--- go-lastrelease.obo 2026-09-13 05:37:42.205294383 +0000
+++ go.obo 2026-09-13 05:51:22.471894714 +0000
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2026-07-26
+data-version: releases/2026-09-13
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"
@@ -8,7 +8,7 @@
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"
-subsetdef: goslim_euk_cellular_processes_ribbon "GO ribbon for eukaroytic cellular processes"
+subsetdef: goslim_euk_cellular_processes_ribbon "GO ribbon for eukaryotic cellular processes"
subsetdef: goslim_flybase_ribbon "Insecta GO ribbon slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_metagenomics "Metagenomics GO slim"
@@ -22,6 +22,7 @@
subsetdef: goslim_synapse "synapse GO slim"
subsetdef: goslim_virus "GO subset for viruses"
subsetdef: goslim_yeast "Yeast GO slim"
+subsetdef: noctua_allowed "ChEBI terms allowed for use in Noctua, comprising the Rhea pH 7.3 subset and the GO ChEBI allow-list."
synonymtypedef: syngo_official_label "label approved by the SynGO project"
synonymtypedef: systematic_synonym "Systematic synonym" EXACT
default-namespace: gene_ontology
@@ -44,7 +45,7 @@
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 "2026-07-26" xsd:string
+property_value: owl:versionInfo "2026-09-13" xsd:string
property_value: terms:license http://creativecommons.org/licenses/by/4.0/
[Term]
@@ -474,7 +475,7 @@
is_a: GO:0070925 ! organelle assembly
is_a: GO:1905037 ! autophagosome organization
relationship: has_part GO:0019778 ! Atg12 activating enzyme activity
-relationship: has_part GO:0019786 ! protein-phosphatidylethanolamide deconjugating activity
+relationship: has_part GO:0019786 ! protein-phosphatidylethanolamine deconjugating activity
relationship: has_part GO:0061651 ! Atg12 conjugating enzyme activity
relationship: has_part GO:0061660 ! Atg12 ligase activity
relationship: has_part GO:1904745 ! Atg1/ULK1 kinase complex assembly
@@ -1071,8 +1072,12 @@
xref: MetaCyc:SO4ASSIM-PWY
xref: MetaCyc:SULFMETII-PWY
is_a: GO:0006790 ! sulfur compound metabolic process
+is_a: GO:0044281 ! small molecule metabolic process
+is_a: GO:7770097 ! nutrient assimilation
property_value: skos:narrowMatch MetaCyc:SO4ASSIM-PWY
property_value: skos:narrowMatch MetaCyc:SULFMETII-PWY
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32287" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32376" xsd:anyURI
[Term]
id: GO:0000104
@@ -4618,42 +4623,49 @@
[Term]
id: GO:0000429
-name: carbon catabolite regulation of transcription from RNA polymerase II promoter
+name: obsolete carbon catabolite regulation of transcription from RNA polymerase II promoter
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, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc, GOC:mah]
+def: "OBSOLETE. A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc, GOC:mah]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
synonym: "regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah]
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-is_a: GO:0045990 ! carbon catabolite regulation of transcription
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:0000430
-name: regulation of transcription from RNA polymerase II promoter by glucose
+name: obsolete regulation of transcription from RNA polymerase II promoter by glucose
namespace: biological_process
-def: "Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
-is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter
-is_a: GO:0046015 ! regulation of transcription by glucose
+def: "OBSOLETE. Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:0000431
-name: regulation of transcription from RNA polymerase II promoter by galactose
+name: obsolete regulation of transcription from RNA polymerase II promoter by galactose
namespace: biological_process
-def: "Any process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
-is_a: GO:0000409 ! regulation of transcription by galactose
-is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter
+def: "OBSOLETE. Any process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0006357
[Term]
id: GO:0000432
-name: positive regulation of transcription from RNA polymerase II promoter by glucose
+name: obsolete positive regulation of transcription from RNA polymerase II promoter by glucose
namespace: biological_process
-def: "Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc]
+def: "OBSOLETE. Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
synonym: "activation of transcription from RNA polymerase II promoter by glucose" NARROW []
synonym: "stimulation of transcription from RNA polymerase II promoter by glucose" NARROW []
synonym: "up regulation of transcription from RNA polymerase II promoter by glucose" EXACT []
synonym: "up-regulation of transcription from RNA polymerase II promoter by glucose" EXACT []
synonym: "upregulation of transcription from RNA polymerase II promoter by glucose" EXACT []
-is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose
-is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter
-is_a: GO:0046016 ! positive regulation of transcription by glucose
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0045944
[Term]
id: GO:0000433
@@ -4678,32 +4690,35 @@
synonym: "down-regulation of transcription from RNA polymerase II promoter by galactose" EXACT []
synonym: "downregulation of transcription from RNA polymerase II promoter by galactose" EXACT []
synonym: "inhibition of transcription from RNA polymerase II promoter by galactose" NARROW []
-property_value: term_tracker_item "The reason for obsoletion is that these terms represent GO-CAM models." xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
is_obsolete: true
+consider: GO:0000122
[Term]
id: GO:0000435
-name: positive regulation of transcription from RNA polymerase II promoter by galactose
+name: obsolete positive regulation of transcription from RNA polymerase II promoter by galactose
namespace: biological_process
-def: "Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc]
+def: "OBSOLETE. Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
synonym: "activation of transcription from RNA polymerase II promoter by galactose" NARROW []
synonym: "stimulation of transcription from RNA polymerase II promoter by galactose" NARROW []
synonym: "up regulation of transcription from RNA polymerase II promoter by galactose" EXACT []
synonym: "up-regulation of transcription from RNA polymerase II promoter by galactose" EXACT []
synonym: "upregulation of transcription from RNA polymerase II promoter by galactose" EXACT []
-is_a: GO:0000411 ! positive regulation of transcription by galactose
-is_a: GO:0000431 ! regulation of transcription from RNA polymerase II promoter by galactose
-is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0045944
[Term]
id: GO:0000436
-name: carbon catabolite activation of transcription from RNA polymerase II promoter
+name: obsolete carbon catabolite activation of transcription from RNA polymerase II promoter
namespace: biological_process
-def: "Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
+def: "OBSOLETE. Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
synonym: "positive regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah]
-is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:0045991 ! carbon catabolite activation of transcription
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0045944
[Term]
id: GO:0000437
@@ -6503,7 +6518,7 @@
id: GO:0000815
name: ESCRT III complex
namespace: cellular_component
-def: "A complex with membrane scission activity that plays a major role in many processes where membranes are remodelled - including endosomal transport (vesicle budding), nuclear envelope organisation (membrane closure, mitotic bridge cleavage), and cytokinesis (abscission)." [PMID:17556548, PMID:22361144, PMID:28242692, PMID:31132588, PMID:32243490, PMID:34449766]
+def: "A complex with membrane scission activity that plays a major role in many processes where membranes are remodelled - including endosomal transport (vesicle budding), nuclear envelope organization (membrane closure, mitotic bridge cleavage), and cytokinesis (abscission)." [PMID:17556548, PMID:22361144, PMID:28242692, PMID:31132588, PMID:32243490, PMID:34449766]
synonym: "endosomal sorting complex required for transport" BROAD []
is_a: GO:0036452 ! ESCRT complex
is_a: GO:0098796 ! membrane protein complex
@@ -6731,9 +6746,10 @@
id: GO:0000836
name: Hrd1p ubiquitin ligase complex
namespace: cellular_component
-def: "A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal and membrane domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p. In mammals, this complex contains the ubiquitin ligase HRD1 (Synoviolin) or AMFR (gp78)." [GOC:bf, GOC:elh, PMID:16619026, PMID:16873066, PMID:21454652]
+def: "A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal and membrane domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p. In mammals, this complex contains the ubiquitin ligase HRD1 (Synoviolin)." [GOC:bf, GOC:elh, PMID:16619026, PMID:16873066, PMID:20100910, PMID:21454652]
synonym: "HRD1 ubiquitin ligase complex" RELATED [GOC:bf]
is_a: GO:0000835 ! ER ubiquitin ligase complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32529" xsd:anyURI
[Term]
id: GO:0000837
@@ -10748,6 +10764,7 @@
synonym: "ganglioside metabolism" EXACT []
is_a: GO:0006672 ! ceramide metabolic process
is_a: GO:0006687 ! glycosphingolipid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32322" xsd:anyURI
[Term]
id: GO:0001574
@@ -12201,6 +12218,7 @@
xref: Reactome:R-HSA-72095 "Internal Methylation of mRNA"
xref: RHEA:55584
is_a: GO:0008174 ! mRNA methyltransferase activity
+is_a: GO:7770107 ! RNA (adenine-N6)-methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.348
property_value: skos:exactMatch RHEA:55584
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27389" xsd:anyURI
@@ -13477,7 +13495,6 @@
is_a: GO:0007040 ! lysosome organization
is_a: GO:0016050 ! vesicle organization
is_a: GO:0070925 ! organelle assembly
-relationship: part_of GO:0006909 ! phagocytosis
relationship: part_of GO:0090382 ! phagosome maturation
[Term]
@@ -14067,13 +14084,14 @@
name: leukocyte mediated cytotoxicity
namespace: biological_process
def: "The directed killing of a target cell by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149, PMID:11911826]
-comment: Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system.
+comment: Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. The is_a links to GO:0001906 and GO:0002443 are asserted rather than inferred because this term has no logical definition; they must be maintained by hand (see #20574).
synonym: "immune cell mediated cell death" EXACT []
synonym: "immune cell mediated cell killing" EXACT []
synonym: "immune cell mediated cytotoxicity" EXACT []
synonym: "leucocyte mediated cytotoxicity" EXACT []
is_a: GO:0001906 ! cell killing
is_a: GO:0002443 ! leukocyte mediated immunity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0001910
@@ -16017,13 +16035,13 @@
[Term]
id: GO:0002084
-name: protein depalmitoylation
+name: obsolete protein depalmitoylation
namespace: biological_process
-def: "The removal of palymitoyl groups from a lipoprotein." [GOC:hjd]
-subset: gocheck_obsoletion_candidate
-is_a: GO:0035601 ! protein deacylation
-is_a: GO:0042159 ! lipoprotein catabolic process
-is_a: GO:0098734 ! macromolecule depalmitoylation
+def: "OBSOLETE. The removal of palymitoyl groups from a lipoprotein." [GOC:hjd]
+comment: The reason for obsoletion is that this term represents a molecular function, not a biological process. Consider instead annotating to the molecular function 'palmitoyl-(protein) hydrolase activity' (GO:0008474).
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32290" xsd:anyURI
+is_obsolete: true
+consider: GO:0008474
[Term]
id: GO:0002085
@@ -17458,12 +17476,13 @@
[Term]
id: GO:0002234
-name: detection of endoplasmic reticulum overloading
+name: obsolete detection of endoplasmic reticulum overloading
namespace: biological_process
-def: "The series of events in which a stimulus generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum is received and converted into a molecular signal." [GOC:add, PMID:10390516]
+def: "OBSOLETE. The series of events in which a stimulus generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum is received and converted into a molecular signal." [GOC:add, PMID:10390516]
+comment: The reason for obsoletion is that the term was made in error and describes a molecular function.
synonym: "detection of ER overloading" EXACT []
-is_a: GO:0006983 ! ER overload response
-is_a: GO:0009595 ! detection of biotic stimulus
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32516" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0002235
@@ -18514,7 +18533,7 @@
id: GO:0002330
name: pre-B cell receptor expression
namespace: biological_process
-def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunuglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, PMID:15263090, PMID:22949502, PMID:9834086]
+def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunoglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, PMID:15263090, PMID:22949502, PMID:9834086]
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0002329 ! pre-B cell differentiation
@@ -18965,21 +18984,23 @@
name: dendritic cell cytokine production
namespace: biological_process
def: "Any process that contributes to cytokine production by a dendritic cell." [GOC:add, ISBN:0781735149]
-comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. The is_a link to GO:0002443 is asserted rather than inferred because GO:0002443 has no logical definition; it must be maintained by hand (see #20574).
subset: gocheck_do_not_annotate
is_a: GO:0002367 ! cytokine production involved in immune response
is_a: GO:0002443 ! leukocyte mediated immunity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002372
name: myeloid dendritic cell cytokine production
namespace: biological_process
def: "Any process that contributes to cytokine production by a myeloid dendritic cell." [GOC:add, ISBN:0781735149]
-comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms. The is_a link to GO:0002444 is asserted rather than inferred because GO:0002444 has no logical definition; it must be maintained by hand (see #20574).
subset: gocheck_do_not_annotate
is_a: GO:0002371 ! dendritic cell cytokine production
is_a: GO:0002444 ! myeloid leukocyte mediated immunity
is_a: GO:0061082 ! myeloid leukocyte cytokine production
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002373
@@ -19201,19 +19222,21 @@
id: GO:0002402
name: B cell tolerance induction in mucosal-associated lymphoid tissue
namespace: biological_process
-def: "Tolerance induction taking place in the mucosal-associated lymphoid tissue (MALT) mediated by B cells." [GOC:jal, ISBN:0781735149]
+def: "Tolerance induction taking place in a B cell within the mucosal-associated lymphoid tissue (MALT)." [GOC:jal, ISBN:0781735149]
synonym: "B cell tolerance induction in MALT" EXACT []
is_a: GO:0002401 ! tolerance induction in mucosal-associated lymphoid tissue
is_a: GO:0002451 ! peripheral B cell tolerance induction
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002403
name: T cell tolerance induction in mucosal-associated lymphoid tissue
namespace: biological_process
-def: "Tolerance induction taking place in the mucosal-associated lymphoid tissue (MALT) mediated by T cells." [GOC:jal, ISBN:0781735149, PMID:16551263]
+def: "Tolerance induction taking place in a T cell within the mucosal-associated lymphoid tissue (MALT)." [GOC:jal, ISBN:0781735149, PMID:16551263]
synonym: "T cell tolerance induction in MALT" EXACT []
is_a: GO:0002401 ! tolerance induction in mucosal-associated lymphoid tissue
is_a: GO:0002458 ! peripheral T cell tolerance induction
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002404
@@ -19277,10 +19300,11 @@
id: GO:0002411
name: T cell tolerance induction to tumor cell
namespace: biological_process
-def: "A process of tolerance induction dependent on T cells which leads to immunological tolerance of a tumor." [GOC:add, ISBN:0781735149, PMID:16730260]
+def: "A process of tolerance induction taking place in a T cell which leads to immunological tolerance of a tumor." [GOC:add, ISBN:0781735149, PMID:16730260]
is_a: GO:0002413 ! tolerance induction to tumor cell
is_a: GO:0002424 ! T cell mediated immune response to tumor cell
is_a: GO:0002458 ! peripheral T cell tolerance induction
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002412
@@ -19569,6 +19593,7 @@
alt_id: GO:0019723
alt_id: GO:0042087
def: "Any process involved in the carrying out of an immune response by a leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+comment: This term intentionally has no logical definition: it is a grouping class covering everything leukocytes do immunologically, and no relation in GO expresses that role as necessary and sufficient conditions. Subclasses must be asserted by hand (see #20574).
synonym: "cell-mediated immune response" RELATED []
synonym: "cellular immune response" RELATED []
synonym: "immune cell effector process" EXACT []
@@ -19577,16 +19602,19 @@
synonym: "leucocyte mediated immunity" EXACT []
synonym: "leukocyte immune effector process" EXACT []
is_a: GO:0002252 ! immune effector process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002444
name: myeloid leukocyte mediated immunity
namespace: biological_process
def: "Any process involved in the carrying out of an immune response by a myeloid leukocyte." [GO_REF:0000022, GOC:add, ISBN:0781735149]
+comment: This term intentionally has no logical definition: it is a grouping class covering everything myeloid leukocytes do immunologically, and no relation in GO expresses that role as necessary and sufficient conditions. Subclasses must be asserted by hand (see #20574).
synonym: "myeloid leucocyte immune effector process" EXACT []
synonym: "myeloid leucocyte mediated immunity" EXACT []
synonym: "myeloid leukocyte immune effector process" EXACT []
is_a: GO:0002443 ! leukocyte mediated immunity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0002445
@@ -23269,6 +23297,7 @@
namespace: biological_process
def: "Antigen processing and presentation which is initiated by uptake of antigen via phagocytosis." [GOC:add, ISBN:0781735149]
is_a: GO:0019882 ! antigen processing and presentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32152" xsd:anyURI
[Term]
id: GO:0002748
@@ -31525,6 +31554,7 @@
def: "OBSOLETE. Assists in the correct, non-covalent assembly of glycoproteins in vivo, but is not a component of the assembled structures when performing its normal biological function. Utilizes a lectin site as a means to associate with the unfolded glycoproteins." [GOC:jl, PMID:11337494]
comment: This term was made obsolete because it represents a class of gene products and a biological process rather than a molecular function.
synonym: "glycoprotein-specific chaperone activity" EXACT []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32494" xsd:anyURI
is_obsolete: true
consider: GO:0006457
consider: GO:0044183
@@ -33624,7 +33654,7 @@
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
+relationship: part_of GO:0006096 ! glycolysis
property_value: skos:exactMatch EC:2.7.1.11
property_value: skos:exactMatch RHEA:16109
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -34490,7 +34520,7 @@
id: GO:0003919
name: FMN adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + FMN = diphosphate + FAD." [EC:2.7.7.2, RHEA:17237]
+def: "Catalysis of the reaction: FMN + ATP + H+ = FAD + diphosphate." [RHEA:17237]
synonym: "adenosine triphosphate-riboflavin mononucleotide transadenylase activity" RELATED [EC:2.7.7.2]
synonym: "adenosine triphosphate-riboflavine mononucleotide transadenylase activity" RELATED [EC:2.7.7.2]
synonym: "ATP:FMN adenylyltransferase activity" EXACT []
@@ -34510,6 +34540,7 @@
property_value: skos:exactMatch EC:2.7.7.2
property_value: skos:exactMatch RHEA:17237
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/32345" xsd:anyURI
[Term]
id: GO:0003920
@@ -36658,7 +36689,6 @@
xref: RHEA:10736
xref: RHEA:10740
xref: RHEA:12216
-xref: RHEA:12785
xref: RHEA:13221
xref: RHEA:15757
xref: RHEA:16317
@@ -36731,7 +36761,6 @@
property_value: skos:narrowMatch RHEA:10736
property_value: skos:narrowMatch RHEA:10740
property_value: skos:narrowMatch RHEA:12216
-property_value: skos:narrowMatch RHEA:12785
property_value: skos:narrowMatch RHEA:13221
property_value: skos:narrowMatch RHEA:15757
property_value: skos:narrowMatch RHEA:16317
@@ -37086,26 +37115,32 @@
[Term]
id: GO:0004032
-name: aldose reductase (NADPH) activity
+name: aldose reductase [NAD(P)H] activity
namespace: molecular_function
-def: "Catalysis of the reaction: an alditol + NADP+ = an aldose + NADPH + H+." [EC:1.1.1.21]
+def: "Catalysis of the reaction: an alditol + NAD(P)+ = an aldose + NAD(P)H + H+." [EC:1.1.1.21]
synonym: "aldehyde reductase activity" RELATED [EC:1.1.1.21]
-synonym: "alditol:NADP+ 1-oxidoreductase activity" EXACT []
-synonym: "aldose reductase activity" RELATED [EC:1.1.1.21]
+synonym: "alditol:NAD(P)+ 1-oxidoreductase activity" EXACT [EC:1.1.1.21]
+synonym: "alditol:NADP+ 1-oxidoreductase activity" NARROW []
+synonym: "aldose reductase (NADPH) activity" NARROW []
+synonym: "aldose reductase activity" EXACT [EC:1.1.1.21]
synonym: "polyol dehydrogenase (NADP(+)) activity" RELATED [EC:1.1.1.21]
+xref: EC:1.1.1.21
xref: KEGG_REACTION:R02820
+xref: MetaCyc:ALDEHYDE-REDUCTASE-RXN
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:12785
xref: RHEA:12789
xref: RHEA:37967
xref: RHEA:59924
xref: RHEA:59932
-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
+is_a: GO:0018455 ! alcohol dehydrogenase [NAD(P)+] activity
+property_value: skos:exactMatch EC:1.1.1.21
+property_value: skos:exactMatch MetaCyc:ALDEHYDE-REDUCTASE-RXN
+property_value: skos:narrowMatch KEGG_REACTION:R02820
+property_value: skos:narrowMatch RHEA:12785
+property_value: skos:narrowMatch RHEA:12789
property_value: skos:narrowMatch RHEA:37967
property_value: skos:narrowMatch RHEA:59924
property_value: skos:narrowMatch RHEA:59932
@@ -39822,12 +39857,14 @@
property_value: skos:broadMatch RHEA:27758
property_value: skos:broadMatch RHEA:27786
property_value: skos:broadMatch RHEA:28042
+property_value: skos:broadMatch RHEA:30795
property_value: skos:exactMatch EC:1.8.1.4
property_value: skos:exactMatch MetaCyc:1.8.1.4-RXN
property_value: skos:exactMatch RHEA:15045
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24350" 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/30262" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32557" xsd:anyURI
[Term]
id: GO:0004149
@@ -53051,7 +53088,7 @@
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
+relationship: part_of GO:0006096 ! glycolysis
property_value: skos:exactMatch EC:2.7.1.40
property_value: skos:exactMatch MetaCyc:PEPDEPHOS-RXN
property_value: skos:exactMatch RHEA:18157
@@ -56679,7 +56716,7 @@
id: GO:0004972
name: NMDA glutamate receptor activity
namespace: molecular_function
-def: "A cation channel that opens in response to binding by extracellular glutmate, but only if glycine or D-serine is also bound and the membrane is depolarized. Voltage gating is indirect, due to ejection of bound magnesium from the pore at permissive voltages." [GOC:mah, PMID:10049997, PMID:7790891]
+def: "A cation channel that opens in response to binding by extracellular glutamate, but only if glycine or D-serine is also bound and the membrane is depolarized. Voltage gating is indirect, due to ejection of bound magnesium from the pore at permissive voltages." [GOC:mah, PMID:10049997, PMID:7790891]
comment: The name of this receptor comes from its selective activation by N-methyl-D-aspartate (NMDA). Note that this term represents an activity and not a gene product.
synonym: "N-methyl-D-aspartate selective glutamate receptor activity" EXACT []
synonym: "NMDA receptor" EXACT []
@@ -59183,7 +59220,7 @@
name: transporter activity
namespace: molecular_function
alt_id: GO:0005478
-def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf]
+def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, across or in between cells." [GOC:ai, GOC:dgf]
comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
subset: gocheck_do_not_annotate
subset: goslim_agr
@@ -61237,11 +61274,13 @@
name: binding
namespace: molecular_function
def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732]
+subset: gocheck_do_not_annotate
subset: goslim_pir
subset: goslim_plant
synonym: "ligand" NARROW []
xref: Wikipedia:Binding_(molecular)
is_a: GO:0003674 ! molecular_function
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0005489
@@ -66695,14 +66734,18 @@
[Term]
id: GO:0006041
-name: D-glucosamine metabolic process
+name: obsolete D-glucosamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC:jl, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC:jl, ISBN:0198506732]
+comment: The reason for obsoletion is that these terms were added in error.
