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Renamed and merged terms. #26122 #26827

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Renamed and merged terms. #26122 #26827

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10e3b9e
Renamed and merged terms. #26122
raymond91105 Jan 18, 2024
704bf10
Removed taxon constraints. #26122
raymond91105 Jan 18, 2024
bbc69fa
Merge branch 'master' of github.com:geneontology/go-ontology into iss…
raymond91105 Jan 22, 2024
0aea920
Merge branch 'master' of github.com:geneontology/go-ontology into iss…
raymond91105 Jan 22, 2024
cb8d2f4
Added relationships to multiple terms. #26122
raymond91105 Jan 23, 2024
d1172c3
Fixed a weird error in Typedef.
raymond91105 Jan 23, 2024
cc5a3be
Removed some SubClassOf relationships. #26122
raymond91105 Jan 23, 2024
926b973
Merge branch 'master' of github.com:geneontology/go-ontology into iss…
raymond91105 Jan 24, 2024
570ffd3
Fixed a weird error in Typedef again.
raymond91105 Jan 24, 2024
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50 changes: 26 additions & 24 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -56485,12 +56485,14 @@ relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005947
name: mitochondrial alpha-ketoglutarate dehydrogenase complex
name: obsolete mitochondrial alpha-ketoglutarate dehydrogenase complex
namespace: cellular_component
def: "Mitochondrial complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah, GOC:mtg_sensu]
def: "OBSOLETE. Mitochondrial complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is equivalent to mitochondrial oxoglutarate dehydrogenase complex.
synonym: "2-oxoglutarate dehydrogenase complex" BROAD []
intersection_of: GO:0045240 ! dihydrolipoyl dehydrogenase complex
intersection_of: part_of GO:0005739 ! mitochondrion
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26122" xsd:anyURI
is_obsolete: true
replaced_by: GO:0009353

[Term]
id: GO:0005948
Expand Down Expand Up @@ -89561,9 +89563,6 @@ comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succ
is_a: GO:0098798 ! mitochondrial protein-containing complex
intersection_of: GO:0045252 ! oxoglutarate dehydrogenase complex
intersection_of: part_of GO:0005739 ! mitochondrion
relationship: capable_of GO:0004148 ! dihydrolipoyl dehydrogenase activity
relationship: capable_of GO:0004149 ! dihydrolipoyllysine-residue succinyltransferase activity
relationship: capable_of GO:0004591 ! oxoglutarate dehydrogenase (succinyl-transferring) activity
relationship: part_of GO:0005759 ! mitochondrial matrix

[Term]
Expand Down Expand Up @@ -262636,23 +262635,26 @@ relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0045240
name: dihydrolipoyl dehydrogenase complex
name: alpha-ketoacid dehydrogenase complex
namespace: cellular_component
def: "A protein complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah]
synonym: "2-oxoglutarate dehydrogenase complex" EXACT []
synonym: "alpha-ketoglutarate dehydrogenase complex" EXACT []
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0004148 ! dihydrolipoyl dehydrogenase activity
def: "A multi-enzyme complex that catalyzes the oxidative decarboxylation of an alpha-ketoacid - pyruvate, a branched-chain alpha-ketoacid or alpha-ketoglutarate (also known as 2-oxoglutarate). The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: a dihydrolipoyl transacylase (E2) forms the core of the complex, with an alpha-ketoacid dehydrogenase (E1) and a dihydrolipoamide dehydrogenase (E3) attached through non-covalent bonds. The E1 and E2 components are specific to different alpha-ketoacid dehydrogenase complexes, whereas the E3 component is the same. Additional proteins may also be present." [GOC:mah, PMID:10745006]
synonym: "2-oxoacid dehydrogenase complex" EXACT []
synonym: "2-oxoglutarate dehydrogenase complex" NARROW []
synonym: "alpha-ketoglutarate dehydrogenase complex" NARROW []
synonym: "dihydrolipoyl dehydrogenase complex" EXACT []
is_a: GO:1990204 ! oxidoreductase complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26122" xsd:anyURI

[Term]
id: GO:0045241
name: cytosolic alpha-ketoglutarate dehydrogenase complex
name: obsolete cytosolic alpha-ketoglutarate dehydrogenase complex
namespace: cellular_component
def: "Cytosolic complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah, GOC:mtg_sensu]
def: "OBSOLETE. Cytosolic complex that possesses alpha-ketoglutarate dehydrogenase activity." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is equivalent to cytosolic oxoglutarate dehydrogenase complex.
synonym: "2-oxoglutarate dehydrogenase complex" BROAD []
is_a: GO:0045240 ! dihydrolipoyl dehydrogenase complex
is_a: GO:0045246 ! cytosolic tricarboxylic acid cycle enzyme complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26122" xsd:anyURI
is_obsolete: true
replaced_by: GO:0045248

