Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Obsoleted multiple terms under TCA cycle enzyme complex, #26882. #26950

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Obsoleted multiple terms under TCA cycle enzyme complex, #26882. #26950

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c334a34
Obsoleted multiple terms under TCA cycle enzyme complex, #26882.
raymond91105 Feb 3, 2024
12f37b8
Changed term label, fixes #26882.
raymond91105 Feb 6, 2024
1cd9667
Tried to resolve conflicts in go_taxon_constraints.owl.
raymond91105 Feb 6, 2024
2de50c7
Removed a taxon constraint, again, #26882
raymond91105 Feb 6, 2024
b44f8ae
Updated taxon constraint files to master
raymond91105 Feb 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
56 changes: 30 additions & 26 deletions src/ontology/go-edit.obo
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56644,12 +56644,13 @@ relationship: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0005962
name: mitochondrial isocitrate dehydrogenase complex (NAD+)
name: obsolete mitochondrial isocitrate dehydrogenase complex (NAD+)
namespace: cellular_component
def: "Mitochondrial complex that possesses isocitrate dehydrogenase (NAD+) activity." [GOC:mah, GOC:mtg_sensu]
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'isocitrate dehydrogenase (NAD+) activity ; GO:0004449'.
intersection_of: GO:0045242 ! isocitrate dehydrogenase complex (NAD+)
intersection_of: part_of GO:0005739 ! mitochondrion
def: "OBSOLETE. Mitochondrial complex that possesses isocitrate dehydrogenase (NAD+) activity." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is unnecessarily taxon-specific.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26882" xsd:anyURI
is_obsolete: true
replaced_by: GO:0045242

[Term]
id: GO:0005963
Expand Down Expand Up @@ -156407,13 +156408,14 @@ relationship: part_of GO:0031966 ! mitochondrial membrane

[Term]
id: GO:0030062
name: mitochondrial tricarboxylic acid cycle enzyme complex
name: obsolete mitochondrial tricarboxylic acid cycle enzyme complex
namespace: cellular_component
def: "Any of the heteromeric enzymes, located in the mitochondrion, that act in the tricarboxylic acid (TCA) cycle." [GOC:mah, GOC:mtg_sensu]
def: "OBSOLETE. Any of the heteromeric enzymes, located in the mitochondrion, that act in the tricarboxylic acid (TCA) cycle." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is unnecessarily taxon-specific.
synonym: "TCA cycle enzyme complex" BROAD []
intersection_of: GO:0045239 ! tricarboxylic acid cycle enzyme complex
intersection_of: part_of GO:0005739 ! mitochondrion
relationship: part_of GO:0005759 ! mitochondrial matrix
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26882" xsd:anyURI
is_obsolete: true
replaced_by: GO:0045239

[Term]
id: GO:0030063
Expand Down Expand Up @@ -238020,7 +238022,7 @@ id: GO:0042709
name: succinate-CoA ligase complex
namespace: cellular_component
def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP." [GOC:jl, PMID:10671455]
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
is_a: GO:0045239 ! tricarboxylic acid cycle heteromeric enzyme complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0004774 ! succinate-CoA ligase activity

Expand Down Expand Up @@ -262722,7 +262724,7 @@ is_a: GO:0005153 ! interleukin-8 receptor binding

[Term]
id: GO:0045239
name: tricarboxylic acid cycle enzyme complex
name: tricarboxylic acid cycle heteromeric enzyme complex
namespace: cellular_component
def: "Any of the heteromeric enzymes that act in the TCA cycle." [GOC:mah]
subset: goslim_pir
Expand Down Expand Up @@ -262757,19 +262759,20 @@ id: GO:0045242
name: isocitrate dehydrogenase complex (NAD+)
namespace: cellular_component
def: "Complex that possesses isocitrate dehydrogenase (NAD+) activity." [GOC:mah]
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
is_a: GO:0045239 ! tricarboxylic acid cycle heteromeric enzyme complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0004449 ! isocitrate dehydrogenase (NAD+) activity