synonym: "chitosamine metabolic process" EXACT []
synonym: "chitosamine metabolism" EXACT []
synonym: "glucosamine metabolic process" EXACT []
synonym: "glucosamine metabolism" EXACT []
-is_a: GO:0006040 ! amino sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0006042
+consider: GO:0006043
[Term]
id: GO:0006042
@@ -66716,7 +66759,6 @@
synonym: "glucosamine biosynthetic process" EXACT []
synonym: "glucosamine formation" EXACT []
synonym: "glucosamine synthesis" EXACT []
-is_a: GO:0006041 ! D-glucosamine metabolic process
is_a: GO:1901073 ! glucosamine-containing compound biosynthetic process
[Term]
@@ -66730,18 +66772,21 @@
synonym: "glucosamine catabolic process" EXACT []
synonym: "glucosamine catabolism" EXACT []
synonym: "glucosamine degradation" EXACT []
-is_a: GO:0006041 ! D-glucosamine metabolic process
is_a: GO:1901072 ! glucosamine-containing compound catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
[Term]
id: GO:0006044
-name: N-acetylglucosamine metabolic process
+name: obsolete N-acetylglucosamine metabolic process
namespace: biological_process
-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]
+def: "OBSOLETE. 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]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0006045
+consider: GO:0006046
[Term]
id: GO:0006045
@@ -66752,7 +66797,6 @@
synonym: "N-acetylglucosamine biosynthesis" EXACT []
synonym: "N-acetylglucosamine formation" EXACT []
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
@@ -66766,7 +66810,6 @@
synonym: "N-acetylglucosamine degradation" EXACT []
xref: MetaCyc:GLUAMCAT-PWY
xref: MetaCyc:PWY-6517
-is_a: GO:0006044 ! N-acetylglucosamine metabolic process
is_a: GO:1901072 ! glucosamine-containing compound catabolic process
property_value: skos:narrowMatch MetaCyc:GLUAMCAT-PWY
property_value: skos:narrowMatch MetaCyc:PWY-6517
@@ -66776,12 +66819,14 @@
[Term]
id: GO:0006047
-name: UDP-N-acetylglucosamine metabolic process
+name: obsolete UDP-N-acetylglucosamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC:ai]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "UDP-N-acetylglucosamine metabolism" EXACT []
-is_a: GO:0006040 ! amino sugar metabolic process
-is_a: GO:0009225 ! nucleotide-sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0006048
[Term]
id: GO:0006048
@@ -66797,7 +66842,6 @@
xref: MetaCyc:UDPNACETYLGALSYN-PWY
xref: MetaCyc:UDPNAGSYN-PWY
xref: Reactome:R-HSA-446210 "Synthesis of UDP-N-acetyl-glucosamine"
-is_a: GO:0006047 ! UDP-N-acetylglucosamine metabolic process
is_a: GO:0009226 ! nucleotide-sugar biosynthetic process
is_a: GO:0046349 ! amino sugar biosynthetic process
property_value: skos:narrowMatch MetaCyc:UDPNACETYLGALSYN-PWY
@@ -66829,11 +66873,15 @@
[Term]
id: GO:0006051
-name: N-acetylmannosamine metabolic process
+name: obsolete N-acetylmannosamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose." [GOC:ai, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose." [GOC:ai, ISBN:0198506732]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "N-acetylmannosamine metabolism" EXACT []
-is_a: GO:0006040 ! amino sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0006052
+consider: GO:0006053
[Term]
id: GO:0006052
@@ -66844,7 +66892,6 @@
synonym: "N-acetylmannosamine biosynthesis" EXACT []
synonym: "N-acetylmannosamine formation" EXACT []
synonym: "N-acetylmannosamine synthesis" EXACT []
-is_a: GO:0006051 ! N-acetylmannosamine metabolic process
is_a: GO:0046347 ! mannosamine biosynthetic process
[Term]
@@ -66855,19 +66902,21 @@
synonym: "N-acetylmannosamine breakdown" EXACT []
synonym: "N-acetylmannosamine catabolism" EXACT []
synonym: "N-acetylmannosamine degradation" EXACT []
-is_a: GO:0006051 ! N-acetylmannosamine metabolic process
is_a: GO:0046346 ! mannosamine catabolic process
[Term]
id: GO:0006054
-name: N-acetylneuraminate metabolic process
+name: obsolete N-acetylneuraminate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "N-acetylneuraminate metabolism" EXACT []
synonym: "sialic acid metabolic process" BROAD []
synonym: "sialic acid metabolism" BROAD []
-is_a: GO:0006040 ! amino sugar metabolic process
-is_a: GO:0019752 ! carboxylic acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0019262
+consider: GO:0046380
[Term]
id: GO:0006055
@@ -66958,6 +67007,7 @@
is_a: GO:0019406 ! hexitol biosynthetic process
property_value: skos:narrowMatch MetaCyc:PWY-5054
property_value: skos:narrowMatch MetaCyc:PWY-5530
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32269" xsd:anyURI
[Term]
id: GO:0006062
@@ -67371,7 +67421,7 @@
[Term]
id: GO:0006096
-name: glycolytic process
+name: glycolysis
namespace: biological_process
alt_id: GO:0019641
alt_id: GO:0019642
@@ -67379,10 +67429,15 @@
synonym: "anaerobic glycolysis" RELATED []
synonym: "Embden-Meyerhof pathway" RELATED []
synonym: "Embden-Meyerhof-Parnas pathway" RELATED []
-synonym: "glycolysis" RELATED [GOC:dph]
+synonym: "glycolytic process" EXACT []
synonym: "modified Embden-Meyerhof pathway" RELATED []
+xref: MetaCyc:ANAGLYCOLYSIS-PWY
+xref: MetaCyc:GLYCOLYSIS
xref: MetaCyc:GLYCOLYSIS-VARIANTS
xref: MetaCyc:P341-PWY
+xref: MetaCyc:PWY-1042
+xref: MetaCyc:PWY-5484
+xref: MetaCyc:PWY-8404
is_a: GO:0006090 ! pyruvate metabolic process
is_a: GO:0006091 ! generation of precursor metabolites and energy
is_a: GO:0016052 ! carbohydrate catabolic process
@@ -67397,9 +67452,15 @@
relationship: has_part GO:0043891 ! glyceraldehyde-3-phosphate dehydrogenase (phosphorylating, [NAD(P)+] ) activity
relationship: part_of GO:0009060 ! aerobic respiration
property_value: skos:exactMatch MetaCyc:GLYCOLYSIS-VARIANTS
+property_value: skos:narrowMatch MetaCyc:ANAGLYCOLYSIS-PWY
+property_value: skos:narrowMatch MetaCyc:GLYCOLYSIS
property_value: skos:narrowMatch MetaCyc:P341-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-1042
+property_value: skos:narrowMatch MetaCyc:PWY-5484
+property_value: skos:narrowMatch MetaCyc:PWY-8404
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21176" 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/32471" xsd:anyURI
[Term]
id: GO:0006097
@@ -67575,19 +67636,21 @@
[Term]
id: GO:0006110
-name: regulation of glycolytic process
+name: regulation of glycolysis
namespace: biological_process
alt_id: GO:0090525
def: "Any process that modulates the frequency, rate or extent of glycolysis." [GOC:curators]
synonym: "regulation of glycolysis involved in cellular glucose homeostasis" EXACT []
+synonym: "regulation of glycolytic process" EXACT []
xref: Reactome:R-HSA-170822 "Regulation of Glucokinase by Glucokinase Regulatory Protein"
is_a: GO:0033121 ! regulation of purine nucleotide catabolic process
is_a: GO:0043467 ! regulation of generation of precursor metabolites and energy
is_a: GO:0043470 ! regulation of carbohydrate catabolic process
is_a: GO:1903578 ! regulation of ATP metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0006096 ! glycolytic process
-relationship: regulates GO:0006096 ! glycolytic process
+intersection_of: regulates GO:0006096 ! glycolysis
+relationship: regulates GO:0006096 ! glycolysis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
[Term]
id: GO:0006111
@@ -70229,7 +70292,7 @@
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:curators]
+def: "Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase 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
@@ -70635,7 +70698,7 @@
id: GO:0006392
name: transcription elongation by mitochondrial RNA polymerase
namespace: biological_process
-def: "The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase." [GOC:mah, GOC:txnOH]
+def: "The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitochondrial RNA polymerase." [GOC:mah, GOC:txnOH]
synonym: "RNA elongation from mitochondrial promoter" EXACT []
synonym: "transcription elongation from mitochondrial promoter" EXACT []
is_a: GO:0000959 ! mitochondrial RNA metabolic process
@@ -70932,152 +70995,210 @@
namespace: biological_process
def: "The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis." [GOC:ma]
subset: goslim_yeast
-synonym: "tRNA charging" NARROW []
xref: MetaCyc:TRNA-CHARGING-PWY
xref: Reactome:R-HSA-379724 "tRNA Aminoacylation"
-is_a: GO:0043039 ! tRNA aminoacylation
+is_a: GO:0043039 ! tRNA charging
relationship: part_of GO:0006412 ! translation
[Term]
id: GO:0006419
-name: alanyl-tRNA aminoacylation
+name: obsolete alanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004813 alanine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006420
-name: arginyl-tRNA aminoacylation
+name: obsolete arginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004814 arginine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006421
-name: asparaginyl-tRNA aminoacylation
+name: obsolete asparaginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004816 asparagine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006422
-name: aspartyl-tRNA aminoacylation
+name: obsolete aspartyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA." [GOC:mah, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA." [GOC:mah, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004815 aspartate-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006423
-name: cysteinyl-tRNA aminoacylation
+name: obsolete cysteinyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling L-cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling L-cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004817 cysteine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006424
-name: glutamyl-tRNA aminoacylation
+name: obsolete glutamyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004818 glutamate-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006425
-name: glutaminyl-tRNA aminoacylation
+name: obsolete glutaminyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. The glutaminyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. The glutaminyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004819 glutamine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006426
-name: glycyl-tRNA aminoacylation
+name: obsolete glycyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004820 glycine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006427
-name: histidyl-tRNA aminoacylation
+name: obsolete histidyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004821 histidine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006428
-name: isoleucyl-tRNA aminoacylation
+name: obsolete isoleucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004822 isoleucine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006429
-name: leucyl-tRNA aminoacylation
+name: obsolete leucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004823 leucine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006430
-name: lysyl-tRNA aminoacylation
+name: obsolete lysyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004824 lysine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006431
-name: methionyl-tRNA aminoacylation
+name: obsolete methionyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. The methionyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a methionine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004825 methionine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006432
-name: phenylalanyl-tRNA aminoacylation
+name: obsolete phenylalanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004826 phenylalanine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006433
-name: prolyl-tRNA aminoacylation
+name: obsolete prolyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA." [GOC:mah, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA." [GOC:mah, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004827 proline-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006434
-name: seryl-tRNA aminoacylation
+name: obsolete seryl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
-relationship: has_part GO:0001717 ! conversion of seryl-tRNAsec to selenocys-tRNAsec
+def: "OBSOLETE. The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004828 serine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006435
-name: threonyl-tRNA aminoacylation
+name: obsolete threonyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004829 threonine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006436
-name: tryptophanyl-tRNA aminoacylation
+name: obsolete tryptophanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004830 tryptophan-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006437
-name: tyrosyl-tRNA aminoacylation
+name: obsolete tyrosyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004831 tyrosine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006438
-name: valyl-tRNA aminoacylation
+name: obsolete valyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
-is_a: GO:0006418 ! tRNA aminoacylation for protein translation
+def: "OBSOLETE. The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004832 valine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
[Term]
id: GO:0006439
@@ -71811,17 +71932,21 @@
[Term]
id: GO:0006515
-name: protein quality control for misfolded or incompletely synthesized proteins
+name: protein quality control
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins." [GOC:jl]
-synonym: "degradation of misfolded or incompletely synthesized proteins" EXACT []
-synonym: "misfolded or incompletely synthesized protein breakdown" EXACT []
-synonym: "misfolded or incompletely synthesized protein catabolic process" EXACT []
-synonym: "misfolded or incompletely synthesized protein catabolism" EXACT []
-synonym: "misfolded or incompletely synthesized protein degradation" EXACT []
-synonym: "protein quality control (PQC)" EXACT []
-synonym: "protein quality control by the ubiquitin-proteasome system" BROAD []
-is_a: GO:0030163 ! protein catabolic process
+def: "A cellular process that monitors the folding, integrity, and assembly state of proteins and acts on those recognized as aberrant, including misfolded, damaged, dysfunctional, or incompletely synthesized proteins, and orphan subunits that fail to assemble into their cognate protein complex, by refolding, stabilizing, sequestering, retaining, or degrading them." [PMID:21746797, PMID:30075143, PMID:32075773, PMID:35316660]
+synonym: "degradation of misfolded or incompletely synthesized proteins" NARROW []
+synonym: "misfolded or incompletely synthesized protein breakdown" NARROW []
+synonym: "misfolded or incompletely synthesized protein catabolic process" NARROW []
+synonym: "misfolded or incompletely synthesized protein catabolism" NARROW []
+synonym: "misfolded or incompletely synthesized protein degradation" NARROW []
+synonym: "PQC" EXACT []
+synonym: "protein quality control by the ubiquitin-proteasome system" NARROW []
+synonym: "protein quality control for misfolded or incompletely synthesized proteins" NARROW []
+is_a: GO:0009987 ! cellular process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32274" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32442" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32546" xsd:anyURI
[Term]
id: GO:0006516
@@ -73107,6 +73232,7 @@
xref: Reactome:R-HSA-71288 "Creatine metabolism"
is_a: GO:0006575 ! modified amino acid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32279" xsd:anyURI
[Term]
id: GO:0006601
@@ -73148,6 +73274,7 @@
synonym: "phosphocreatine metabolism" EXACT []
is_a: GO:0006575 ! modified amino acid metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32279" xsd:anyURI
[Term]
id: GO:0006604
@@ -76575,6 +76702,7 @@
intersection_of: GO:0099024 ! plasma membrane invagination
intersection_of: part_of GO:0006909 ! phagocytosis
relationship: part_of GO:0006909 ! phagocytosis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32152" xsd:anyURI
[Term]
id: GO:0006912
@@ -77269,6 +77397,8 @@
is_a: GO:0006984 ! ER-nucleus signaling pathway
is_a: GO:0034976 ! response to endoplasmic reticulum stress
is_a: GO:0071216 ! cellular response to biotic stimulus
+relationship: part_of GO:0170080 ! endoplasmic reticulum protein quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20914" xsd:anyURI
[Term]
id: GO:0006984
@@ -77490,11 +77620,9 @@
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
synonym: "mitochondrial membrane organisation" EXACT []
synonym: "mitochondrial membrane organization and biogenesis" RELATED [GOC:mah]
-is_a: GO:0007005 ! mitochondrion organization
is_a: GO:0061024 ! membrane organization
-intersection_of: GO:0061024 ! membrane organization
-intersection_of: occurs_in GO:0005739 ! mitochondrion
-relationship: occurs_in GO:0005739 ! mitochondrion
+relationship: part_of GO:0007005 ! mitochondrion organization
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32356" xsd:anyURI
[Term]
id: GO:0007007
@@ -81065,17 +81193,19 @@
id: GO:0007350
name: blastoderm segmentation
namespace: biological_process
-def: "The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo." [ISBN:0879694238]
is_a: GO:0009880 ! embryonic pattern specification
is_a: GO:0035282 ! segmentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007351
name: tripartite regional subdivision
namespace: biological_process
-def: "Subdivision of the embryo along the anterior/posterior axis into anterior, posterior and terminal regions." [GOC:dph, GOC:isa_complete, http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "Subdivision of the embryo along the anterior/posterior axis into anterior, posterior and terminal regions." [GOC:dph, GOC:isa_complete, ISBN:0879694238]
is_a: GO:0003002 ! regionalization
relationship: part_of GO:0007350 ! blastoderm segmentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007352
@@ -81102,24 +81232,27 @@
id: GO:0007354
name: zygotic determination of anterior/posterior axis, embryo
namespace: biological_process
-def: "The specification of the anterior/posterior axis of the embryo by products of genes expressed in the zygote; exemplified in insects by the gap genes, pair rule genes and segment polarity gene cascade." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The specification of the anterior/posterior axis of the embryo by products of genes expressed in the zygote; exemplified in insects by the gap genes, pair rule genes and segment polarity gene cascade." [ISBN:0879694238]
is_a: GO:0008595 ! anterior/posterior axis specification, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007355
name: anterior region determination
namespace: biological_process
-def: "Specification of the anterior (head and thoracic segments) of the embryo by the gap genes; exemplified in insects by the actions of hunchback gene product." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "Specification of the anterior (head and thoracic segments) of the embryo by the gap genes; exemplified in insects by the actions of hunchback gene product." [ISBN:0879694238]
is_a: GO:0009952 ! anterior/posterior pattern specification
relationship: part_of GO:0007354 ! zygotic determination of anterior/posterior axis, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007356
name: thorax and anterior abdomen determination
namespace: biological_process
-def: "Specification of the central (trunk) regions of the embryo by the gap genes; exemplified in insects by the actions of the Kruppel gene product." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "Specification of the central (trunk) regions of the embryo by the gap genes; exemplified in insects by the actions of the Kruppel gene product." [ISBN:0879694238]
is_a: GO:0009952 ! anterior/posterior pattern specification
relationship: part_of GO:0007354 ! zygotic determination of anterior/posterior axis, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007357
@@ -81139,8 +81272,9 @@
id: GO:0007358
name: obsolete establishment of central gap gene boundaries
namespace: biological_process
-def: "OBSOLETE. Specification of the borders of central gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by knirps repression of Kruppel." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "OBSOLETE. Specification of the borders of central gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by knirps repression of Kruppel." [ISBN:0879694238]
comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22546" xsd:anyURI
is_obsolete: true
@@ -81148,10 +81282,11 @@
id: GO:0007359
name: posterior abdomen determination
namespace: biological_process
-def: "The regionalization process in which the posterior (abdominal) regions of the embryo are specified by the gap genes." [GOC:dph, GOC:isa_complete, http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The regionalization process in which the posterior (abdominal) regions of the embryo are specified by the gap genes." [GOC:dph, GOC:isa_complete, ISBN:0879694238]
comment: Note that this process is exemplified in insects by the actions of the knirps gene product.
is_a: GO:0009952 ! anterior/posterior pattern specification
relationship: part_of GO:0007354 ! zygotic determination of anterior/posterior axis, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007360
@@ -81172,7 +81307,7 @@
id: GO:0007361
name: obsolete establishment of posterior gap gene boundaries
namespace: biological_process
-def: "OBSOLETE. Specification of the borders of posterior gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by hunchback and tailless repression of knirps." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "OBSOLETE. Specification of the borders of posterior gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by hunchback and tailless repression of knirps." [ISBN:0879694238]
comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22546" xsd:anyURI
is_obsolete: true
@@ -81181,9 +81316,10 @@
id: GO:0007362
name: terminal region determination
namespace: biological_process
-def: "Specification of the terminal regions (the two non-segmented ends) of the embryo by the gap genes; exemplified in insects by the actions of huckebein and tailless gene products." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "Specification of the terminal regions (the two non-segmented ends) of the embryo by the gap genes; exemplified in insects by the actions of huckebein and tailless gene products." [ISBN:0879694238]
is_a: GO:0009880 ! embryonic pattern specification
relationship: part_of GO:0007354 ! zygotic determination of anterior/posterior axis, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007363
@@ -81203,7 +81339,7 @@
id: GO:0007364
name: obsolete establishment of terminal gap gene boundary
namespace: biological_process
-def: "OBSOLETE. Specification of the borders of terminal gap gene expression mediated largely by the effects of other gap genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "OBSOLETE. Specification of the borders of terminal gap gene expression mediated largely by the effects of other gap genes." [ISBN:0879694238]
comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22546" xsd:anyURI
is_obsolete: true
@@ -81221,16 +81357,18 @@
id: GO:0007366
name: periodic partitioning by pair rule gene
namespace: biological_process
-def: "Allocation of cells to parasegments in the embryo, through the action of overlapping series of pair rule gene activities." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0632030488, ISBN:0879694238]
+def: "Allocation of cells to parasegments in the embryo, through the action of overlapping series of pair rule gene activities." [ISBN:0632030488, ISBN:0879694238]
is_a: GO:0007365 ! periodic partitioning
is_a: GO:0009952 ! anterior/posterior pattern specification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007367
name: segment polarity determination
namespace: biological_process
-def: "Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0632030488, ISBN:0879694238]
+def: "Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products." [ISBN:0632030488, ISBN:0879694238]
is_a: GO:0007365 ! periodic partitioning
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007368
@@ -81319,9 +81457,10 @@
id: GO:0007379
name: segment specification
namespace: biological_process
-def: "The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes." [ISBN:0879694238]
is_a: GO:0007389 ! pattern specification process
relationship: part_of GO:0035282 ! segmentation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007380
@@ -81376,24 +81515,27 @@
id: GO:0007386
name: compartment pattern specification
namespace: biological_process
-def: "The regionalization process in which embryonic segments are divided into compartments that will result in differences in cell differentiation." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The regionalization process in which embryonic segments are divided into compartments that will result in differences in cell differentiation." [ISBN:0879694238]
synonym: "compartment specification" RELATED [GOC:dph]
is_a: GO:0009952 ! anterior/posterior pattern specification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007387
name: anterior compartment pattern formation
namespace: biological_process
-def: "The process giving rise to specification of cell identity in the anterior compartments of the segmented embryo." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The process giving rise to specification of cell identity in the anterior compartments of the segmented embryo." [ISBN:0879694238]
synonym: "anterior compartment pattern specification" RELATED [GOC:dph]
is_a: GO:0007386 ! compartment pattern specification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007388
name: posterior compartment specification
namespace: biological_process
-def: "The process involved in the specification of cell identity in the posterior compartments of the segmented embryo." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The process involved in the specification of cell identity in the posterior compartments of the segmented embryo." [ISBN:0879694238]
is_a: GO:0007386 ! compartment pattern specification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007389
@@ -82047,9 +82189,10 @@
id: GO:0007469
name: antennal development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the antenna over time, from its formation to the mature structure. The antenna are the sensory structures on the head that are capable of detecting various environmental stimuli." [http://fly.ebi.ac.uk/.bin/cvreport2?id=FBcv0004526]
+def: "The process whose specific outcome is the progression of the antenna over time, from its formation to the mature structure. The antenna are the sensory structures on the head that are capable of detecting various environmental stimuli." [FBbt:00004511]
is_a: GO:0035114 ! imaginal disc-derived appendage morphogenesis
relationship: part_of GO:0035214 ! eye-antennal disc development
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0007470
@@ -82388,7 +82531,7 @@
id: GO:0007508
name: larval heart development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the larval heart over time, from its formation to the mature structure. In Drosophila the larval heart (dorsal vessel) is a continuous tube of mesodormal cells that runs beneath the dorsal midline of the epidermis, divided into an anterior aorta and a posterior heart proper." [GOC:bf, ISBN:0879694238]
+def: "The process whose specific outcome is the progression of the larval heart over time, from its formation to the mature structure. In Drosophila the larval heart (dorsal vessel) is a continuous tube of mesodermal cells that runs beneath the dorsal midline of the epidermis, divided into an anterior aorta and a posterior heart proper." [GOC:bf, ISBN:0879694238]
is_a: GO:0007507 ! heart development
relationship: part_of GO:0002164 ! larval development
@@ -84132,9 +84275,10 @@
id: GO:0008056
name: ocellus development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the ocellus over time, from its formation to the mature structure. The ocellus is a simple visual organ of insects." [http://fly.ebi.ac.uk/.bin/cvreport2?id=FBcv0004540]
+def: "The process whose specific outcome is the progression of the ocellus over time, from its formation to the mature structure. The ocellus is a simple visual organ of insects." [FBbt:00004505]
is_a: GO:0007423 ! sensory organ development
relationship: part_of GO:0035214 ! eye-antennal disc development
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0008057
@@ -84150,12 +84294,14 @@
[Term]
id: GO:0008058
-name: ocellus pigment granule organization
+name: obsolete ocellus pigment granule 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 intracellular pigment storage granules in the ocellus." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm]
+def: "OBSOLETE. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of intracellular pigment storage granules in the ocellus." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm]
+comment: The reason for obsoletion is that this term was made in error.
synonym: "ocellus pigment granule organisation" EXACT []
synonym: "ocellus pigment granule organization and biogenesis" RELATED [GOC:mah]
-is_a: GO:0048753 ! pigment granule organization
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0008061
@@ -87871,8 +88017,9 @@
id: GO:0008358
name: maternal determination of anterior/posterior axis, embryo
namespace: biological_process
-def: "The specification of the anterior/posterior axis of the embryo by gradients of maternally-transcribed gene products; exemplified in insects by the morphogens, bicoid and nanos." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The specification of the anterior/posterior axis of the embryo by gradients of maternally-transcribed gene products; exemplified in insects by the morphogens, bicoid and nanos." [ISBN:0879694238]
is_a: GO:0008595 ! anterior/posterior axis specification, embryo
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0008359
@@ -88071,24 +88218,24 @@
[Term]
id: GO:0008379
-name: thioredoxin peroxidase activity
+name: obsolete thioredoxin peroxidase activity
namespace: molecular_function
alt_id: GO:0009031
-def: "Catalysis of the reaction: [thioredoxin]-dithiol + H2O2 = [thioredoxin]-disulfide + H2O." [RHEA:63528]
+def: "OBSOLETE. Catalysis of the reaction: [thioredoxin]-dithiol + H2O2 = [thioredoxin]-disulfide + H2O." [RHEA:63528]
+comment: This term was obsoleted because it is redundant with GO:0140824 thioredoxin-dependent peroxiredoxin activity. Both enzyme activities use thioredoxin; the nominal distinction was that GO:0008379/RHEA:63528 specified hydrogen peroxide as substrate while GO:0140824/RHEA:62620 uses a hydroperoxide (of which H2O2 is a subtype). RHEA:63528 has no proteins associated with it and this term has been misannotated for enzymes with broader hydroperoxide specificity.
