_value: skos:narrowMatch RHEA:85931
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22757" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29636" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30578" xsd:anyURI
@@ -485724,6 +491260,7 @@
synonym: "protein substrate chaperone activity" RELATED []
synonym: "protein-substrate adaptor activity" BROAD []
xref: Reactome:R-HSA-202137 "AKT1 binds eNOS complex via HSP90"
+xref: Reactome:R-HSA-5653886 "B4GALT1 binds LALBA"
is_a: GO:0030674 ! protein-macromolecule adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22972" xsd:anyURI
created_by: pg
@@ -485757,8 +491294,10 @@
namespace: molecular_function
def: "Catalysis of the reaction: L-lysyl-[protein] + tetradecanoyl-CoA = CoA + H+ + N(6)-tetradecanoyl-L-lysyl-[protein]." [PMID:1402651, RHEA:59752]
xref: RHEA:59752
+xref: RHEA:70671
is_a: GO:0018030 ! peptidyl-lysine N6-myristoyltransferase activity
property_value: skos:exactMatch RHEA:59752
+property_value: skos:narrowMatch RHEA:70671
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22968" xsd:anyURI
created_by: pg
creation_date: 2022-03-02T12:45:16Z
@@ -486435,11 +491974,13 @@
synonym: "mRNA 5'-phosphatase activity" EXACT []
xref: EC:3.6.1.74
xref: MetaCyc:POLYNUCLEOTIDE-5-PHOSPHATASE-RXN
+xref: RHEA:11008
xref: RHEA:67004
is_a: GO:0016462 ! pyrophosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
property_value: skos:exactMatch EC:3.6.1.74
property_value: skos:exactMatch RHEA:67004
+property_value: skos:narrowMatch RHEA:11008
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23319" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25810" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26929" xsd:anyURI
@@ -486462,6 +492003,7 @@
name: cytosol to Golgi apparatus transport
namespace: biological_process
def: "The directed movement of substances from the cytosol into the Golgi apparatus of a cell." [PMID:28373556]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0055085 ! transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21524" xsd:anyURI
created_by: pg
@@ -486520,9 +492062,13 @@
def: "Catalysis of the reaction: [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O." [PMID:12707274, PMID:19820102, RHEA:62620]
xref: EC:1.11.1.24
xref: RHEA:62620
+xref: RHEA:63840
+xref: RHEA:63844
is_a: GO:0051920 ! peroxiredoxin activity
property_value: skos:exactMatch EC:1.11.1.24
property_value: skos:exactMatch RHEA:62620
+property_value: skos:narrowMatch RHEA:63840
+property_value: skos:narrowMatch RHEA:63844
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23121" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -486533,6 +492079,7 @@
name: lactoperoxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O." [PMID:19339248, RHEA:56136]
+synonym: "heme peroxidase activity" RELATED []
synonym: "peroxidase activity" BROAD []
xref: EC:1.11.1.7
xref: MetaCyc:PEROXID-RXN
@@ -487012,9 +492559,11 @@
synonym: "medicarpin synthase activity" EXACT [EC:4.2.1.139]
xref: EC:4.2.1.139
xref: RHEA:35407
+xref: RHEA:35811
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.139
property_value: skos:exactMatch RHEA:35407
+property_value: skos:narrowMatch RHEA:35811
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23521" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28937" xsd:anyURI
@@ -487030,11 +492579,13 @@
synonym: "vestitone reductase activity" NARROW [EC:1.1.1.348]
xref: EC:1.1.1.348
xref: MetaCyc:RXN-18747
+xref: RHEA:35403
xref: RHEA:56284
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.348
property_value: skos:exactMatch MetaCyc:RXN-18747
property_value: skos:exactMatch RHEA:56284
+property_value: skos:narrowMatch RHEA:35403
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23521" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28324" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30910" xsd:anyURI
@@ -487690,6 +493241,11 @@
name: halogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: R-CH + a halogen + oxygen donor = R-C-halogen +H2O." [PMID:28466644, PMID:34368824]
+xref: Reactome:R-HSA-209815 "Tyrosine is monoiodinated"
+xref: Reactome:R-HSA-209840 "Two DITs combine to form thyroxine"
+xref: Reactome:R-HSA-209925 "DIT and MIT combine to form triiodothyronine"
+xref: Reactome:R-HSA-209973 "Tyrosine is diiodinated"
+xref: Reactome:R-HSA-350901 "Iodide is organified"
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23587" xsd:anyURI
created_by: pg
@@ -487794,6 +493350,7 @@
name: zinc ion import into secretory vesicle
namespace: biological_process
def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a secretory vesicle." [PMID:19496757]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0062111 ! zinc ion import into organelle
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23879" xsd:anyURI
created_by: pg
@@ -487815,6 +493372,7 @@
namespace: biological_process
def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a lysosome." [PMID:25808614]
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0062111 ! zinc ion import into organelle
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23907" xsd:anyURI
@@ -487826,6 +493384,7 @@
name: zinc ion import into mitochondrion
namespace: biological_process
def: "The directed import of zinc(2+) from the cytosol, across an organelle membrane, into a mitochondrion." [PMID:21289295]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0062111 ! zinc ion import into organelle
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23890" xsd:anyURI
created_by: pg
@@ -488028,10 +493587,12 @@
def: "Catalysis of the reaction: a 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + N7-methyl-GDP + H+." [PMID:18820299, PMID:29483298]
synonym: "m(7)GpppN-mRNA hydrolase activity" EXACT []
xref: EC:3.6.1.62
+xref: RHEA:37371
xref: RHEA:67484
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.62
property_value: skos:exactMatch RHEA:67484
+property_value: skos:narrowMatch RHEA:37371
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23290" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -488775,9 +494336,13 @@
def: "Catalysis of the reaction: an omega-methyl-medium-chain fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy-medium-chain fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]. A medium-chain fatty acid has an aliphatic tail containing 6 to 12 carbons." [RHEA:75279]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
xref: MetaCyc:RXN-19719
+xref: RHEA:38947
xref: RHEA:75279
+xref: RHEA:75283
is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
property_value: skos:exactMatch RHEA:75279
+property_value: skos:narrowMatch RHEA:38947
+property_value: skos:narrowMatch RHEA:75283
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24661" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -489155,6 +494720,7 @@
namespace: biological_process
def: "The directed import of purine nucleotide from the cytosol, across the lysosomal membrane, into the lysosome." [PMID:18375752, PMID:23876310]
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0072530 ! purine-containing compound transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25075" xsd:anyURI
@@ -489393,10 +494959,14 @@
xref: EC:1.1.1.330
xref: MetaCyc:RXN-7698
xref: Reactome:R-HSA-548818 "HSD17B3,12 hydrogenates 3OOD-CoA to 3HODC-CoA"
+xref: RHEA:39267
xref: RHEA:48680
+xref: RHEA:85831
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.330
property_value: skos:exactMatch RHEA:48680
+property_value: skos:narrowMatch RHEA:39267
+property_value: skos:narrowMatch RHEA:85831
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25302" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25805" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25814" xsd:anyURI
@@ -490001,6 +495571,7 @@
namespace: molecular_function
def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of glucose." [PMID:17470517]
synonym: "glucose sensing activity" EXACT []
+xref: Reactome:R-HSA-170810 "nucleoplasmic GCK1:GCKR complex => glucokinase (GCK1) + glucokinase regulatory protein (GCKR)"
is_a: GO:0140299 ! molecular sensor activity
relationship: has_part GO:0005536 ! D-glucose binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25267" xsd:anyURI
@@ -490117,10 +495688,11 @@
[Term]
id: GO:0141098
-name: tRNA (cytidine(34)-2'-O)-methyltransferase activity
+name: tRNA (cytidine(34)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: cytidine(34) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(34) in tRNA + H+ + S-adenosyl-L-homocysteine." [PMID:31943105, RHEA:43084]
synonym: "tRNA (cytidine 34-2'-O)-methyltransferase activity" EXACT []
+synonym: "tRNA (cytidine(34)-2'-O)-methyltransferase activity" EXACT []
xref: MetaCyc:RXN-11860
xref: RHEA:43084
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
@@ -490134,9 +495706,10 @@
[Term]
id: GO:0141100
-name: tRNA (guanine(18)-2'-O)-methyltransferase activity
+name: tRNA (guanine(18)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanosine 18 in tRNA= S-adenosyl-L-homocysteine + 2'-O-methylguanosine 18 in tRNA + H+." [PMID:25404562]
+synonym: "tRNA (guanine(18)-2'-O-)-methyltransferase activity" EXACT []
synonym: "tRNA (guanosine(18)-2'-O)-methyltransferase activity" EXACT []
xref: EC:2.1.1.34
xref: MetaCyc:2.1.1.34-RXN
@@ -490151,10 +495724,11 @@
[Term]
id: GO:0141101
-name: tRNA(Ser) (uridine(44)-2'-O-)-methyltransferase activity
+name: tRNA(Ser) (uridine(44)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: Catalysis of the reaction: S-adenosyl-L-methionine + uridine44 in tRNASer = 2'-O-methyluridine44 in tRNASer + H+ + S-adenosyl-L-homocysteine." [PMID:18025252, RHEA:43100]
synonym: "tRNA(Ser) (uracil(44)-2'-O-)-methyltransferase activity" EXACT []
+synonym: "tRNA(Ser) (uridine(44)-2'-O-)-methyltransferase activity" EXACT []
xref: EC:2.1.1.211
xref: MetaCyc:RXN-12368
xref: Reactome:R-HSA-6788707 "TRMT44 2'-O-methylates uridine-44 in tRNA(Ser)"
@@ -490169,9 +495743,10 @@
[Term]
id: GO:0141102
-name: tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity
+name: tRNA (5-carboxymethylaminomethyluridine(34)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 5-carboxymethylaminomethyluridine34 in tRNA(Leu) + S-adenosyl-L-methionine = 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNA(Leu) + H+ + S-adenosyl-L-homocysteine." [PMID:20855540, RHEA:43088]
+synonym: "tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity" EXACT []
synonym: "tRNA (cytidine(34)/5-carboxymethylaminomethyluridine(34)-2'-O)- methyltransferase activity" EXACT []
xref: RHEA:43088
is_a: GO:0016300 ! tRNA (uridine) methyltransferase activity
@@ -490360,6 +495935,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: Fe(II)-heme b-[protein] + nitric oxide + O2 = Fe(III)-heme b-[protein] + nitrate." [PMID:20511233]
comment: Note that this activity is similar to nitric oxide dioxygenase activity ; GO:0008941, but GO:000894 uses NADPH as the electron donor.
+xref: Reactome:R-HSA-5340226 "CYGB dioxygenates NO"
xref: RHEA:78091
is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
property_value: skos:exactMatch RHEA:78091
@@ -490442,11 +496018,38 @@
namespace: molecular_function
def: "Catalysis of the reaction: a short-chain fatty acyl-CoA + H2O = a short fatty acid + CoA + H+. A short-chain fatty acid has an aliphatic tail of less than 6 carbons." [RHEA:68180]
comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
+xref: EC:3.1.2.18
xref: MetaCyc:3.1.2.18-RXN
+xref: RHEA:31251
+xref: RHEA:40103
+xref: RHEA:40111
+xref: RHEA:40799
+xref: RHEA:45156
+xref: RHEA:55052
+xref: RHEA:55064
+xref: RHEA:55084
+xref: RHEA:55096
+xref: RHEA:65204
+xref: RHEA:65208
+xref: RHEA:66980
+xref: RHEA:66984
xref: RHEA:68180
is_a: GO:0047617 ! fatty acyl-CoA hydrolase activity
property_value: skos:exactMatch RHEA:68180
-property_value: skos:relatedMatch EC:3.1.2.18
+property_value: skos:narrowMatch EC:3.1.2.18
+property_value: skos:narrowMatch RHEA:31251
+property_value: skos:narrowMatch RHEA:40103
+property_value: skos:narrowMatch RHEA:40111
+property_value: skos:narrowMatch RHEA:40799
+property_value: skos:narrowMatch RHEA:45156
+property_value: skos:narrowMatch RHEA:55052
+property_value: skos:narrowMatch RHEA:55064
+property_value: skos:narrowMatch RHEA:55084
+property_value: skos:narrowMatch RHEA:55096
+property_value: skos:narrowMatch RHEA:65204
+property_value: skos:narrowMatch RHEA:65208
+property_value: skos:narrowMatch RHEA:66980
+property_value: skos:narrowMatch RHEA:66984
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26441" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -490704,12 +496307,14 @@
xref: EC:1.3.1.39
xref: MetaCyc:ENOYL-ACP-REDUCT-NADPH-RXN
xref: RHEA:22564
+xref: RHEA:41812
is_a: GO:0016631 ! enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity
property_value: skos:exactMatch EC:1.3.1.104
property_value: skos:exactMatch MetaCyc:ENOYL-ACP-REDUCT-NADPH-RXN
property_value: skos:exactMatch RHEA:22564
property_value: skos:narrowMatch EC:1.3.1.10
property_value: skos:narrowMatch EC:1.3.1.39
+property_value: skos:narrowMatch RHEA:41812
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25699" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28173" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30035" xsd:anyURI
@@ -490721,7 +496326,7 @@
name: regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:35931019]
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
+is_a: GO:1902531 ! regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -490734,8 +496339,8 @@
name: positive regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:14615391]
-is_a: GO:0010750 ! positive regulation of nitric oxide mediated signal transduction
is_a: GO:0141149 ! regulation of nitric oxide-cGMP mediated signal transduction
+is_a: GO:1902533 ! positive regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: positively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -490748,8 +496353,8 @@
name: negative regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:35931019]
-is_a: GO:0010751 ! negative regulation of nitric oxide mediated signal transduction
is_a: GO:0141149 ! regulation of nitric oxide-cGMP mediated signal transduction
+is_a: GO:1902532 ! negative regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: negatively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -490836,6 +496441,7 @@
synonym: "cAMP/PKA signaling cassette" EXACT []
synonym: "PKA signaling" BROAD []
synonym: "protein kinase A signaling" BROAD []
+xref: Reactome:R-HSA-163358 "PKA-mediated phosphorylation of key metabolic factors"
is_a: GO:0141124 ! intracellular signaling cassette
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI
created_by: pg
@@ -491485,10 +497091,20 @@
def: "Catalysis of the reaction: N6-acyl-L-lysyl-[protein] + NAD+ + H2O = 2''-O-acyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein]." [PMID:35044827, RHEA:54172]
synonym: "protein lysine deacylase activity" BROAD []
xref: RHEA:54172
+xref: RHEA:70627
+xref: RHEA:70631
+xref: RHEA:70635
+xref: RHEA:70639
+xref: RHEA:85159
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140096 ! catalytic activity, acting on a protein
is_a: GO:0160215 ! deacylase activity
property_value: skos:exactMatch RHEA:54172
+property_value: skos:narrowMatch RHEA:70627
+property_value: skos:narrowMatch RHEA:70631
+property_value: skos:narrowMatch RHEA:70635
+property_value: skos:narrowMatch RHEA:70639
+property_value: skos:narrowMatch RHEA:85159
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28920" xsd:anyURI
created_by: pg
creation_date: 2024-09-19T14:13:12Z
@@ -492485,9 +498101,10 @@
id: GO:0150103
name: reactive gliosis
namespace: biological_process
-def: "A neuroinflammatory response, occurring over several days, during which glial cells undergo nonspecific reactive changes in response to damage to the central nervous system (CNS); typically involves the proliferation or hypertrophy of different types of glial cells." [GOC:aruk, GOC:bc, PMID:24462092]
+def: "A coordinated response of central nervous system (CNS) glial cells-including astrocytes, microglia, and NG2 glia-to injury, infection, or disease, characterized by changes in gene expression, morphology, proliferation, and extracellular matrix production. Reactive gliosis can range from transient glial activation to the formation of a persistent glial scar border." [GOC:aruk, GOC:bc, PMID:20012068, PMID:24267886, PMID:24462092, PMID:27049947]
synonym: "gliosis" BROAD []
is_a: GO:0150076 ! neuroinflammatory response
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30886" xsd:anyURI
created_by: bc
creation_date: 2019-05-21T12:37:31Z
@@ -493270,6 +498887,7 @@
name: glutathione import into mitochondrion
namespace: biological_process
def: "The process in which glutathione is transported from the cytosol into the mitochondrial matrix." [PMID:34707288]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034775 ! glutathione transmembrane transport
created_by: rynl
creation_date: 2021-11-11T22:53:16Z
@@ -493982,8 +499600,9 @@
def: "The binding activity of a molecule that brings together an ubiquitin ligase and an ubiquitin ligase-substrate adaptor, permitting those molecules to function in a coordinated way." [PMID:27664236]
synonym: "core protein activity for the CUL-RING ubiquitin ligase complex" NARROW []
synonym: "core protein activity for the Cullin-RING ubiquitin ligase complex" NARROW []
-is_a: GO:0030674 ! protein-macromolecule adaptor activity
+is_a: GO:0140378 ! protein complex scaffold activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24591" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31499" xsd:anyURI
created_by: rynl
creation_date: 2022-12-21T22:41:32Z
@@ -494013,6 +499632,8 @@
name: non-canonical inflammasome complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a non-canonical inflammasome complex." [PMID:27291964]
+xref: Reactome:R-HSA-9948001 "CASP4 inflammasome assembly"
+xref: Reactome:R-HSA-9948011 "CASP5 inflammasome assembly"
is_a: GO:0065003 ! protein-containing complex assembly
created_by: rynl
creation_date: 2023-01-25T22:38:01Z
@@ -494216,7 +499837,7 @@
id: GO:0160096
name: nematode pharyngeal muscle development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the nematode pharyngeal muscle over time, from its formation to the mature structure." [GOC:go_curators]
+def: "The process whose specific outcome is the progression of the nematode pharyngeal muscle over time, from its formation to the mature structure." [GOC:curators]
is_a: GO:0007517 ! muscle organ development
relationship: part_of GO:0160094 ! nematode pharynx development
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18285" xsd:anyURI
@@ -494514,9 +500135,17 @@
name: bis(monoacylglycero)phosphate synthase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 3-acyl-sn-glycero-1-phospho-(1'-sn-glycerol) = 3-acyl-sn-glycero-1-phospho-(3'-acyl-1'-sn-glycerol) + sn-glycero-1-phospho-(1'-sn-glycerol)." [PMID:37708259, RHEA:77619]
+xref: RHEA:77599
+xref: RHEA:77603
+xref: RHEA:77607
+xref: RHEA:77611
xref: RHEA:77619
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:77619
+property_value: skos:narrowMatch RHEA:77599
+property_value: skos:narrowMatch RHEA:77603
+property_value: skos:narrowMatch RHEA:77607