[Term]
id: GO:0045243
name: cytosolic isocitrate dehydrogenase complex (NAD+)
name: obsolete cytosolic isocitrate dehydrogenase complex (NAD+)
namespace: cellular_component
def: "Cytosolic complex that possesses isocitrate dehydrogenase (NAD+) activity." [GOC:mah, GOC:mtg_sensu]
def: "OBSOLETE. Cytosolic complex that possesses isocitrate dehydrogenase (NAD+) activity." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is unnecessarily taxon-specific.
synonym: "isocitrate dehydrogenase complex (NAD+)" BROAD []
is_a: GO:0045246 ! cytosolic tricarboxylic acid cycle enzyme complex
intersection_of: GO:0045242 ! isocitrate dehydrogenase complex (NAD+)
intersection_of: part_of GO:0005829 ! cytosol
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26882" xsd:anyURI
is_obsolete: true
replaced_by: GO:0045242

[Term]
id: GO:0045244
Expand All @@ -262779,21 +262782,20 @@ alt_id: GO:0008325
alt_id: GO:0045245
def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming GTP." [GOC:jl, PMID:27487822]
synonym: "succinyl-CoA synthetase, GDP-forming" EXACT [CORUM:392]
is_a: GO:0030062 ! mitochondrial tricarboxylic acid cycle enzyme complex
is_a: GO:0042709 ! succinate-CoA ligase complex
intersection_of: GO:0030062 ! mitochondrial tricarboxylic acid cycle enzyme complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0004776 ! succinate-CoA ligase (GDP-forming) activity
intersection_of: part_of GO:0005739 ! mitochondrion

[Term]
id: GO:0045246
name: cytosolic tricarboxylic acid cycle enzyme complex
name: obsolete cytosolic tricarboxylic acid cycle enzyme complex
namespace: cellular_component
def: "Any of the heteromeric enzymes, located in the cytosol, that act in the tricarboxylic acid (TCA) cycle." [GOC:mah, GOC:mtg_sensu]
def: "OBSOLETE. Any of the heteromeric enzymes, located in the cytosol, that act in the tricarboxylic acid (TCA) cycle." [GOC:mah, GOC:mtg_sensu]
comment: The reason for obsoletion is that this term is unnecessarily taxon-specific.
synonym: "TCA cycle enzyme complex" BROAD []
synonym: "tricarboxylic acid cycle enzyme complex" BROAD []
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
relationship: part_of GO:0005829 ! cytosol
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26882" xsd:anyURI
is_obsolete: true
replaced_by: GO:0045239

[Term]
id: GO:0045247
Expand Down Expand Up @@ -262855,6 +262857,7 @@ synonym: "alpha-ketoglutarate dehydrogenase complex" EXACT []
synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT []
synonym: "KGDHC" EXACT []
xref: Wikipedia:Oxoglutarate_dehydrogenase_complex
is_a: GO:0045239 ! tricarboxylic acid cycle heteromeric enzyme complex
is_a: GO:0045240 ! alpha-ketoacid dehydrogenase complex
intersection_of: GO:0032991 ! protein-containing complex
intersection_of: capable_of GO:0034602 ! oxoglutarate dehydrogenase (NAD+) activity
Expand Down Expand Up @@ -262893,6 +262896,7 @@ id: GO:0045257
name: succinate dehydrogenase complex (ubiquinone)
namespace: cellular_component
def: "The enzyme that catalyzes the oxidation of succinate and ubiquinone to fumarate and ubiquinol; involved in aerobic respiration, repressed in anaerobic respiration." [GOC:kd, ISBN:0198547684]
is_a: GO:0045239 ! tricarboxylic acid cycle heteromeric enzyme complex
is_a: GO:0045281 ! succinate dehydrogenase complex
intersection_of: GO:0045281 ! succinate dehydrogenase complex
intersection_of: capable_of GO:0008177 ! succinate dehydrogenase (quinone) activity
Expand Down
Loading
Loading