synonym: "thiol peroxidase activity" EXACT []
synonym: "TPx activity" EXACT []
synonym: "TrxPx activity" EXACT []
-xref: MetaCyc:RXN0-267
xref: Reactome:R-HSA-3322995 "PRDX3,5 catalyze TXN2 reduced + H2O2 => TXN2 oxidized + 2H2O"
xref: Reactome:R-HSA-3341343 "PRDX1,2,5 catalyze TXN reduced + H2O2 => TXN oxidized + 2H2O"
xref: Reactome:R-HSA-3697882 "PRDX5 reduces peroxynitrite to nitrite using TXN"
xref: Reactome:R-HSA-3697894 "PRDX5 reduces peroxynitrite to nitrite using TXN2"
-xref: RHEA:63528
-is_a: GO:0140824 ! thioredoxin-dependent peroxiredoxin activity
-property_value: skos:exactMatch RHEA:63528
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32388" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0140824
[Term]
id: GO:0008380
@@ -90289,7 +90436,7 @@
id: GO:0008531
name: riboflavin kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H+." [EC:2.7.1.26, RHEA:14357]
+def: "Catalysis of the reaction: riboflavin + ATP = FMN + ADP + H+." [RHEA:14357]
synonym: "ATP:riboflavin 5'-phosphotransferase activity" RELATED [EC:2.7.1.26]
synonym: "FK" RELATED [EC:2.7.1.26]
synonym: "flavokinase activity" RELATED [EC:2.7.1.26]
@@ -90305,6 +90452,7 @@
property_value: skos:exactMatch EC:2.7.1.26
property_value: skos:exactMatch RHEA:14357
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/32345" xsd:anyURI
[Term]
id: GO:0008532
@@ -90547,6 +90695,7 @@
namespace: molecular_function
alt_id: GO:0008561
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Cd2+(in) = ADP + phosphate + Cd2+(out)." [PMID:17326661]
+comment: Note that RHEA:12132 represents both the ABC and the P-type cadmium transporters.
synonym: "cadmium exporting ATPase activity" EXACT []
synonym: "cadmium transmembrane transporter activity, phosphorylative mechanism" RELATED []
synonym: "cadmium-exporting ATPase activity" NARROW []
@@ -90555,12 +90704,12 @@
synonym: "Cd2+-exporting ATPase activity" RELATED [EC:7.2.2.21]
xref: EC:7.2.2.21
xref: MetaCyc:3.6.3.3-RXN
-xref: RHEA:12132
is_a: GO:0015086 ! cadmium ion transmembrane transporter activity
is_a: GO:0015662 ! P-type ion transporter activity
is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
+property_value: skos:broadMatch RHEA:12132
property_value: skos:exactMatch EC:7.2.2.21
-property_value: skos:exactMatch RHEA:12132
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20824" 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/28183" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -90729,7 +90878,7 @@
id: GO:0008564
name: protein-exporting ATPase 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: ATP + H2O + protein+(in) = ADP + phosphate + protein+(out); drives the concomitant secretion of proteins." [EC:7.4.2.8, PMID:30346996]
+def: "Enables the transfer of a protein from one side of a membrane to the other according to the reaction: ATP + H2O + protein+(in) = ADP + phosphate + protein+(out); drives the concomitant secretion of proteins." [EC:7.4.2.8, PMID:30346996]
comment: Represents ATP- hydrolyzing enzymes of the general secretory pathway (Sec or Type II), of the virulence-related secretory pathway (Type III) and of the conjugal DNA-protein transfer pathway (Type IV). Type II enzymes occur in bacteria, archaea and eukaryotes, whereas type III and type IV enzymes occur in bacteria where they form components of a multi-subunit complex.
synonym: "ATPase-coupled protein transporter activity" EXACT []
xref: EC:7.4.2.8
@@ -90739,6 +90888,7 @@
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32395" xsd:anyURI
[Term]
id: GO:0008565
@@ -90754,19 +90904,17 @@
[Term]
id: GO:0008566
-name: mitochondrial protein-transporting ATPase activity
+name: obsolete mitochondrial protein-transporting ATPase 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: ATP + H2O = ADP + phosphate; drives the transport of proteins into the mitochondrion via the mitochondrial inner membrane translocase complex." [EC:7.4.2.3]
-comment: See also the cellular component term 'mitochondrial inner membrane presequence translocase complex ; GO:0005744'.
+def: "OBSOLETE. Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate; drives the transport of proteins into the mitochondrion via the mitochondrial inner membrane translocase complex." [EC:7.4.2.3]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
synonym: "ATPase-coupled mitochondrial protein transporter activity" EXACT []
xref: EC:7.4.2.3
xref: MetaCyc:3.6.3.51-RXN
-is_a: GO:0015450 ! protein-transporting ATPase activity
-intersection_of: GO:0015450 ! protein-transporting ATPase activity
-intersection_of: occurs_in GO:0005739 ! mitochondrion
-relationship: occurs_in GO:0005739 ! mitochondrion
property_value: skos:exactMatch EC:7.4.2.3
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/32393" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0008567
@@ -91066,7 +91214,7 @@
id: GO:0008595
name: anterior/posterior axis specification, embryo
namespace: biological_process
-def: "The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+def: "The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote." [ISBN:0879694238]
synonym: "anterior/posterior axis determination, embryo" RELATED [GOC:dph]
is_a: GO:0000578 ! embryonic axis specification
is_a: GO:0009948 ! anterior/posterior axis specification
@@ -95317,22 +95465,24 @@
[Term]
id: GO:0008876
-name: quinoprotein glucose dehydrogenase activity
+name: glucose dehydrogenase (PQQ, quinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol." [RHEA:22152]
+def: "Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol, using PQQ as a cofactor." [EC:1.1.5.2]
synonym: "D-glucose:(pyrroloquinoline-quinone) 1-oxidoreductase activity" RELATED [EC:1.1.5.2]
synonym: "D-glucose:ubiquinone oxidoreductase activity" RELATED [EC:1.1.5.2]
synonym: "glucose dehydrogenase (PQQ-dependent) activity" RELATED [EC:1.1.5.2]
synonym: "glucose dehydrogenase (pyrroloquinoline-quinone) activity" EXACT []
synonym: "quinoprotein D-glucose dehydrogenase activity" RELATED [EC:1.1.5.2]
+synonym: "quinoprotein glucose dehydrogenase (PQQ, quinone) activity" EXACT []
+synonym: "quinoprotein glucose dehydrogenase activity" BROAD []
xref: EC:1.1.5.2
-xref: KEGG_REACTION:R00305
-xref: MetaCyc:RXN0-6373
-xref: RHEA:22152
is_a: GO:0004344 ! glucose dehydrogenase activity
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
+property_value: skos:broadMatch KEGG_REACTION:R06620
+property_value: skos:broadMatch MetaCyc:RXN0-6373
+property_value: skos:broadMatch RHEA:22152
property_value: skos:exactMatch EC:1.1.5.2
-property_value: skos:exactMatch RHEA:22152
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32504" xsd:anyURI
[Term]
id: GO:0008877
@@ -97203,7 +97353,8 @@
xref: TC:4.A
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
+is_a: GO:7770111 ! group translocator activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27496" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31586" xsd:anyURI
[Term]
@@ -97323,8 +97474,8 @@
xref: RHEA:58724
xref: RHEA:58728
xref: RHEA:62612
-is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity
+is_a: GO:7770107 ! RNA (adenine-N6)-methyltransferase activity
property_value: skos:exactMatch RHEA:58728
property_value: skos:narrowMatch RHEA:58724
property_value: skos:narrowMatch RHEA:62612
@@ -98146,19 +98297,34 @@
id: GO:0009038
name: undecaprenol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + undecaprenol = ADP + undecaprenyl phosphate." [GOC:curators]
+def: "Catalysis of the reaction: ATP + undecaprenol = ADP + undecaprenyl phosphate." [GOC:curators, PMID:33310291]
+comment: Undecaprenol kinase has broad substrate specificity and is capable of phosphorylating all-trans-undecaprenol as well as di-trans,poly-cis-undecaprenol (PMID:33310291).
+synonym: "all-trans undecaprenol kinase activity" RELATED []
synonym: "ATP:undecaprenol phosphotransferase activity" RELATED [EC:2.7.1.66]
synonym: "C55-isoprenoid alcohol kinase activity" RELATED [EC:2.7.1.66]
synonym: "C55-isoprenoid alcohol phosphokinase activity" RELATED [EC:2.7.1.66]
synonym: "C55-isoprenyl alcohol phosphokinase activity" RELATED [EC:2.7.1.66]
+synonym: "di-trans, poly-cis-undecaprenol kinase activity" RELATED []
+synonym: "ditrans,polycis-undecaprenol kinase activity" NARROW []
synonym: "isoprenoid alcohol kinase (phosphorylating)" BROAD [EC:2.7.1.66]
synonym: "isoprenoid alcohol kinase activity" BROAD [EC:2.7.1.66]
synonym: "isoprenoid alcohol phosphokinase activity" BROAD [EC:2.7.1.66]
synonym: "isoprenoid-alcohol kinase activity" BROAD [EC:2.7.1.66]
synonym: "polyisoprenol kinase activity" BROAD [EC:2.7.1.66]
+xref: EC:2.7.1.66
+xref: KEGG_REACTION:R05626
+xref: MetaCyc:UNDECAPRENOL-KINASE-RXN
+xref: RHEA:23752
+xref: RHEA:28122
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
+property_value: skos:exactMatch EC:2.7.1.66
+property_value: skos:narrowMatch KEGG_REACTION:R05626
+property_value: skos:narrowMatch MetaCyc:UNDECAPRENOL-KINASE-RXN
+property_value: skos:narrowMatch RHEA:23752
+property_value: skos:narrowMatch RHEA:28122
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/32370" xsd:anyURI
[Term]
id: GO:0009039
@@ -99098,10 +99264,11 @@
[Term]
id: GO:0009107
-name: lipoate biosynthetic process
+name: obsolete lipoate biosynthetic process
namespace: biological_process
alt_id: GO:0009105
-def: "The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid." [GOC:ai, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid." [GOC:ai, ISBN:0198506732]
+comment: The reason for obsoletion is that the term usage has been inconsistent.
synonym: "lipoate anabolism" EXACT []
synonym: "lipoate biosynthesis" EXACT []
synonym: "lipoate formation" EXACT []
@@ -99111,9 +99278,9 @@
synonym: "lipoic acid biosynthetic process" EXACT []
synonym: "lipoic acid formation" EXACT []
synonym: "lipoic acid synthesis" EXACT []
-is_a: GO:0006633 ! fatty acid biosynthetic process
-is_a: GO:0009106 ! lipoate metabolic process
-is_a: GO:0044272 ! sulfur compound biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32418" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009249
[Term]
id: GO:0009108
@@ -100705,13 +100872,18 @@
name: protein lipoylation
namespace: biological_process
alt_id: GO:0018055
-def: "The lipoylation of peptidyl-lysine to form peptidyl-N6-lipoyl-L-lysine." [RESID:AA0118]
+def: "The chemical reactions and pathways resulting in the attachment of a lipoyl group to a lipoyl carrier protein, either by de novo assembly on the carrier protein via transfer of an octanoyl group followed by sulfur insertion, or by ligation of exogenous lipoate." [PMID:29987032, RESID:AA0118]
+synonym: "lipoate biosynthesis" NARROW []
+synonym: "lipoate biosynthetic process" NARROW []
+synonym: "lipoic acid biosynthetic process" NARROW []
synonym: "peptidyl-lysine lipoylation" EXACT []
synonym: "protein-lipoic acid cofactor linkage" EXACT []
xref: Reactome:R-HSA-9857492 "Protein lipoylation"
+is_a: GO:0009106 ! lipoate metabolic process
is_a: GO:0018205 ! peptidyl-lysine modification
is_a: GO:0051604 ! protein maturation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29772" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32418" xsd:anyURI
[Term]
id: GO:0009250
@@ -100802,19 +100974,20 @@
[Term]
id: GO:0009257
-name: 10-formyltetrahydrofolate biosynthetic process
+name: obsolete 10-formyltetrahydrofolate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 10-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of 10-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate." [GOC:ai]
+comment: This term was obsoleted because it represents the same process as folate cycle ; GO:0035999.
synonym: "10-formyl-THF biosynthesis" EXACT []
synonym: "10-formyl-THF biosynthetic process" EXACT []
synonym: "10-formyltetrahydrofolate anabolism" EXACT []
synonym: "10-formyltetrahydrofolate biosynthesis" EXACT []
synonym: "10-formyltetrahydrofolate formation" EXACT []
synonym: "10-formyltetrahydrofolate synthesis" EXACT []
-is_a: GO:0009256 ! 10-formyltetrahydrofolate metabolic process
-is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
-is_a: GO:0046654 ! tetrahydrofolate biosynthetic process
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/32289" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0035999
[Term]
id: GO:0009258
@@ -111145,7 +111318,7 @@
id: GO:0010278
name: chloroplast outer membrane translocon
namespace: cellular_component
-def: "The protein transport machinery of the chloroplast outer membrane that contains at least three components Toc159, Toc75 and Toc34, interacts with precursor proteins which are imported into the chloroplast in a GTP dependant manner." [PMID:11299338]
+def: "The protein transport machinery of the chloroplast outer membrane that contains at least three components Toc159, Toc75 and Toc34, interacts with precursor proteins which are imported into the chloroplast in a GTP-dependent manner." [PMID:11299338]
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0009707 ! chloroplast outer membrane
@@ -121917,9 +122090,9 @@
[Term]
id: GO:0015056
-name: corticotrophin-releasing factor receptor activity
+name: corticotropin-releasing factor receptor activity
namespace: molecular_function
-def: "Combining with the corticotrophin-releasing factor family of ligands, including the urocortins, to initiate a change in cell activity." [PMID:12032352]
+def: "Combining with the corticotropin-releasing factor family of ligands, including the urocortins, to initiate a change in cell activity." [PMID:12032352]
is_a: GO:0004930 ! G protein-coupled receptor activity
relationship: part_of GO:0071376 ! cellular response to corticotropin-releasing hormone stimulus
@@ -125811,6 +125984,7 @@
name: ABC-type cadmium transporter 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: ATP + H2O + Cd (cytosol) = ADP + phosphate + Cd (vacuole)." [PMID:12455987]
+comment: Note that RHEA:12132 represents both the ABC and the P-type cadmium transporters.
synonym: "ATP-dependent cadmium transmembrane transporter activity" RELATED []
synonym: "ATPase-coupled cadmium transmembrane transporter activity" RELATED []
synonym: "cadmium ABC transporter" EXACT []
@@ -125820,7 +125994,9 @@
is_a: GO:0015086 ! cadmium ion transmembrane transporter activity
is_a: GO:0019829 ! ATPase-coupled monoatomic cation transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
+property_value: skos:broadMatch RHEA:12132
property_value: skos:exactMatch EC:7.2.2.2
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20824" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -126160,7 +126336,7 @@
id: GO:0015462
name: ABC-type protein transporter 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: ATP + H2O + protein(out) = ADP + phosphate + protein(in)." [GOC:jl]
+def: "Enables the transfer of a protein from one side of a membrane to the other according to the reaction: ATP + H2O + protein(out) = ADP + phosphate + protein(in)." [GOC:jl]
comment: Enzymes with this activity include bacterial enzymes dedicated to the secretion of one or several closely related proteins belonging to the toxin, protease and lipase families, for example alpha-hemolysin, cyclolysin, colicin V, siderophores, bacteriocin, subtilin, competence factor and pediocin (from EC:7.4.2.5).
synonym: "ABC-type protein transmembrane transporter activity" EXACT []
synonym: "ATPase-coupled protein transmembrane transporter activity" RELATED []
@@ -126171,6 +126347,7 @@
is_a: GO:0015450 ! protein-transporting ATPase activity
is_a: GO:0140359 ! ABC-type transporter activity
property_value: skos:broadMatch EC:7.4.2.5
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32395" xsd:anyURI
[Term]
id: GO:0015464
@@ -135396,7 +135573,7 @@
id: GO:0016464
name: chloroplast protein-transporting ATPase 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: ATP + H2O = ADP + phosphate; drives the transport of proteins into the chloroplast stroma." [EC:7.4.2.4]
+def: "Enables the transfer of a protein from one side of a membrane to the other according to the reaction: ATP + H2O = ADP + phosphate; drives the transport of proteins into the chloroplast stroma." [EC:7.4.2.4]
synonym: "AAA chloroplast protein-transporting ATPase" EXACT []
synonym: "ATPase-coupled chloroplast protein transporter activity" EXACT []
xref: EC:7.4.2.4
@@ -135404,6 +135581,7 @@
is_a: GO:0015450 ! protein-transporting ATPase activity
property_value: skos:exactMatch EC:7.4.2.4
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/32395" xsd:anyURI
[Term]
id: GO:0016465
@@ -140644,8 +140822,9 @@
comment: This term was made obsolete because it represents a gene product and not a molecular function.
synonym: "ligand-dependent thyroid hormone receptor interactor activity" EXACT []
synonym: "TRIP4" RELATED []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
is_obsolete: true
-consider: GO:0046966
+consider: GO:0016922
[Term]
id: GO:0016925
@@ -141157,7 +141336,7 @@
xref: Reactome:R-HSA-6793591 "LIAS synthesizes lipoyl-GCSH"
xref: RHEA:16585
is_a: GO:0016783 ! sulfurtransferase activity
-relationship: part_of GO:0009107 ! lipoate biosynthetic process
+relationship: part_of GO:0009249 ! protein lipoylation
property_value: skos:exactMatch EC:2.8.1.8
property_value: skos:exactMatch MetaCyc:RXN0-949
property_value: skos:exactMatch RHEA:16585
@@ -142973,11 +143152,13 @@
[Term]
id: GO:0017162
-name: aryl hydrocarbon receptor binding
+name: obsolete aryl hydrocarbon receptor binding
namespace: molecular_function
-def: "Binding to an aryl hydrocarbon receptor." [GOC:ai]
-is_a: GO:0005102 ! signaling receptor binding
-is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
+def: "OBSOLETE. Binding to an aryl hydrocarbon receptor." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a gene product. Better captured with GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding, with aryl hydrocarbon receptor as 'has_input' in annotation extension.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32477" xsd:anyURI
+is_obsolete: true
+consider: GO:0061629
[Term]
id: GO:0017163
@@ -157306,7 +157487,6 @@
synonym: "N-acetylneuraminate catabolism" EXACT []
synonym: "N-acetylneuraminate degradation" EXACT []
xref: MetaCyc:P441-PWY
-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
@@ -157451,12 +157631,14 @@
[Term]
id: GO:0019276
-name: UDP-N-acetylgalactosamine metabolic process
+name: obsolete UDP-N-acetylgalactosamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving UDP-N-acetylgalactosamine, a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving UDP-N-acetylgalactosamine, a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC:ai]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "UDP-N-acetylgalactosamine metabolism" EXACT []
-is_a: GO:0006040 ! amino sugar metabolic process
-is_a: GO:0009225 ! nucleotide-sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0019277
[Term]
id: GO:0019277
@@ -157471,7 +157653,6 @@
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
@@ -159257,7 +159438,7 @@
synonym: "dissimilatory sulphate reduction" EXACT []
xref: MetaCyc:DISSULFRED-PWY
xref: Wikipedia:Sulfate-reducing_microorganism
-is_a: GO:0000103 ! sulfate assimilation
+is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0009061 ! anaerobic respiration
relationship: has_part GO:0018551 ! dissimilatory sulfite reductase (NADH) activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26582" xsd:anyURI
@@ -159772,11 +159953,12 @@
id: GO:0019464
name: glycine decarboxylation via glycine cleavage system
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex." [MetaCyc:GLYCLEAV-PWY]
+def: "The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex." [MetaCyc:GLYCLEAV-PWY, PMID:36347252, PMID:41521798]
synonym: "glycine cleavage system" BROAD []
xref: MetaCyc:GLYCLEAV-PWY
is_a: GO:0006546 ! glycine 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/32362" xsd:anyURI
[Term]
id: GO:0019465
@@ -161770,7 +161952,6 @@
synonym: "urate degradation" EXACT []
synonym: "uric acid catabolic process" EXACT []
xref: MetaCyc:P165-PWY
-is_a: GO:0044282 ! small molecule catabolic process
is_a: GO:0046415 ! urate metabolic process
is_a: GO:0072523 ! purine-containing compound catabolic process
@@ -161886,10 +162067,12 @@
name: organophosphate metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving organophosphates, any phosphate-containing organic compound." [ISBN:0198506732]
+subset: gocheck_do_not_annotate
subset: goslim_pombe
synonym: "organophosphate metabolism" EXACT []
is_a: GO:0006793 ! phosphorus metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26992" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0019638
@@ -162018,6 +162201,7 @@
xref: MetaCyc:PWY-1622
xref: MetaCyc:PWY-1861
is_a: GO:0046292 ! formaldehyde metabolic process
+is_a: GO:7770097 ! nutrient assimilation
property_value: skos:narrowMatch MetaCyc:P185-PWY
property_value: skos:narrowMatch MetaCyc:PWY-1622
property_value: skos:narrowMatch MetaCyc:PWY-1861
@@ -162409,11 +162593,13 @@
is_a: GO:0006536 ! glutamate metabolic process
is_a: GO:0006541 ! L-glutamine metabolic process
is_a: GO:0019740 ! nitrogen utilization
+is_a: GO:7770097 ! nutrient assimilation
property_value: skos:narrowMatch MetaCyc:AMMASSIM-PWY
property_value: skos:narrowMatch MetaCyc:PWY-3282
property_value: skos:narrowMatch MetaCyc:PWY-6963
property_value: skos:narrowMatch MetaCyc:PWY-6964
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/32376" xsd:anyURI
[Term]
id: GO:0019677
@@ -163520,18 +163706,21 @@
[Term]
id: GO:0019786
-name: protein-phosphatidylethanolamide deconjugating activity
+name: protein-phosphatidylethanolamine deconjugating activity
namespace: molecular_function
-def: "Catalysis of the reaction: [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine. An example of this reaction is the removal of ATG8 from membranes to which it is covalently linked to a phosphatidylethanolamid via its terminal glycine residue." [PMID:22240591, PMID:22652539, PMID:28330855, PMID:2882172, PMID:28901328]
-synonym: "APG8-PE hydrolase" RELATED []
+def: "Catalysis of the reaction: [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine. An example of this reaction is the removal of ATG8 from membranes to which it is covalently linked to a phosphatidylethanolamine via its terminal glycine residue." [PMID:22240591, PMID:22652539, PMID:28330855, PMID:28821724, PMID:28901328, RHEA:67548]
+synonym: "APG8-PE hydrolase" NARROW []
synonym: "APG8-specific protease activity" NARROW [GOC:vw]
synonym: "ATG8-PE deconjugation activity" NARROW []
synonym: "ATG8-PE hydrolase activity" NARROW []
synonym: "Atg8-specific peptidase activity" NARROW []
-synonym: "Atg8-specific protease activity" EXACT []
+synonym: "Atg8-specific protease activity" NARROW []
+xref: RHEA:67548
is_a: GO:0016787 ! hydrolase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
+property_value: skos:exactMatch RHEA:67548
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25472" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32575" xsd:anyURI
[Term]
id: GO:0019787
@@ -163994,7 +164183,7 @@
id: GO:0019813
name: type III site-specific deoxyribonuclease complex
namespace: cellular_component
-def: "A heterodimeric enzyme complex composed of two subunits, Res and Mod, that functions as an endonuclease and cleaves DNA. Cleavage will only occur when there are two un-methylated copies of a specific recognition site in an inverse orientation on the DNA. Cleavage occurs at a specific distance away from one of the recognition sites. The Mod subunit can act alone as a methyltansferase. DNA restriction systems such as this are used by bacteria to defend against phage and other foreign DNA that may enter a cell." [PMID:12654995]
+def: "A heterodimeric enzyme complex composed of two subunits, Res and Mod, that functions as an endonuclease and cleaves DNA. Cleavage will only occur when there are two un-methylated copies of a specific recognition site in an inverse orientation on the DNA. Cleavage occurs at a specific distance away from one of the recognition sites. The Mod subunit can act alone as a methyltransferase. DNA restriction systems such as this are used by bacteria to defend against phage and other foreign DNA that may enter a cell." [PMID:12654995]
synonym: "type III restriction enzyme complex" EXACT []
is_a: GO:1905347 ! endodeoxyribonuclease complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -164637,14 +164826,14 @@
name: obsolete diaminopimelate biosynthetic process
namespace: biological_process
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.