+property_value: skos:narrowMatch RHEA:77611
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26277" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: rynl
@@ -495268,10 +500897,14 @@
synonym: "nitrate reductase Z activity" RELATED [EC:1.7.5.1]
synonym: "quinol-nitrate oxidoreductase activity" RELATED [EC:1.7.5.1]
xref: EC:1.7.5.1
+xref: RHEA:29119
+xref: RHEA:29127
xref: RHEA:56144
is_a: GO:0008940 ! nitrate reductase activity
property_value: skos:exactMatch EC:1.7.5.1
property_value: skos:exactMatch RHEA:56144
+property_value: skos:narrowMatch RHEA:29119
+property_value: skos:narrowMatch RHEA:29127
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27675" xsd:anyURI
created_by: rynl
creation_date: 2024-04-24T22:45:01Z
@@ -495446,6 +501079,7 @@
def: "Catalysis of the reaction: a di-trans,poly-cis-polyprenol + NAD+ = a di-trans,poly-cis-polyprenal + NADH + H+." [PMID:38821050, RHEA:80719]
synonym: "polyprenol dehydrogenase activity" BROAD []
xref: MetaCyc:RXN-24567
+xref: Reactome:R-HSA-9937298 "DHRSX oxidizes polyprenol to polyprenal"
xref: RHEA:80719
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:broadMatch EC:1.1.1.441
@@ -495478,6 +501112,7 @@
def: "Catalysis of the reaction: ditrans,polycis-polyprenal+ H+ + NADPH = ditrans,polycis-dolichal+ NADP." [PMID:38821050, RHEA:80727]
xref: EC:1.3.1.94
xref: MetaCyc:RXN-9971
+xref: Reactome:R-HSA-9937295 "SRD5A3 reduces polyprenal to dolichal"
xref: RHEA:80727
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.94
@@ -495564,10 +501199,11 @@
[Term]
id: GO:0160206
-name: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity
+name: tRNA (cytidine(32)/uridine(32)-2'-O-ribose)-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: cytidine(32)/uridine(32) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(32)/2'-O-methyluridine(32) in tRNA + H+ + S-adenosyl-L-homocysteine." [EC:2.1.1.200]
synonym: "TrMet(Xm32) activity" EXACT []
+synonym: "tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity" EXACT []
xref: EC:2.1.1.200
xref: RHEA:42936
is_a: GO:0016300 ! tRNA (uridine) methyltransferase activity
@@ -495717,11 +501353,8 @@
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions." [PMID:26942675, PMID:36849569, PMID:37754565]
synonym: "negative regulation of acetyl-CoA biosynthetic process from pyruvate" EXACT []
-is_a: GO:0009890 ! negative regulation of biosynthetic process
is_a: GO:0010510 ! regulation of pyruvate decarboxylation to acetyl-CoA
-is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
+is_a: GO:0140391 ! negative regulation of acetyl-CoA biosynthesis
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006086 ! pyruvate decarboxylation to acetyl-CoA
relationship: negatively_regulates GO:0006086 ! pyruvate decarboxylation to acetyl-CoA
@@ -495804,9 +501437,15 @@
synonym: "5-methoxy-2-methyl-3-(all-trans-polyprenyl)benzoquinone,NADH:oxygen oxidoreductase (5-hydroxylating) activity" EXACT []
xref: EC:1.14.13.253
xref: RHEA:81211
+xref: RHEA:82851
+xref: RHEA:82855
+xref: RHEA:82859
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
property_value: skos:exactMatch EC:1.14.13.253
property_value: skos:exactMatch RHEA:81211
+property_value: skos:narrowMatch RHEA:82851
+property_value: skos:narrowMatch RHEA:82855
+property_value: skos:narrowMatch RHEA:82859
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29305" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: rynl
@@ -495957,9 +501596,11 @@
namespace: molecular_function
def: "Catalysis of the reaction: reduced [NADPH-hemoprotein reductase] + O2 + a long-chain fatty aldehyde = oxidized [NADPH-hemoprotein reductase] + CO2 + H2O + H+ + a long-chain alkane." [PMID:22927409, RHEA:83563]
synonym: "aldehyde oxidative decarbonylase activity" BROAD []
+xref: RHEA:83559
xref: RHEA:83563
is_a: GO:0016830 ! carbon-carbon lyase activity
property_value: skos:exactMatch RHEA:83563
+property_value: skos:narrowMatch RHEA:83559
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28217" xsd:anyURI
created_by: rynl
creation_date: 2025-01-22T22:31:47Z
@@ -495993,8 +501634,10 @@
namespace: molecular_function
def: "Catalysis of the reaction: a cardiolipin + NAD+ = a diphosphatidylglycerone + NADH + H+." [PMID:26338420, RHEA:81091]
xref: RHEA:81091
+xref: RHEA:81095
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch RHEA:81091
+property_value: skos:narrowMatch RHEA:81095
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29557" xsd:anyURI
created_by: rynl
creation_date: 2025-01-30T18:41:21Z
@@ -496050,6 +501693,7 @@
name: NADPH-iron-sulfur [2Fe-2S] protein oxidoreductase activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 oxidized [2Fe-2S]-[protein] + NADPH = 2 reduced [2Fe-2S]-[protein] + NADP+ + H+." [RHEA:67716]
+xref: Reactome:R-HSA-2564824 "NADPH reduces NDOR1:CIAPIN1"
xref: RHEA:67716
is_a: GO:0016731 ! oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor
property_value: skos:exactMatch RHEA:67716
@@ -496332,7 +501976,6 @@
namespace: molecular_function
def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(out) + a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(in) + a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out). This reaction results in the exchange of phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between membranes." [PMID:34249917, PMID:39106189, RHEA:81667]
xref: RHEA:81667
-is_a: GO:0008526 ! phosphatidylinositol transfer activity
is_a: GO:0140343 ! phosphatidylserine transfer activity
is_a: GO:7770011 ! lipid exchange activity
property_value: skos:exactMatch RHEA:81667
@@ -496358,9 +502001,11 @@
id: GO:0160272
name: RNA 2',3'-cyclic phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + 2 H2O = a 3'-end ribonucleotide-RNA + phosphate + H+." [PMID:32732418]
+def: "Catalysis of the reaction: a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + 2 H2O = a 3'-end ribonucleotide-RNA + phosphate + H+." [PMID:32732418, RHEA:85011]
+xref: RHEA:85011
is_a: GO:0016791 ! phosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
+property_value: skos:exactMatch RHEA:85011
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28001" xsd:anyURI
created_by: rynl
creation_date: 2025-05-28T05:44:27Z
@@ -496369,11 +502014,13 @@
id: GO:0160273
name: RNA 2'-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + a 3'-end 2'-phospho-ribonucleotide-RNA = a 3'-end ribonucleotide-RNA + phosphate." [PMID:36180430]
+def: "Catalysis of the reaction: H2O + a 3'-end 2'-phospho-ribonucleotide-RNA = a 3'-end ribonucleotide-RNA + phosphate." [PMID:36180430, RHEA:85191]
synonym: "Ribonucleic acid 2'-phosphatase activity" EXACT []
synonym: "RNA 2'-Pase activity" EXACT []
+xref: RHEA:85191
is_a: GO:0016791 ! phosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
+property_value: skos:exactMatch RHEA:85191
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28002" xsd:anyURI
created_by: rynl
creation_date: 2025-05-28T16:38:49Z
@@ -496420,12 +502067,13 @@
id: GO:0160277
name: lumenal side of cis-Golgi cisternae membrane
namespace: cellular_component
-def: "The membrane leaflet of the cis-Golgi cisternae membrane that faces the Golgi lumen and is involved in glycosylation and lumen-facing cargo recognition." [PMID:23913272, PMID:34597626]
+def: "The leaflet of the cis-Golgi cisternae membrane that faces the Golgi lumen, including any protein embedded in, attached to, or peripherally associated with it. This is the site where glycosylation and lumen-facing cargo recognition occur." [PMID:23913272, PMID:34597626]
synonym: "lumenal face of cis-Golgi cisternae membrane" EXACT []
synonym: "lumenal leaflet of cis-Golgi cisternae membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:1990674 ! Golgi cis cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-21T00:29:16Z
@@ -496433,12 +502081,13 @@
id: GO:0160278
name: cytoplasmic side of cis-Golgi cisternae membrane
namespace: cellular_component
-def: "The membrane leaflet of the cis-Golgi cisternae membrane that faces the cytoplasm and is the site of interactions with cytosolic proteins, including those involved in vesicle budding, membrane tethering, and lipid or protein trafficking." [PMID:10922460, PMID:34597626, PMID:39331042]
+def: "The leaflet of the cis-Golgi cisternae membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it. This is the site of interactions with cytosolic proteins, including those involved in vesicle budding, membrane tethering, and lipid or protein trafficking." [PMID:10922460, PMID:34597626, PMID:39331042]
synonym: "cytoplasmic face of cis-Golgi cisternae membrane" EXACT []
synonym: "cytoplasmic leaflet of cis-Golgi cisternae membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:1990674 ! Golgi cis cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30406" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-22T17:19:30Z
@@ -496446,12 +502095,13 @@
id: GO:0160279
name: cytoplasmic side of medial-Golgi cisterna membrane
namespace: cellular_component
-def: "The membrane leaflet of the medial-Golgi cisternae that faces the cytoplasm participates in interactions with cytosolic proteins involved in membrane trafficking, vesicle docking, and cargo sorting." [PMID:28777890, PMID:34597626, PMID:39658747]
+def: "The leaflet of the medial-Golgi cisternae membrane that faces the cytoplasm,including any protein embedded in, attached to, or peripherally associated with it. This is the site of interactions with cytosolic proteins involved in membrane trafficking, vesicle docking, and cargo sorting." [PMID:28777890, PMID:34597626, PMID:39658747]
synonym: "cytoplasmic face of Golgi medial cisterna membrane" EXACT []
synonym: "cytoplasmic leaflet of Golgi medial cisterna membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:1990675 ! Golgi medial cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30407" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-22T21:12:40Z
@@ -496459,12 +502109,13 @@
id: GO:0160280
name: lumenal side of medial-Golgi cisterna membrane
namespace: cellular_component
-def: "The membrane leaflet of the medial-Golgi cisternae that directly contacts the Golgi lumen, hosts glycosyltransferases and enzymes to modify N-linked oligosaccharides by trimming mannose and adding N-acetylglucosamine." [PMID:28777890, PMID:34597626, PMID:36658747, PMID:39331042]
+def: "The leaflet of the medial-Golgi cisternae membrane that faces the Golgi lumen, including any protein embedded in, attached to, or peripherally associated with it. This is the site where protein glycosylation occur." [PMID:28777890, PMID:34597626, PMID:36658747, PMID:39331042]
synonym: "lumenal face of medial-Golgi cisterna membrane" EXACT []
synonym: "lumenal leaflet of Golgi medial cisterna membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:1990675 ! Golgi medial cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30418" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-22T21:36:28Z
@@ -496472,13 +502123,14 @@
id: GO:0160281
name: cytoplasmic side of trans-Golgi network membrane
namespace: cellular_component
-def: "The leaflet of the membrane bilayer of the trans-Golgi network faces the cytoplasm and is crucial for lipid and protein sorting and trafficking, as it interacts with cytoplasmic proteins involved in vesicle formation and targeting." [PMID:10922460, PMID:23913272, PMID:34597626]
+def: "The leaflet of the trans-Golgi network membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it. This is the site of interaction where cytoplasmic proteins interact with proteins involved in vesicle formation and targeting." [PMID:10922460, PMID:23913272, PMID:34597626]
synonym: "cytoplasmic face of trans-Golgi network membrane" EXACT []
synonym: "cytoplasmic leaflet of trans-Golgi network membrane" EXACT []
synonym: "cytoplasmic side of trans-Golgi network" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:0032588 ! trans-Golgi network membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30427" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-22T23:41:33Z
@@ -496486,13 +502138,14 @@
id: GO:0160282
name: lumenal side of trans-Golgi network membrane
namespace: cellular_component
-def: "The membrane leaflet of the trans-Golgi network membrane that faces the Golgi lumen." [PMID:23913272, PMID:34597626, PMID:38307322]
+def: "The leaflet of the trans-Golgi network membrane that faces the Golgi lumen, including any protein embedded in, attached to, or peripherally associated with it." [PMID:23913272, PMID:34597626, PMID:38307322]
synonym: "lumenal face of trans-Golgi network membrane" EXACT []
synonym: "lumenal leaflet of trans-Golgi network membrane" EXACT []
synonym: "lumenal side of trans-Golgi network" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:0032588 ! trans-Golgi network membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30428" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-23T00:11:57Z
@@ -496500,9 +502153,11 @@
id: GO:0160283
name: queuine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of queuine from one side of a membrane to the other according to the reaction: queuine(out) = queuine(in)." [PMID:40526720]
+def: "Enables the transfer of queuine from one side of a membrane to the other according to the reaction: queuine(out) = queuine(in)." [PMID:40526720, RHEA:85679]
+xref: RHEA:85679
is_a: GO:0022857 ! transmembrane transporter activity
relationship: part_of GO:0160284 ! queuine import across plasma membrane
+property_value: skos:exactMatch RHEA:85679
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30470" xsd:anyURI
created_by: rynl
creation_date: 2025-06-24T17:27:38Z
@@ -496522,9 +502177,11 @@
id: GO:0160286
name: queuosine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of queuosine from one side of a membrane to the other according to the reaction: queuosine(out) = queuosine(in)." [PMID:40526720]
+def: "Enables the transfer of queuosine from one side of a membrane to the other according to the reaction: queuosine(out) = queuosine(in)." [PMID:40526720, RHEA:85683]
+xref: RHEA:85683
is_a: GO:0005337 ! nucleoside transmembrane transporter activity
relationship: part_of GO:0160287 ! queuosine import across plasma membrane
+property_value: skos:exactMatch RHEA:85683
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30470" xsd:anyURI
created_by: rynl
creation_date: 2025-06-27T00:30:53Z
@@ -496544,13 +502201,14 @@
id: GO:0160288
name: cytoplasmic side of trans-Golgi cisterna membrane
namespace: cellular_component
-def: "The membrane leaflet of the trans-Golgi cisternae that faces the cytoplasm. It is the site of protein and lipid interaction, vesicle formation, and cargo sorting towards post-Golgi destinations such as endosomes, lysosomes, and the plasma membrane." [PMID:23913272, PMID:34597626, PMID:37566051]
+def: "The leaflet of the trans-Golgi cisternae membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it. This is the site where vesicle formation, and cargo sorting towards post-Golgi destinations such as endosomes, lysosomes and the plasma membrane occur." [PMID:23913272, PMID:34597626, PMID:37566051]
synonym: "cytoplasmic face of Golgi trans cisterna membrane" EXACT []
synonym: "cytoplasmic leaflet of Golgi trans cisterna membrane" EXACT []
synonym: "cytoplasmic side of Golgi trans cisternae membrane" EXACT []
is_a: GO:0098562 ! cytoplasmic side of membrane
relationship: part_of GO:1990676 ! Golgi trans cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30509" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-27T05:51:59Z
@@ -496558,13 +502216,14 @@
id: GO:0160289
name: lumenal side of trans-Golgi cisternae membrane
namespace: cellular_component
-def: "The membrane leaflet of the trans-Golgi cisternae membrane that faces the Golgi lumen. It is involved in the final steps of glycan processing, proteolytic modification, and cargo maturation prior to sorting at the trans-Golgi network." [PMID:34597626, PMID:38307322, PMID:6121819]
+def: "The leaflet of the trans-Golgi cisternae membrane that faces the Golgi lumen, including any protein embedded in, attached to, or peripherally associated with it. This is the site where the final steps of glycan processing, proteolytic modification, and cargo maturation prior to sorting at the trans-Golgi network occur." [PMID:34597626, PMID:38307322, PMID:6121819]
synonym: "lumenal face of trans-Golgi cisternae membrane" EXACT []
synonym: "lumenal leaflet of trans-Golgi cisternae membrane" EXACT []
synonym: "lumenal side of Golgi trans cisternae membrane" EXACT []
is_a: GO:0098576 ! lumenal side of membrane
relationship: part_of GO:1990676 ! Golgi trans cisterna membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30510" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: rynl
creation_date: 2025-06-27T06:11:48Z
@@ -496584,10 +502243,12 @@
id: GO:0160291
name: phosphatidylinositol-4-phosphate-cholesterol exchange activity
namespace: molecular_function
-def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(out) + cholesterol(in) = 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(in) + cholesterol(out). This reaction results in the exchange of cholesterol for phosphatidylinositol-4-phosphate (PI(4)P) between membranes." [PMID:24209621, PMID:29596003]
-is_a: GO:0008526 ! phosphatidylinositol transfer activity
+def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(out) + cholesterol(in) = 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol 4-phosphate)(in) + cholesterol(out). This reaction results in the exchange of cholesterol for phosphatidylinositol-4-phosphate (PI(4)P) between membranes." [PMID:24209621, PMID:29596003, RHEA:84179]
+xref: RHEA:84179
+is_a: GO:0120014 ! phospholipid transfer activity
is_a: GO:0120020 ! cholesterol transfer activity
is_a: GO:7770011 ! lipid exchange activity
+property_value: skos:exactMatch RHEA:84179
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30432" xsd:anyURI
created_by: rynl
@@ -496663,9 +502324,13 @@
id: GO:0160298
name: pyridinol guanylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-carboxymethyl-3,5-dimethyl-4-hydroxypyridin-2-ol + GTP + H+ = guanylylpyridinol + diphosphate." [PMID:24249552]
+def: "Catalysis of the reaction: 6-carboxymethyl-3,5-dimethyl-4-hydroxypyridin-2-ol + GTP + H+ = guanylylpyridinol + diphosphate." [PMID:24249552, RHEA:85479]
+xref: EC:2.7.7.109
xref: KEGG_REACTION:R13518
+xref: RHEA:85479
is_a: GO:0070568 ! guanylyltransferase activity
+property_value: skos:exactMatch EC:2.7.7.109
+property_value: skos:exactMatch RHEA:85479
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30718" xsd:anyURI
created_by: rynl
creation_date: 2025-08-21T00:46:39Z
@@ -496685,9 +502350,13 @@
id: GO:0160301
name: guanylylpyridinol adenylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: guanylylpyridinol + ATP + H+ = guanylylpyridinol-AMP + diphosphate." [PMID:25882909]
+def: "Catalysis of the reaction: guanylylpyridinol + ATP + H+ = guanylylpyridinol-AMP + diphosphate." [PMID:25882909, RHEA:85487]
+xref: EC:2.7.7.110
xref: KEGG_REACTION:R13520
+xref: RHEA:85487
is_a: GO:0016779 ! nucleotidyltransferase activity
+property_value: skos:exactMatch EC:2.7.7.110
+property_value: skos:exactMatch RHEA:85487