[Term]
id: GO:0045242
Expand Down Expand Up @@ -262712,9 +262714,6 @@ namespace: cellular_component
def: "A cytosolic complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [GOC:mtg_sensu, PMID:10848975]
intersection_of: GO:0045252 ! oxoglutarate dehydrogenase complex
intersection_of: part_of GO:0005829 ! cytosol
relationship: capable_of GO:0004148 ! dihydrolipoyl dehydrogenase activity
relationship: capable_of GO:0004149 ! dihydrolipoyllysine-residue succinyltransferase activity
relationship: capable_of GO:0004591 ! oxoglutarate dehydrogenase (succinyl-transferring) activity

[Term]
id: GO:0045249
Expand Down Expand Up @@ -262753,10 +262752,9 @@ namespace: cellular_component
def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
subset: goslim_pir
synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT []
is_a: GO:0045240 ! alpha-ketoacid dehydrogenase complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0004148 ! dihydrolipoyl dehydrogenase activity
intersection_of: capable_of GO:0004149 ! dihydrolipoyllysine-residue succinyltransferase activity
intersection_of: capable_of GO:0004591 ! oxoglutarate dehydrogenase (succinyl-transferring) activity
intersection_of: capable_of GO:0034602 ! oxoglutarate dehydrogenase (NAD+) activity

[Term]
id: GO:0045253
Expand All @@ -262780,6 +262778,7 @@ subset: goslim_pir
synonym: "dihydrolipoyl dehydrogenase complex" BROAD []
synonym: "pyruvate dehydrogenase complex (lipoamide)" EXACT []
xref: Wikipedia:Pyruvate_dehydrogenase_complex
is_a: GO:0045240 ! alpha-ketoacid dehydrogenase complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0034604 ! pyruvate dehydrogenase (NAD+) activity
relationship: part_of GO:0005737 ! cytoplasm
Expand Down Expand Up @@ -460151,7 +460150,10 @@ name: branched-chain alpha-keto acid dehydrogenase complex
namespace: cellular_component
def: "A mitochondrial complex that catalyzes the oxidative decarboxylation of branched-chain alpha-keto acids derived from L-leucine, L-isoleucine, and L-valine to branched-chain acyl-CoAs. The complex is organized around a 24-meric cubic core of the dihydrolipoyl transacylase (E2) with multiple (about 6 to 12) copies of the branched-chain alpha-ketoacid dehydrogenase (E1, consisting of alpha and beta subunits), about 6 copies of the dimeric dihydrolipoyl dehydrogenase (E3), and a small number of copies of the E1-specific kinase and phosphatase." [PMID:10745006, PMID:3593587, PMID:9582350]
synonym: "BCKD complex" EXACT []
is_a: GO:0045240 ! alpha-ketoacid dehydrogenase complex
is_a: GO:0098798 ! mitochondrial protein-containing complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0047101 ! branched-chain alpha-keto acid dehydrogenase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26121" xsd:anyURI
created_by: rynl
creation_date: 2023-10-27T23:46:26Z
Expand Down
6 changes: 0 additions & 6 deletions src/taxon_constraints/only_in_taxon.ofn
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Expand Up @@ -101,7 +101,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005917>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005918>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005921>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005929>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005947>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0006264>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0006390>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0006393>))
Expand Down Expand Up @@ -1419,11 +1418,6 @@ SubClassOf(<http://purl.obolibrary.org/obo/GO_0005921> ObjectAllValuesFrom(<http
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005929> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005929> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))

# Class: <http://purl.obolibrary.org/obo/GO_0005947> (<http://purl.obolibrary.org/obo/GO_0005947>)

SubClassOf(<http://purl.obolibrary.org/obo/GO_0005947> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))
SubClassOf(<http://purl.obolibrary.org/obo/GO_0005947> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))

# Class: <http://purl.obolibrary.org/obo/GO_0006264> (<http://purl.obolibrary.org/obo/GO_0006264>)

SubClassOf(<http://purl.obolibrary.org/obo/GO_0006264> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002160> <http://purl.obolibrary.org/obo/NCBITaxon_2759>))
Expand Down
1 change: 0 additions & 1 deletion src/taxon_constraints/only_in_taxon.tsv
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Expand Up @@ -67,7 +67,6 @@ GO:0005917 nephrocyte diaphragm NCBITaxon:50557 Insecta
GO:0005918 septate junction NCBITaxon:6656 Arthropoda
GO:0005921 gap junction NCBITaxon:6072 Eumetazoa
GO:0005929 cilium NCBITaxon:2759 Eukaryota
GO:0005947 mitochondrial alpha-ketoglutarate dehydrogenase complex NCBITaxon:2759 Eukaryota
GO:0006914 autophagy NCBITaxon:2759 Eukaryota
GO:0006915 apoptotic process NCBITaxon:33154 Opisthokonta
GO:0006954 inflammatory response NCBITaxon:7742 Vertebrata <Metazoa>
Expand Down
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