+comment: This term was obsoleted because it represents an intermediate in L-lysine biosynthesis.
synonym: "diaminopimelate anabolism" EXACT []
synonym: "diaminopimelate biosynthesis" EXACT []
synonym: "diaminopimelate formation" EXACT []
synonym: "diaminopimelate synthesis" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
is_obsolete: true
-consider: GO:0009098
+consider: GO:0009085
[Term]
id: GO:0019878
@@ -173177,10 +173366,11 @@
xref: Reactome:R-HSA-9856871 "MDH1 reduces OA"
xref: RHEA:21432
is_a: GO:0016615 ! malate dehydrogenase activity
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+is_a: GO:0102443 ! L-2-hydroxycarboxylate dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.1.1.37
property_value: skos:exactMatch RHEA:21432
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/32501" xsd:anyURI
[Term]
id: GO:0030061
@@ -176116,12 +176306,15 @@
[Term]
id: GO:0030331
-name: nuclear estrogen receptor binding
+name: obsolete nuclear estrogen receptor binding
namespace: molecular_function
-def: "Binding to a nuclear estrogen receptor." [GOC:ai]
+def: "OBSOLETE. Binding to a nuclear estrogen receptor." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and estrogen receptor as 'has_input'.
synonym: "estrogen receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0030332
@@ -176629,11 +176822,15 @@
[Term]
id: GO:0030389
-name: fructosamine metabolic process
+name: obsolete fructosamine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving fructosamine, a fructose molecule containing an amino group in place of a hydroxyl group." [GOC:jl, ISBN:0192801023]
+def: "OBSOLETE. The chemical reactions and pathways involving fructosamine, a fructose molecule containing an amino group in place of a hydroxyl group." [GOC:jl, ISBN:0192801023]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "fructosamine metabolism" EXACT []
-is_a: GO:0006040 ! amino sugar metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
+consider: GO:0030391
+consider: GO:0030392
[Term]
id: GO:0030391
@@ -176644,7 +176841,6 @@
synonym: "fructosamine biosynthesis" EXACT []
synonym: "fructosamine formation" EXACT []
synonym: "fructosamine synthesis" EXACT []
-is_a: GO:0030389 ! fructosamine metabolic process
is_a: GO:0046349 ! amino sugar biosynthetic process
[Term]
@@ -176655,7 +176851,6 @@
synonym: "fructosamine breakdown" EXACT []
synonym: "fructosamine catabolism" EXACT []
synonym: "fructosamine degradation" EXACT []
-is_a: GO:0030389 ! fructosamine metabolic process
is_a: GO:0046348 ! amino sugar catabolic process
[Term]
@@ -176664,8 +176859,8 @@
namespace: biological_process
def: "The chemical reactions and pathways involving fructoselysine, a fructose molecule containing a lysine group in place of a hydroxyl group." [GOC:ai]
synonym: "fructoselysine metabolism" EXACT []
+is_a: GO:0006040 ! amino sugar metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
-is_a: GO:0030389 ! fructosamine metabolic process
[Term]
id: GO:0030394
@@ -177862,11 +178057,12 @@
name: regulation of axon extension
namespace: biological_process
def: "Any process that modulates the rate, direction or extent of axon extension." [GOC:curators]
+is_a: GO:0001558 ! regulation of cell growth
is_a: GO:0048638 ! regulation of developmental growth
-is_a: GO:0061387 ! regulation of extent of cell growth
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0048675 ! axon extension
relationship: regulates GO:0048675 ! axon extension
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
[Term]
id: GO:0030517
@@ -178613,11 +178809,14 @@
[Term]
id: GO:0030592
-name: DNA ADP-ribosylation
+name: obsolete DNA ADP-ribosylation
namespace: biological_process
-def: "The covalent attachment of an ADP-ribosyl group to a residue in double-stranded DNA." [PMID:11592983, PMID:27471034, PMID:29361132, PMID:29520010]
-is_a: GO:0006304 ! DNA modification
+def: "OBSOLETE. The covalent attachment of an ADP-ribosyl group to a residue in double-stranded DNA." [PMID:11592983, PMID:27471034, PMID:29361132, PMID:29520010]
+comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16614" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
+is_obsolete: true
+consider: GO:0140294
[Term]
id: GO:0030593
@@ -179723,21 +179922,20 @@
[Term]
id: GO:0030701
-name: NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity
+name: obsolete NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NAD+ + [dinitrogen reductase] = nicotinamide + ADP-D-ribosyl-[dinitrogen reductase]." [EC:2.4.2.37]
+def: "OBSOLETE. Catalysis of the reaction: L-arginyl-[dinitrogen reductase] + NAD+ = N(omega)-alpha-(ADP-D-ribosyl)-L-arginyl-[dinitrogen reductase] + nicotinamide + H+." [RHEA:18077]
+comment: The reason for obsoletion is that this term represents a specific substrate of the parent GO:0106274 NAD+-protein-arginine ADP-ribosyltransferase activity.
synonym: "ADP-ribosyltransferase activity" BROAD [EC:2.4.2.37]
synonym: "NAD+:[dinitrogen reductase] (ADP-D-ribosyl)transferase activity" RELATED [EC:2.4.2.37]
synonym: "NAD--azoferredoxin (ADP-ribose)transferase activity" RELATED [EC:2.4.2.37]
synonym: "NAD-azoferredoxin (ADPribose)transferase activity" RELATED [EC:2.4.2.37]
synonym: "NAD-dinitrogen-reductase ADP-D-ribosyltransferase activity" EXACT []
-xref: EC:2.4.2.37
-xref: MetaCyc:2.4.2.37-RXN
-xref: RHEA:18077
-is_a: GO:0016763 ! pentosyltransferase activity
-property_value: skos:exactMatch EC:2.4.2.37
-property_value: skos:exactMatch RHEA:18077
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/32501" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32503" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0106274
[Term]
id: GO:0030703
@@ -183154,6 +183352,8 @@
is_a: GO:0034976 ! response to endoplasmic reticulum stress
is_a: GO:0035556 ! intracellular signal transduction
relationship: part_of GO:0034620 ! cellular response to unfolded protein
+relationship: part_of GO:0170080 ! endoplasmic reticulum protein quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20914" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28057" xsd:anyURI
[Term]
@@ -183191,7 +183391,7 @@
synonym: "protein retrotranslocation, ER to cytosol" EXACT [GOC:bf]
synonym: "retrograde protein transport, endoplasmic reticulum to cytosol" EXACT []
is_a: GO:0015031 ! protein transport
-relationship: part_of GO:0036503 ! ERAD pathway
+relationship: part_of GO:0036503 ! ERAD quality control pathway
[Term]
id: GO:0030971
@@ -183956,7 +184156,7 @@
namespace: biological_process
alt_id: GO:0070924
alt_id: GO:0140458
-def: "A heterochromatin formation-based gene silencing process mediated by a regulatory non-coding RNA molecule that occur before the beginning of trancription." [PMID:19239886, PMID:21420348]
+def: "A heterochromatin formation-based gene silencing process mediated by a regulatory non-coding RNA molecule that occurs before the beginning of transcription." [PMID:19239886, PMID:21420348]
synonym: "chromatin silencing by small RNA" RELATED []
synonym: "heterochromatin assembly by small RNA" NARROW []
synonym: "heterochromatin assembly involved in chromatin silencing by small RNA" RELATED []
@@ -188711,7 +188911,7 @@
id: GO:0031500
name: Tea1 cell-end complex
namespace: cellular_component
-def: "A high molecular weight complex characterized in S. pombe containing the cell-end anchoring protein Tea1. This complex is transported to the cell ends by microtubules and is involved in bipolar growth and the maintennce of normal cell polarity." [PMID:15936270]
+def: "A high molecular weight complex characterized in S. pombe containing the cell-end anchoring protein Tea1. This complex is transported to the cell ends by microtubules and is involved in bipolar growth and the maintenance of normal cell polarity." [PMID:15936270]
is_a: GO:0005875 ! microtubule associated complex
relationship: part_of GO:0000133 ! polarisome
@@ -188877,12 +189077,12 @@
synonym: "telomeric heterochromatin formation" RELATED []
synonym: "telomeric silencing" EXACT [GOC:bf]
is_a: GO:0140719 ! constitutive heterochromatin formation
-relationship: occurs_in GO:0000781 ! chromosome, telomeric region
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19188" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19308" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22027" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23553" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29160" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32403" xsd:anyURI
[Term]
id: GO:0031510
@@ -190693,7 +190893,7 @@
id: GO:0031680
name: G-protein beta/gamma-subunit complex
namespace: cellular_component
-def: "The heterodimer formed by the beta and gamma subunits of a heterotrimeric G protein, which dissociates from the alpha subunit upon guanine nuclotide exchange." [GOC:mah]
+def: "The heterodimer formed by the beta and gamma subunits of a heterotrimeric G protein, which dissociates from the alpha subunit upon guanine nucleotide exchange." [GOC:mah]
comment: See also the cellular component term 'heterotrimeric G-protein complex ; GO:0005834'.
synonym: "G-beta/G-gamma complex" EXACT []
synonym: "heterotrimeric G-protein GTPase, beta-subunit" NARROW []
@@ -193218,21 +193418,27 @@
[Term]
id: GO:0031961
-name: nuclear cortisol receptor binding
+name: obsolete nuclear cortisol receptor binding
namespace: molecular_function
-def: "Binding to a nuclear cortisol receptor." [GOC:mah, PMID:12511169]
+def: "OBSOLETE. Binding to a nuclear cortisol receptor." [GOC:mah, PMID:12511169]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and cortisol receptor as 'has_input'.
synonym: "cortisol receptor binding" BROAD []
-is_a: GO:0035259 ! nuclear glucocorticoid receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0031962
-name: nuclear mineralocorticoid receptor binding
+name: obsolete nuclear mineralocorticoid receptor binding
namespace: molecular_function
-def: "Binding to a nuclear mineralocorticoid receptor." [GOC:mah, PMID:12511169]
+def: "OBSOLETE. Binding to a nuclear mineralocorticoid receptor." [GOC:mah, PMID:12511169]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and mineralocorticoid receptor as 'has_input'.
synonym: "mineralocorticoid receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0031963
@@ -195656,7 +195862,7 @@
alt_id: GO:0006320
alt_id: GO:0006321
alt_id: GO:0006322
-def: "A type of transposition in which a transposable element (transposon) copies and pastes itself into a different genomic location by transcription and convertsion of the transcribed RNA back into DNA through reverse transcription." [ISBN:1555812090, PMID:26912865, PMID:30416149, PMID:30958115, PMID:32588192]
+def: "A type of transposition in which a transposable element (transposon) copies and pastes itself into a different genomic location by transcription and conversion of the transcribed RNA back into DNA through reverse transcription." [ISBN:1555812090, PMID:26912865, PMID:30416149, PMID:30958115, PMID:32588192]
synonym: "Class I transposition" EXACT []
synonym: "retrotransposon transposition" EXACT []
synonym: "RNA-mediated transposition" EXACT [GOC:dph, GOC:tb]
@@ -196670,7 +196876,7 @@
id: GO:0032280
name: symmetric synapse
namespace: cellular_component
-def: "A synapse that lacks an electron dense postsynaptic specialization. In vertebtrates, these occur primarily on dendrite shafts and neuronal cell bodies and involve persynapses containing clusters of predominantly flattened or elongated vesicles and are typically inhibitory." [GOC:dgh, GOC:ef]
+def: "A synapse that lacks an electron dense postsynaptic specialization. In vertebrates, these occur primarily on dendrite shafts and neuronal cell bodies and involve presynapses containing clusters of predominantly flattened or elongated vesicles and are typically inhibitory." [GOC:dgh, GOC:ef]
comment: The term 'symmetric' in this name refers only to gross morphology. There is no implication of functional symmetry.
synonym: "Gray's type II synapse" EXACT []
is_a: GO:0098984 ! neuron to neuron synapse
@@ -203927,11 +204133,13 @@
xref: EC:1.1.1.431
xref: MetaCyc:RXN-8773
xref: RHEA:27445
-is_a: GO:0004032 ! aldose reductase (NADPH) activity
+is_a: GO:0004032 ! aldose reductase [NAD(P)H] activity
+is_a: GO:0008106 ! alcohol dehydrogenase (NADP+) activity
property_value: skos:exactMatch EC:1.1.1.431
property_value: skos:exactMatch MetaCyc:RXN-8773
property_value: skos:exactMatch RHEA:27445
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30910" xsd:anyURI
[Term]
@@ -203946,9 +204154,11 @@
xref: MetaCyc:RXN-8772
xref: RHEA:25229
xref: SABIO-RK:1858
-is_a: GO:0004032 ! aldose reductase (NADPH) activity
+is_a: GO:0004032 ! aldose reductase [NAD(P)H] activity
+is_a: GO:0008106 ! alcohol dehydrogenase (NADP+) activity
property_value: skos:exactMatch RHEA:25229
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -205354,9 +205564,9 @@
xref: Reactome:R-HSA-9906955 "MT-ND4 is translated"
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32404" xsd:anyURI
[Term]
id: GO:0032978
@@ -207092,12 +207302,15 @@
[Term]
id: GO:0033142
-name: nuclear progesterone receptor binding
+name: obsolete nuclear progesterone receptor binding
namespace: molecular_function
-def: "Binding to a nuclear progesterone receptor." [GOC:mah]
+def: "OBSOLETE. Binding to a nuclear progesterone receptor." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and progesterone receptor as 'has_input'.
synonym: "progesterone receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0033143
@@ -207338,7 +207551,7 @@
id: GO:0033165
name: interphotoreceptor matrix
namespace: cellular_component
-def: "A specialized extracellularc matrix that surrounds the photoreceptors of the retina and lies between them and the apical surface of the retinal pigment epithelium. The IPM has been implicated in several important activities required for photoreceptor function and maintenance." [PMID:1862095, PMID:2194288]
+def: "A specialized extracellular matrix that surrounds the photoreceptors of the retina and lies between them and the apical surface of the retinal pigment epithelium. The IPM has been implicated in several important activities required for photoreceptor function and maintenance." [PMID:1862095, PMID:2194288]
is_a: GO:0140047 ! specialized extracellular matrix
[Term]
@@ -209095,11 +209308,14 @@
[Term]
id: GO:0033331
-name: ent-kaurene metabolic process
+name: obsolete ent-kaurene metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ent-kaur-16-ene. Ent-kaurene is a tetracyclic diterpenoid that is a precursor of several plant isoprenoids, including gibberellins." [GOC:mah, PMID:17064690]
+def: "OBSOLETE. The chemical reactions and pathways involving ent-kaur-16-ene. Ent-kaurene is a tetracyclic diterpenoid that is a precursor of several plant isoprenoids, including gibberellins." [GOC:mah, PMID:17064690]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
synonym: "ent-kaurene metabolism" EXACT []
-is_a: GO:0042214 ! terpene metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28120" xsd:anyURI
+is_obsolete: true
+consider: GO:0033332
[Term]
id: GO:0033332
@@ -209112,7 +209328,6 @@
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
@@ -209311,7 +209526,7 @@
id: GO:0033353
name: L-methionine cycle
namespace: biological_process
-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]
+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:32961717, PMID:39394448]
synonym: "activated methyl cycle" EXACT []
synonym: "S-adenosylmethionine cycle" EXACT []
synonym: "SAM cycle" EXACT []
@@ -209319,6 +209534,7 @@
xref: MetyaCyc:PWY-6151
is_a: GO:0006555 ! L-methionine metabolic process
is_a: GO:0006575 ! modified amino acid metabolic process
+is_a: GO:0006730 ! one-carbon metabolic process
is_a: GO:0046128 ! purine ribonucleoside metabolic process
is_a: GO:0046500 ! S-adenosylmethionine metabolic process
is_a: GO:0050667 ! homocysteine metabolic process
@@ -209326,6 +209542,7 @@
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31840" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32362" xsd:anyURI
[Term]
id: GO:0033354
@@ -211302,9 +211519,11 @@
id: GO:0033528
name: S-methylmethionine cycle
namespace: biological_process
-def: "A cyclic series of interconversions involving S-methyl-L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, L-homocysteine, and L-methionine. Converts the methionine group of adenosylmethionine back to free methionine, and may serve regulate the cellular adenosylmethionine level." [GOC:mah, MetaCyc:PWY-5441]
+def: "A cyclic series of interconversions involving S-methyl-L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, L-homocysteine, and L-methionine. Converts the methionine group of S-adenosylmethionine back to free L-methionine, and may serve regulate the cellular adenosylmethionine level." [GOC:mah, MetaCyc:PWY-5441, PMID:11337394]
xref: MetaCyc:PWY-5441
+is_a: GO:0006730 ! one-carbon metabolic process
is_a: GO:0033477 ! S-methylmethionine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32362" xsd:anyURI
[Term]
id: GO:0033529
@@ -218705,15 +218924,17 @@
[Term]
id: GO:0034045
-name: phagophore assembly site membrane
+name: obsolete phagophore assembly site membrane
namespace: cellular_component
-def: "A cellular membrane associated with the phagophore assembly site." [GOC:mah, GOC:rph, PMID:16874040, PMID:17382324]
+def: "OBSOLETE. A cellular membrane associated with the phagophore assembly site." [GOC:mah, GOC:rph, PMID:16874040, PMID:17382324]
+comment: This term was obsoleted because the phagophore assembly site (PAS) is not itself a membrane-bounded compartment, and the class had become a catch-all for membranes at, or associated with, the site of phagophore biogenesis. Annotations should be moved to phagophore membrane (GO:7770114), which captures the membrane of the nascent phagophore, or to another more appropriate term (e.g. GO:0000407 phagophore assembly site, GO:0061908 phagophore) depending on the evidence.
synonym: "isolation membrane" RELATED []
synonym: "PAS membrane" EXACT []
synonym: "phagophore" RELATED [PMID:20811355]
synonym: "pre-autophagosomal structure membrane" NARROW []
-is_a: GO:0016020 ! membrane
-relationship: part_of GO:0000407 ! phagophore assembly site
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29437" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:7770114
[Term]
id: GO:0034046
@@ -222163,6 +222384,7 @@
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/31588" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32456" xsd:anyURI
[Term]
id: GO:0034355
@@ -230532,7 +230754,7 @@
id: GO:0035225
name: determination of genital disc primordium
namespace: biological_process
-def: "Allocation of embryonic cells to the genital imaginal disc founder populations. Early in development at the blastoderm stage, the anlage of the genital disc of both sexes consists of three primordia: the female genital primoridum lcoated anteriorly, the anal primoridum located posteriorly, and the male gential primordium between the two." [GOC:bf, PMID:11494318]
+def: "Allocation of embryonic cells to the genital imaginal disc founder populations. Early in development at the blastoderm stage, the anlage of the genital disc of both sexes consists of three primordia: the female genital primordium located anteriorly, the anal primordium located posteriorly, and the male genital primordium between the two." [GOC:bf, PMID:11494318]
is_a: GO:0007445 ! determination of imaginal disc primordium
relationship: part_of GO:0035215 ! genital disc development
@@ -230871,12 +231093,15 @@
[Term]
id: GO:0035259
-name: nuclear glucocorticoid receptor binding
+name: obsolete nuclear glucocorticoid receptor binding
namespace: molecular_function
-def: "Binding to a nuclear glucocorticoid receptor." [GOC:bf]
+def: "OBSOLETE. Binding to a nuclear glucocorticoid receptor." [GOC:bf]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and glucocorticoid receptor as 'has_input'.
synonym: "glucocorticoid receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0035260
@@ -239543,11 +239768,13 @@
[Term]
id: GO:0035999
-name: tetrahydrofolate interconversion
+name: folate cycle
namespace: biological_process
-def: "The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules." [GOC:yaf, PMID:1825999]
-synonym: "folate cycle" EXACT []
+def: "A cyclic series of interconversions of the one-carbon unit carried by tetrahydrofolate - as 10-formyltetrahydrofolate, 5,10-methenyltetrahydrofolate, 5,10-methylenetetrahydrofolate and 5-methyltetrahydrofolate. Couples the acquisition of a one-carbon unit from donors such as serine, glycine or formate with its transfer, in the appropriate oxidation state, to biosynthetic acceptors, and with regeneration of tetrahydrofolate." [PMID:1825999, PMID:18804690, PMID:27641100]
synonym: "folate transformations" EXACT []
+synonym: "folate-mediated one-carbon metabolism" EXACT []
+synonym: "folic acid cycle" EXACT []
+synonym: "tetrahydrofolate interconversion" EXACT []
xref: MetaCyc:1CMET2-PWY
xref: MetaCyc:PWY-2201
xref: MetaCyc:PWY-3841
@@ -239558,6 +239785,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-3841
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/32289" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32362" xsd:anyURI
created_by: bf
creation_date: 2011-09-02T01:35:49Z
@@ -240947,7 +241175,6 @@
name: very long-chain fatty-acyl-CoA catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of very long-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a very long-chain fatty-acyl group. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons." [GOC:pm]
-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 fatty-acyl-CoA breakdown" EXACT [GOC:bf]
synonym: "very long-chain fatty-acyl-CoA catabolism" EXACT [GOC:bf]
synonym: "very long-chain fatty-acyl-CoA degradation" EXACT [GOC:bf]
@@ -242784,7 +243011,7 @@
id: GO:0036261
name: 7-methylguanosine cap hypermethylation
namespace: biological_process
-def: "Hypermethylation of the 7-(mono)methylguanosine (m(7)G) cap structure at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. This type of cap modification occurs on small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) and is dependent on prior guanine-N7 methylation." [GOC:bf, GOC:BHF, GOC:krc, GOC:mah, GOC:rl, PMID:11983179, PMID:18775984]
+def: "Hypermethylation of the 7-(mono)methylguanosine (m(7)G) cap structure at the N2 position of the guanine base to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. This type of cap modification occurs on small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) and is dependent on prior guanine-N7 methylation." [GOC:bf, GOC:BHF, GOC:krc, GOC:mah, GOC:rl, PMID:11983179, PMID:15590684, PMID:18775984]
synonym: "2,2,7-trimethylguanosine cap formation" EXACT [PMID:11983179]
synonym: "conversion of m(7)G to m(3)G" EXACT [PMID:11983179]
synonym: "hypermethylation of snoRNA cap" NARROW [GOC:bf, GOC:krc, GOC:mah]
@@ -242796,6 +243023,7 @@
is_a: GO:0001510 ! RNA methylation
is_a: GO:0036260 ! RNA capping
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26208" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27628" xsd:anyURI
created_by: bf
creation_date: 2012-06-15T02:21:39Z
@@ -244161,11 +244389,11 @@
[Term]
id: GO:0036381
-name: pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
+name: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing) 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 + 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]
+synonym: "pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity" RELATED [EC:4.3.3.6]
xref: EC:4.3.3.6
xref: KEGG_REACTION:R10089
xref: MetaCyc:RXN-11322
@@ -244859,32 +245087,27 @@
[Term]
id: GO:0036432
-name: all-trans undecaprenol kinase activity
+name: obsolete all-trans undecaprenol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + undecaprenol + all-trans-undecaprenyl phosphate + ADP + H+." [RHEA:23752]
-xref: RHEA:23752
-is_a: GO:0009038 ! undecaprenol kinase activity
-property_value: skos:exactMatch RHEA:23752
+def: "OBSOLETE. Catalysis of the reaction: ATP + undecaprenol + all-trans-undecaprenyl phosphate + ADP + H+." [RHEA:23752]
+comment: This term was obsoleted because undecaprenol kinase (UdpK) has broad substrate specificity and phosphorylates both all-trans- and di-trans,poly-cis-undecaprenol (PMID:33310291), so a single grouping term (GO:0009038, undecaprenol kinase activity) is sufficient rather than splitting by isomer.