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30720" xsd:anyURI
created_by: rynl
creation_date: 2025-08-21T22:49:37Z
@@ -496696,9 +502365,11 @@
id: GO:0160302
name: 6-carboxymethyl-5-methyl-4-hydroxypyridin-2-ol 3-C-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 6-carboxymethyl-5-methyl-4-hydroxypyridin-2-ol + S-adenosyl-L-methionine = 6-carboxymethyl-3,5-dimethyl-4-hydroxypyridin-2-ol + S-adenosyl-L-homocysteine + H+." [PMID:27391308]
+def: "Catalysis of the reaction: 6-carboxymethyl-5-methyl-4-hydroxypyridin-2-ol + S-adenosyl-L-methionine = 6-carboxymethyl-3,5-dimethyl-4-hydroxypyridin-2-ol + S-adenosyl-L-homocysteine + H+." [PMID:27391308, RHEA:85483]
xref: KEGG_REACTION:R13499
+xref: RHEA:85483
is_a: GO:0008168 ! methyltransferase activity
+property_value: skos:exactMatch RHEA:85483
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30721" xsd:anyURI
created_by: rynl
creation_date: 2025-08-21T23:15:13Z
@@ -496721,9 +502392,11 @@
id: GO:0160304
name: 4-vinylphenol methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-vinylphenol + S-adenosyl-L-methionine = 4-vinylanisole + S-adenosyl-L-homocysteine + H+." [PMID:40562929]
+def: "Catalysis of the reaction: 4-vinylphenol + S-adenosyl-L-methionine = 4-vinylanisole + S-adenosyl-L-homocysteine + H+." [PMID:40562929, RHEA:86075]
+xref: RHEA:86075
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
+property_value: skos:exactMatch RHEA:86075
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30708" xsd:anyURI
created_by: rynl
creation_date: 2025-08-23T00:16:21Z
@@ -496789,6 +502462,39 @@
creation_date: 2025-11-19T23:57:27Z
[Term]
+id: GO:0160310
+name: dopamine loading into synaptic vesicle
+namespace: biological_process
+def: "The active transport of dopamine neurotransmitters into a synaptic vesicle." [PMID:29666153]
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
+is_a: GO:0015872 ! dopamine transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+created_by: rynl
+creation_date: 2025-12-02T22:02:35Z
+
+[Term]
+id: GO:0160311
+name: tyramine loading into synaptic vesicle
+namespace: biological_process
+def: "The active transport of tyramine neurotransmitters into a synaptic vesicle." [PMID:15849736, PMID:9870940]
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
+is_a: GO:7770032 ! tyramine transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+created_by: rynl
+creation_date: 2025-12-02T23:16:14Z
+
+[Term]
+id: GO:0160312
+name: octopamine loading into synaptic vesicle
+namespace: biological_process
+def: "The active transport of octopamine neurotransmitters into a synaptic vesicle." [PMID:15849736, PMID:9870940]
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
+is_a: GO:7770033 ! octopamine transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+created_by: rynl
+creation_date: 2025-12-02T23:21:33Z
+
+[Term]
id: GO:0160313
name: endosomal intralumenal vesicle
namespace: cellular_component
@@ -496890,17 +502596,13 @@
[Term]
id: GO:0160320
-name: protein-tyrosine iodotransferase activity
+name: obsolete protein-tyrosine iodotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: [thyroglobulin]-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3-iodo-L-tyrosine + 2 H2O and [thyroglobulin]-3-iodo-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3,5-diiodo-L-tyrosine + 2 H2O." [PMID:36537574, PMID:8651700]
-xref: RHEA:48956
-xref: RHEA:48960
-is_a: GO:0140905 ! haloperoxidase activity
-property_value: skos:narrowMatch RHEA:48956
-property_value: skos:narrowMatch RHEA:48960
+def: "OBSOLETE. Catalysis of the reaction: [thyroglobulin]-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3-iodo-L-tyrosine + 2 H2O and [thyroglobulin]-3-iodo-L-tyrosine + iodide + H2O2 + H+ = [thyroglobulin]-3,5-diiodo-L-tyrosine + 2 H2O." [PMID:36537574, PMID:8651700]
+comment: The reason for obsoletion is that the reactions covered by this term (RHEA:48956 and RHEA:48960) are now subsumed by the updated GO:0004447 (iodide peroxidase activity), which covers all 5 thyroid peroxidase reactions.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30596" xsd:anyURI
-created_by: rynl
-creation_date: 2026-01-21T23:56:40Z
+is_obsolete: true
+replaced_by: GO:0004447
[Term]
id: GO:0170001
@@ -496970,6 +502672,8 @@
name: endoplasmic reticulum-lipid droplet tether activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together a lipid droplet with an endoplasmic reticulum membrane, via membrane lipid binding, to establish membrane contact sites and mediate exchange and communication." [PMID:35389430]
+xref: Reactome:R-HSA-8857686 "FITM2 binds TAGs"
+xref: Reactome:R-HSA-9942190 "FITM1 binds TAGs"
is_a: GO:0043495 ! protein-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25428" xsd:anyURI
created_by: ew
@@ -497135,6 +502839,8 @@
def: "The chemical reactions and pathways involving an L-amino acid." [GOC:edw]
synonym: "L-alpha-amino acid metabolism" EXACT []
synonym: "L-amino acid metabolism" EXACT []
+xref: Reactome:R-HSA-8963693 "Aspartate and asparagine metabolism"
+xref: Reactome:R-HSA-8964539 "Glutamate and glutamine metabolism"
is_a: GO:1901605 ! alpha-amino acid metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23268" xsd:anyURI
created_by: ew
@@ -497174,6 +502880,7 @@
name: import into the mitochondrion
namespace: biological_process
def: "The directed movement of substances from the cytosol into the mitochondrion." [GOC:ew]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:1990542 ! mitochondrial transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26201" xsd:anyURI
created_by: ew
@@ -497184,6 +502891,7 @@
name: export from the mitochondrion
namespace: biological_process
def: "The directed movement of substances from the mitochondrion to the cytosol." [GOC:ew]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:1990542 ! mitochondrial transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26201" xsd:anyURI
created_by: ew
@@ -497278,7 +502986,6 @@
def: "Enables the transfer of isopentenyl pyrophosphate from one side of a membrane to the other." [GOC:ew, PMID:37813972]
synonym: "IPP transmembrane transport activity" EXACT []
synonym: "isopentenyl diphosphate transmembrane transport activity" EXACT []
-is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
is_a: GO:0170055 ! lipid transmembrane transporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26285" xsd:anyURI
@@ -497393,7 +503100,6 @@
namespace: molecular_function
def: "Enables the transfer of a lipid from one side of a membrane to the other." [GOC:curators]
subset: gocheck_do_not_annotate
-is_a: GO:0005319 ! lipid transporter activity
is_a: GO:0022857 ! transmembrane transporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27252" xsd:anyURI
created_by: ew
@@ -497479,7 +503185,9 @@
name: transmembrane transport from lysosomal lumen to cytosol
namespace: biological_process
def: "The directed movement of a solute from the lysosomal lumen across the lysosomal membrane and into the cytosol." [PMID:26631267]
+synonym: "export from lysosome lumen to cytosol" EXACT []
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20070" xsd:anyURI
created_by: ew
@@ -497512,15 +503220,16 @@
[Term]
id: GO:0170067
-name: L-arginine biosynthetic process via N-acetyl-L-citrulline
+name: obsolete L-arginine biosynthetic process via N-acetyl-L-citrulline
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound N-acetyl-L-citrulline." [PMID:16585758]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound N-acetyl-L-citrulline." [PMID:16585758]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "arginine biosynthesis via N-acetyl intermediates" EXACT []
synonym: "arginine biosynthesis, N-acetylated pathway" EXACT []
-xref: MetaCyc:PWY-5154
-is_a: GO:0006526 ! L-arginine biosynthetic process
-property_value: skos:exactMatch MetaCyc:PWY-5154
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29602" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006526
created_by: ew
creation_date: 2025-03-14T17:04:09Z
@@ -497583,6 +503292,35 @@
creation_date: 2025-08-12T21:56:57Z
[Term]
+id: GO:0170074
+name: RADAR pathway
+namespace: biological_process
+def: "A quality control pathway that degrades peroxisomal matrix protein receptors when the recycling machinery is blocked. When recycling to the cytosol fails, cargo-free receptors accumulate at the peroxisomal membrane, where they are polyubiquitinated and subsequently degraded by the ubiquitin-proteasome system (UPS)." [PMID:16390998, PMID:17011644, PMID:41076631]
+synonym: "Receptor Accumulation and Degradation in the Absence of Recycling" EXACT []
+is_a: GO:0043161 ! proteasome-mediated ubiquitin-dependent protein catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31570" xsd:anyURI
+created_by: ew
+creation_date: 2026-02-17T22:02:27Z
+
+[Term]
+id: GO:0170075
+name: negative regluation of nuclear-transribed mRNA catabolic process, no-go decay
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, no-go decay." [PMID:41607283]
+synonym: "negative regulation of no-go decay" EXACT []
+synonym: "negative regulation of no-go mRNA decay" EXACT []
+synonym: "negative regulation of nuclear-transcribed mRNA breakdown, no-go decay" EXACT []
+synonym: "negative regulation of nuclear-transcribed mRNA catabolism, no-go decay" EXACT []
+synonym: "negative regulation of nuclear-transcribed mRNA degradation, no-go decay" EXACT []
+is_a: GO:1902373 ! negative regulation of mRNA catabolic process
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: negatively_regulates GO:0070966 ! nuclear-transcribed mRNA catabolic process, no-go decay
+relationship: negatively_regulates GO:0070966 ! nuclear-transcribed mRNA catabolic process, no-go decay
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31747" xsd:anyURI
+created_by: ew
+creation_date: 2026-03-23T21:12:37Z
+
+[Term]
id: GO:0180000
name: histone methyltransferase inhibitor activity
namespace: molecular_function
@@ -497729,6 +503467,7 @@
def: "Any process involved in transcription termination-coupled 3' processing of RNA polymerase II mRNA transcripts by the 3' end cleavage and addition of a poly(A) tail." [PMID:31499460]
synonym: "cotranscriptional 3' processing of RNA polymerase II mRNA transcripts" EXACT []
synonym: "mRNA polyadenylation" RELATED []
+xref: Reactome:R-HSA-9770562 "mRNA Polyadenylation"
is_a: GO:0031124 ! mRNA 3'-end processing
is_a: GO:0180012 ! co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24921" xsd:anyURI
@@ -497853,7 +503592,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + U6 snRNA = S-adenosyl-L-homocysteine + U6 containing a 3'-terminal 2'-O-methylnucleotide + H+." [PMID:37403782, RHEA:63088]
xref: RHEA:63088
-is_a: GO:0090486 ! small RNA 2'-O-methyltransferase activity
+is_a: GO:0090486 ! small RNA 2'-O-ribose methyltransferase activity
property_value: skos:exactMatch RHEA:63088
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25706" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -498110,6 +503849,7 @@
name: polyphosphate import into vacuole
namespace: biological_process
def: "The directed movement of polyphosphate into the vacuole across the vacuolar membrane." [PMID:37066886]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015698 ! inorganic anion transport
is_a: GO:0034486 ! vacuolar transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27870" xsd:anyURI
@@ -498402,6 +504142,21 @@
creation_date: 2025-06-27T07:22:01Z
[Term]
+id: GO:0180067
+name: terreate biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of terreate, a fungal metabolite with ecological, antimicrobial, antiproliferative, and antioxidative activities." [PMID:25265334]
+synonym: "terreic acid biosynthetic process" RELATED []
+is_a: GO:0097176 ! epoxide metabolic process
+is_a: GO:0120255 ! olefinic compound biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+is_a: GO:1901663 ! quinone biosynthetic process
+is_a: GO:1902645 ! tertiary alcohol biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31114" xsd:anyURI
+created_by: PomBase:vw
+creation_date: 2026-02-23T10:27:33Z
+
+[Term]
id: GO:0180068
name: negative regulation of carbohydrate utilization
namespace: biological_process
@@ -498412,6 +504167,20 @@
creation_date: 2026-01-19T11:52:03Z
[Term]
+id: GO:0180069
+name: positive regulation of terreate biosynthetic process
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of terreate." [PMID:25265334]
+is_a: GO:0010566 ! regulation of ketone biosynthetic process
+is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: positively_regulates GO:0180067 ! terreate biosynthetic process
+relationship: positively_regulates GO:0180067 ! terreate biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31114" xsd:anyURI
+created_by: PomBase:vw
+creation_date: 2026-02-23T15:24:17Z
+
+[Term]
id: GO:0198738
name: obsolete cell-cell signaling by wnt
namespace: biological_process
@@ -506319,7 +512088,7 @@
id: GO:1900371
name: regulation of purine nucleotide biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:go_curators, GOC:TermGenie]
+def: "Any process that modulates the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:curators, GOC:TermGenie]
synonym: "regulation of purine nucleotide anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of purine nucleotide biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of purine nucleotide formation" EXACT [GOC:TermGenie]
@@ -506336,7 +512105,7 @@
id: GO:1900372
name: negative regulation of purine nucleotide biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:go_curators, GOC:TermGenie]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:curators, GOC:TermGenie]
synonym: "down regulation of purine nucleotide anabolism" EXACT [GOC:TermGenie]
synonym: "down regulation of purine nucleotide biosynthesis" EXACT [GOC:TermGenie]
synonym: "down regulation of purine nucleotide biosynthetic process" EXACT [GOC:TermGenie]
@@ -506374,7 +512143,7 @@
id: GO:1900373
name: positive regulation of purine nucleotide biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:go_curators, GOC:TermGenie]
+def: "Any process that activates or increases the frequency, rate or extent of purine nucleotide biosynthetic processes." [GOC:curators, GOC:TermGenie]
synonym: "activation of purine nucleotide anabolism" EXACT [GOC:TermGenie]
synonym: "activation of purine nucleotide biosynthesis" EXACT [GOC:TermGenie]
synonym: "activation of purine nucleotide biosynthetic process" NARROW [GOC:TermGenie]
@@ -506412,7 +512181,7 @@
id: GO:1900374
name: obsolete positive regulation of mating type switching by regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching." [GOC:go_curators, GOC:TermGenie, PMID:8804308]
+def: "OBSOLETE. A regulation of transcription from RNA polymerase II promoter that results in positive regulation of mating type switching." [GOC:curators, GOC:TermGenie, PMID:8804308]
comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of mating type switching by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
synonym: "stimulation of mating type switching by regulation of transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
@@ -506427,7 +512196,7 @@
id: GO:1900375
name: obsolete positive regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "OBSOLETE. A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of inositol biosynthetic process." [GOC:go_curators, GOC:TermGenie, PMID:2004420]
+def: "OBSOLETE. A positive regulation of transcription from RNA polymerase II promoter that results in positive regulation of inositol biosynthetic process." [GOC:curators, GOC:TermGenie, PMID:2004420]
comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "activation of inositol anabolism by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "activation of inositol biosynthesis by positive regulation of transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
@@ -507294,12 +513063,14 @@
name: regulation of alcohol catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of alcohol catabolic process within a cell." [GOC:TermGenie]
+subset: gocheck_do_not_annotate
is_a: GO:0009894 ! regulation of catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0046164 ! alcohol catabolic process
relationship: regulates GO:0046164 ! alcohol catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: krc
creation_date: 2012-04-20T10:21:18Z
@@ -507308,6 +513079,7 @@
name: negative regulation of alcohol catabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of alcohol catabolic process within a cell." [GOC:TermGenie]
+subset: gocheck_do_not_annotate
synonym: "down regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "down-regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "downregulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
@@ -507318,6 +513090,7 @@
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0046164 ! alcohol catabolic process
relationship: negatively_regulates GO:0046164 ! alcohol catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: krc
creation_date: 2012-04-20T10:21:28Z
@@ -507326,6 +513099,7 @@
name: positive regulation of alcohol catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of alcohol catabolic process within a cell." [GOC:TermGenie]
+subset: gocheck_do_not_annotate
synonym: "activation of cellular alcohol catabolic process" NARROW [GOC:TermGenie]
synonym: "up regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellular alcohol catabolic process" EXACT [GOC:TermGenie]
@@ -507337,6 +513111,7 @@
intersection_of: positively_regulates GO:0046164 ! alcohol catabolic process
relationship: positively_regulates GO:0046164 ! alcohol catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: krc
creation_date: 2012-04-20T10:21:46Z
@@ -507432,6 +513207,7 @@
synonym: "negative regulation of defence response to bacterium" EXACT [GOC:TermGenie]
synonym: "negative regulation of defense response to bacteria" EXACT [GOC:TermGenie]
synonym: "negative regulation of defense response to bacterium, incompatible interaction" NARROW []
+xref: Reactome:R-HSA-9968551 "Regulation of GBP-mediated host defense"
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
@@ -509733,7 +515509,21 @@
synonym: "protoheme catabolic process" EXACT []
synonym: "protoheme degradation" EXACT []
xref: MetaCyc:PWY-5874
+xref: MetaCyc:PWY-7843
+xref: MetaCyc:PWY-7844
+xref: MetaCyc:PWY-7845
+xref: MetaCyc:PWY-7846
+xref: MetaCyc:PWY-7847
+xref: MetaCyc:PWY-7848
is_a: GO:0042167 ! heme catabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5874
+property_value: skos:narrowMatch MetaCyc:PWY-7843
+property_value: skos:narrowMatch MetaCyc:PWY-7844
+property_value: skos:narrowMatch MetaCyc:PWY-7845
+property_value: skos:narrowMatch MetaCyc:PWY-7846
+property_value: skos:narrowMatch MetaCyc:PWY-7847
+property_value: skos:narrowMatch MetaCyc:PWY-7848
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: pr
creation_date: 2012-05-14T12:35:18Z
@@ -515476,14 +521266,15 @@
[Term]
id: GO:1900829
-name: D-tyrosine catabolic process
+name: obsolete D-tyrosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-tyrosine." [GOC:TermGenie, PMID:10766779]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-tyrosine." [GOC:TermGenie, PMID:10766779]
+comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-tyrosine.
synonym: "D-tyrosine breakdown" EXACT [GOC:TermGenie]
synonym: "D-tyrosine catabolism" EXACT [GOC:TermGenie]
synonym: "D-tyrosine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009074 ! aromatic amino acid family catabolic process
-is_a: GO:0019478 ! D-amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
created_by: se
creation_date: 2012-06-06T09:27:24Z
@@ -515516,28 +521307,30 @@
[Term]
id: GO:1900832
-name: D-leucine catabolic process
+name: obsolete D-leucine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-leucine." [GOC:TermGenie, PMID:10918062]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-leucine." [GOC:TermGenie, PMID:10918062]
+comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-leucine.
synonym: "D-leucine breakdown" EXACT [GOC:TermGenie]
synonym: "D-leucine catabolism" EXACT [GOC:TermGenie]
synonym: "D-leucine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
-is_a: GO:0019478 ! D-amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
created_by: se
creation_date: 2012-06-06T09:37:40Z
[Term]
id: GO:1900833
-name: D-leucine biosynthetic process
+name: obsolete D-leucine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of D-leucine." [GOC:TermGenie, PMID:10918062]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of D-leucine." [GOC:TermGenie, PMID:10918062]
+comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
synonym: "D-leucine anabolism" EXACT [GOC:TermGenie]
synonym: "D-leucine biosynthesis" EXACT [GOC:TermGenie]
synonym: "D-leucine formation" EXACT [GOC:TermGenie]
synonym: "D-leucine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
-is_a: GO:0046437 ! D-amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
created_by: se
creation_date: 2012-06-06T09:37:47Z
@@ -519781,44 +525574,46 @@
[Term]
id: GO:1901052
-name: sarcosine metabolic process
+name: obsolete sarcosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
+def: "OBSOLETE. The chemical reactions and pathways involving sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
+comment: This term was obsoleted because sarcosine is an intermediate and byproduct in glycine synthesis and degradation.
synonym: "sarcosine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+consider: GO:0006545
+consider: GO:0006546
created_by: yaf
creation_date: 2012-06-28T04:52:04Z
[Term]
id: GO:1901053
-name: sarcosine catabolic process
+name: obsolete sarcosine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:17951379]
+comment: This term was obsoleted because there is no evidence that a specific pathway for sarcosine degradation exists.
synonym: "sarcosine breakdown" EXACT [GOC:TermGenie]
synonym: "sarcosine catabolism" EXACT [GOC:TermGenie]
synonym: "sarcosine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0042219 ! modified amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
-is_a: GO:1901052 ! sarcosine metabolic process
-is_a: GO:1901606 ! alpha-amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
created_by: yaf
creation_date: 2012-06-28T04:52:29Z
[Term]
id: GO:1901054
-name: sarcosine biosynthetic process
+name: obsolete sarcosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:31402327]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of sarcosine." [GOC:TermGenie, GOC:yaf, PMID:31402327]
+comment: This term was obsoleted because sarcosine is an intermediate and byproduct in glycine synthesis and degradation.
synonym: "sarcosine anabolism" EXACT [GOC:TermGenie]
synonym: "sarcosine biosynthesis" EXACT [GOC:TermGenie]
synonym: "sarcosine formation" EXACT [GOC:TermGenie]
synonym: "sarcosine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0042398 ! modified amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
-is_a: GO:1901052 ! sarcosine metabolic process
-is_a: GO:1901607 ! alpha-amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
+consider: GO:0006545
+consider: GO:0006546
created_by: yaf
creation_date: 2012-06-28T04:52:37Z
@@ -526262,8 +532057,9 @@
synonym: "regulation of tetrapyrrole biosynthesis from glutamate" EXACT [GOC:TermGenie]
synonym: "regulation of tetrapyrrole formation from glutamate" EXACT [GOC:TermGenie]
synonym: "regulation of tetrapyrrole synthesis from glutamate" EXACT [GOC:TermGenie]
+is_a: GO:0006521 ! regulation of amino acid metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:1901463 ! regulation of tetrapyrrole biosynthetic process
-is_a: GO:2000211 ! regulation of glutamate metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0033526 ! tetrapyrrole biosynthetic process from glutamate
relationship: regulates GO:0033526 ! tetrapyrrole biosynthetic process from glutamate
@@ -526299,9 +532095,10 @@
synonym: "negative regulation of tetrapyrrole biosynthesis from glutamate" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole formation from glutamate" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole synthesis from glutamate" EXACT [GOC:TermGenie]
+is_a: GO:0045763 ! negative regulation of amino acid metabolic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1901410 ! regulation of tetrapyrrole biosynthetic process from glutamate
is_a: GO:1901464 ! negative regulation of tetrapyrrole biosynthetic process
-is_a: GO:2000212 ! negative regulation of glutamate metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0033526 ! tetrapyrrole biosynthetic process from glutamate
relationship: negatively_regulates GO:0033526 ! tetrapyrrole biosynthetic process from glutamate
@@ -527525,7 +533322,7 @@
name: azole transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0045118
-def: "Enables the directed movement of azoles, heterocyclic compound found in many biologically important substances, from one side of a membrane to the other." [GOC:go_curators, ISBN:3527307206, Wikipedia:Azole]
+def: "Enables the directed movement of azoles, heterocyclic compound found in many biologically important substances, from one side of a membrane to the other." [GOC:curators, ISBN:3527307206, Wikipedia:Azole]
synonym: "azole transporter activity" RELATED []
is_a: GO:0022857 ! transmembrane transporter activity
relationship: part_of GO:0045117 ! azole transmembrane transport
@@ -527843,16 +533640,13 @@
[Term]
id: GO:1901494
-name: regulation of cysteine metabolic process
+name: obsolete regulation of cysteine metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cysteine metabolic process." [GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cysteine metabolic process." [GOC:TermGenie]
+comment: This term was obsoleted because it was an unnecessray grouping term.
synonym: "regulation of cysteine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0042762 ! regulation of sulfur metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006534 ! cysteine metabolic process
-relationship: regulates GO:0006534 ! cysteine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31281" xsd:anyURI
+is_obsolete: true
created_by: vw
creation_date: 2012-10-16T14:28:42Z
@@ -528870,7 +534664,6 @@
namespace: biological_process
def: "OBSOLETE. The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie]
comment: The reason for obsoletion is that this term was an unnecessary grouping term.
-xref: Reactome:R-HSA-71291 "Metabolism of amino acids and derivatives"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI
is_obsolete: true
@@ -530336,7 +536129,7 @@
name: quinone metabolic process
namespace: biological_process
alt_id: GO:0042375
-def: "The chemical reactions and pathways involving quinone." [GOC:go_curators, GOC:pr, GOC:TermGenie]
+def: "The chemical reactions and pathways involving quinone." [GOC:curators, GOC:pr, GOC:TermGenie]
synonym: "quinone cofactor metabolic process" RELATED []
synonym: "quinone cofactor metabolism" RELATED []
synonym: "quinone metabolism" EXACT [GOC:TermGenie]
@@ -530349,7 +536142,7 @@
name: quinone catabolic process
namespace: biological_process
alt_id: GO:0042378
-def: "The chemical reactions and pathways resulting in the breakdown of quinone." [GOC:go_curators, GOC:pr, GOC:TermGenie]
+def: "The chemical reactions and pathways resulting in the breakdown of quinone." [GOC:curators, GOC:pr, GOC:TermGenie]
synonym: "quinone breakdown" EXACT [GOC:TermGenie]
synonym: "quinone catabolism" EXACT [GOC:TermGenie]
synonym: "quinone cofactor breakdown" RELATED []
@@ -531282,8 +537075,12 @@
synonym: "L-glutamine biosynthesis" EXACT [GOC:TermGenie]
synonym: "L-glutamine formation" EXACT [GOC:TermGenie]
synonym: "L-glutamine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0006541 ! glutamine metabolic process
+xref: MetaCyc:GLNSYN-PWY
+is_a: GO:0006541 ! L-glutamine metabolic process
is_a: GO:0009084 ! L-glutamine family amino acid biosynthetic process
+property_value: skos:broadMatch MetaCyc:PWY-5505
+property_value: skos:narrowMatch MetaCyc:GLNSYN-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: pde
creation_date: 2012-12-13T23:32:52Z
@@ -531296,8 +537093,21 @@
synonym: "L-isoleucine biosynthesis" EXACT [GOC:TermGenie]
synonym: "L-isoleucine formation" EXACT [GOC:TermGenie]
synonym: "L-isoleucine synthesis" EXACT [GOC:TermGenie]
+xref: MetaCyc:ILEUSYN-PWY
+xref: MetaCyc:PWY-5101
+xref: MetaCyc:PWY-5103
+xref: MetaCyc:PWY-5104
+xref: MetaCyc:PWY-5108
+is_a: GO:0006549 ! isoleucine metabolic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
-is_a: GO:0009097 ! isoleucine biosynthetic process
+is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
+property_value: skos:narrowMatch MetaCyc:ILEUSYN-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-5101
+property_value: skos:narrowMatch MetaCyc:PWY-5103
+property_value: skos:narrowMatch MetaCyc:PWY-5104
+property_value: skos:narrowMatch MetaCyc:PWY-5108
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30848" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
created_by: pde
creation_date: 2012-12-13T23:32:56Z
@@ -531520,30 +537330,30 @@
[Term]
id: GO:1901715
-name: regulation of gamma-aminobutyric acid catabolic process
+name: regulation of GABA catabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of gamma-aminobutyric acid catabolic process." [GOC:TermGenie]
synonym: "regulation of 4-aminobutanoate catabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of 4-aminobutanoate catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of 4-aminobutyrate catabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of 4-aminobutyrate catabolism" EXACT [GOC:TermGenie]
-synonym: "regulation of GABA catabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of GABA catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of gamma-aminobutyric acid breakdown" EXACT [GOC:TermGenie]
+synonym: "regulation of gamma-aminobutyric acid catabolic process" EXACT [GOC:TermGenie]
synonym: "regulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie]
is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:0009894 ! regulation of catabolic process
is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
-relationship: regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
+intersection_of: regulates GO:0009450 ! GABA catabolic process
+relationship: regulates GO:0009450 ! GABA catabolic process
created_by: mcc
creation_date: 2012-12-19T16:13:24Z
[Term]
id: GO:1901716
-name: negative regulation of gamma-aminobutyric acid catabolic process
+name: negative regulation of GABA catabolic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of gamma-aminobutyric acid catabolic process." [GOC:TermGenie]
synonym: "down regulation of 4-aminobutanoate catabolic process" EXACT [GOC:TermGenie]
@@ -531590,24 +537400,24 @@
synonym: "negative regulation of 4-aminobutanoate catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of 4-aminobutyrate catabolic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of 4-aminobutyrate catabolism" EXACT [GOC:TermGenie]
-synonym: "negative regulation of GABA catabolic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of GABA catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of gamma-aminobutyric acid breakdown" EXACT [GOC:TermGenie]
+synonym: "negative regulation of gamma-aminobutyric acid catabolic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie]
is_a: GO:0009895 ! negative regulation of catabolic process
is_a: GO:0045763 ! negative regulation of amino acid metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-is_a: GO:1901715 ! regulation of gamma-aminobutyric acid catabolic process
+is_a: GO:1901715 ! regulation of GABA catabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
-relationship: negatively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
+intersection_of: negatively_regulates GO:0009450 ! GABA catabolic process
+relationship: negatively_regulates GO:0009450 ! GABA catabolic process
created_by: mcc
creation_date: 2012-12-19T16:13:31Z
[Term]
id: GO:1901717
-name: positive regulation of gamma-aminobutyric acid catabolic process
+name: positive regulation of GABA catabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of gamma-aminobutyric acid catabolic process." [GOC:TermGenie]
synonym: "activation of 4-aminobutanoate catabolic process" EXACT [GOC:TermGenie]
@@ -531624,9 +537434,9 @@
synonym: "positive regulation of 4-aminobutanoate catabolism" EXACT [GOC:TermGenie]
synonym: "positive regulation of 4-aminobutyrate catabolic process" EXACT [GOC:TermGenie]
synonym: "positive regulation of 4-aminobutyrate catabolism" EXACT [GOC:TermGenie]
-synonym: "positive regulation of GABA catabolic process" EXACT [GOC:TermGenie]
synonym: "positive regulation of GABA catabolism" EXACT [GOC:TermGenie]
synonym: "positive regulation of gamma-aminobutyric acid breakdown" EXACT [GOC:TermGenie]
+synonym: "positive regulation of gamma-aminobutyric acid catabolic process" EXACT [GOC:TermGenie]
synonym: "positive regulation of gamma-aminobutyric acid catabolism" EXACT [GOC:TermGenie]
synonym: "positive regulation of gamma-aminobutyric acid degradation" EXACT [GOC:TermGenie]
synonym: "up regulation of 4-aminobutanoate catabolic process" EXACT [GOC:TermGenie]
@@ -531662,10 +537472,10 @@
is_a: GO:0009896 ! positive regulation of catabolic process
is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
-is_a: GO:1901715 ! regulation of gamma-aminobutyric acid catabolic process
+is_a: GO:1901715 ! regulation of GABA catabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
-relationship: positively_regulates GO:0009450 ! gamma-aminobutyric acid catabolic process
+intersection_of: positively_regulates GO:0009450 ! GABA catabolic process
+relationship: positively_regulates GO:0009450 ! GABA catabolic process
created_by: mcc
creation_date: 2012-12-19T16:13:36Z
@@ -533560,6 +539370,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving nicotinate." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00830]
synonym: "nicotinate metabolism" EXACT [GOC:TermGenie]
+xref: Reactome:R-HSA-196807 "Nicotinate metabolism"
is_a: GO:0009820 ! alkaloid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0072524 ! pyridine-containing compound metabolic process
@@ -533574,10 +539385,17 @@
synonym: "nicotinate breakdown" EXACT [GOC:TermGenie]
synonym: "nicotinate catabolism" EXACT [GOC:TermGenie]
synonym: "nicotinate degradation" EXACT [GOC:TermGenie]
+xref: MetaCyc:PWY-5033
+xref: MetaCyc:PWY-5055
+xref: MetaCyc:PWY-722
is_a: GO:0009822 ! alkaloid catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:0072526 ! pyridine-containing compound catabolic process
is_a: GO:1901847 ! nicotinate metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-5033
+property_value: skos:narrowMatch MetaCyc:PWY-5055
+property_value: skos:narrowMatch MetaCyc:PWY-722
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: yaf
creation_date: 2013-01-28T11:23:52Z
@@ -535599,6 +541417,7 @@
namespace: biological_process
def: "The directed movement of substances from endoplasmic reticulum to chloroplast." [GOC:TermGenie, PMID:18689504]
synonym: "ER to chloroplast transport" EXACT [GOC:TermGenie]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
created_by: tb
creation_date: 2013-02-20T23:48:52Z
@@ -535884,7 +541703,7 @@
name: phosphatidylinositol phosphate binding
namespace: molecular_function
def: "Binding to phosphatidylinositol phosphate." [GOC:TermGenie, PMID:23445487]
-is_a: GO:0035091 ! phosphatidylinositol binding
+is_a: GO:0005543 ! phospholipid binding
created_by: tb
creation_date: 2013-03-12T18:21:22Z
@@ -536147,8 +541966,9 @@
synonym: "regulation of indoleacetic acid anabolism via tryptophan" EXACT [GOC:TermGenie]
synonym: "regulation of indoleacetic acid formation via tryptophan" EXACT [GOC:TermGenie]
synonym: "regulation of indoleacetic acid synthesis via tryptophan" EXACT [GOC:TermGenie]
+is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:0010600 ! regulation of auxin biosynthetic process
-is_a: GO:0090357 ! regulation of L-tryptophan metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0009848 ! indoleacetic acid biosynthetic process via tryptophan
relationship: regulates GO:0009848 ! indoleacetic acid biosynthetic process via tryptophan
@@ -536302,7 +542122,7 @@
synonym: "regulation of proline biosynthetic process" BROAD []
synonym: "regulation of proline formation" EXACT [GOC:TermGenie]
synonym: "regulation of proline synthesis" EXACT [GOC:TermGenie]
-is_a: GO:2000214 ! regulation of L-proline metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:2000282 ! regulation of amino acid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0055129 ! L-proline biosynthetic process
@@ -537728,15 +543548,15 @@
[Term]
id: GO:1902079
-name: D-valine catabolic process
+name: obsolete D-valine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-valine." [GOC:TermGenie, PMID:23085840]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of D-valine." [GOC:TermGenie, PMID:23085840]
+comment: This term was obsoleted because there is no evidence that there is a specific pathway to degrade D-valine.