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/32370" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009038
created_by: bf
creation_date: 2013-09-16T14:21:04Z
[Term]
id: GO:0036433
-name: di-trans, poly-cis-undecaprenol kinase activity
+name: obsolete di-trans, poly-cis-undecaprenol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: di-trans, octa-cis-undecaprenol + ATP = di-trans,octa-cis-undecaprenyl phosphate + ADP + H+." [RHEA:28122]
-synonym: "ditrans,polycis-undecaprenol kinase activity" RELATED []
-xref: EC:2.7.1.66
-xref: KEGG_REACTION:R05626
-xref: MetaCyc:UNDECAPRENOL-KINASE-RXN
-xref: RHEA:28122
-is_a: GO:0009038 ! undecaprenol kinase activity
-property_value: skos:exactMatch EC:2.7.1.66
-property_value: skos:exactMatch KEGG_REACTION:R05626
-property_value: skos:exactMatch MetaCyc:UNDECAPRENOL-KINASE-RXN
-property_value: skos:exactMatch RHEA:28122
+def: "OBSOLETE. Catalysis of the reaction: di-trans, octa-cis-undecaprenol + ATP = di-trans,octa-cis-undecaprenyl phosphate + ADP + H+." [RHEA:28122]
+comment: This term was obsoleted because undecaprenol kinase (UdpK) has broad substrate specificity and phosphorylates both all-trans- and di-trans,poly-cis-undecaprenol (PMID:33310291), so a single grouping term (GO:0009038, undecaprenol kinase activity) is sufficient rather than splitting by isomer.
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/32370" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009038
created_by: bf
creation_date: 2013-09-16T14:21:12Z
@@ -245744,17 +245967,20 @@
[Term]
id: GO:0036503
-name: ERAD pathway
+name: ERAD quality control pathway
namespace: biological_process
-def: "The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome." [GOC:bf, GOC:PARL, PMID:20940304, PMID:21969857]
+def: "The protein catabolic pathway which constitutively monitors and targets misfolded/aberrant endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome." [GOC:bf, GOC:PARL, PMID:20940304, PMID:21969857]
comment: ER-associated protein degradation (ERAD) pathways target misfolded ER lumenal proteins (ERAD-L), ER membrane proteins (ERAD-M), and ER proteins with misfolded cytosolic domains (ERAD-C) by recognizing aberrant proteins, retrotranslocating these substrates to the cytosol, followed by substrate ubiquitination and proteosomal-mediated degradation. In contrast the stress-induced homeostatically regulated protein degradation (SHRED) pathway (GO:0120174), although inducible by stress, targets diverse ER membrane, and cytosolic proteins as well as numerous other native proteins in the absence of stress. Stress results in the protease-mediated (Nma111p) generation of a Roq1p cleavage product that then binds to the type-1 active site of Ubr1p, altering its substrate specificity, and leading to the proteasome-mediated degradation of both misfolded and native proteins. Although the SHRED pathway may contain some components in common with ERAD pathways (GO:0036503), such as UBR1, RAD6 and CDC48, other ERAD components, such as HRD1 and DOA10, do not appear to be involved, and as such these pathways are currently considered to be distinct.
-synonym: "endoplasmic reticulum-associated degradation" EXACT [PMID:22535891]
+synonym: "endoplasmic reticulum-associated degradation" BROAD [PMID:22535891]
synonym: "endoplasmic reticulum-associated protein degradation pathway" RELATED [GOC:bf]
synonym: "ER-associated degradation pathway" RELATED [PMID:24699081]
-synonym: "protein degradation by ERAD" EXACT [GOC:bf]
+synonym: "ERAD pathway" BROAD []
+synonym: "protein degradation by ERAD" BROAD [GOC:bf]
is_a: GO:0010498 ! proteasomal protein catabolic process
-is_a: GO:0034976 ! response to endoplasmic reticulum stress
-is_a: GO:0042221 ! response to chemical
+is_a: GO:0170080 ! endoplasmic reticulum protein quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20914" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32527" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32532" xsd:anyURI
created_by: bf
creation_date: 2015-05-14T11:43:06Z
@@ -246714,6 +246940,7 @@
synonym: "IL-5-mediated signaling pathway" EXACT [GOC:bf]
synonym: "interleukin-5-mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
+relationship: part_of GO:7770103 ! cellular response to interleukin-5
created_by: bf
creation_date: 2011-11-03T04:18:21Z
@@ -248084,6 +248311,7 @@
synonym: "granulocyte colony-stimulating factor receptor signaling pathway" EXACT [GOC:nhn]
synonym: "granulocyte colony-stimulating factor signalling pathway" RELATED [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32373" xsd:anyURI
created_by: bf
creation_date: 2012-05-14T01:30:28Z
@@ -253176,6 +253404,7 @@
xref: MetaCyc:PWY490-3
is_a: GO:0042126 ! nitrate metabolic process
is_a: GO:0071941 ! nitrogen cycle metabolic process
+is_a: GO:7770097 ! nutrient assimilation
relationship: has_part GO:0015112 ! nitrate transmembrane transporter activity
relationship: has_part GO:0098809 ! nitrite reductase activity
property_value: skos:narrowMatch MetaCyc:PWY-381
@@ -253184,6 +253413,7 @@
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32376" xsd:anyURI
[Term]
id: GO:0042129
@@ -253252,7 +253482,7 @@
synonym: "fructose diphosphatase activity" RELATED [EC:3.1.3.11]
synonym: "fructose diphosphate phosphatase activity" RELATED [EC:3.1.3.11]
synonym: "fructose-1,6-bisphosphatase activity" RELATED [EC:3.1.3.11]
-synonym: "fructose-bisphosphatase activity" BROAD [EC:3.1.3.00]
+synonym: "fructose-bisphosphatase activity" BROAD [EC:3.1.3.11]
synonym: "hexose bisphosphatase activity" RELATED [EC:3.1.3.11]
synonym: "hexose diphosphatase activity" RELATED [EC:3.1.3.11]
synonym: "hexosediphosphatase activity" BROAD [EC:3.1.3.11]
@@ -259024,11 +259254,10 @@
def: "mitochondrial protein-containing complex localised in the mitochondrial inner membrane space that chaperones proteins to the TIM22 complex for insertion into the mitochondrial inner membrane." [GOC:vw]
synonym: "mitochondrial intermembrane space protein transporter complex" RELATED []
synonym: "small TIM complex" EXACT []
-synonym: "Tim8-Tim13 complex" NARROW []
-synonym: "Tim9-Tim10 complex" NARROW []
is_a: GO:0098798 ! mitochondrial protein-containing complex
relationship: part_of GO:0005758 ! mitochondrial intermembrane space
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30351" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32408" xsd:anyURI
[Term]
id: GO:0042720
@@ -260084,14 +260313,17 @@
[Term]
id: GO:0042809
-name: nuclear vitamin D receptor binding
+name: obsolete nuclear vitamin D receptor binding
namespace: molecular_function
-def: "Binding to a nuclear vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
+def: "OBSOLETE. Binding to a nuclear vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and vitamin D3 receptor as 'has_input'.
synonym: "calciferol receptor binding" NARROW []
synonym: "VDR binding" EXACT []
synonym: "vitamin D receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0042810
@@ -260158,7 +260390,7 @@
name: bipolar cell growth
namespace: biological_process
def: "The process in which a cell irreversibly increases in size along one axis through simultaneous polarized growth from opposite ends of a cell, resulting in morphogenesis of the cell." [GOC:vw]
-comment: Bipolar cell growth refers to a change in both cell size and cell shape. For shape changes where cell size is not affected, consider instead the term 'establishment or maintenance of bipolar cell polarity resulting in cell shape ; GO:0061246' and its children.
+comment: Bipolar cell growth refers to a change in both cell size and cell shape. For shape changes where cell size is not affected, consider instead the term 'establishment or maintenance of bipolar cell polarity; GO:0061245' and its children.
synonym: "bipolar cell elongation" NARROW []
synonym: "bipolar growth" BROAD []
synonym: "polar cell elongation" RELATED []
@@ -261737,13 +261969,16 @@
[Term]
id: GO:0042974
-name: nuclear retinoic acid receptor binding
+name: obsolete nuclear retinoic acid receptor binding
namespace: molecular_function
-def: "Binding to a nuclear retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
+def: "OBSOLETE. Binding to a nuclear retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and retinoic acid receptor as 'has_input'.
synonym: "RAR binding" EXACT []
synonym: "retinoic acid receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0042975
@@ -262433,22 +262668,26 @@
[Term]
id: GO:0043038
-name: amino acid activation
+name: obsolete amino acid activation
namespace: biological_process
-def: "The modification of an amino acid to an active form, for incorporation into a peptide, protein or other macromolecule." [GOC:jl]
-is_a: GO:0006520 ! amino acid metabolic process
+def: "OBSOLETE. The modification of an amino acid to an active form, for incorporation into a peptide, protein or other macromolecule." [GOC:jl]
+comment: The reason for obsoletion is that this term grouped two processes that do not share a common biology: tRNA aminoacylation (GO:0043039), in which the amino acid is esterified to a tRNA and is not itself metabolized, and nonribosomal amino acid activation (GO:0043041), in which the amino acid is covalently modified (adenylylated). Its placement under 'amino acid metabolic process' therefore caused tRNA aminoacylation and all of its descendants to be inferred as amino acid metabolism, which the GO editors rejected. Because no residual process is common to both children, the grouping term has been obsoleted rather than redefined. Consider GO:0043039 for tRNA charging and GO:7770118 for nonribosomal activation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+consider: GO:0043039
+consider: GO:7770118
[Term]
id: GO:0043039
-name: tRNA aminoacylation
+name: tRNA charging
namespace: biological_process
def: "The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules." [GOC:ma, GOC:mah]
synonym: "amino acid activation" RELATED []
+synonym: "aminoacyl tRNA synthesis" EXACT []
synonym: "aminoacyl-tRNA biosynthesis" EXACT [GOC:mah]
synonym: "aminoacyl-tRNA biosynthetic process" EXACT [GOC:mah]
-synonym: "tRNA charging" EXACT []
+synonym: "tRNA aminoacylation" EXACT []
is_a: GO:0006399 ! tRNA metabolic process
-is_a: GO:0043038 ! amino acid activation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
[Term]
@@ -262460,26 +262699,33 @@
synonym: "tRNA aminoacylation for nonribosomal peptide biosynthesis" EXACT []
synonym: "tRNA aminoacylation for nonribosomal peptide formation" EXACT []
synonym: "tRNA aminoacylation for nonribosomal peptide synthesis" EXACT []
-is_a: GO:0043039 ! tRNA aminoacylation
-is_a: GO:0043041 ! amino acid activation for nonribosomal peptide biosynthetic process
+is_a: GO:0043039 ! tRNA charging
+relationship: part_of GO:0019184 ! nonribosomal peptide biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
[Term]
id: GO:0043041
-name: amino acid activation for nonribosomal peptide biosynthetic process
+name: obsolete amino acid activation for nonribosomal peptide biosynthetic process
namespace: biological_process
-def: "Activation of an amino acid for incorporation into a peptide by a nonribosomal process." [GOC:jl]
+def: "OBSOLETE. Activation of an amino acid for incorporation into a peptide by a nonribosomal process." [GOC:jl]
+comment: The reason for obsoletion is that this term restates a single molecular function. Activation of an amino acid for nonribosomal incorporation is one catalysed reaction, adenylation of the amino acid followed by its transfer as a thioester onto the phosphopantetheine group of a carrier protein, and is fully covered by GO:7770118. Consider GO:7770118.
synonym: "nonribosomal amino acid activation" RELATED []
-is_a: GO:0043038 ! amino acid activation
-relationship: part_of GO:0019184 ! nonribosomal peptide biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30872" xsd:anyURI
+is_obsolete: true
+consider: GO:7770118
[Term]
id: GO:0043042
-name: amino acid adenylylation by nonribosomal peptide synthase
+name: obsolete amino acid adenylylation by nonribosomal peptide synthase
namespace: biological_process
-def: "Activation of an amino acid for incorporation into a peptide by a nonribosomal process, catalyzed by subunits of nonribosomal peptide synthase. The amino acid is adenylated at its carboxylate group (ATP-dependent) then transferred to the thiol group of an enzyme-bound phosphopantetheine cofactor." [GOC:jl, PMID:9250661, PMID:9712910]
+def: "OBSOLETE. Activation of an amino acid for incorporation into a peptide by a nonribosomal process, catalyzed by subunits of nonribosomal peptide synthase. The amino acid is adenylated at its carboxylate group (ATP-dependent) then transferred to the thiol group of an enzyme-bound phosphopantetheine cofactor." [GOC:jl, PMID:9250661, PMID:9712910]
+comment: The reason for obsoletion is that this term restates a single molecular function, and names the same reaction as its former parent GO:0043041 with the gene product carrying it out. The reaction is fully covered by GO:7770118. Consider GO:7770118.
synonym: "amino acid adenylation by nonribosomal peptide synthase" EXACT []
synonym: "amino acid adenylation by NRPS" EXACT []
-is_a: GO:0043041 ! amino acid activation for nonribosomal peptide biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30872" xsd:anyURI
+is_obsolete: true
+consider: GO:7770118
[Term]
id: GO:0043043
@@ -262643,7 +262889,7 @@
id: GO:0043060
name: meiotic metaphase I homologous chromosome alignment
namespace: biological_process
-def: "A cell cycle process whereby homlogous chromosomes are positioned in a specific order and orientation at the metaphase plate (spindle equator) by the spindle machinery and centromere/kinetochore arrangement during meiosis I chromosome segregation. This alignment ensures that each daughter cell will receive the correct number of chromosomes during cell division." [PMID:10809666]
+def: "A cell cycle process whereby homologous chromosomes are positioned in a specific order and orientation at the metaphase plate (spindle equator) by the spindle machinery and centromere/kinetochore arrangement during meiosis I chromosome segregation. This alignment ensures that each daughter cell will receive the correct number of chromosomes during cell division." [PMID:10809666]
synonym: "meiotic metaphase I chromosome alignment" EXACT []
is_a: GO:0051311 ! meiotic metaphase chromosome alignment
relationship: part_of GO:0045143 ! homologous chromosome segregation
@@ -266171,7 +266417,7 @@
alt_id: GO:0031636
def: "Combining with corticotropin-releasing hormone and transmitting the signal to initiate a change in cell activity." [GOC:signaling, ISBN:0838577016, PMID:11027914, PMID:15134857]
synonym: "adrenocorticotropin-releasing hormone receptor activity" EXACT []
-synonym: "corticotropin-releasing factor receptor activity" EXACT [GOC:bf]
+synonym: "corticotropin releasing factor receptor activity" EXACT [GOC:bf]
synonym: "CRF receptor activity" EXACT [GOC:bf]
synonym: "CRH receptor activity" EXACT [GOC:bf]
is_a: GO:0038023 ! signaling receptor activity
@@ -270664,7 +270910,7 @@
[Term]
id: GO:0043802
-name: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) activity
+name: hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolyzing) activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 L-glutamine + 2 ATP + 2 H2O + hydrogenobyrinate = 2 L-glutamate + 2 ADP + 4 H+ + hydrogenobyrinate a,c-diamide + 2 phosphate." [EC:6.3.5.9, RHEA:12544]
synonym: "CobB" RELATED []
@@ -272349,7 +272595,7 @@
synonym: "negative regulation by host of viral transcription" EXACT []
synonym: "negative regulation of viral transcription by host" EXACT []
is_a: GO:0043921 ! host-mediated perturbation of viral transcription
-is_a: GO:0044793 ! host-mediated suppression of viral proces
+is_a: GO:0044793 ! host-mediated suppression of viral process
[Term]
id: GO:0043923
@@ -278118,66 +278364,81 @@
[Term]
id: GO:0044472
-name: venom-mediated perturbation of calcium channel activity
+name: obsolete venom-mediated perturbation of calcium channel activity
namespace: biological_process
-def: "A process in which an organism alters or subverts the activity of a calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+def: "OBSOLETE. A process in which an organism alters or subverts the activity of a calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in modulation of calcium channel activity in another organism" EXACT []
synonym: "envenomation resulting in modulation of calcium channel activity in other organism" EXACT []
-is_a: GO:0044560 ! venom-mediated perturbation of ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0005246
created_by: jl
creation_date: 2012-01-19T02:17:25Z
[Term]
id: GO:0044473
-name: venom-mediated inhibition of calcium channel activity
+name: obsolete venom-mediated inhibition of calcium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of calcium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of calcium channel activity in other organism" EXACT []
-is_a: GO:0044472 ! venom-mediated perturbation of calcium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0019855
created_by: jl
creation_date: 2012-01-19T02:19:46Z
[Term]
id: GO:0044474
-name: venom-mediated inhibition of voltage-gated calcium channel activity
+name: obsolete venom-mediated inhibition of voltage-gated calcium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of voltage-gated calcium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism" EXACT []
-is_a: GO:0044473 ! venom-mediated inhibition of calcium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0019855
created_by: jl
creation_date: 2012-01-19T02:25:04Z
[Term]
id: GO:0044475
-name: venom-mediated inhibition of high voltage-gated calcium channel activity
+name: obsolete venom-mediated inhibition of high voltage-gated calcium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a high voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a high voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of high voltage-gated calcium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of high voltage-gated calcium channel activity in other organism" EXACT []
-is_a: GO:0044474 ! venom-mediated inhibition of voltage-gated calcium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0019855
created_by: jl
creation_date: 2012-01-19T02:28:11Z
[Term]
id: GO:0044476
-name: venom-mediated inhibition of low voltage-gated calcium channel activity
+name: obsolete venom-mediated inhibition of low voltage-gated calcium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a low voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a low voltage-gated calcium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:20920515]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of low voltage-gated calcium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of low voltage-gated calcium channel activity in other organism" EXACT []
-is_a: GO:0044474 ! venom-mediated inhibition of voltage-gated calcium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0019855
created_by: jl
creation_date: 2012-01-19T02:28:42Z
@@ -278380,38 +278641,47 @@
[Term]
id: GO:0044492
-name: venom-mediated perturbation of voltage-gated sodium channel activity
+name: obsolete venom-mediated perturbation of voltage-gated sodium channel activity
namespace: biological_process
-def: "A process in which an organism alters or subverts the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+def: "OBSOLETE. A process in which an organism alters or subverts the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in modulation of voltage-gated sodium channel activity in another organism" EXACT []
synonym: "envenomation resulting in modulation of voltage-gated sodium channel activity in other organism" EXACT []
-is_a: GO:0044560 ! venom-mediated perturbation of ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0017080
created_by: jl
creation_date: 2012-02-01T01:23:04Z
[Term]
id: GO:0044493
-name: venom-mediated inhibition of voltage-gated sodium channel activity
+name: obsolete venom-mediated inhibition of voltage-gated sodium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of voltage-gated sodium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of voltage-gated sodium channel activity in other organism" EXACT []
-is_a: GO:0044492 ! venom-mediated perturbation of voltage-gated sodium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0019871
created_by: jl
creation_date: 2012-02-01T01:26:59Z
[Term]
id: GO:0044494
-name: venom-mediated activation of voltage-gated sodium channel activity
+name: obsolete venom-mediated activation of voltage-gated sodium channel activity
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+def: "OBSOLETE. A process in which an organism initiates, promotes, or enhances the activity of a voltage-gated sodium channel in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:21781281]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in positive regulation of voltage-gated sodium channel activity in another organism" EXACT []
synonym: "envenomation resulting in positive regulation of voltage-gated sodium channel activity in other organism" EXACT []
-is_a: GO:0044492 ! venom-mediated perturbation of voltage-gated sodium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:7770087
created_by: jl
creation_date: 2012-02-01T01:29:25Z
@@ -278474,7 +278744,7 @@
id: GO:0044499
name: venom-mediated vasoconstriction
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances the narrowing (constriction) of blood vessels by small muscles in their walls in another organism via the action of a venom, concomittantly increasing blood pressure in the bitten/stung organism." [GOC:fj, PMID:19837656]
+def: "A process in which an organism initiates, promotes, or enhances the narrowing (constriction) of blood vessels by small muscles in their walls in another organism via the action of a venom, concomitantly increasing blood pressure in the bitten/stung organism." [GOC:fj, PMID:19837656]
synonym: "envenomation resulting in positive regulation of blood pressure in another organism" EXACT []
synonym: "envenomation resulting in positive regulation of blood pressure in other organism" EXACT []
synonym: "venom-mediated increase in blood pressure in another organism" EXACT []
@@ -279118,7 +279388,7 @@
id: GO:0044551
name: venom-mediated vasodilation
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances the widening of blood vessels by small muscles in their walls in another organism via the action of a venom, concomittantly reducing blood pressure in the bitten/stung organism." [GOC:ecd, GOC:jl, PMID:21050868]
+def: "A process in which an organism initiates, promotes, or enhances the widening of blood vessels by small muscles in their walls in another organism via the action of a venom, concomitantly reducing blood pressure in the bitten/stung organism." [GOC:ecd, GOC:jl, PMID:21050868]
synonym: "envenomation resulting in modulation of vasodilation in other organism" RELATED []
synonym: "envenomation resulting in regulation of vasodilation in other organism" RELATED []
synonym: "envenomation resulting in vasodilation in another organism" EXACT []
@@ -279221,28 +279491,33 @@
[Term]
id: GO:0044559
-name: venom-mediated perturbation of voltage-gated potassium channel activity
+name: obsolete venom-mediated perturbation of voltage-gated potassium channel activity
namespace: biological_process
-def: "A process in which an organism alters or subverts the activity of a voltage-gated potassium channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+def: "OBSOLETE. A process in which an organism alters or subverts the activity of a voltage-gated potassium channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in modulation of voltage-gated potassium channel activity in another organism" EXACT []
synonym: "envenomation resulting in modulation of voltage-gated potassium channel activity in other organism" EXACT []
-is_a: GO:0044560 ! venom-mediated perturbation of ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0015459
created_by: jl
creation_date: 2012-04-05T03:35:20Z
[Term]
id: GO:0044560
-name: venom-mediated perturbation of ion channel activity
+name: obsolete venom-mediated perturbation of ion channel activity
namespace: biological_process
-def: "A process in which an organism alters or subverts the activity of an ion channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+def: "OBSOLETE. A process in which an organism alters or subverts the activity of an ion channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in modulation of ion channel activity in another organism" EXACT []
synonym: "envenomation resulting in modulation of ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in regulation of ion channel activity in other organism" EXACT []
-is_a: GO:0035738 ! venom-mediated perturbation of biological process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
created_by: jl
creation_date: 2012-04-05T03:46:35Z
@@ -279261,13 +279536,16 @@
[Term]