synonym: "D-valine breakdown" EXACT [GOC:TermGenie]
synonym: "D-valine catabolism" EXACT [GOC:TermGenie]
synonym: "D-valine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
-is_a: GO:0019478 ! D-amino acid catabolic process
-is_a: GO:1902114 ! D-valine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
created_by: al
creation_date: 2013-04-23T21:34:29Z
@@ -538446,12 +544266,13 @@
[Term]
id: GO:1902114
-name: D-valine metabolic process
+name: obsolete D-valine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving D-valine." [GOC:TermGenie, PMID:23085840]
+def: "OBSOLETE. The chemical reactions and pathways involving D-valine." [GOC:TermGenie, PMID:23085840]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "D-valine metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006573 ! valine metabolic process
-is_a: GO:0046416 ! D-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31357" xsd:anyURI
+is_obsolete: true
created_by: al
creation_date: 2013-05-13T23:27:23Z
@@ -540295,6 +546116,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving ketone body." [GOC:pr, GOC:TermGenie]
synonym: "ketone body metabolism" EXACT [GOC:TermGenie]
+xref: Reactome:R-HSA-74182 "Ketone body metabolism"
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0044281 ! small molecule metabolic process
is_a: GO:1901568 ! fatty acid derivative metabolic process
@@ -542227,6 +548049,7 @@
namespace: biological_process
def: "The directed movement of fructose from vacuole to cytoplasm." [GOC:TermGenie, PMID:23583552]
synonym: "fructose transport from vacuole to cytoplasm" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0015755 ! fructose transmembrane transport
is_a: GO:0034486 ! vacuolar transmembrane transport
created_by: tb
@@ -544318,6 +550141,7 @@
name: chloride transmembrane transport
namespace: biological_process
def: "The process in which chloride is transported across a membrane." [GOC:TermGenie, GOC:vw]
+xref: Reactome:R-HSA-426117 "Cation-coupled Chloride cotransporters"
is_a: GO:0006821 ! chloride transport
is_a: GO:0098656 ! monoatomic anion transmembrane transport
created_by: bf
@@ -546702,7 +552526,7 @@
def: "The chemical reactions and pathways involving 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate." [GO_REF:0000068, GOC:di, GOC:TermGenie, PMID:22562153]
comment: Phosphatidylinositol-4,5-bisphosphate, PtdIns(4,5)P(2) common name.
synonym: "1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046488 ! phosphatidylinositol metabolic process
+is_a: GO:0006650 ! glycerophospholipid metabolic process
created_by: di
creation_date: 2014-01-18T00:34:27Z
@@ -546715,7 +552539,7 @@
synonym: "1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate breakdown" EXACT [GOC:TermGenie]
synonym: "1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate catabolism" EXACT [GOC:TermGenie]
synonym: "1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate degradation" EXACT [GOC:TermGenie]
-is_a: GO:0031161 ! phosphatidylinositol catabolic process
+is_a: GO:0046475 ! glycerophospholipid catabolic process
is_a: GO:1902633 ! 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate metabolic process
created_by: di
creation_date: 2014-01-18T00:34:36Z
@@ -546925,7 +552749,7 @@
synonym: "regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate formation" EXACT [GOC:TermGenie]
synonym: "regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010511 ! regulation of phosphatidylinositol biosynthetic process
+is_a: GO:0071071 ! regulation of phospholipid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:1902635 ! 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
relationship: regulates GO:1902635 ! 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
@@ -546961,7 +552785,7 @@
synonym: "negative regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010512 ! negative regulation of phosphatidylinositol biosynthetic process
+is_a: GO:0071072 ! negative regulation of phospholipid biosynthetic process
is_a: GO:1902646 ! regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:1902635 ! 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
@@ -546998,7 +552822,7 @@
synonym: "upregulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate formation" EXACT [GOC:TermGenie]
synonym: "upregulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0010513 ! positive regulation of phosphatidylinositol biosynthetic process
+is_a: GO:0071073 ! positive regulation of phospholipid biosynthetic process
is_a: GO:1902646 ! regulation of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:1902635 ! 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process
@@ -548263,7 +554087,7 @@
namespace: cellular_component
def: "A protein complex which is capable of GABA receptor activity. Upon binding of gamma-aminobutyric acid (GABA) it transmits the signal from one side of the membrane to the other to initiate a change in cell activity. Major inhibitory receptor in vertebrate brain. Also found in other vertebrate tissues, invertebrates and possibly in plants. Effective benzodiazepine receptor." [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:18790874]
synonym: "gamma-aminobutyric acid receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bhm
creation_date: 2014-02-20T16:07:48Z
@@ -548947,8 +554771,7 @@
synonym: "sulfurated eukaryotic molybdenum cofactor(2-) formation" EXACT [GOC:TermGenie]
synonym: "sulfurated eukaryotic molybdenum cofactor(2-) synthesis" EXACT [GOC:TermGenie]
xref: MetaCyc:PWY-5963
-is_a: GO:0006793 ! phosphorus metabolic process
-is_a: GO:0009058 ! biosynthetic process
+is_a: GO:0006777 ! Mo-molybdopterin cofactor biosynthetic process
relationship: has_part GO:0008265 ! molybdenum cofactor sulfurtransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
created_by: dph
@@ -549009,6 +554832,7 @@
synonym: "Mo-molybdopterin-cytosine-dinucleotide cofactor biosynthetic process" EXACT []
xref: MetaCyc:PWY-6476
is_a: GO:0006777 ! Mo-molybdopterin cofactor biosynthetic process
+is_a: GO:0009165 ! nucleotide biosynthetic process
relationship: has_part GO:0061602 ! molybdenum cofactor cytidylyltransferase activity
created_by: dph
creation_date: 2014-03-06T14:00:43Z
@@ -549250,6 +555074,7 @@
comment: an example of this is snapin in mouse (Q9Z266) in PMID:20920792 inferred from mutant phenotype
synonym: "prevacuolar compartment to lysosome transport" BROAD [GOC:TermGenie]
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0010496 ! intercellular transport
created_by: pad
creation_date: 2014-03-17T16:32:36Z
@@ -550717,8 +556542,13 @@
synonym: "propionyl-CoA breakdown" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA catabolism" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA degradation" EXACT [GOC:TermGenie]
+xref: MetaCyc:PROPIONMET-PWY
+xref: MetaCyc:PWY-7574
is_a: GO:0036115 ! fatty-acyl-CoA catabolic process
is_a: GO:1902858 ! propionyl-CoA metabolic process
+property_value: skos:narrowMatch MetaCyc:PROPIONMET-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-7574
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31668" xsd:anyURI
created_by: tt
creation_date: 2014-04-03T03:10:23Z
@@ -552035,6 +557865,7 @@
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0046165 ! alcohol biosynthetic process
relationship: regulates GO:0046165 ! alcohol biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: tt
creation_date: 2014-04-22T21:55:03Z
@@ -552043,6 +557874,7 @@
name: negative regulation of alcohol biosynthetic process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of alcohol biosynthetic process." [GO_REF:0000058, GOC:mengo_curators, GOC:TermGenie, PMID:23332010]
+subset: gocheck_do_not_annotate
synonym: "down regulation of alcohol anabolism" EXACT [GOC:TermGenie]
synonym: "down regulation of alcohol biosynthesis" EXACT [GOC:TermGenie]
synonym: "down regulation of alcohol biosynthetic process" EXACT [GOC:TermGenie]
@@ -552074,6 +557906,7 @@
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0046165 ! alcohol biosynthetic process
relationship: negatively_regulates GO:0046165 ! alcohol biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: tt
creation_date: 2014-04-22T21:55:13Z
@@ -552082,6 +557915,7 @@
name: positive regulation of alcohol biosynthetic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of alcohol biosynthetic process." [GO_REF:0000058, GOC:mengo_curators, GOC:TermGenie, PMID:23332010]
+subset: gocheck_do_not_annotate
synonym: "activation of alcohol anabolism" NARROW [GOC:TermGenie]
synonym: "activation of alcohol biosynthesis" NARROW [GOC:TermGenie]
synonym: "activation of alcohol biosynthetic process" NARROW [GOC:TermGenie]
@@ -552113,6 +557947,7 @@
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0046165 ! alcohol biosynthetic process
relationship: positively_regulates GO:0046165 ! alcohol biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31485" xsd:anyURI
created_by: tt
creation_date: 2014-04-22T21:55:19Z
@@ -552160,6 +557995,7 @@
namespace: molecular_function
def: "Binding to phosphatidylinositol bisphosphate." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:18690034]
comment: An example of this is KCNJ2 in human (P63252) in PMID:18690034 (inferred from direct assay)
+xref: Reactome:R-HSA-8870332 "PTPN13:PLEKHA1,2 bind PI(3,4)P2"
is_a: GO:0043168 ! anion binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
created_by: bhm
@@ -552349,7 +558185,6 @@
synonym: "metalloendoproteinase activity involved in amyloid precursor protein degradation" NARROW [GOC:TermGenie]
synonym: "metalloendoproteinase activity involved in APP catabolic process" NARROW [GOC:TermGenie]
synonym: "metalloendoproteinase activity involved in APP catabolism" NARROW [GOC:TermGenie]
-xref: Reactome:R-HSA-9010034 "ADAM10:Zn2+:TSPANs cleaves APP(18-770)"
is_a: GO:0004222 ! metalloendopeptidase activity
intersection_of: GO:0004222 ! metalloendopeptidase activity
intersection_of: part_of GO:0042987 ! amyloid precursor protein catabolic process
@@ -552593,7 +558428,6 @@
synonym: "upregulation of TPK I" RELATED [GOC:TermGenie]
synonym: "upregulation of TPK II" RELATED [GOC:TermGenie]
synonym: "upregulation of TTK" RELATED [GOC:TermGenie]
-xref: Reactome:R-HSA-9032845 "Activated NTRK2 signals through CDK5"
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22455" xsd:anyURI
is_obsolete: true
created_by: sjp
@@ -552700,31 +558534,25 @@
[Term]
id: GO:1902954
-name: regulation of early endosome to recycling endosome transport
+name: obsolete regulation of early endosome to recycling endosome transport
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of early endosome to recycling endosome transport." [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:22621900]
-is_a: GO:0032386 ! regulation of intracellular transport
-is_a: GO:0060627 ! regulation of vesicle-mediated transport
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0061502 ! early endosome to recycling endosome transport
-relationship: regulates GO:0061502 ! early endosome to recycling endosome transport
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of early endosome to recycling endosome transport." [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:22621900]
+comment: This term is described by another GO term
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31240" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:2001135
created_by: sjp
creation_date: 2014-05-02T09:06:23Z
[Term]
id: GO:1902955
-name: positive regulation of early endosome to recycling endosome transport
+name: obsolete positive regulation of early endosome to recycling endosome transport
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of early endosome to recycling endosome transport." [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:22621900]
-synonym: "activation of early endosome to recycling endosome transport" NARROW [GOC:TermGenie]
-synonym: "up regulation of early endosome to recycling endosome transport" EXACT [GOC:TermGenie]
-synonym: "up-regulation of early endosome to recycling endosome transport" EXACT [GOC:TermGenie]
-synonym: "upregulation of early endosome to recycling endosome transport" EXACT [GOC:TermGenie]
-is_a: GO:0032388 ! positive regulation of intracellular transport
-is_a: GO:1902954 ! regulation of early endosome to recycling endosome transport
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0061502 ! early endosome to recycling endosome transport
-relationship: positively_regulates GO:0061502 ! early endosome to recycling endosome transport
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of early endosome to recycling endosome transport." [GO_REF:0000058, GOC:sjp, GOC:TermGenie, PMID:22621900]
+comment: This term is described by another GO term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31240" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:2001137
created_by: sjp
creation_date: 2014-05-02T09:06:29Z
@@ -553770,16 +559598,17 @@
is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:2000282 ! regulation of amino acid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
-relationship: regulates GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
+intersection_of: regulates GO:0009085 ! L-lysine biosynthetic process
+relationship: regulates GO:0009085 ! L-lysine biosynthetic process
created_by: al
creation_date: 2014-05-07T08:07:08Z
[Term]
id: GO:1902987
-name: negative regulation of lysine biosynthetic process via aminoadipic acid
+name: obsolete negative regulation of lysine biosynthetic process via aminoadipic acid
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of lysine biosynthetic process via aminoadipic acid." [GO_REF:0000058, GOC:TermGenie, PMID:8590464]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of lysine biosynthetic process via aminoadipic acid." [GO_REF:0000058, GOC:TermGenie, PMID:8590464]
+comment: The reason for obsoletion is that this term was created unnecessarily.
synonym: "down regulation of lysine anabolism via aminoadipic acid" EXACT [GOC:TermGenie]
synonym: "down regulation of lysine biosynthesis, aminoadipic acid pathway" EXACT [GOC:TermGenie]
synonym: "down regulation of lysine biosynthesis, aminoadipic pathway" EXACT [GOC:TermGenie]
@@ -553819,12 +559648,8 @@
synonym: "negative regulation of lysine biosynthetic process, aminoadipic pathway" EXACT [GOC:TermGenie]
synonym: "negative regulation of lysine formation via aminoadipic acid" EXACT [GOC:TermGenie]
synonym: "negative regulation of lysine synthesis via aminoadipic acid" EXACT [GOC:TermGenie]
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-is_a: GO:1902986 ! regulation of lysine biosynthetic process via aminoadipic acid
-is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
-relationship: negatively_regulates GO:0019878 ! L-lysine biosynthetic process via aminoadipic acid
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
created_by: al
creation_date: 2014-05-07T08:07:15Z
@@ -556129,7 +561954,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate." [GO_REF:0000068, GOC:bhm, GOC:TermGenie, PMID:19037259]
synonym: "1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046488 ! phosphatidylinositol metabolic process
+is_a: GO:0006650 ! glycerophospholipid metabolic process
created_by: bhm
creation_date: 2014-06-04T14:14:24Z
@@ -556141,7 +561966,7 @@
synonym: "1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate breakdown" EXACT [GOC:TermGenie]
synonym: "1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate catabolism" EXACT [GOC:TermGenie]
synonym: "1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate degradation" EXACT [GOC:TermGenie]
-is_a: GO:0031161 ! phosphatidylinositol catabolic process
+is_a: GO:0046475 ! glycerophospholipid catabolic process
is_a: GO:1903100 ! 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process
created_by: bhm
creation_date: 2014-06-04T14:14:30Z
@@ -558015,13 +563840,16 @@
[Term]
id: GO:1903212
-name: protein localization to mating-type region heterochromatin
+name: obsolete protein localization to mating-type region heterochromatin
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a mating-type region heterochromatin." [GO_REF:0000087, GOC:TermGenie, PMID:18761674]
+def: "OBSOLETE. A process in which a protein is transported to, or maintained in, a location within a mating-type region heterochromatin." [GO_REF:0000087, GOC:TermGenie, PMID:18761674]
+comment: This term was obsoleted because it represents a precomposed term.
synonym: "protein localisation in mating-type region heterochromatin" EXACT [GOC:TermGenie]
synonym: "protein localisation to mating-type region heterochromatin" EXACT [GOC:TermGenie]
synonym: "protein localization in mating-type region heterochromatin" EXACT [GOC:TermGenie]
-is_a: GO:0097355 ! protein localization to heterochromatin
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31529" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071168
created_by: mah
creation_date: 2014-07-24T09:38:12Z
@@ -559071,8 +564899,9 @@
synonym: "regulation of ornithine breakdown" EXACT [GOC:TermGenie]
synonym: "regulation of ornithine catabolism" EXACT [GOC:TermGenie]
synonym: "regulation of ornithine degradation" EXACT [GOC:TermGenie]
+is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:0009894 ! regulation of catabolic process
-is_a: GO:0090368 ! regulation of ornithine metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006593 ! L-ornithine catabolic process
relationship: regulates GO:0006593 ! L-ornithine catabolic process
@@ -562112,7 +567941,7 @@
namespace: biological_process
def: "The directed movement of flavonoid from endoplasmic reticulum to plant-type vacuole." [GO_REF:0000078, GOC:tb, GOC:TermGenie, PMID:25116949]
synonym: "flavonoid accumulation in vacuole" RELATED []
-is_a: GO:0006810 ! transport
+is_a: GO:0010496 ! intercellular transport
created_by: tb
creation_date: 2014-09-05T00:35:34Z
@@ -563887,6 +569716,7 @@
namespace: biological_process
def: "The directed movement of substances from endoplasmic reticulum to cytosol." [GO_REF:0000076, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:16402920]
synonym: "ER to cytosol transport" EXACT [GOC:TermGenie]
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0046907 ! intracellular transport
created_by: rl
creation_date: 2014-10-02T11:24:34Z
@@ -564778,30 +570608,29 @@
[Term]
id: GO:1903559
-name: 3-cyano-L-alanine catabolic process
+name: obsolete 3-cyano-L-alanine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
+comment: This term was obsoleted because there is no evidence that a specific pathway for 3-cyano-L-alanine degradation exists.
synonym: "3-cyano-L-alanine breakdown" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine catabolism" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0050899 ! nitrile catabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+is_obsolete: true
created_by: kmv
creation_date: 2014-10-21T17:13:10Z
[Term]
id: GO:1903560
-name: 3-cyano-L-alanine biosynthetic process
+name: obsolete 3-cyano-L-alanine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 3-cyano-L-alanine." [GO_REF:0000068, GOC:kmv, GOC:TermGenie, PMID:24100226, PMID:24843024]
+comment: The reason for merging the above terms is to clean up this branch, consistent to what has been done previously.
synonym: "3-cyano-L-alanine anabolism" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine biosynthesis" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine formation" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0080028 ! nitrile biosynthetic process
-is_a: GO:0170034 ! L-amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+is_obsolete: true
created_by: kmv
creation_date: 2014-10-21T17:13:26Z
@@ -568820,7 +574649,7 @@
name: taste receptor complex
namespace: cellular_component
def: "A protein complex which is capable of taste receptor activity." [GO_REF:0000088, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:16720576]
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: rl
creation_date: 2014-12-22T16:53:45Z
@@ -569622,8 +575451,7 @@
synonym: "L-glutamine import" BROAD []
synonym: "L-glutamine import into cell" EXACT []
synonym: "L-glutamine uptake" EXACT [GOC:bf]
-is_a: GO:0006868 ! glutamine transport
-is_a: GO:0015695 ! organic cation transport
+is_a: GO:0006868 ! L-glutamine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
created_by: bf
@@ -573940,12 +579768,12 @@
synonym: "regulation of homofermentative pathway" EXACT [GOC:TermGenie]
synonym: "regulation of homolactate fermentation" EXACT [GOC:TermGenie]
synonym: "regulation of homolactic fermentation" EXACT [GOC:TermGenie]
-is_a: GO:0010906 ! regulation of glucose metabolic process
+is_a: GO:0009894 ! regulation of catabolic process
is_a: GO:0043465 ! regulation of fermentation
-is_a: GO:0043470 ! regulation of carbohydrate catabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0019661 ! homolactic fermentation
-relationship: regulates GO:0019661 ! homolactic fermentation
+intersection_of: regulates GO:0019244 ! pyruvate fermentation to lactate
+relationship: regulates GO:0019244 ! pyruvate fermentation to lactate
created_by: dph
creation_date: 2015-03-11T16:57:32Z
@@ -573989,13 +579817,12 @@
synonym: "negative regulation of homolactate fermentation" EXACT [GOC:TermGenie]
synonym: "negative regulation of homolactic fermentation" EXACT [GOC:TermGenie]
is_a: GO:0009895 ! negative regulation of catabolic process
-is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1901003 ! negative regulation of fermentation
is_a: GO:1904023 ! regulation of glucose catabolic process to lactate via pyruvate
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0019661 ! homolactic fermentation
-relationship: negatively_regulates GO:0019661 ! homolactic fermentation
+intersection_of: negatively_regulates GO:0019244 ! pyruvate fermentation to lactate
+relationship: negatively_regulates GO:0019244 ! pyruvate fermentation to lactate
created_by: dph
creation_date: 2015-03-11T16:57:38Z
@@ -574039,11 +579866,11 @@
synonym: "upregulation of homolactate fermentation" EXACT [GOC:TermGenie]
synonym: "upregulation of homolactic fermentation" EXACT [GOC:TermGenie]
is_a: GO:0009896 ! positive regulation of catabolic process
-is_a: GO:0010907 ! positive regulation of glucose metabolic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1904023 ! regulation of glucose catabolic process to lactate via pyruvate
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0019661 ! homolactic fermentation
-relationship: positively_regulates GO:0019661 ! homolactic fermentation
+intersection_of: positively_regulates GO:0019244 ! pyruvate fermentation to lactate
+relationship: positively_regulates GO:0019244 ! pyruvate fermentation to lactate
created_by: dph
creation_date: 2015-03-11T16:57:44Z
@@ -584736,7 +590563,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving phosphatidylinositol 5-phosphate." [GO_REF:0000068, GOC:autophagy, GOC:dph, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:23916588]
synonym: "phosphatidylinositol 5-phosphate metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0046488 ! phosphatidylinositol metabolic process
+is_a: GO:0006650 ! glycerophospholipid metabolic process
created_by: dph
creation_date: 2015-08-18T16:21:44Z
@@ -589048,6 +594875,8 @@
name: all-trans-retinol binding
namespace: molecular_function
def: "Binding to all-trans-retinol." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
+xref: Reactome:R-HSA-2404135 "RBP4 binds atROL"
+xref: Reactome:R-HSA-975633 "atROL binds to RBP2"
is_a: GO:0019841 ! retinol binding
created_by: kmv
creation_date: 2015-10-27T21:14:47Z
@@ -592716,6 +598545,7 @@
namespace: biological_process
def: "The process in which folic acid is transported from the cytosol into the mitochondrial matrix." [GO_REF:0000075, GOC:BHF, GOC:rph, GOC:TermGenie, PMID:15140890]
synonym: "folic acid import into mitochondrion" RELATED []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0098838 ! folate transmembrane transport
created_by: rph
creation_date: 2016-02-03T12:10:14Z
@@ -593101,6 +598931,7 @@
synonym: "regulation of warburg's respiratory enzyme activity" RELATED [GOC:TermGenie]
is_a: GO:0010155 ! regulation of proton transport
is_a: GO:0022898 ! regulation of transmembrane transporter activity
+is_a: GO:0051341 ! regulation of oxidoreductase activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0004129 ! cytochrome-c oxidase activity
relationship: regulates GO:0004129 ! cytochrome-c oxidase activity
@@ -593193,6 +599024,7 @@
synonym: "upregulation of NADH cytochrome c oxidase" EXACT [GOC:TermGenie]
synonym: "upregulation of warburg's respiratory enzyme activity" RELATED [GOC:TermGenie]
is_a: GO:0032414 ! positive regulation of ion transmembrane transporter activity
+is_a: GO:0051353 ! positive regulation of oxidoreductase activity
is_a: GO:1904959 ! regulation of cytochrome-c oxidase activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0004129 ! cytochrome-c oxidase activity
@@ -593217,6 +599049,7 @@
def: "The vesicle-mediated and directed movement of substances from plastid to vacuole." [GO_REF:0000076, GOC:TermGenie, PMID:25281689]
synonym: "plastid to vacuolar carboxypeptidase Y vesicle-mediated transport" RELATED [GOC:TermGenie]
is_a: GO:0007034 ! vacuolar transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0016192 ! vesicle-mediated transport
is_a: GO:0016482 ! cytosolic transport
created_by: tb
@@ -594241,6 +600074,7 @@
alt_id: GO:0007037
def: "The directed movement of phosphate ions from the cytosol across the vacuolar membrane and into the vacuolar lumen." [GO_REF:0000078, GOC:TermGenie, PMID:26554016]
synonym: "vacuolar phosphate transport" BROAD []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0034486 ! vacuolar transmembrane transport
is_a: GO:0035435 ! phosphate ion transmembrane transport
created_by: tb
@@ -594253,7 +600087,7 @@
def: "Any process that modulates the frequency, rate or extent of 'de novo' NAD biosynthetic process from L-tryptophan." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:12140278, PMID:19843166]
synonym: "regulation of 'de novo' NAD biosynthetic process from tryptophan" BROAD []
synonym: "regulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
-is_a: GO:0090357 ! regulation of L-tryptophan metabolic process
+is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:1900371 ! regulation of purine nucleotide biosynthetic process
is_a: GO:1902688 ! regulation of NAD metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -594304,7 +600138,7 @@
synonym: "up-regulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
synonym: "upregulation of 'de novo' NAD biosynthetic process from tryptophan" EXACT [GOC:TermGenie]
synonym: "upregulation of de novo NAD biosynthetic process from tryptophan" RELATED [GOC:TermGenie]
-is_a: GO:0090358 ! positive regulation of L-tryptophan metabolic process
+is_a: GO:0045764 ! positive regulation of amino acid metabolic process
is_a: GO:1900373 ! positive regulation of purine nucleotide biosynthetic process
is_a: GO:1902690 ! positive regulation of NAD metabolic process
is_a: GO:1905012 ! regulation of 'de novo' NAD biosynthetic process from L-tryptophan
@@ -604651,47 +610485,45 @@
[Term]
id: GO:1905526
-name: regulation of Golgi lumen acidification
+name: obsolete regulation of Golgi lumen acidification
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
-is_a: GO:0032847 ! regulation of cellular pH reduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0061795 ! Golgi lumen acidification
-relationship: regulates GO:0061795 ! Golgi lumen acidification
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
+comment: This term was added in error. Regulating regulation is redundant. Direction is unspecified.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+consider: GO:0061795
created_by: dph
creation_date: 2016-10-05T13:16:25Z
[Term]
id: GO:1905527
-name: negative regulation of Golgi lumen acidification
+name: obsolete negative regulation of Golgi lumen acidification
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
+comment: This term was added in error. Regulating regulation is redundant.
synonym: "down regulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
synonym: "down-regulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
synonym: "downregulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
synonym: "inhibition of Golgi lumen acidification" NARROW [GOC:TermGenie]
-is_a: GO:0032848 ! negative regulation of cellular pH reduction
-is_a: GO:1905526 ! regulation of Golgi lumen acidification
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0061795 ! Golgi lumen acidification
-relationship: negatively_regulates GO:0061795 ! Golgi lumen acidification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061795
created_by: dph
creation_date: 2016-10-05T13:16:33Z
[Term]
id: GO:1905528
-name: positive regulation of Golgi lumen acidification
+name: obsolete positive regulation of Golgi lumen acidification
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of Golgi lumen acidification." [GO_REF:0000058, GOC:dph, GOC:TermGenie, PMID:23447592]
+comment: This term was added in error. Regulating regulation is redundant.
synonym: "activation of Golgi lumen acidification" NARROW [GOC:TermGenie]
synonym: "up regulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
synonym: "up-regulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
synonym: "upregulation of Golgi lumen acidification" EXACT [GOC:TermGenie]
-is_a: GO:0032849 ! positive regulation of cellular pH reduction
-is_a: GO:1905526 ! regulation of Golgi lumen acidification
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0061795 ! Golgi lumen acidification
-relationship: positively_regulates GO:0061795 ! Golgi lumen acidification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061795
created_by: dph
creation_date: 2016-10-05T13:16:41Z
@@ -604896,7 +610728,7 @@
synonym: "IL-7-receptor complex" EXACT []
synonym: "IL7 receptor complex" EXACT []
synonym: "IL7-receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bhm
creation_date: 2016-10-10T07:44:05Z
@@ -604948,7 +610780,7 @@
synonym: "IL15 receptor complex" EXACT []
synonym: "IL15-receptor complex" EXACT []
synonym: "interleukin-15-receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bhm
creation_date: 2016-10-10T13:38:12Z
@@ -605801,7 +611633,7 @@
synonym: "IL-10-receptor complex" EXACT []
synonym: "IL10 receptor complex" EXACT []
synonym: "interleukin-10-receptor complex" EXACT []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: bhm
creation_date: 2016-10-19T09:45:22Z
@@ -613699,7 +619531,9 @@
def: "Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex." [GOC:bhm, PMID:20378773]
synonym: "OMP complex" EXACT []
is_a: GO:0098796 ! membrane protein complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0031241 ! periplasmic side of cell outer membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31720" xsd:anyURI
created_by: bhm
creation_date: 2013-03-20T15:42:57Z
@@ -614860,6 +620694,8 @@
namespace: molecular_function
def: "Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA." [GOC:dgf, PMID:20802481]
synonym: "G(5')pppN pyrophosphatase activity" RELATED []
+xref: Reactome:R-HSA-9935300 "DXO decaps NAD-capped RNA (NAD-RNA)"
+xref: Reactome:R-HSA-9935319 "DXO decaps incompletely capped RNA (GpppN-RNA)"
is_a: GO:0016891 ! RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism
created_by: tb
creation_date: 2013-08-26T17:51:00Z
@@ -614944,14 +620780,16 @@
[Term]
id: GO:1990181
-name: acetyl-CoA biosynthetic process from pantothenate
+name: obsolete acetyl-CoA biosynthetic process from pantothenate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetyl-CoA from pantothenate via phosphopantothenate and CoA." [GOC:mah, PMID:23091701]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetyl-CoA from pantothenate via phosphopantothenate and CoA." [GOC:mah, PMID:23091701]
+comment: The reason for obsoletion is that these represent GO-CAMs.
synonym: "acetyl-CoA anabolism from pantothenate" EXACT []
synonym: "acetyl-CoA formation from pantothenate" RELATED []
synonym: "acetyl-CoA synthesis from pantothenate" RELATED []
-is_a: GO:0006085 ! acetyl-CoA biosynthetic process
-is_a: GO:0015939 ! pantothenate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31666" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006085
created_by: mah
creation_date: 2013-08-30T16:20:44Z
@@ -615037,10 +620875,16 @@
def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-seryl-[protein] = CoA + H+ + N-terminal Nalpha-acetyl-L-seryl-[protein]." [PMID:23912279, RHEA:50504]
synonym: "peptide-serine-alpha-N-acetyltransferase activity" EXACT []
xref: EC:2.3.1.257
+xref: RHEA:43760
xref: RHEA:50504
+xref: RHEA:50596
+xref: RHEA:50600
is_a: GO:0004596 ! protein-N-terminal amino-acid acetyltransferase activity
property_value: skos:exactMatch RHEA:50504
property_value: skos:narrowMatch EC:2.3.1.257
+property_value: skos:narrowMatch RHEA:43760
+property_value: skos:narrowMatch RHEA:50596
+property_value: skos:narrowMatch RHEA:50600
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27532" xsd:anyURI
created_by: tb
creation_date: 2013-09-11T20:13:40Z
@@ -615982,7 +621826,7 @@
synonym: "PDGF-DD-receptor beta complex" NARROW []
synonym: "receptor-ligand complex" BROAD []
is_a: GO:0098797 ! plasma membrane protein complex
-relationship: has_part GO:0043235 ! receptor complex
+relationship: has_part GO:0043235 ! signaling receptor complex
relationship: has_part GO:1990265 ! platelet-derived growth factor complex
created_by: bhm
creation_date: 2014-01-14T11:12:22Z
@@ -616353,6 +622197,7 @@
def: "A collagen homotrimer made of three alpha1(XIX) collagen chains, each presenting interrupted triple helical collagen domains. Localizes to basement membrane ECMs, not known to associate with any fibrillar collagens that are predominantly found in the interstitial extracellular matrix." [PMID:10585282, PMID:12579531, PMID:12788917, PMID:17876790, PMID:31823868, PMID:35346795, PMID:9403723]
comment: The collagen XIX trimer is often classified as a FACIT collagen trimer (which stands for Fibril Associated Collagens with Interrupted Triple helices) because of the presence of interrupted triple helical collagen domains, similar to other FACIT members. However, evidence show that collagen XIX localizes to basement membrane ECMs, and none of the basement membrane collagens are fibrillar.