id: GO:0044562
-name: venom-mediated inhibition of voltage-gated potassium channel activity
+name: obsolete venom-mediated inhibition of voltage-gated potassium channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a voltage-gated potassium channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a voltage-gated potassium channel in another organism via the action of a venom." [GOC:fj, GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of voltage-gated potassium channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism" EXACT []
-is_a: GO:0044559 ! venom-mediated perturbation of voltage-gated potassium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:7770090
created_by: jl
creation_date: 2012-04-05T04:01:49Z
@@ -279281,7 +279559,6 @@
synonym: "voltage-dependence of activation shift (to the left)" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29857" xsd:anyURI
is_obsolete: true
-replaced_by: GO:0044562
created_by: jl
creation_date: 2012-04-05T04:06:29Z
@@ -279294,7 +279571,6 @@
synonym: "envenomation resulting in occlusion of the pore of voltage-gated potassium channel in other organism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29857" xsd:anyURI
is_obsolete: true
-replaced_by: GO:0044562
created_by: jl
creation_date: 2012-04-05T04:14:24Z
@@ -281044,49 +281320,58 @@
[Term]
id: GO:0044733
-name: venom-mediated perturbation of pH-gated ion channel activity
+name: obsolete venom-mediated perturbation of pH-gated ion channel activity
namespace: biological_process
-def: "A process in which an organism alters or subverts the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+def: "OBSOLETE. A process in which an organism alters or subverts the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in modulation of acid-sensing ion channel activity in another organism" EXACT []
synonym: "envenomation resulting in modulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in modulation of ASIC channel activity in other organism" EXACT []
synonym: "venom-mediated perturbation of acid-sensing ion channel activity" EXACT []
-is_a: GO:0044560 ! venom-mediated perturbation of ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29859" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0099106
created_by: jl
creation_date: 2012-11-06T15:58:36Z
[Term]
id: GO:0044734
-name: venom-mediated activation of pH-gated ion channel activity
+name: obsolete venom-mediated activation of pH-gated ion channel activity
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+def: "OBSOLETE. A process in which an organism initiates, promotes, or enhances the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in positive regulation of acid-sensing ion channel activity in another organism" EXACT []
synonym: "envenomation resulting in positive regulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in positive regulation of ASIC channel activity in other organism" EXACT []
synonym: "venom-mediated activation of acid-sensing ion channel activity" RELATED []
-is_a: GO:0044733 ! venom-mediated perturbation of pH-gated ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29859" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0099103
created_by: jl
creation_date: 2012-11-06T16:02:01Z
[Term]
id: GO:0044735
-name: venom-mediated inhibition of pH-gated ion channel activity
+name: obsolete venom-mediated inhibition of pH-gated ion channel activity
namespace: biological_process
-def: "A process in which an organism inhibits or disrupts the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+def: "OBSOLETE. A process in which an organism inhibits or disrupts the activity of a pH-gated (also known as acid-sensing ion channel (ASIC)) in another organism via the action of a venom." [GOC:fj, GOC:jl, PMID:23034652]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "envenomation resulting in negative regulation of acid-sensing ion channel activity in another organism" EXACT []
synonym: "envenomation resulting in negative regulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in negative regulation of ASIC channel activity in other organism" EXACT []
synonym: "venom-mediated inhibition of acid-sensing ion channel activity" RELATED []
-is_a: GO:0044733 ! venom-mediated perturbation of pH-gated ion channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29375" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29851" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29859" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32401" xsd:anyURI
+is_obsolete: true
+consider: GO:0008200
created_by: jl
creation_date: 2012-11-06T16:05:58Z
@@ -281674,7 +281959,7 @@
[Term]
id: GO:0044793
-name: host-mediated suppression of viral proces
+name: host-mediated suppression of viral process
namespace: biological_process
def: "A process in which a host organism interferes with, inhibits or disrupts a process being mediated by a virus with which it is infected." [GOC:jl]
synonym: "negative regulation by host of viral process" EXACT []
@@ -282496,7 +282781,7 @@
name: negative regulation by host of viral glycoprotein metabolic process
namespace: biological_process
def: "A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral glycoprotein metabolic process." [GOC:jl]
-is_a: GO:0044793 ! host-mediated suppression of viral proces
+is_a: GO:0044793 ! host-mediated suppression of viral process
is_a: GO:0044870 ! modulation by host of viral glycoprotein metabolic process
is_a: GO:0048525 ! negative regulation of viral process
is_a: GO:1903019 ! negative regulation of glycoprotein metabolic process
@@ -287032,8 +287317,9 @@
id: GO:0045498
name: sex comb development
namespace: biological_process
-def: "The process whose specific outcome is the progression of the sex comb over time, from its formation to the mature structure. The sex combs are the male specific chaetae located on the prothoracic tarsal segment of the prothoracic leg." [http://fly.ebi.ac.uk]
+def: "The process whose specific outcome is the progression of the sex comb over time, from its formation to the mature structure. The sex combs are the male specific chaetae located on the prothoracic tarsal segment of the prothoracic leg." [FBbt:00004296]
is_a: GO:0007423 ! sensory organ development
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0045499
@@ -290068,6 +290354,7 @@
synonym: "metabolic burst after phagocytosis" EXACT []
synonym: "oxidative burst after phagocytosis" EXACT []
is_a: GO:0002679 ! respiratory burst involved in defense response
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32152" xsd:anyURI
[Term]
id: GO:0045729
@@ -291375,38 +291662,40 @@
[Term]
id: GO:0045820
-name: negative regulation of glycolytic process
+name: negative regulation of glycolysis
namespace: biological_process
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 []
synonym: "inhibition of glycolysis" NARROW []
-is_a: GO:0006110 ! regulation of glycolytic process
+synonym: "negative regulation of glycolytic process" EXACT []
+is_a: GO:0006110 ! regulation of glycolysis
is_a: GO:0033122 ! negative regulation of purine nucleotide catabolic process
is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
is_a: GO:1903579 ! negative regulation of ATP metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0006096 ! glycolytic process
-relationship: negatively_regulates GO:0006096 ! glycolytic process
+intersection_of: negatively_regulates GO:0006096 ! glycolysis
+relationship: negatively_regulates GO:0006096 ! glycolysis
[Term]
id: GO:0045821
-name: positive regulation of glycolytic process
+name: positive regulation of glycolysis
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of glycolysis." [GOC:curators]
synonym: "activation of glycolysis" NARROW []
+synonym: "positive regulation of glycolytic process" EXACT []
synonym: "stimulation of glycolysis" NARROW []
synonym: "up regulation of glycolysis" EXACT []
synonym: "up-regulation of glycolysis" EXACT []
synonym: "upregulation of glycolysis" EXACT []
-is_a: GO:0006110 ! regulation of glycolytic process
+is_a: GO:0006110 ! regulation of glycolysis
is_a: GO:0033123 ! positive regulation of purine nucleotide catabolic process
is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
is_a: GO:1903580 ! positive regulation of ATP metabolic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0006096 ! glycolytic process
-relationship: positively_regulates GO:0006096 ! glycolytic process
+intersection_of: positively_regulates GO:0006096 ! glycolysis
+relationship: positively_regulates GO:0006096 ! glycolysis
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29024" xsd:anyURI
[Term]
@@ -298746,7 +299035,6 @@
synonym: "N-acetylneuraminate biosynthesis" EXACT []
synonym: "N-acetylneuraminate formation" EXACT []
synonym: "N-acetylneuraminate synthesis" EXACT []
-is_a: GO:0006054 ! N-acetylneuraminate metabolic process
is_a: GO:0046349 ! amino sugar biosynthetic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
@@ -298885,23 +299173,27 @@
name: carboxylic acid biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732]
+subset: gocheck_do_not_annotate
synonym: "carboxylic acid anabolism" EXACT []
synonym: "carboxylic acid biosynthesis" EXACT []
synonym: "carboxylic acid formation" EXACT []
synonym: "carboxylic acid synthesis" EXACT []
is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0044283 ! small molecule biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0046395
name: carboxylic acid catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." [ISBN:0198506732]
+subset: gocheck_do_not_annotate
synonym: "carboxylic acid breakdown" EXACT []
synonym: "carboxylic acid catabolism" EXACT []
synonym: "carboxylic acid degradation" EXACT []
is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0044282 ! small molecule catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0046396
@@ -299390,11 +299682,13 @@
name: organophosphate catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of organophosphates, any phosphate-containing organic compound." [GOC:ai]
+subset: gocheck_do_not_annotate
synonym: "organophosphate breakdown" EXACT []
synonym: "organophosphate catabolism" EXACT []
synonym: "organophosphate degradation" EXACT []
is_a: GO:0009056 ! catabolic process
is_a: GO:0019637 ! organophosphate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0046435
@@ -304207,7 +304501,7 @@
name: ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity
namespace: molecular_function
alt_id: GO:0018236
-def: "Binds to and iincreases the activity of rubisco by the removal of otherwise inhibitory sugar phosphates: RuBP, and in some plants, 2-carboxyarabinitol 1-phosphate." [PMID:10430961, PMID:10965036, PMID:2404515]
+def: "Binds to and increases the activity of rubisco by the removal of otherwise inhibitory sugar phosphates: RuBP, and in some plants, 2-carboxyarabinitol 1-phosphate." [PMID:10430961, PMID:10965036, PMID:2404515]
comment: See also the molecular function term 'ribulose-bisphosphate carboxylase activity ; GO:0016984'.
synonym: "ribulose-1,5-bisphosphate carboxylase/oxygenase activase activity" EXACT [GOC:dph, GOC:tb]
synonym: "ribulose-bisphosphate carboxylase activase activity" EXACT []
@@ -304916,16 +305210,18 @@
id: GO:0046923
name: ER lumen protein retrieval receptor activity
namespace: molecular_function
-def: "Binding to an endoplasmic reticulum (ER) retention sequence, a short stretch of amino acids found in a protein that acts as a signal to retain the protein within the ER." [GOC:ai]
+def: "Binding to a C-terminal ER retrieval signal, such as KDEL, HDEL or DDEL, present on soluble lumenal proteins that have escaped from the endoplasmic reticulum (ER) to the Golgi, and mediating their return to the ER." [PMID:33037041]
synonym: "DDEL sequence binding" NARROW []
-synonym: "DDEL signal sequence receptor activity" NARROW []
-synonym: "endoplasmic reticulum retention sequence binding" EXACT []
-synonym: "ER retention sequence binding" NARROW []
+synonym: "DDEL signal sequence receptor activity" RELATED []
+synonym: "endoplasmic reticulum retention sequence binding" RELATED []
+synonym: "ER retention sequence binding" RELATED []
synonym: "HDEL sequence binding" NARROW []
-synonym: "HDEL signal sequence receptor activity" NARROW []
+synonym: "HDEL signal sequence receptor activity" RELATED []
synonym: "KDEL sequence binding" NARROW []
-synonym: "KDEL signal sequence receptor activity" NARROW []
-is_a: GO:0005048 ! signal sequence receptor activity
+synonym: "KDEL signal sequence receptor activity" RELATED []
+is_a: GO:0038024 ! cargo receptor activity
+relationship: part_of GO:0006890 ! retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32307" xsd:anyURI
[Term]
id: GO:0046924
@@ -305471,23 +305767,29 @@
[Term]
id: GO:0046965
-name: nuclear retinoid X receptor binding
+name: obsolete nuclear retinoid X receptor binding
namespace: molecular_function
-def: "Binding to a nuclear retinoid X receptor." [GOC:ai]
+def: "OBSOLETE. Binding to a nuclear retinoid X receptor." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and retinoid X receptor as 'has_input'.
synonym: "retinoid X receptor binding" BROAD []
synonym: "RXR binding" EXACT []
-is_a: GO:0042974 ! nuclear retinoic acid receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0046966
-name: nuclear thyroid hormone receptor binding
+name: obsolete nuclear thyroid hormone receptor binding
namespace: molecular_function
-def: "Binding to a nuclear thyroid hormone receptor." [GOC:ai]
+def: "OBSOLETE. Binding to a nuclear thyroid hormone receptor." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and thyroid hormone receptor as 'has_input'.
synonym: "ligand-dependent thyroid hormone receptor interactor activity" NARROW []
synonym: "thyroid hormone receptor binding" BROAD []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0046967
@@ -306595,9 +306897,9 @@
def: "Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP+ = biopterin + 2 H+ + 2 NADPH." [EC:1.5.1.33, RHEA:19509]
synonym: "5,6,7,8-tetrahydrobiopterin:NADP+ oxidoreductase activity" RELATED [EC:1.5.1.33]
synonym: "dihydrobiopterin reduction" RELATED []
-synonym: "pteridine reductase 1 activity" NARROW [EC:1.5.1.33e]
+synonym: "pteridine reductase 1 activity" NARROW [EC:1.5.1.33]
synonym: "PTR1" RELATED [EC:1.5.1.33]
-synonym: "ptr1 activity" NARROW [EC:1.5.1.33e]
+synonym: "ptr1 activity" NARROW [EC:1.5.1.33]
xref: EC:1.5.1.33
xref: KEGG_REACTION:R01812
xref: MetaCyc:1.1.1.253-RXN
@@ -316323,19 +316625,18 @@
[Term]
id: GO:0047576
-name: 4-chlorobenzoate dehalogenase activity
+name: obsolete 4-chlorobenzoate dehalogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chlorobenzoate + H2O = 4-hydroxybenzoate + chloride + H+." [RHEA:23440]
+def: "OBSOLETE. Catalysis of the reaction: 4-chlorobenzoate + H2O = 4-hydroxybenzoate + chloride + H+." [RHEA:23440]
+comment: The reason for obsoletion is that this activity is not known to be catalyzed by any gene product, there is no evidence that this function/process/component exists, and the EC number (EC 3.8.1.6) on which this GO term was based has been deleted in the IUBMB EC list.
synonym: "4-chlorobenzoate chlorohydrolase activity" RELATED [EC:3.8.1.6]
synonym: "halobenzoate dehalogenase activity" RELATED [EC:3.8.1.6]
-xref: EC:3.8.1.6
-xref: KEGG_REACTION:R01307
-xref: MetaCyc:4-CHLOROBENZOATE-DEHALOGENASE-RXN
-xref: RHEA:23440
-is_a: GO:0019120 ! hydrolase activity, acting on halide bonds, in C-halide compounds
-property_value: skos:exactMatch EC:3.8.1.6
-property_value: skos:exactMatch RHEA:23440
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/32542" xsd:anyURI
+is_obsolete: true
+consider: GO:0018739
+consider: GO:0018787
+consider: GO:0018861
[Term]
id: GO:0047577
@@ -330005,12 +330306,13 @@
name: regulation of collateral sprouting
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of collateral sprouting." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
+is_a: GO:0001558 ! regulation of cell growth
is_a: GO:0048638 ! regulation of developmental growth
is_a: GO:0050770 ! regulation of axonogenesis
-is_a: GO:0061387 ! regulation of extent of cell growth
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0048668 ! collateral sprouting
relationship: regulates GO:0048668 ! collateral sprouting
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
[Term]
id: GO:0048671
@@ -330195,12 +330497,13 @@
name: regulation of sprouting of injured axon
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sprouting of an injured axon." [GOC:dgh, GOC:dph, GOC:jid, GOC:lm]
+is_a: GO:0001558 ! regulation of cell growth
is_a: GO:0022603 ! regulation of anatomical structure morphogenesis
is_a: GO:0048638 ! regulation of developmental growth
-is_a: GO:0061387 ! regulation of extent of cell growth
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0048682 ! sprouting of injured axon
relationship: regulates GO:0048682 ! sprouting of injured axon
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
[Term]
id: GO:0048687
@@ -331504,11 +331807,12 @@
id: GO:0048816
name: ocellus morphogenesis
namespace: biological_process
-def: "The process in which the anatomical structures of the ocellus are generated and organized. The ocellus is a simple visual organ of insects." [http://fly.ebi.ac.uk/.bin/cvreport2?id=FBcv0004540]
+def: "The process in which the anatomical structures of the ocellus are generated and organized. The ocellus is a simple visual organ of insects." [FBbt:00004505]
is_a: GO:0009886 ! post-embryonic animal morphogenesis
is_a: GO:0090596 ! sensory organ morphogenesis
relationship: part_of GO:0007455 ! eye-antennal disc morphogenesis
relationship: part_of GO:0008056 ! ocellus development
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18983" xsd:anyURI
[Term]
id: GO:0048817
@@ -336074,7 +336378,7 @@
id: GO:0050197
name: phytanate-CoA ligase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + CoA + phytanate = AMP + diphosphate + H+ + phytanoyl-CoA." [EC:6.2.1.24, RHEA:21380]
+def: "Catalysis of the reaction: ATP + CoA + phytanate = AMP + diphosphate + H+ + phytanoyl-CoA." [RHEA:21380]
synonym: "phytanate:CoA ligase (AMP-forming)" RELATED [EC:6.2.1.24]
synonym: "phytanoyl-CoA ligase activity" RELATED [EC:6.2.1.24]
xref: EC:6.2.1.24
@@ -336082,10 +336386,11 @@
xref: MetaCyc:PHYTANATE--COA-LIGASE-RXN
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:0120515 ! fatty acid-CoA 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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32501" xsd:anyURI
[Term]
id: GO:0050198
@@ -341373,7 +341678,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UDP-N-acetyl-alpha-D-glucosamine = beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamm-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H+ + UDP." [RHEA:23192]
synonym: "MurG transferase activity" RELATED [EC:2.4.1.227]
-synonym: "UDP-N-acetyl-D-glucosamine:N-acetyl-alpha-D-muramyl(oyl-L-Ala- gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol beta-1,4-N-acetylglucosaminlytransferase activity" RELATED [EC:2.4.1.227]
+synonym: "UDP-N-acetyl-D-glucosamine:N-acetyl-alpha-D-muramyl(oyl-L-Ala- gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol beta-1,4-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.227]
synonym: "UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase activity" RELATED [EC:2.4.1.227]
synonym: "undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase activity" RELATED [EC:2.4.1.227]
synonym: "undecaprenyldiphospho-muramoylpentapeptide b-N-acetylglucosaminyltransferase activity" EXACT []
@@ -343428,7 +343733,7 @@
id: GO:0050633
name: acetyl-CoA C-myristoyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: myristoyl-CoA + acetyl-CoA = 3-oxopalmitoyl-CoA + CoA." [EC:2.3.1.155, MetaCyc:2.3.1.155-RXN]
+def: "Catalysis of the reaction: tetradecanoyl-CoA + acetyl-CoA = 3-oxohexadecanoyl-CoA + CoA." [RHEA:18161]
synonym: "3-oxopalmitoyl-CoA hydrolase activity" RELATED [EC:2.3.1.155]
synonym: "3-oxopalmitoyl-CoA-CoA acetyltransferase activity" RELATED [EC:2.3.1.155]
synonym: "myristoyl-CoA C-acetyltransferase activity" RELATED [EC:2.3.1.155]
@@ -343436,10 +343741,12 @@
xref: EC:2.3.1.155
xref: MetaCyc:2.3.1.155-RXN
xref: RHEA:18161
+is_a: GO:0003988 ! acetyl-CoA C-acyltransferase activity
is_a: GO:0019107 ! myristoyltransferase activity
property_value: skos:exactMatch EC:2.3.1.155
property_value: skos:exactMatch RHEA:18161
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/32501" xsd:anyURI
[Term]
id: GO:0050634
@@ -343707,7 +344014,7 @@
id: GO:0050651
name: dermatan sulfate proteoglycan biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycans, which consist of a core protein linked to a dermatan sulfate glycosaminoglycan. The dermatan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-D-hexuronic acid-beta-(1,3)-N-acetyl-D-galactosamine. Tthe former can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids, and the latter can be O-sulfated. Dermatan sulfate chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate)." [PMID:17239763]
+def: "The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycans, which consist of a core protein linked to a dermatan sulfate glycosaminoglycan. The dermatan sulfate chain is composed of the repeating disaccharide unit beta-(1,4)-D-hexuronic acid-beta-(1,3)-N-acetyl-D-galactosamine. The former can be a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids, and the latter can be O-sulfated. Dermatan sulfate chains are covalently linked to serine/threonine residues (O-linked) of the core protein via a tetrasaccharide linker sequence (xylose-galactose-galactose-glucuronate)." [PMID:17239763]
synonym: "chondroitin sulfate B proteoglycan biosynthesis" EXACT []
synonym: "chondroitin sulfate B proteoglycan biosynthetic process" EXACT []
synonym: "dermatan sulfate proteoglycan anabolism" EXACT []
@@ -344096,13 +344403,16 @@
[Term]
id: GO:0050681
-name: nuclear androgen receptor binding
+name: obsolete nuclear androgen receptor binding
namespace: molecular_function
-def: "Binding to a nuclear androgen receptor." [GOC:ai]
+def: "OBSOLETE. Binding to a nuclear androgen receptor." [GOC:ai]
+comment: The reason for obsoletion is that this term represents a gene product. Better to annotate with GO:0016922 nuclear receptor binding and androgen receptor as 'has_input'.
synonym: "androgen receptor binding" BROAD []
synonym: "AR binding" EXACT []
-is_a: GO:0016922 ! nuclear receptor binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32475" xsd:anyURI
+is_obsolete: true
+consider: GO:0016922
[Term]
id: GO:0050682
@@ -350108,7 +350418,6 @@
synonym: "protein-mitochondrion membrane insertion" EXACT []
is_a: GO:0007006 ! mitochondrial membrane organization
is_a: GO:0051205 ! protein insertion into membrane
-is_a: GO:0051649 ! establishment of localization in cell
is_a: GO:0072594 ! establishment of protein localization to organelle
relationship: part_of GO:0070585 ! protein localization to mitochondrion
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15800" xsd:anyURI
@@ -358521,7 +358830,7 @@
id: GO:0051920
name: peroxiredoxin activity
namespace: molecular_function
-def: "Catalysis of the reaction: [protein]-dithol + ROOH = [protein]-disulfide + H2O + ROH." [RHEA:10008]
+def: "Catalysis of the reaction: [protein]-dithiol + ROOH = [protein]-disulfide + H2O + ROH." [RHEA:10008]
comment: Includes redox chemistry as part of the catalytic reaction (2 R'-SH = R'-S-S-R'), where R' refers to peroxiredoxin itself).
synonym: "PRDX activity" EXACT []
synonym: "Prx activity" EXACT []
@@ -358529,16 +358838,13 @@
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31239" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32405" xsd:anyURI
[Term]
id: GO:0051921
@@ -359519,7 +359825,7 @@
[Term]
id: GO:0051991
-name: UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase activity
+name: UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-glucosamine = di-trans-octa-cis-undecaprenyl diphospho-[N-acetyl-alpha-D-glucosaminyl-(1->4)]-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + H+ + UDP." [RHEA:31227]
xref: MetaCyc:NACGLCTRANS-RXN
@@ -369018,19 +369324,19 @@
[Term]
id: GO:0052869
-name: arachidonate omega-hydroxylase activity
+name: obsolete arachidonate omega-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = 20-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate + H+ + H2O + oxidized [NADPH--hemoprotein reductase]. (5Z,8Z,11Z,14Z)-icosatetraenoic acid is also known as arachidonic acid is also and 20-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate as 20-HETE." [RHEA:39755]
+def: "OBSOLETE. Catalysis of the reaction: (5Z,8Z,11Z,14Z)-eicosatetraenoate + O2 + reduced [NADPH--hemoprotein reductase] = 20-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate + H+ + H2O + oxidized [NADPH--hemoprotein reductase]. (5Z,8Z,11Z,14Z)-icosatetraenoic acid is also known as arachidonic acid is also and 20-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoate as 20-HETE." [RHEA:39755]
+comment: The reason for obsoletion is that this term represents a specific substrate of the parent term.
synonym: "arachidonic acid hydroxylase activity" BROAD []
synonym: "arachidonic acid omega-hydroxylase activity" EXACT []
-synonym: "arachidonic acid:oxygen 1-oxidoreductase activity" EXACT systematic_synonym []
-xref: KEGG_REACTION:R07041
-xref: MetaCyc:RXN-19677
-xref: RHEA:39755
-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:39755
+synonym: "arachidonic acid:oxygen 1-oxidoreductase activity" EXACT []
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/28648" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32501" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32503" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0102033
created_by: ai
creation_date: 2012-01-30T03:05:27Z
@@ -383918,22 +384224,25 @@
[Term]
id: GO:0061160
-name: regulation of establishment of bipolar cell polarity regulating cell shape
+name: obsolete regulation of establishment of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of the establishment of bipolar cell polarity that contributes to the shape of a cell." [GOC:dph, GOC:vw]
-is_a: GO:0061172 ! regulation of establishment of bipolar cell polarity
-is_a: GO:2000100 ! regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that modulates the rate, frequency or extent of the establishment of bipolar cell polarity that contributes to the shape of a cell." [GOC:dph, GOC:vw]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-06-23T09:21:36Z
[Term]
id: GO:0061161
-name: positive regulation of establishment of bipolar cell polarity regulating cell shape
+name: obsolete positive regulation of establishment of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of the establishment of bipolar cell polarity that regulates the shape of a cell." [GOC:dph, GOC:vw]
-is_a: GO:0061160 ! regulation of establishment of bipolar cell polarity regulating cell shape
-is_a: GO:0061173 ! positive regulation of establishment of bipolar cell polarity
-is_a: GO:2000247 ! positive regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that increases the rate, frequency or extent of the establishment of bipolar cell polarity that regulates the shape of a cell." [GOC:dph, GOC:vw]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-06-23T09:26:45Z
@@ -384867,11 +385176,13 @@
[Term]
id: GO:0061246
-name: establishment or maintenance of bipolar cell polarity regulating cell shape
+name: obsolete establishment or maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any cellular process that results in the specification, formation or maintenance of a bipolar intracellular organization or cell growth patterns that regulates the shaping of a cell." [GOC:dph, GOC:vw]
-is_a: GO:0061245 ! establishment or maintenance of bipolar cell polarity
-is_a: GO:0071963 ! establishment or maintenance of cell polarity regulating cell shape
+def: "OBSOLETE. Any cellular process that results in the specification, formation or maintenance of a bipolar intracellular organization or cell growth patterns that regulates the shaping of a cell." [GOC:dph, GOC:vw]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-08-23T09:46:01Z
@@ -385528,10 +385839,13 @@
[Term]
id: GO:0061305
-name: maintenance of bipolar cell polarity regulating cell shape
+name: obsolete maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "The maintenance of established bipolar anisotropic intracellular organization or cell growth patterns that results in the shaping of a cell." [GOC:dph, GOC:vw]
-is_a: GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. The maintenance of established bipolar anisotropic intracellular organization or cell growth patterns that results in the shaping of a cell." [GOC:dph, GOC:vw]
+comment: The reason for obsoletion is that these terms were added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-09-16T09:25:18Z
@@ -386203,23 +386517,25 @@
[Term]
id: GO:0061361
-name: positive regulation of maintenance of bipolar cell polarity regulating cell shape
+name: obsolete positive regulation of maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of maintenance of bipolar cell polarity regulating cell shape." [GOC:dph]
-is_a: GO:2000115 ! regulation of maintenance of bipolar cell polarity regulating cell shape
-is_a: GO:2000247 ! positive regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
-relationship: positively_regulates GO:0061305 ! maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that increases the frequency, rate or extent of maintenance of bipolar cell polarity regulating cell shape." [GOC:dph]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-10-13T09:00:59Z
[Term]
id: GO:0061362
-name: negative regulation of maintenance of bipolar cell polarity regulating cell shape
+name: obsolete negative regulation of maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of maintenance of bipolar cell polarity regulating cell shape." [GOC:dph]
-is_a: GO:2000115 ! regulation of maintenance of bipolar cell polarity regulating cell shape
-is_a: GO:2000750 ! negative regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
-relationship: negatively_regulates GO:0061305 ! maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that decreases the frequency, rate or extent of maintenance of bipolar cell polarity regulating cell shape." [GOC:dph]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-10-13T09:03:42Z
@@ -386482,9 +386798,10 @@
id: GO:0061387
name: regulation of extent of cell growth
namespace: biological_process
-def: "Any process that modulates the extent of cell growth." [GOC:mah, GOC:vw]
+def: "Any process that modulates how much additional mass a cell adds during cell growth before growth ceases." [GOC:mah, GOC:vw]
is_a: GO:0001558 ! regulation of cell growth
relationship: part_of GO:0008361 ! regulation of cell size
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
created_by: dph
creation_date: 2011-07-14T10:15:42Z
@@ -386492,8 +386809,9 @@
id: GO:0061388
name: regulation of rate of cell growth
namespace: biological_process
-def: "Any process that modulates the rate of cell growth." [GOC:mah, GOC:vw]
+def: "Any process that modulates how fast a cell adds additional mass during cell growth." [GOC:mah, GOC:vw]
is_a: GO:0001558 ! regulation of cell growth
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
created_by: dph
creation_date: 2011-07-14T10:18:06Z
@@ -386501,9 +386819,10 @@
id: GO:0061389
name: regulation of direction of cell growth
namespace: biological_process
-def: "Any process that modulates the direction of cell growth." [GOC:mah, GOC:vw]
+def: "Any process that modulates where in a cell additional mass is added during cell growth." [GOC:mah, GOC:vw]
is_a: GO:0001558 ! regulation of cell growth
is_a: GO:0008360 ! regulation of cell shape
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19737" xsd:anyURI
created_by: dph
creation_date: 2011-07-14T10:19:46Z
@@ -386987,10 +387306,13 @@
[Term]
id: GO:0061429
-name: positive regulation of transcription from RNA polymerase II promoter by oleic acid
+name: obsolete positive regulation of transcription from RNA polymerase II promoter by oleic acid
namespace: biological_process
-def: "Any process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dph, PMID:20395639]
-is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter
+def: "OBSOLETE. Any process involving oleic acid that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:dph, PMID:20395639]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0045944
created_by: dph
creation_date: 2012-02-07T09:54:49Z
@@ -387452,7 +387774,8 @@
id: GO:0061474
name: phagolysosome membrane
namespace: cellular_component
-def: "The lipid bilayer surrounding a phagolysosome." [GOC:dph, PMID:22073313]
+def: "The lipid bilayer surrounding a phagolysosome." [GOC:dph, PMID:22073313, PMID:29471269]
+synonym: "phagolysosome vesicle membrane" EXACT []
is_a: GO:0005765 ! lysosomal membrane
is_a: GO:0030670 ! phagocytic vesicle membrane
relationship: part_of GO:0032010 ! phagolysosome
@@ -387461,13 +387784,13 @@
[Term]
id: GO:0061475
-name: cytosolic valyl-tRNA aminoacylation
+name: obsolete cytosolic valyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling valine to valyl-tRNA in the cytosol, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:dph]
-is_a: GO:0006438 ! valyl-tRNA aminoacylation
-intersection_of: GO:0006438 ! valyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005829 ! cytosol
-relationship: occurs_in GO:0005829 ! cytosol
+def: "OBSOLETE. The process of coupling valine to valyl-tRNA in the cytosol, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:dph]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004832 valine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
created_by: dph
creation_date: 2012-11-06T12:29:42Z
@@ -388975,32 +389298,28 @@
[Term]
id: GO:0061615
-name: glycolytic process through fructose-6-phosphate
+name: obsolete glycolytic process through fructose-6-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "glycolysis through fructose-6-phosphate" EXACT [GOC:dph]
-xref: MetaCyc:PWY-5484
-is_a: GO:0006096 ! glycolytic process
-intersection_of: GO:0006096 ! glycolytic process
-intersection_of: has_part GO:0003872 ! 6-phosphofructokinase activity
-intersection_of: has_part GO:0004332 ! fructose-bisphosphate aldolase activity
-intersection_of: has_part GO:0004807 ! triose-phosphate isomerase activity
-relationship: has_part GO:0003872 ! 6-phosphofructokinase activity
-relationship: has_part GO:0004332 ! fructose-bisphosphate aldolase activity
-relationship: has_part GO:0004807 ! triose-phosphate isomerase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-08T10:08:49Z
[Term]
id: GO:0061616
-name: glycolytic process from fructose through fructose-6-phosphate
+name: obsolete glycolytic process from fructose through fructose-6-phosphate
namespace: biological_process
-def: "The glycolytic process through fructose-6-phosphate in which fructose is catabolized into pyruvate." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+def: "OBSOLETE. The glycolytic process through fructose-6-phosphate in which fructose is catabolized into pyruvate." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "glycolysis from fructose through fructose-6-phosphate" EXACT [GOC:dph]
-is_a: GO:0006001 ! fructose catabolic process
-is_a: GO:0061615 ! glycolytic process through fructose-6-phosphate
-relationship: has_part GO:0008865 ! fructokinase activity
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/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-08T10:20:37Z
@@ -389029,64 +389348,66 @@
[Term]
id: GO:0061619
-name: glycolytic process from mannose through fructose-6-phosphate
+name: obsolete glycolytic process from mannose through fructose-6-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of mannose into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
-is_a: GO:0019309 ! mannose catabolic process
-is_a: GO:0061615 ! glycolytic process through fructose-6-phosphate
-relationship: has_part GO:0061611 ! mannose to fructose-6-phosphate catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of mannose into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-14T09:13:13Z
[Term]
id: GO:0061620
-name: glycolytic process through glucose-6-phosphate
+name: obsolete glycolytic process through glucose-6-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, occurring through a glucose-6-phosphate intermediate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
-is_a: GO:0061615 ! glycolytic process through fructose-6-phosphate
-relationship: has_part GO:0004347 ! glucose-6-phosphate isomerase activity
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, occurring through a glucose-6-phosphate intermediate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26642" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29187" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-14T09:17:48Z
[Term]
id: GO:0061621
-name: canonical glycolysis
+name: obsolete canonical glycolysis
namespace: biological_process
-def: "The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
-xref: MetaCyc:ANAGLYCOLYSIS-PWY
+def: "OBSOLETE. The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
xref: Reactome:R-HSA-70171 "Glycolysis"
-xref: Wikipedia:Glycolysis
-is_a: GO:0006007 ! glucose catabolic process
-is_a: GO:0061620 ! glycolytic process through glucose-6-phosphate
-relationship: has_part GO:0004340 ! glucokinase activity
-relationship: has_part GO:0004365 ! glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28968" 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/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-14T09:21:54Z
[Term]
id: GO:0061622
-name: glycolytic process through glucose-1-phosphate
+name: obsolete glycolytic process through glucose-1-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways through a glucose-1-phosphate intermediate that result in the catabolism of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910]
-is_a: GO:0061620 ! glycolytic process through glucose-6-phosphate
-intersection_of: GO:0061620 ! glycolytic process through glucose-6-phosphate
-intersection_of: has_part GO:0004614 ! phosphoglucomutase activity
-relationship: has_part GO:0004614 ! phosphoglucomutase activity
+def: "OBSOLETE. The chemical reactions and pathways through a glucose-1-phosphate intermediate that result in the catabolism of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-28T08:08:01Z
[Term]
id: GO:0061623
-name: glycolytic process from galactose
+name: obsolete glycolytic process from galactose
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of galactose into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910]
-is_a: GO:0019388 ! galactose catabolic process
-is_a: GO:0061622 ! glycolytic process through glucose-1-phosphate
-relationship: has_part GO:0033499 ! beta-D-galactose catabolic process via UDP-galactose, Leloir pathway
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of galactose into pyruvate, with the concomitant production of a small amount of ATP." [GOC:dph, ISBN:0201090910]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-28T08:13:38Z
@@ -389106,12 +389427,14 @@
[Term]
id: GO:0061625
-name: glycolytic process through fructose-1-phosphate
+name: obsolete glycolytic process through fructose-1-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of fructose into pyruvate through a fructose-1-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910]
-xref: MetaCyc:PWY-8404
-is_a: GO:0006096 ! glycolytic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of fructose into pyruvate through a fructose-1-phosphate intermediate, with the concomitant production of ATP and NADH." [GOC:dph, ISBN:0201090910]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27616" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-04-29T13:04:10Z
@@ -389338,14 +389661,14 @@
[Term]
id: GO:0061633
-name: transport-coupled glycolytic process through glucose-6-phosphate
+name: obsolete transport-coupled glycolytic process through glucose-6-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glucose into pyruvate, in which the glucose is converted to glucose-6-phosphate intermediate coupled to transmembrane transport." [GOC:dph]
-xref: MetaCyc:GLYCOLYSIS
-is_a: GO:0006007 ! glucose catabolic process
-is_a: GO:0061620 ! glycolytic process through glucose-6-phosphate
-relationship: has_part GO:0022855 ! protein-N(PI)-phosphohistidine-glucose phosphotransferase system transporter activity
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of glucose into pyruvate, in which the glucose is converted to glucose-6-phosphate intermediate coupled to transmembrane transport." [GOC:dph]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26642" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2014-06-19T09:12:37Z
@@ -390143,11 +390466,13 @@
[Term]
id: GO:0061704
-name: glycolytic process from sucrose
+name: obsolete glycolytic process from sucrose
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a sucrose into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules." [GOC:dph, GOC:glycolysis, PMID:15012287]
-is_a: GO:0005987 ! sucrose catabolic process
-is_a: GO:0006096 ! glycolytic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a sucrose into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules." [GOC:dph, GOC:glycolysis, PMID:15012287]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2015-06-11T13:26:28Z
@@ -390165,11 +390490,13 @@
[Term]
id: GO:0061706
-name: glycolytic process from sucrose through glucose and fructose
+name: obsolete glycolytic process from sucrose through glucose and fructose
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of sucrose into pyruvate through both glucose and fructose intermediates, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules." [GOC:dph, GOC:glycolysis, MetaCyc:PWY-1042, PMID:15012287]
-xref: MetaCyc:PWY-1042
-is_a: GO:0061704 ! glycolytic process from sucrose
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of sucrose into pyruvate through both glucose and fructose intermediates, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules." [GOC:dph, GOC:glycolysis, MetaCyc:PWY-1042, PMID:15012287]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
created_by: dph
creation_date: 2015-06-11T13:40:32Z
@@ -390717,13 +391044,14 @@
[Term]
id: GO:0061753
-name: substrate localization to autophagosome
+name: obsolete substrate localization to autophagosome
namespace: biological_process
-def: "The localization process by which an autophagic substrate is delivered to a forming autophagosome." [GOC:dph, GOC:pad, GOC:PARL, PMID:23545414]
+def: "OBSOLETE. The localization process by which an autophagic substrate is delivered to a forming autophagosome." [GOC:dph, GOC:pad, GOC:PARL, PMID:23545414]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term: localization terms that are not transport terms are largely uninformative about biological process. The intended biology in every observed use is better captured by a specific selective-autophagy term (e.g. mitophagy, glycophagy, reticulophagy). See the annotation review at https://github.com/geneontology/go-annotation/issues/6497 for per-annotation transfer recommendations.
synonym: "substrate sequestration to autophagosome" EXACT []
synonym: "substrate sequestration to phagophore" EXACT []
-is_a: GO:0051649 ! establishment of localization in cell
-relationship: part_of GO:0000045 ! autophagosome assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32304" xsd:anyURI
+is_obsolete: true
created_by: dph
creation_date: 2015-11-20T11:14:22Z
@@ -391218,13 +391546,13 @@
[Term]
id: GO:0061796
-name: membrane addition at site of mitotic cytokinesis
+name: obsolete membrane addition at site of mitotic cytokinesis
namespace: biological_process
-def: "A mitotic cell cycle process involved in the net addition of membrane at the site of cytokinesis; includes vesicle recruitment and fusion, local lipid synthesis and insertion." [GOC:dph, GOC:vw]
-is_a: GO:0007107 ! membrane addition at site of cytokinesis
-is_a: GO:1902410 ! mitotic cytokinetic process
-intersection_of: GO:0007107 ! membrane addition at site of cytokinesis
-intersection_of: part_of GO:0000278 ! mitotic cell cycle
+def: "OBSOLETE. A mitotic cell cycle process involved in the net addition of membrane at the site of cytokinesis; includes vesicle recruitment and fusion, local lipid synthesis and insertion." [GOC:dph, GOC:vw]
+comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31687" xsd:anyURI
+is_obsolete: true
+consider: GO:0006887
created_by: dph
creation_date: 2016-10-05T12:06:11Z
@@ -391393,14 +391721,14 @@
xref: Reactome:R-HSA-8938076 "CD38 hydrolyses NAD+ to NAM and ADP-ribose"
xref: Reactome:R-HSA-9637699 "CpnT hydrolyses NAD+"
xref: RHEA:38611
-xref: RHEA:38615
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
+relationship: has_part GO:0061812 ! cyclic ADP-ribose hydrolase activity
property_value: skos:broadMatch RHEA:16301
property_value: skos:exactMatch EC:3.2.2.6
property_value: skos:narrowMatch RHEA:38611
-property_value: skos:narrowMatch RHEA:38615
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26011" 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/32457" xsd:anyURI
created_by: dph
creation_date: 2016-11-11T13:14:13Z
@@ -391430,13 +391758,16 @@
[Term]
id: GO:0061812
-name: obsolete cyclic ADP-ribose hydrolase
+name: cyclic ADP-ribose hydrolase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: cyclic ADP-ribose + H20 = ADP-ribose (ADPR)." [GOC:dph, GOC:pad, GOC:PARL, PMID:11866528]
-comment: This term was obsoleted because it represents a step in a multi-step reaction.
+def: "Catalysis of the reaction: cyclic ADP-beta-D-ribose + H2O = ADP-D-ribose." [PMID:42243876, RHEA:38615]
+comment: Note that this term was reinstated from obsolete.
+synonym: "cADPR hydrolase activity" EXACT []
+xref: RHEA:38615
+is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
+property_value: skos:exactMatch RHEA:38615
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26011" xsd:anyURI
-is_obsolete: true
-replaced_by: GO:0061809
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32457" xsd:anyURI
created_by: dph
creation_date: 2016-11-11T13:32:43Z
@@ -391860,11 +392191,13 @@
id: GO:0061857
name: endoplasmic reticulum stress-induced pre-emptive quality control
namespace: biological_process
-def: "The response to endoplasimic reticulum stress in which nascent proteins are degraded by attenuation of their translocation into the ER followed by rerouting to the cytosol without cleavage of the signal peptide, and subsequent degradation by the proteasome." [PMID:17129784, PMID:26565908]
+def: "The response to endoplasmic reticulum stress in which nascent proteins are degraded by attenuation of their translocation into the ER followed by rerouting to the cytosol without cleavage of the signal peptide, and subsequent degradation by the proteasome." [PMID:17129784, PMID:26565908]
synonym: "ER pQC" EXACT []
-synonym: "ER stress-indiced pre-emptive quality control" EXACT []
+synonym: "ER stress-induced pre-emptive quality control" EXACT []
is_a: GO:0034976 ! response to endoplasmic reticulum stress
+is_a: GO:0170080 ! endoplasmic reticulum protein quality control
relationship: has_part GO:0043161 ! proteasome-mediated ubiquitin-dependent protein catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20914" xsd:anyURI
created_by: dph
creation_date: 2017-03-28T13:05:03Z
@@ -393085,7 +393418,7 @@
id: GO:0061983
name: meiosis II cell cycle process
namespace: biological_process
-def: "A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes." [PMID:29385397]
+def: "A process that contributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes." [PMID:29385397]
synonym: "second meiotic division" EXACT [PMID:29385397]
is_a: GO:1903046 ! meiotic cell cycle process
created_by: dph
@@ -393121,11 +393454,13 @@
[Term]
id: GO:0061987
-name: negative regulation of transcription from RNA polymerase II promoter by glucose
+name: obsolete negative regulation of transcription from RNA polymerase II promoter by glucose
namespace: biological_process
-def: "Any process involving glucose that decreases the frequency, rate or extent or transcription from an RNA polymerase II promoter." [PMID:11875061]
-is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose
-is_a: GO:0061986 ! negative regulation of transcription by glucose
+def: "OBSOLETE. Any process involving glucose that decreases the frequency, rate or extent or transcription from an RNA polymerase II promoter." [PMID:11875061]
+comment: The reason for obsoletion is that these terms represent GO-CAM models.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21442" xsd:anyURI
+is_obsolete: true
+consider: GO:0000122
created_by: dph
creation_date: 2018-02-15T17:48:00Z
@@ -393218,7 +393553,7 @@
id: GO:0062000
name: positive regulation of cardiac endothelial to mesenchymal transition
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cardiac endothelial to mesenchymal trnasition." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:26857067]
+def: "Any process that activates or increases the frequency, rate or extent of cardiac endothelial to mesenchymal transition." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:26857067]
is_a: GO:0045597 ! positive regulation of cell differentiation
is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:0061999 ! regulation of cardiac endothelial to mesenchymal transition
@@ -393385,7 +393720,7 @@
id: GO:0062025
name: regulation of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
namespace: biological_process
-def: "Any process that modualtes the rate, frequency or extent of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, 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, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome." [PMID:28007894]
+def: "Any process that modulates the rate, frequency or extent of SCF-dependent proteasomal ubiquitin-dependent protein catabolic process, 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, with ubiquitin-protein ligation catalyzed by an SCF (Skp1/Cul1/F-box protein) complex, and mediated by the proteasome." [PMID:28007894]
is_a: GO:0032434 ! regulation of proteasomal ubiquitin-dependent protein catabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0031146 ! SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
@@ -393935,7 +394270,7 @@
id: GO:0062077
name: phenylacetyl-CoA 1,2-epoxidase complex
namespace: cellular_component
-def: "A protein complex capable of catalysing the reaction: phenylacetyl-CoA + H+ + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP+." [GOC:bhm, PMID:21247899]
+def: "A protein complex capable of catalyzing the reaction: phenylacetyl-CoA + H+ + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP+." [GOC:bhm, PMID:21247899]
synonym: "paaABCE complex" NARROW []
is_a: GO:1990204 ! oxidoreductase complex
created_by: dph
@@ -393958,7 +394293,8 @@
namespace: cellular_component
def: "A protein complex essential for autophagy during nutrient deprivation, a catabolic process that sequesters undesired cellular material into autophagosomes for delivery to lysosomes for degradation. Contributes to nutrition homeostasis and damage control in eukaryotic cells. Functions at a late step of autophagosome formation for efficient completion of sequestration, probably through facilitating recruitment of ATG8-phosphatidylethanolamine (PE) to the preautophagosomal structure (PAS) and/or its protection from deconjugation by ATG4. Composed of ATG2 and ATG18 in Saccharomyces cerevisiae." [GOC:bhm, PMID:23230146]
is_a: GO:0098796 ! membrane protein complex
-relationship: part_of GO:0034045 ! phagophore assembly site membrane
+relationship: part_of GO:7770114 ! phagophore membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29437" xsd:anyURI
created_by: dph
creation_date: 2018-10-12T13:47:25Z
@@ -394849,7 +395185,7 @@
id: GO:0062160
name: spongiome
namespace: cellular_component
-def: "A cellular anatomical entity which is a network of tubules and vessicles and is part of the contractile vacuole complex. It is involved in the discharge of water externally. One of its functions is osmoregulatory." [PMID:23890380]
+def: "A cellular anatomical entity which is a network of tubules and vesicles and is part of the contractile vacuole complex. It is involved in the discharge of water externally. One of its functions is osmoregulatory." [PMID:23890380]
is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0062159 ! contractile vacuole complex
created_by: dph
@@ -395070,7 +395406,7 @@
id: GO:0062176
name: R-loop processing
namespace: biological_process
-def: "A DNA metabolic process that results in the disassembly of R-loops. R-loops are three-stranded nucleic acid structures consisitng of an RNA:DNA heteroduplex and a looped-out non-template strand. Aberrant formation and persistence of R-loops block transcription elongation and cause DNA damage. Mechanisms that resolve R-loops are essential for genome stability." [PMID:27252122, PMID:28790157, PMID:33986538]
+def: "A DNA metabolic process that results in the disassembly of R-loops. R-loops are three-stranded nucleic acid structures consisting of an RNA:DNA heteroduplex and a looped-out non-template strand. Aberrant formation and persistence of R-loops block transcription elongation and cause DNA damage. Mechanisms that resolve R-loops are essential for genome stability." [PMID:27252122, PMID:28790157, PMID:33986538]
synonym: "R-loop disassembly" EXACT []
is_a: GO:0006338 ! chromatin remodeling
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18012" xsd:anyURI
@@ -395112,7 +395448,7 @@
id: GO:0062181
name: 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity
namespace: molecular_function
-def: "Catatlysis of the reaction: calcitriol + 2 H+ + O2 + 2 reduced [adrenodoxin] = 1alpha,23S,25-trihydroxycholecalciferol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:49192]
+def: "Catalysis of the reaction: calcitriol + 2 H+ + O2 + 2 reduced [adrenodoxin] = 1alpha,23S,25-trihydroxycholecalciferol + H2O + 2 oxidized [adrenodoxin]." [PMID:22100522, PMID:30205156, RHEA:49192]
xref: RHEA:49192
is_a: GO:0062179 ! vitamin D 23-hydroxylase activity
property_value: skos:exactMatch RHEA:49192
@@ -395986,10 +396322,12 @@
name: intracellular organelle lumen
namespace: cellular_component
def: "An organelle lumen that is part of an intracellular organelle." [GOC:mah]
+subset: gocheck_do_not_annotate
is_a: GO:0043233 ! organelle lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: part_of GO:0043229 ! intracellular organelle
relationship: part_of GO:0043229 ! intracellular organelle
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