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140143 ! collagenous component of basement membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29569" xsd:anyURI
created_by: bhm
@@ -616409,6 +622254,7 @@
namespace: cellular_component
def: "A collagen homotrimer of alpha1(XXVI) chains." [GOC:bhm, PMID:17876790]
is_a: GO:0005581 ! collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140152 ! collagenous component of interstitial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30146" xsd:anyURI
created_by: bhm
@@ -616429,6 +622275,7 @@
namespace: cellular_component
def: "A collagen homotrimer of alpha1(XXVIII) chains." [PMID:17876790]
is_a: GO:0140158 ! von-Willerbrand-factor-A-domain-rich collagen trimer
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140143 ! collagenous component of basement membrane
created_by: bhm
creation_date: 2014-03-16T23:15:28Z
@@ -616568,7 +622415,7 @@
name: thrombospondin complex
namespace: cellular_component
def: "A homotrimeric or homopentameric glycoprotein that functions at the interface of the cell membrane and the extracellular matrix through its interactions with proteins and proteoglycans, such as collagens, integrins and fibronectin, to regulate matrix structure and cellular behaviour." [GOC:bhm, PMID:15094109, PMID:18193164]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0140149 ! non-collagenous component of interstitial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31065" xsd:anyURI
created_by: bhm
@@ -617749,7 +623596,7 @@
id: GO:1990451
name: cellular stress response to acidic pH
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in the homeostasis of organismal or cellular pH (with pH < 7). pH is a measure of the acidity or basicity of an aqueous solution." [GOC:BHF, GOC:go_curators, GOC:rl, PMID:10615049]
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in the homeostasis of organismal or cellular pH (with pH < 7). pH is a measure of the acidity or basicity of an aqueous solution." [GOC:BHF, GOC:curators, GOC:rl, PMID:10615049]
comment: An example of this is NOX1 in human (Q9Y5S8) in PMID:10615049.
synonym: "cellular stress response to acidity" BROAD []
is_a: GO:0062197 ! cellular response to chemical stress
@@ -618507,6 +624354,7 @@
def: "The process in which a pyrimidine nucleotide is transported across the mitochondrial inner membrane, into the mitochondrial matrix." [PMID:16194150]
synonym: "mitochondrial pyrimidine nucleotide import" EXACT []
is_a: GO:0006864 ! pyrimidine nucleotide transport
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
is_a: GO:1901679 ! nucleotide transmembrane transport
created_by: vw
@@ -618952,7 +624800,7 @@
comment: An example of this is SCD1 in human (UniProt symbol P18827) in PMID:22660413 (inferred from physical interaction).
synonym: "exosome complex" EXACT []
synonym: "extracellular vesicular exosome complex" EXACT [GOC:vesicles]
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0070062 ! extracellular exosome
created_by: bhm
creation_date: 2014-11-25T16:35:53Z
@@ -619029,7 +624877,9 @@
alt_id: GO:0015784
def: "The process in which GDP-mannose is transported across a membrane." [PMID:9395539]
synonym: "GDP-mannose transport" RELATED []
+is_a: GO:0015711 ! organic anion transport
is_a: GO:0090480 ! purine nucleotide-sugar transmembrane transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
created_by: vw
creation_date: 2014-11-27T12:05:09Z
@@ -619348,12 +625198,14 @@
[Term]
id: GO:1990599
-name: 3' overhang single-stranded DNA endodeoxyribonuclease activity
+name: 3' overhang single-stranded DNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within 3' overhang single-stranded deoxyribonucleic acid by creating internal breaks." [PMID:25203555]
+synonym: "3' overhang single-stranded DNA endodeoxyribonuclease activity" EXACT []
xref: EC:3.1.31.1
-is_a: GO:0000014 ! single-stranded DNA endodeoxyribonuclease activity
+is_a: GO:0000014 ! single-stranded DNA endonuclease activity
property_value: skos:narrowMatch EC:3.1.31.1
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31721" xsd:anyURI
created_by: al
creation_date: 2015-01-06T15:21:28Z
@@ -619363,16 +625215,18 @@
namespace: molecular_function
def: "Increases the activity of a single-stranded DNA endodeoxyribonuclease activator activity." [PMID:25203555]
is_a: GO:0140656 ! endodeoxyribonuclease activator activity
-relationship: positively_regulates GO:0000014 ! single-stranded DNA endodeoxyribonuclease activity
+relationship: positively_regulates GO:0000014 ! single-stranded DNA endonuclease activity
created_by: al
creation_date: 2015-01-06T15:35:36Z
[Term]
id: GO:1990601
-name: 5' overhang single-stranded DNA endodeoxyribonuclease activity
+name: 5' overhang single-stranded DNA endonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within 5' overhang single-stranded deoxyribonucleic acid by creating internal breaks." [PMID:25203555]
-is_a: GO:0000014 ! single-stranded DNA endodeoxyribonuclease activity
+synonym: "5' overhang single-stranded DNA endodeoxyribonuclease activity" EXACT []
+is_a: GO:0000014 ! single-stranded DNA endonuclease activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31721" xsd:anyURI
created_by: al
creation_date: 2015-01-06T16:24:39Z
@@ -619522,6 +625376,7 @@
namespace: biological_process
def: "The directed movement of magnesium ions out of mitochondrial matrix into the cytosol by means of some agent such as a transporter or pore." [PMID:25585246]
synonym: "magnesium ion efflux from mitochondrion" EXACT []
+is_a: GO:0010496 ! intercellular transport
is_a: GO:0045016 ! mitochondrial magnesium ion transmembrane transport
created_by: mcc
creation_date: 2015-01-21T22:06:42Z
@@ -619569,7 +625424,7 @@
def: "A receptor complex composed of two ANPR-A molecules and expressed in the heart atrium in mammals; it plays a major role in the regulation of blood pressure and salt-fluid volume homeostasis. Binding of the ligand AMP in response to atrial distension (high blood volume) leads to guanylate cyclase activity of the ANPR-A receptor complex, thereby elevating intracellular cGMP levels. The end result is a reduction in blood volume and, therefore, a reduction in cardiac output and systemic blood pressure." [GOC:ame, PMID:15117952]
comment: An example of this is Npr1 in rat (UniProt symbol P18910) in PMID:15117952 (inferred from direct assay).
synonym: "NPR1 receptor complex" RELATED []
-is_a: GO:0043235 ! receptor complex
+is_a: GO:0043235 ! signaling receptor complex
created_by: ame
creation_date: 2015-01-28T16:03:22Z
@@ -621301,9 +627156,10 @@
id: GO:1990780
name: cytoplasmic side of dendritic spine plasma membrane
namespace: cellular_component
-def: "The leaflet of the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface surrounding a dendritic spine." [PMID:9275233]
+def: "The leaflet of the plasma membrane in the dendritic spine region that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it." [PMID:9275233]
is_a: GO:0009898 ! cytoplasmic side of plasma membrane
relationship: part_of GO:0032591 ! dendritic spine membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31515" xsd:anyURI
created_by: sl
creation_date: 2015-06-23T18:35:39Z
@@ -621719,8 +627575,11 @@
synonym: "RNA adenylyltransferase activity" EXACT []
xref: EC:2.7.7.19
xref: MetaCyc:POLYNUCLEOTIDE-ADENYLYLTRANSFERASE-RXN
-xref: Reactome:R-HSA-72185 "mRNA polyadenylation"
xref: Reactome:R-HSA-9833031 "Polyadenylation of respiratory syncytial virus subgenomic positive-sense mRNAs"
+xref: Reactome:R-HSA-9936998 "MTPAP polyadenylates mitochondrial mRNA"
+xref: Reactome:R-HSA-9970189 "PABPN1-stimulated PAPOL synthesizes polyA tail at distal 3'UTR PAS"
+xref: Reactome:R-HSA-9970318 "PABPN1-stimulated PAPOL synthesizes polyA tail at proximal 3'UTR PAS"
+xref: Reactome:R-HSA-9970320 "PABPN1-stimulated PAPOL synthesizes polyA tail at intronic PAS"
xref: RHEA:11332
is_a: GO:0070566 ! adenylyltransferase activity
property_value: skos:exactMatch EC:2.7.7.19
@@ -622461,6 +628320,7 @@
def: "Catalysis of the reaction: a cytidine in 18S rRNA + acetyl-CoA + ATP + H2O = an N(4)-acetylcytidine in 18S rRNA + ADP + phosphate + CoA + H+." [PMID:25402480, RHEA:51424]
xref: RHEA:51424
is_a: GO:0008080 ! N-acetyltransferase activity
+is_a: GO:0140102 ! catalytic activity, acting on a rRNA
property_value: skos:exactMatch RHEA:51424
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29506" xsd:anyURI
created_by: al
@@ -622746,7 +628606,8 @@
name: response to psychosocial stress
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to aversive or demanding psychological and social conditions that tax or exceed the behavioral resources of the organism." [PMID:22922217, PMID:26458179]
-is_a: GO:0006950 ! response to stress
+is_a: GO:0033555 ! multicellular organismal response to stress
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31407" xsd:anyURI
created_by: sl
creation_date: 2015-12-07T20:38:35Z
@@ -623091,12 +628952,15 @@
[Term]
id: GO:1990943
-name: mating type region replication fork barrier binding
+name: obsolete mating type region replication fork barrier binding
namespace: molecular_function
-def: "Binding to the replication fork barrier found in the mating type region of fission yeast." [PMID:18723894]
+def: "OBSOLETE. Binding to the replication fork barrier found in the mating type region of fission yeast." [PMID:18723894]
+comment: This term was obsoleted because it represents a precomposed term.
synonym: "RTS1 barrier binding" EXACT []
synonym: "RTS1 element binding" EXACT []
-is_a: GO:0031634 ! replication fork barrier binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31529" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0031634
created_by: mah
creation_date: 2016-04-06T16:08:43Z
@@ -623376,6 +629240,7 @@
synonym: "EMILIN-1 complex" NARROW []
synonym: "EMILIN-2 complex" NARROW []
is_a: GO:0098637 ! protein complex involved in cell-matrix adhesion
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0071953 ! elastic fiber
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31133" xsd:anyURI
created_by: bhm
@@ -623395,6 +629260,7 @@
synonym: "p155 complex" NARROW []
synonym: "Platelet glycoprotein Ia* complex" NARROW []
is_a: GO:0098637 ! protein complex involved in cell-matrix adhesion
+is_a: GO:0140392 ! extracellular protein-containing complex
relationship: part_of GO:0071953 ! elastic fiber
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31134" xsd:anyURI
created_by: bhm
@@ -623699,16 +629565,16 @@
[Term]
id: GO:2000013
-name: regulation of arginine biosynthetic process via ornithine
+name: obsolete regulation of arginine biosynthetic process via ornithine
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of arginine biosynthetic process via ornithine." [GOC:obol]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of arginine biosynthetic process via ornithine." [GOC:obol]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
synonym: "regulation of arginine anabolism via ornithine" EXACT [GOC:obol]
synonym: "regulation of arginine formation via ornithine" EXACT [GOC:obol]
synonym: "regulation of arginine synthesis via ornithine" EXACT [GOC:obol]
-is_a: GO:1900079 ! regulation of arginine biosynthetic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0042450 ! L-arginine biosynthetic process via ornithine
-relationship: regulates GO:0042450 ! L-arginine biosynthetic process via ornithine
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:1900079
created_by: tb
creation_date: 2010-08-05T11:21:51Z
@@ -624154,6 +630020,7 @@
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cell-cell adhesion mediated by cadherin." [GOC:obol]
xref: Reactome:R-HSA-9764260 "Regulation of Expression and Function of Type II Classical Cadherins"
+xref: Reactome:R-HSA-9764274 "Regulation of Expression and Function of Type I Classical Cadherins"
is_a: GO:0022407 ! regulation of cell-cell adhesion
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0044331 ! cell-cell adhesion mediated by cadherin
@@ -626542,34 +632409,29 @@
[Term]
id: GO:2000211
-name: regulation of glutamate metabolic process
+name: obsolete regulation of glutamate metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of glutamate metabolic process." [GOC:sl]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of glutamate metabolic process." [GOC:sl]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
synonym: "regulation of glutamate metabolism" EXACT [GOC:obol]
synonym: "regulation of glutamic acid metabolic process" EXACT [GOC:obol]
synonym: "regulation of glutamic acid metabolism" EXACT [GOC:obol]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006536 ! glutamate metabolic process
-relationship: regulates GO:0006536 ! glutamate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: mah
creation_date: 2010-11-03T02:43:51Z
[Term]
id: GO:2000212
-name: negative regulation of glutamate metabolic process
+name: obsolete negative regulation of glutamate metabolic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glutamate metabolic process." [GOC:sl]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of glutamate metabolic process." [GOC:sl]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
synonym: "negative regulation of glutamate metabolism" EXACT [GOC:obol]
synonym: "negative regulation of glutamic acid metabolic process" EXACT [GOC:obol]
synonym: "negative regulation of glutamic acid metabolism" EXACT [GOC:obol]
-is_a: GO:0045763 ! negative regulation of amino acid metabolic process
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-is_a: GO:2000211 ! regulation of glutamate metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0006536 ! glutamate metabolic process
-relationship: negatively_regulates GO:0006536 ! glutamate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: mah
creation_date: 2010-11-03T02:43:55Z
@@ -626589,16 +632451,14 @@
[Term]
id: GO:2000214
-name: regulation of L-proline metabolic process
+name: obsolete regulation of L-proline metabolic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of L-proline metabolic process." [GOC:sl]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of L-proline metabolic process." [GOC:sl]
+comment: The reason for obsoletion is that this term was an unnecessary grouping terms and only 'biosynthetic' or 'catabolic' process should be used.
synonym: "regulation of proline metabolic process" BROAD []
synonym: "regulation of proline metabolism" EXACT [GOC:obol]
-is_a: GO:0006521 ! regulation of amino acid metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006560 ! L-proline metabolic process
-relationship: regulates GO:0006560 ! L-proline metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31171" xsd:anyURI
+is_obsolete: true
created_by: mah
creation_date: 2010-11-03T02:45:20Z
@@ -630549,8 +636409,8 @@
is_a: GO:0032890 ! regulation of organic acid transport
is_a: GO:0051955 ! regulation of amino acid transport
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006868 ! glutamine transport
-relationship: regulates GO:0006868 ! glutamine transport
+intersection_of: regulates GO:0006868 ! L-glutamine transport
+relationship: regulates GO:0006868 ! L-glutamine transport
created_by: bf
creation_date: 2011-03-11T09:32:23Z
@@ -630564,8 +636424,8 @@
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:2000485 ! regulation of glutamine transport
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0006868 ! glutamine transport
-relationship: negatively_regulates GO:0006868 ! glutamine transport
+intersection_of: negatively_regulates GO:0006868 ! L-glutamine transport
+relationship: negatively_regulates GO:0006868 ! L-glutamine transport
created_by: bf
creation_date: 2011-03-11T09:33:07Z
@@ -630579,8 +636439,8 @@
is_a: GO:0051957 ! positive regulation of amino acid transport
is_a: GO:2000485 ! regulation of glutamine transport
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0006868 ! glutamine transport
-relationship: positively_regulates GO:0006868 ! glutamine transport
+intersection_of: positively_regulates GO:0006868 ! L-glutamine transport
+relationship: positively_regulates GO:0006868 ! L-glutamine transport
created_by: bf
creation_date: 2011-03-11T09:33:39Z
@@ -639599,8 +645459,9 @@
synonym: "regulation of proline catabolic process to glutamate" BROAD []
synonym: "regulation of proline degradation to glutamate" EXACT [GOC:obol]
synonym: "regulation of proline oxidation" RELATED [GOC:obol]
+is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:0009894 ! regulation of catabolic process
-is_a: GO:2000214 ! regulation of L-proline metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0006562 ! L-proline catabolic process
relationship: regulates GO:0006562 ! L-proline catabolic process
@@ -640073,30 +645934,27 @@
[Term]
id: GO:2001194
-name: regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
+name: obsolete regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of lysine biosynthetic process via alpha-aminoadipate and saccharopine." [GOC:obol]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of lysine biosynthetic process via alpha-aminoadipate and saccharopine." [GOC:obol]
+comment: The reason for obsoletion is that this term was created unnecessarily.
synonym: "regulation of lysine biosynthesis via aminoadipic acid and saccharopine" EXACT [GOC:obol]
synonym: "regulation of lysine biosynthetic process via aminoadipic acid and saccharopine" EXACT [GOC:obol]
-is_a: GO:1902986 ! regulation of lysine biosynthetic process via aminoadipic acid
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
-relationship: regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
created_by: mcc
creation_date: 2011-11-03T07:57:11Z
[Term]
id: GO:2001195
-name: negative regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
+name: obsolete negative regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of lysine biosynthetic process via alpha-aminoadipate and saccharopine." [GOC:obol]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of lysine biosynthetic process via alpha-aminoadipate and saccharopine." [GOC:obol]
+comment: The reason for obsoletion is that this term was created unnecessarily.
synonym: "negative regulation of lysine biosynthesis via aminoadipic acid and saccharopine" EXACT [GOC:obol]
synonym: "negative regulation of lysine biosynthetic process via aminoadipic acid and saccharopine" EXACT [GOC:obol]
-is_a: GO:1902987 ! negative regulation of lysine biosynthetic process via aminoadipic acid
-is_a: GO:2001194 ! regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
-relationship: negatively_regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31525" xsd:anyURI
+is_obsolete: true
created_by: mcc
creation_date: 2011-11-03T07:57:18Z
@@ -640108,11 +645966,11 @@
synonym: "positive regulation of lysine biosynthesis via aminoadipic acid and saccharopine" EXACT [GOC:obol]
synonym: "positive regulation of lysine biosynthetic process via aminoadipic acid and saccharopine" EXACT [GOC:obol]
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
+is_a: GO:1902986 ! regulation of lysine biosynthetic process via aminoadipic acid
is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
-is_a: GO:2001194 ! regulation of lysine biosynthetic process via alpha-aminoadipate and saccharopine
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
-relationship: positively_regulates GO:0051975 ! L-lysine biosynthetic process via alpha-aminoadipate and saccharopine
+intersection_of: positively_regulates GO:0009085 ! L-lysine biosynthetic process
+relationship: positively_regulates GO:0009085 ! L-lysine biosynthetic process
created_by: mcc
creation_date: 2011-11-03T07:57:24Z
@@ -640593,6 +646451,7 @@
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis]
synonym: "regulation of apoptotic signalling pathway" EXACT [GOC:mah]
+xref: Reactome:R-HSA-205025 "NADE modulates death signalling"
is_a: GO:0009966 ! regulation of signal transduction
is_a: GO:0042981 ! regulation of apoptotic process
intersection_of: GO:0065007 ! biological regulation
@@ -640836,8 +646695,9 @@
def: "Any process that modulates the frequency, rate or extent of ammonia assimilation cycle." [GOC:BHF]
synonym: "regulation of glutamate metabolic process via glutamine and ammonia" EXACT [GOC:obol]
synonym: "regulation of glutamate metabolism via glutamine and ammonia" EXACT [GOC:obol]
+is_a: GO:0006521 ! regulation of amino acid metabolic process
is_a: GO:0006808 ! regulation of nitrogen utilization
-is_a: GO:2000211 ! regulation of glutamate metabolic process
+is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0019676 ! ammonia assimilation cycle
relationship: regulates GO:0019676 ! ammonia assimilation cycle
@@ -640851,8 +646711,9 @@
def: "Any process that stops, prevents or reduces the frequency, rate or extent of ammonia assimilation cycle." [GOC:BHF]
synonym: "negative regulation of glutamate metabolic process via glutamine and ammonia" EXACT [GOC:obol]
synonym: "negative regulation of glutamate metabolism via glutamine and ammonia" EXACT [GOC:obol]
+is_a: GO:0045763 ! negative regulation of amino acid metabolic process
is_a: GO:0045847 ! negative regulation of nitrogen utilization
-is_a: GO:2000212 ! negative regulation of glutamate metabolic process
+is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:2001248 ! regulation of ammonia assimilation cycle
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0019676 ! ammonia assimilation cycle
@@ -641552,15 +647413,15 @@
[Term]
id: GO:2001297
-name: N(omega)-methyl-L-arginine catabolic process
+name: obsolete N(omega)-methyl-L-arginine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of N(omega)-methyl-L-arginine." [GOC:rs, PMID:10510241]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of N(omega)-methyl-L-arginine." [GOC:rs, PMID:10510241]
+comment: The reason for obsoletion is that there is no evidence that this function/process/component exists.
synonym: "N(omega)-methyl-L-arginine breakdown" EXACT [GOC:obol]
synonym: "N(omega)-methyl-L-arginine catabolism" EXACT [GOC:obol]
synonym: "N(omega)-methyl-L-arginine degradation" EXACT [GOC:obol]
-is_a: GO:0042219 ! modified amino acid catabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2012-02-14T03:38:21Z
@@ -641578,15 +647439,15 @@
[Term]
id: GO:2001299
-name: N(omega),N(omega)-dimethyl-L-arginine catabolic process
+name: obsolete N(omega),N(omega)-dimethyl-L-arginine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of N(omega),N(omega)-dimethyl-L-arginine, a methyl-L-arginine having two methyl groups both attached to the primary amino moiety of the guanidino group." [GOC:rs, PMID:10510241]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of N(omega),N(omega)-dimethyl-L-arginine, a methyl-L-arginine having two methyl groups both attached to the primary amino moiety of the guanidino group." [GOC:rs, PMID:10510241]
+comment: The reason for obsoletion is that there is no evidence that this function/process/component exists.
synonym: "N(omega),N(omega)-dimethyl-L-arginine breakdown" EXACT [GOC:obol]
synonym: "N(omega),N(omega)-dimethyl-L-arginine catabolism" EXACT [GOC:obol]
synonym: "N(omega),N(omega)-dimethyl-L-arginine degradation" EXACT [GOC:obol]
-is_a: GO:0042219 ! modified amino acid catabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31361" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2012-02-14T03:40:03Z
@@ -641911,8 +647772,10 @@
id: GO:7770002
name: sodium:ammonium:chloride symporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + NH4+(out) + Cl-(out) = Na+(in) + NH4+(in) + Cl-(in)." [PMID:12657561]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + NH4+(out) + Cl-(out) = Na+(in) + NH4+(in) + Cl-(in)." [PMID:12657561, RHEA:85511]
+xref: RHEA:85511
is_a: GO:0015378 ! sodium:chloride symporter activity
+property_value: skos:exactMatch RHEA:85511
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30468" xsd:anyURI
created_by: dragon-ai-agent
creation_date: 2025-06-19T23:39:51Z
@@ -641993,9 +647856,11 @@
id: GO:7770009
name: L-tryptophan conjugated cholate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cholate + L-tryptophan = L-tryptophocholate + H2O." [PMID:40446798]
+def: "Catalysis of the reaction: cholate + L-tryptophan = L-tryptophocholate + H2O." [PMID:40446798, RHEA:85423]
xref: CHEBI:234456
+xref: RHEA:85423
is_a: GO:7770003 ! amino acid conjugated cholate hydrolase activity
+property_value: skos:exactMatch RHEA:85423
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30487" xsd:anyURI
created_by: dragon-ai-agent
creation_date: 2025-06-25T00:18:58Z
@@ -642270,9 +648135,12 @@
def: "The chemical reactions and pathways resulting in the formation of nickel-pincer nucleotide (NPN) cofactor, also known as nickel pyridinium-3,5-bisthiocarboxylic acid mononucleotide." [PMID:24710389, PMID:27114550, PMID:33093595, PMID:39667499, PMID:39827451]
synonym: "NPN cofactor biosynthetic process" EXACT []
xref: MetaCyc:PWY-7928
+xref: MetaCyc:PWY-8561
is_a: GO:0051191 ! prosthetic group biosynthetic process
-property_value: skos:exactMatch MetaCyc:PWY-7928
+property_value: skos:narrowMatch MetaCyc:PWY-7928
+property_value: skos:narrowMatch MetaCyc:PWY-8561
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31252" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
created_by: dragon-ai-agent
[Term]
@@ -642313,6 +648181,235 @@
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30887" xsd:anyURI
created_by: dragon-ai-agent
+[Term]
+id: GO:7770038
+name: melanosomal lumen acidification
+namespace: biological_process
+def: "Any process that reduces the pH of the melanosomal lumen, corresponding to an increase in hydrogen ion concentration." [PMID:23205854, PMID:35469906]
+synonym: "melanosome pH reduction" EXACT []
+is_a: GO:0051452 ! intracellular pH reduction
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28838" xsd:anyURI
+created_by: dragon-ai-agent
+
+[Term]
+id: GO:7770039
+name: melanosomal lumen pH elevation
+namespace: biological_process
+def: "Any process that increases the pH of the melanosomal lumen, corresponding to a decrease in hydrogen ion concentration." [PMID:11310796, PMID:27140606, PMID:32966160, PMID:35469906]
+synonym: "melanosome pH elevation" EXACT []
+is_a: GO:0051454 ! intracellular pH elevation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28838" xsd:anyURI
+created_by: dragon-ai-agent
+
+[Term]
+id: GO:7770040
+name: epiplastidial membrane
+namespace: cellular_component
+def: "The outermost lipid bilayer surrounding complex plastids in organisms that acquired their plastids through secondary endosymbiosis. This membrane is derived from the host cell's endomembrane system and is continuous with the rough endoplasmic reticulum and the outer nuclear envelope. In some species, the cytoplasmic face may be studded with ribosomes." [PMID:15937721, PMID:27179349, PMID:39383259]
+synonym: "cERM" EXACT []
+synonym: "chloroplast ER membrane" EXACT []
+synonym: "epiplastid rough ER" EXACT []
+synonym: "EpM" EXACT []
+synonym: "EPrER" EXACT []
+is_a: GO:0042170 ! plastid membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31421" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-01-29T01:11:34Z
+
+[Term]
+id: GO:7770041
+name: periplastidial membrane
+namespace: cellular_component
+def: "The lipid bilayer that forms the second outermost membrane of complex plastids in organisms that acquired their plastids through secondary endosymbiosis. The periplastidial membrane is evolutionarily derived from the plasma membrane of the engulfed algal endosymbiont and together with the outer envelope membrane of the plastid defines the periplastidial compartment." [PMID:15937721, PMID:27179349, PMID:39383259]
+synonym: "PPM" EXACT []
+is_a: GO:0042170 ! plastid membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31421" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-01-29T01:11:34Z
+
+[Term]
+id: GO:7770042
+name: bindosome complex
+namespace: cellular_component
+def: "A membrane-associated protein complex found in archaea that consists of sugar binding proteins assembled via a type IV pilin-like assembly system. The complex is located at the cell surface and functions in sugar uptake by facilitating the interaction between solute binding proteins and ABC transporters. The complex forms high molecular mass structures (400-600 kDa) that are integrated within or closely associated with the S-layer." [PMID:21234771, PMID:38877064]
+is_a: GO:0098796 ! membrane protein complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31422" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-01-29T01:57:42Z
+
+[Term]
+id: GO:7770043
+name: lipid chaperone activity
+namespace: molecular_function
+def: "Binding to a lipid and delivering it to an acceptor protein, including enzymes, nuclear receptors, and other lipid-binding proteins. The lipid may be presented while bound to the chaperone for enzymatic modification or signaling, or fully transferred to the acceptor protein." [PMID:16216074, PMID:18511927, PMID:25847235, PMID:26658141]
+is_a: GO:0005319 ! lipid carrier activity
+relationship: has_part GO:0008289 ! lipid binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31403" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-01-30T01:54:24Z
+
+[Term]
+id: GO:7770044
+name: phycoerythrobilin synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: biliverdin IXalpha + 2 reduced ferredoxin + 4 H+ = (3Z)-phycoerythrobilin + 2 oxidized ferredoxin." [PMID:18662988, RHEA:25359]
+xref: EC:1.3.7.6
+xref: RHEA:25359
+is_a: GO:0016636 ! oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor
+property_value: skos:exactMatch EC:1.3.7.6
+property_value: skos:exactMatch RHEA:25359
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31443" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-01-30T04:39:58Z
+
+[Term]
+id: GO:7770045
+name: negative regulation of GCN2-mediated signaling
+namespace: biological_process
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of GCN2-mediated signaling." [PMID:23899355]
+is_a: GO:0080135 ! regulation of cellular response to stress
+is_a: GO:1902532 ! negative regulation of intracellular signal transduction
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: negatively_regulates GO:0140469 ! GCN2-mediated signaling
+relationship: negatively_regulates GO:0140469 ! GCN2-mediated signaling
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31453" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-02-04T18:20:09Z
+
+[Term]
+id: GO:7770046
+name: obsolete N6-methyladenosine kinase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: ATP + N6-methyladenosine = ADP + H+ + N6-methyl-AMP." [PMID:40840445]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30800" xsd:anyURI
+is_obsolete: true
+created_by: dragon-ai-agent
+creation_date: 2026-02-09T05:59:37Z
+
+[Term]
+id: GO:7770047
+name: obsolete N6,N6-dimethyladenosine kinase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: ATP + N6,N6-dimethyladenosine = ADP + H+ + N6,N6-dimethyl-AMP." [PMID:40840445]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30800" xsd:anyURI
+is_obsolete: true
+created_by: dragon-ai-agent
+creation_date: 2026-02-09T05:59:37Z
+
+[Term]
+id: GO:7770048
+name: obsolete N6-isopentenyladenosine kinase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: ATP + N6-isopentenyladenosine = ADP + H+ + N6-isopentenyl-AMP." [PMID:40840445]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30800" xsd:anyURI
+is_obsolete: true
+created_by: dragon-ai-agent
+creation_date: 2026-02-09T05:59:37Z
+
+[Term]
+id: GO:7770049
+name: obsolete N6,N6-dimethyl-AMP deaminase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: H2O + H+ + N6,N6-dimethyl-AMP = IMP + dimethylamine." [PMID:40840445]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30800" xsd:anyURI
+is_obsolete: true
+created_by: dragon-ai-agent
+creation_date: 2026-02-09T05:59:37Z
+
+[Term]
+id: GO:7770050
+name: obsolete N6-isopentenyl-AMP deaminase activity
+namespace: molecular_function
+def: "OBSOLETE. Catalysis of the reaction: H2O + H+ + N6-isopentenyl-AMP = IMP + dimethylallylamine." [PMID:40840445]
+comment: The reason for obsoletion is that this term was added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30800" xsd:anyURI
+is_obsolete: true
+created_by: dragon-ai-agent
+creation_date: 2026-02-09T05:59:37Z
+
+[Term]
+id: GO:7770051
+name: mitochondrial-lysosomal membrane contact site
+namespace: cellular_component
+def: "An organelle membrane contact site between the mitochondrial outer membrane and the lysosomal membrane." [PMID:29364868, PMID:30898429, PMID:32703809, PMID:33372681, PMID:33753743, PMID:35249745]
+synonym: "lysosome-mitochondrion membrane contact site" EXACT []
+synonym: "mitochondria-lysosome contact site" EXACT []
+synonym: "mitochondria-lysosome MCS" EXACT []
+synonym: "mitochondria-lysosome membrane contact site" EXACT []
+is_a: GO:1990816 ! vacuole-mitochondrion membrane contact site
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31553" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-02-11T18:32:29Z
+
+[Term]
+id: GO:7770052
+name: endoplasmic reticulum-lysosome membrane contact site
+namespace: cellular_component
+def: "An organelle membrane contact site between the endoplasmic reticulum membrane and the lysosomal membrane." [PMID:31537798, PMID:39370902]
+synonym: "ER-lysosome contact site" EXACT []
+synonym: "ER-lysosome MCS" EXACT []
+synonym: "lysosome-ER membrane contact site" EXACT []
+is_a: GO:0098853 ! endoplasmic reticulum-vacuole membrane contact site
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31541" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-02-12T00:09:12Z
+
+[Term]
+id: GO:7770053
+name: nucleotide-binding leucine-rich repeat receptor complex
+namespace: cellular_component
+def: "A protein complex that contains one or more nucleotide-binding leucine-rich repeat (NLR) proteins and functions as an intracellular innate immune receptor. Upon activation by pathogen effectors or danger signals, the complex oligomerizes with adaptor and effector proteins to trigger downstream immune responses including programmed cell death." [PMID:26355215, PMID:30948526, PMID:30948527]
+synonym: "NLR complex" EXACT []
+synonym: "NLR receptor complex" EXACT []
+synonym: "NOD-like receptor complex" RELATED []
+is_a: GO:0043235 ! signaling receptor complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31604" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-02-19T17:46:49Z
+
+[Term]
+id: GO:7770054
+name: tRNA(Val) (adenine(37)-N6)-methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + adenosine(37) in tRNA(Val) = S-adenosyl-L-homocysteine + N(6)-methyladenosine(37) in tRNA(Val) + H+." [PMID:19383770, RHEA:43160]
+xref: EC:2.1.1.223
+xref: RHEA:43160
+is_a: GO:0008170 ! N-methyltransferase activity
+is_a: GO:0016426 ! tRNA (adenine) methyltransferase activity
+property_value: skos:exactMatch EC:2.1.1.223
+property_value: skos:exactMatch RHEA:43160
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31644" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-02-28T05:25:40Z
+
+[Term]
+id: GO:7770055
+name: intestinal lumen acidification
+namespace: biological_process
+def: "Any process that reduces the pH of the intestinal lumen, corresponding to an increase in hydrogen ion concentration." [PMID:19741196]
+synonym: "intestinal lumen pH reduction" EXACT []
+is_a: GO:7770056 ! multicellular organismal-level extracellular fluid acidification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31657" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-03-03T02:00:57Z
+
+[Term]
+id: GO:7770056
+name: multicellular organismal-level extracellular fluid acidification
+namespace: biological_process
+def: "Any process that reduces the pH of an extracellular fluid of a multicellular organism, corresponding to an increase in hydrogen ion concentration." [PMID:33326313, PMID:35666106]
+synonym: "extracellular fluid pH reduction" EXACT []
+synonym: "multicellular organismal-level extracellular fluid pH reduction" EXACT []
+is_a: GO:0032501 ! multicellular organismal process
+is_a: GO:0045851 ! pH reduction
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29164" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-03-24T17:37:00Z
+
[Typedef]
id: ends_during
name: ends during