[Term]
id: GO:0070014
@@ -397261,173 +397599,173 @@
[Term]
id: GO:0070143
-name: mitochondrial alanyl-tRNA aminoacylation
+name: obsolete mitochondrial alanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling alanine to alanyl-tRNA in a mitochondrion, catalyzed by alanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006419 ! alanyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006419 ! alanyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling alanine to alanyl-tRNA in a mitochondrion, catalyzed by alanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004813 alanine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070144
-name: mitochondrial arginyl-tRNA aminoacylation
+name: obsolete mitochondrial arginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling arginine to arginyl-tRNA in a mitochondrion, catalyzed by arginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006420 ! arginyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006420 ! arginyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling arginine to arginyl-tRNA in a mitochondrion, catalyzed by arginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004814 arginine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070145
-name: mitochondrial asparaginyl-tRNA aminoacylation
+name: obsolete mitochondrial asparaginyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling asparagine to asparaginyl-tRNA in a mitochondrion, catalyzed by asparaginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006421 ! asparaginyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006421 ! asparaginyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling asparagine to asparaginyl-tRNA in a mitochondrion, catalyzed by asparaginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004816 asparagine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070146
-name: mitochondrial aspartyl-tRNA aminoacylation
+name: obsolete mitochondrial aspartyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling aspartate to aspartyl-tRNA in a mitochondrion, catalyzed by aspartyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006422 ! aspartyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006422 ! aspartyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling aspartate to aspartyl-tRNA in a mitochondrion, catalyzed by aspartyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004815 aspartate-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070147
-name: mitochondrial cysteinyl-tRNA aminoacylation
+name: obsolete mitochondrial cysteinyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling L-cysteine to cysteinyl-tRNA in a mitochondrion, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006423 ! cysteinyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006423 ! cysteinyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling L-cysteine to cysteinyl-tRNA in a mitochondrion, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004817 cysteine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070148
-name: mitochondrial glutaminyl-tRNA aminoacylation
+name: obsolete mitochondrial glutaminyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamine to glutaminyl-tRNA in a mitochondrion, catalyzed by glutaminyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006425 ! glutaminyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006425 ! glutaminyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling glutamine to glutaminyl-tRNA in a mitochondrion, catalyzed by glutaminyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function and adds nothing beyond it. Note that the counterpart is not a glutamine-tRNA ligase in most eukaryotes: mitochondria generally encode no mitochondrial GlnRS, and mt-tRNA(Gln) is charged indirectly by a non-discriminating mitochondrial GluRS followed by the GatCAB amidotransferase, which is GO:0050567 glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity. GO:0004819 glutamine-tRNA ligase activity applies only where a mitochondrial GlnRS is present. The biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070149
-name: mitochondrial glutamyl-tRNA aminoacylation
+name: obsolete mitochondrial glutamyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glutamate to glutamyl-tRNA in a mitochondrion, catalyzed by glutamyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006424 ! glutamyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006424 ! glutamyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling glutamate to glutamyl-tRNA in a mitochondrion, catalyzed by glutamyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004818 glutamate-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070150
-name: mitochondrial glycyl-tRNA aminoacylation
+name: obsolete mitochondrial glycyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling glycine to glycyl-tRNA in a mitochondrion, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006426 ! glycyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006426 ! glycyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling glycine to glycyl-tRNA in a mitochondrion, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004820 glycine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070151
-name: mitochondrial histidyl-tRNA aminoacylation
+name: obsolete mitochondrial histidyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling histidine to histidyl-tRNA in a mitochondrion, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006427 ! histidyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006427 ! histidyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling histidine to histidyl-tRNA in a mitochondrion, catalyzed by histidyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004821 histidine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070152
-name: mitochondrial isoleucyl-tRNA aminoacylation
+name: obsolete mitochondrial isoleucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling isoleucine to isoleucyl-tRNA in a mitochondrion, catalyzed by isoleucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006428 ! isoleucyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006428 ! isoleucyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling isoleucine to isoleucyl-tRNA in a mitochondrion, catalyzed by isoleucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004822 isoleucine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070153
-name: mitochondrial leucyl-tRNA aminoacylation
+name: obsolete mitochondrial leucyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling leucine to leucyl-tRNA in a mitochondrion, catalyzed by leucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006429 ! leucyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006429 ! leucyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling leucine to leucyl-tRNA in a mitochondrion, catalyzed by leucyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004823 leucine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070154
-name: mitochondrial lysyl-tRNA aminoacylation
+name: obsolete mitochondrial lysyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling lysine to lysyl-tRNA in a mitochondrion, catalyzed by lysyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006430 ! lysyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006430 ! lysyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling lysine to lysyl-tRNA in a mitochondrion, catalyzed by lysyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004824 lysine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070155
-name: mitochondrial methionyl-tRNA aminoacylation
+name: obsolete mitochondrial methionyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling methionine to methionyl-tRNA in a mitochondrion, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006431 ! methionyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006431 ! methionyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling methionine to methionyl-tRNA in a mitochondrion, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004825 methionine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070156
-name: mitochondrial phenylalanyl-tRNA aminoacylation
+name: obsolete mitochondrial phenylalanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling phenylalanine to phenylalanyl-tRNA in a mitochondrion, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006432 ! phenylalanyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006432 ! phenylalanyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling phenylalanine to phenylalanyl-tRNA in a mitochondrion, catalyzed by phenylalanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004826 phenylalanine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070157
-name: mitochondrial prolyl-tRNA aminoacylation
+name: obsolete mitochondrial prolyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling proline to prolyl-tRNA in a mitochondrion, catalyzed by prolyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006433 ! prolyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006433 ! prolyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling proline to prolyl-tRNA in a mitochondrion, catalyzed by prolyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004827 proline-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070158
-name: mitochondrial seryl-tRNA aminoacylation
+name: obsolete mitochondrial seryl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling serine to seryl-tRNA in a mitochondrion, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006434 ! seryl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006434 ! seryl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling serine to seryl-tRNA in a mitochondrion, catalyzed by seryl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004828 serine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070159
-name: mitochondrial threonyl-tRNA aminoacylation
+name: obsolete mitochondrial threonyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling threonine to threonyl-tRNA in a mitochondrion, catalyzed by threonyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006435 ! threonyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006435 ! threonyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling threonine to threonyl-tRNA in a mitochondrion, catalyzed by threonyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004829 threonine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070160
@@ -397672,33 +398010,33 @@
[Term]
id: GO:0070183
-name: mitochondrial tryptophanyl-tRNA aminoacylation
+name: obsolete mitochondrial tryptophanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling tryptophan to tryptophanyl-tRNA in a mitochondrion, catalyzed by tryptophanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006436 ! tryptophanyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006436 ! tryptophanyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling tryptophan to tryptophanyl-tRNA in a mitochondrion, catalyzed by tryptophanyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004830 tryptophan-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070184
-name: mitochondrial tyrosyl-tRNA aminoacylation
+name: obsolete mitochondrial tyrosyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling tyrosine to tyrosyl-tRNA in a mitochondrion, catalyzed by tyrosyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006437 ! tyrosyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006437 ! tyrosyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling tyrosine to tyrosyl-tRNA in a mitochondrion, catalyzed by tyrosyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004831 tyrosine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070185
-name: mitochondrial valyl-tRNA aminoacylation
+name: obsolete mitochondrial valyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling valine to valyl-tRNA in a mitochondrion, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
-is_a: GO:0006438 ! valyl-tRNA aminoacylation
-is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
-intersection_of: GO:0006438 ! valyl-tRNA aminoacylation
-intersection_of: occurs_in GO:0005739 ! mitochondrion
+def: "OBSOLETE. The process of coupling valine to valyl-tRNA in a mitochondrion, catalyzed by valyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004832 valine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0070127 tRNA aminoacylation for mitochondrial protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0070127
[Term]
id: GO:0070186
@@ -397978,23 +398316,30 @@
[Term]
id: GO:0070212
-name: protein poly-ADP-ribosylation
+name: obsolete protein poly-ADP-ribosylation
namespace: biological_process
-def: "The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain." [GOC:BHF, GOC:mah, GOC:rl, PMID:25043379]
+def: "OBSOLETE. The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain." [GOC:BHF, GOC:mah, GOC:rl, PMID:25043379]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "addition of poly-ADP-ribose to protein" EXACT [GOC:rl]
synonym: "poly(ADP-ribose) addition to protein" EXACT [GOC:rl]
synonym: "protein amino acid poly-ADP-ribosylation" EXACT [GOC:bf]
synonym: "protein poly(ADP-ribose) metabolism" RELATED [GOC:rl]
synonym: "protein poly(ADP-ribose) synthesis" EXACT [GOC:rl]
-is_a: GO:0043687 ! post-translational protein modification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
+is_obsolete: true
+consider: GO:0003950
[Term]
id: GO:0070213
-name: protein auto-ADP-ribosylation
+name: obsolete protein auto-ADP-ribosylation
namespace: biological_process
-def: "The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein." [GOC:BHF, GOC:rl]
+def: "OBSOLETE. The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein." [GOC:BHF, GOC:rl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "protein amino acid auto-ADP-ribosylation" EXACT [GOC:bf]
-is_a: GO:0043687 ! post-translational protein modification
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
+is_obsolete: true
+consider: GO:0003950
+consider: GO:1990404
[Term]
id: GO:0070214
@@ -399284,7 +399629,7 @@
name: inward rectifier potassium channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of an inwardly rectifying potassium channel." [GOC:mah]
-is_a: GO:0019870 ! potassium channel inhibitor activity
+is_a: GO:7770090 ! voltage-gated potassium channel inhibitor activity
relationship: negatively_regulates GO:0005242 ! inward rectifier potassium channel activity
[Term]
@@ -403376,11 +403721,14 @@
[Term]
id: GO:0070681
-name: glutaminyl-tRNAGln biosynthesis via transamidation
+name: obsolete glutaminyl-tRNAGln biosynthesis via transamidation
namespace: biological_process
-def: "A tRNA aminoacylation process in which glutaminyl-tRNAGln is formed by a tRNA-dependent two-step pathway. In the first step a non-discriminating glutamyl-tRNAGlx synthetase generates the misacylated L-glutamyl-tRNAGln species, and in the second step it is amidated to the correctly charged L-glutaminyl-tRNAGln by a glutamyl-tRNAGln amidotransferase." [GOC:mah, MetaCyc:PWY-5921]
-xref: MetaCyc:PWY-5921
-is_a: GO:0043039 ! tRNA aminoacylation
+def: "OBSOLETE. A tRNA aminoacylation process in which glutaminyl-tRNAGln is formed by a tRNA-dependent two-step pathway. In the first step a non-discriminating glutamyl-tRNAGlx synthetase generates the misacylated L-glutamyl-tRNAGln species, and in the second step it is amidated to the correctly charged L-glutaminyl-tRNAGln by a glutamyl-tRNAGln amidotransferase." [GOC:mah, MetaCyc:PWY-5921]
+comment: The reason for obsoletion is that this term represents a specific pathway variant, which is out of scope for GO, following the obsoletion of its structural twin GO:0070680 asparaginyl-tRNAAsn biosynthesis via transamidation. No replaced_by is given because no single term is a safe automatic substitution: the amidotransferase step is GO:0050567 glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity, while GatCAB subunits act on an already-charged tRNA and may belong under GO:0019988 charged-tRNA amino acid modification rather than under tRNA charging at all. Annotations require review rather than migration.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+consider: GO:0043039
+consider: GO:0050567
created_by: mah
creation_date: 2009-06-02T03:15:57Z
@@ -414502,10 +414850,10 @@
synonym: "nucleus-associated proteasomal ubiquitin-dependent protein catabolism" EXACT [GOC:mah]
synonym: "nucleus-associated proteasomal ubiquitin-dependent protein degradation" EXACT [GOC:mah]
synonym: "ubiquitin-dependent catabolism of misfolded proteins by nucleus-associated proteasome" EXACT []
-is_a: GO:0006515 ! protein quality control for misfolded or incompletely synthesized proteins
+is_a: GO:0006515 ! protein quality control
is_a: GO:0043161 ! proteasome-mediated ubiquitin-dependent protein catabolic process
-relationship: part_of GO:0071218 ! cellular response to misfolded protein
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26433" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32546" xsd:anyURI
created_by: mah
creation_date: 2010-02-11T03:31:46Z
@@ -424177,7 +424525,7 @@
synonym: "purine-containing compound breakdown" EXACT [GOC:mah]
synonym: "purine-containing compound catabolism" EXACT [GOC:mah]
synonym: "purine-containing compound degradation" EXACT [GOC:mah]
-is_a: GO:0009056 ! catabolic process
+is_a: GO:0034656 ! nucleobase-containing small molecule catabolic process
is_a: GO:0072521 ! purine-containing compound metabolic process
created_by: mah
creation_date: 2011-01-04T03:17:20Z
@@ -438839,7 +439187,8 @@
def: "A process that is carried out at the cellular level which results in the arrangement of constituent parts of a phagosome within a cell. Phagosome maturation begins with endocytosis and formation of the early phagosome and ends with the formation of the hybrid organelle, the phagolysosome." [GOC:kmv, GOC:tb]
is_a: GO:0006996 ! organelle organization
relationship: has_part GO:0001845 ! phagolysosome assembly
-relationship: has_part GO:0006887 ! exocytosis
+relationship: part_of GO:0006909 ! phagocytosis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32152" xsd:anyURI
created_by: tb
creation_date: 2010-10-19T11:10:34Z
@@ -439031,7 +439380,7 @@
id: GO:0090399
name: replicative senescence
namespace: biological_process
-def: "The process by which normal somatic cells reach an irreversible stage of cell cycle arrest following multiple rounds of replication; this end stage is associated with marked changes in gene expression and function. This is a natural barrier to unlimited proliferation of somatic cells, and is believed to be contolled by telomere shortening." [PMID:17014937, PMID:23061726]
+def: "The process by which normal somatic cells reach an irreversible stage of cell cycle arrest following multiple rounds of replication; this end stage is associated with marked changes in gene expression and function. This is a natural barrier to unlimited proliferation of somatic cells, and is believed to be controlled by telomere shortening." [PMID:17014937, PMID:23061726]
is_a: GO:0022402 ! cell cycle process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22788" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29342" xsd:anyURI
@@ -439115,8 +439464,10 @@
name: organophosphate biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the biosynthesis of deoxyribose phosphate, the phosphorylated sugar 2-deoxy-erythro-pentose." [GOC:chem_mtg]
+subset: gocheck_do_not_annotate
is_a: GO:0009058 ! biosynthetic process
is_a: GO:0019637 ! organophosphate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32294" xsd:anyURI
created_by: tb
creation_date: 2011-02-26T02:22:41Z
@@ -440700,7 +441051,8 @@
def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein S-phosphocysteine + sugar(out) = protein cysteine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:am]
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
+is_a: GO:7770111 ! group translocator activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27496" xsd:anyURI
created_by: tb
creation_date: 2014-04-08T14:58:00Z
@@ -441413,8 +441765,10 @@
name: microglial cell mediated cytotoxicity
namespace: biological_process
def: "The directed killing of a target cell by a microglial cell." [GOC:BHF, GOC:nc, PMID:19100238]
+comment: The is_a link to GO:0002444 is asserted rather than inferred because GO:0002444 has no logical definition; it must be maintained by hand (see #20574).
is_a: GO:0001909 ! leukocyte mediated cytotoxicity
is_a: GO:0002444 ! myeloid leukocyte mediated immunity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
created_by: tb
creation_date: 2015-04-14T14:04:54Z
@@ -442495,11 +442849,13 @@
[Term]
id: GO:0093001
-name: glycolysis from storage polysaccharide through glucose-1-phosphate
+name: obsolete glycolysis from storage polysaccharide through glucose-1-phosphate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a storage polysaccharide into pyruvate through a glucose-1-phosphate intermediate, with the concomitant production of a small amount of ATP and the reduction of NAD to NADH." [GOC:dph, GOC:glycolysis]
-is_a: GO:0000272 ! polysaccharide catabolic process
-is_a: GO:0061622 ! glycolytic process through glucose-1-phosphate
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a storage polysaccharide into pyruvate through a glucose-1-phosphate intermediate, with the concomitant production of a small amount of ATP and the reduction of NAD to NADH." [GOC:dph, GOC:glycolysis]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006096
[Term]
id: GO:0093002
@@ -447625,8 +447981,7 @@
synonym: "gpERAD" EXACT [PMID:25092655]
synonym: "misfolded or incompletely synthesized glycoprotein catabolic process" BROAD []
is_a: GO:0006516 ! glycoprotein catabolic process
-is_a: GO:0036503 ! ERAD pathway
-is_a: GO:1904587 ! response to glycoprotein
+is_a: GO:0036503 ! ERAD quality control pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23092" xsd:anyURI
created_by: pr
creation_date: 2013-02-05T16:37:13Z
@@ -449391,19 +449746,21 @@
[Term]
id: GO:0097620
-name: (R)-mandelate dehydrogenase activity
+name: (R)-mandelate dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: (R)-mandelate + NAD+ = phenylglyoxylate + NADH + H+." [PMID:1731758, RHEA:43112]
comment: In the yeast Rhodotorula graminis, (R)-mandelate dehydrogenase is the first enzyme of the mandelate pathway, and catalyzes the NAD-dependent oxidation of (R)-mandelate to phenylglyoxylate.
-synonym: "D-mandelate dehydrogenase activity" EXACT []
+synonym: "(R)-mandelate dehydrogenase activity" BROAD []
+synonym: "D-mandelate dehydrogenase activity" BROAD []
xref: EC:1.1.1.379
xref: MetaCyc:RXN-15840
xref: RHEA:43112
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+is_a: GO:0140175 ! (2R)-2-hydroxyacid dehydrogenase (NAD+) activity
property_value: skos:exactMatch EC:1.1.1.379
property_value: skos:exactMatch MetaCyc:RXN-15840
property_value: skos:exactMatch RHEA:43112
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30910" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32501" xsd:anyURI
created_by: pr
creation_date: 2014-07-30T09:53:23Z
@@ -449538,16 +449895,18 @@
[Term]
id: GO:0097632
-name: extrinsic component of phagophore assembly site membrane
+name: extrinsic component of phagophore membrane
namespace: cellular_component
-def: "The component of the phagophore assembly site membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:mf]
-synonym: "extrinsic component of pre-autophagosomal structure membrane" NARROW []
-synonym: "extrinsic to phagophore assembly site membrane" EXACT []
+def: "The component of a phagophore membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:mf]
+synonym: "extrinsic component of phagophore assembly site membrane" RELATED []
+synonym: "extrinsic component of pre-autophagosomal structure membrane" RELATED []
+synonym: "extrinsic to phagophore assembly site membrane" RELATED []
synonym: "phagophore assembly site peripheral membrane" RELATED []
-is_a: GO:0031312 ! extrinsic component of organelle membrane
+is_a: GO:0019898 ! extrinsic component of membrane
intersection_of: GO:0019898 ! extrinsic component of membrane
-intersection_of: part_of GO:0034045 ! phagophore assembly site membrane
-relationship: part_of GO:0034045 ! phagophore assembly site membrane
+intersection_of: part_of GO:7770114 ! phagophore membrane
+relationship: part_of GO:7770114 ! phagophore membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29437" xsd:anyURI
[Term]
id: GO:0097633
@@ -449558,7 +449917,7 @@
synonym: "intrinsic to phagophore assembly site membrane" NARROW []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23424" xsd:anyURI
is_obsolete: true
-replaced_by: GO:0034045
+replaced_by: GO:7770114
[Term]
id: GO:0097634
@@ -449570,7 +449929,7 @@
synonym: "phagophore assembly site integral membrane protein" RELATED []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23424" xsd:anyURI
is_obsolete: true
-replaced_by: GO:0034045
+replaced_by: GO:7770114
[Term]
id: GO:0097635
@@ -452278,7 +452637,6 @@
xref: Reactome:R-HSA-5690046 "PPT2 hydrolyses PALMCoA to PALM"
xref: Reactome:R-HSA-9027670 "ESTG binding induces ESR depalmitoylation"
is_a: GO:0016787 ! hydrolase activity
-relationship: part_of GO:0098734 ! macromolecule depalmitoylation
created_by: dos
creation_date: 2014-04-11T17:57:36Z
@@ -453125,7 +453483,7 @@
id: GO:0098683
name: cochlear hair cell ribbon synapse
namespace: cellular_component
-def: "A ribbon synpase of an auditory hair cell of the cochlear. These ribbon synapses contain spherical synaptic ribbons and lack and arciform density." [PMID:15626493]
+def: "A ribbon synapse of an auditory hair cell of the cochlear. These ribbon synapses contain spherical synaptic ribbons and lack arciform density." [PMID:15626493]
subset: goslim_synapse
is_a: GO:0097470 ! ribbon synapse
created_by: dos
@@ -453703,10 +454061,14 @@
[Term]
id: GO:0098734
-name: macromolecule depalmitoylation
+name: obsolete macromolecule depalmitoylation
namespace: biological_process
-def: "The removal of palymitoyl groups from a macromolecule." [GOC:dos]
-is_a: GO:0098732 ! macromolecule deacylation
+def: "OBSOLETE. The removal of palymitoyl groups from a macromolecule." [GOC:dos]
+comment: The reason for obsoletion is that this term represents a molecular function, not a biological process. Consider instead annotating to the molecular function 'palmitoyl hydrolase activity' (GO:0098599), or, for protein substrates, 'palmitoyl-(protein) hydrolase activity' (GO:0008474).
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32290" xsd:anyURI
+is_obsolete: true
+consider: GO:0008474
+consider: GO:0098599
[Term]
id: GO:0098735
@@ -453857,9 +454219,9 @@
[Term]
id: GO:0098755
-name: maintenance of seed dormancy by absisic acid
+name: maintenance of seed dormancy by abscisic acid
namespace: biological_process
-def: "The process by which seed dormancy is maintained by the presence of absisic acid." [GOC:dos, PMID:9580097]
+def: "The process by which seed dormancy is maintained by the presence of abscisic acid." [GOC:dos, PMID:9580097]
is_a: GO:0010231 ! maintenance of seed dormancy
intersection_of: GO:0010231 ! maintenance of seed dormancy
intersection_of: part_of GO:0009737 ! response to abscisic acid
@@ -454092,7 +454454,7 @@
[Term]
id: GO:0098780
-name: response to mitochondrial depolarisation
+name: response to mitochondrial depolarization
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.) in response to the depolarization of one or more mitochondria." [GOC:dos]
xref: Reactome:R-HSA-9840373 "Cellular response to mitochondrial stress"
@@ -454684,7 +455046,7 @@
id: GO:0098842
name: postsynaptic early endosome
namespace: cellular_component
-def: "An early endosome of the postsynapse. It acts as the major sorting station on the endocytic pathway, targeting neurotransmitter receptors for degregation or recycling." [PMID:19603039, PMID:20820847, PMID:24727350]
+def: "An early endosome of the postsynapse. It acts as the major sorting station on the endocytic pathway, targeting neurotransmitter receptors for degradation or recycling." [PMID:19603039, PMID:20820847, PMID:24727350]
comment: Commonly used markers for postsynaptic early endosomes include RAB5A and EEA1.
subset: goslim_synapse
is_a: GO:0005769 ! early endosome
@@ -455534,6 +455896,7 @@
subset: goslim_synapse
is_a: GO:0098920 ! retrograde trans-synaptic signaling by lipid
is_a: GO:0099542 ! trans-synaptic signaling by endocannabinoid
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0098922
@@ -455744,7 +456107,7 @@
id: GO:0098943
name: neurotransmitter receptor transport, postsynaptic endosome to lysosome
namespace: biological_process
-def: "The directed movement of neurotransmitter receptor from the postsynaptic endosome in tranpsort vesicles to the lysosome for degradation." [GOC:dos]
+def: "The directed movement of neurotransmitter receptor from the postsynaptic endosome in transport vesicles to the lysosome for degradation." [GOC:dos]
subset: goslim_synapse
synonym: "postsynaptic neurotransmitter receptor endosomal trafficking" BROAD []
is_a: GO:0006886 ! intracellular protein transport
@@ -455852,7 +456215,7 @@
id: GO:0098953
name: receptor diffusion trapping
namespace: biological_process
-def: "The process by which a membrane receptor, diffusing freely within the plasma membeane, becomes trapped in some plasma membrane region. This can happen when a receptor bind, directly or indirectly, to some component of the underlying matrix." [PMID:18832033]
+def: "The process by which a membrane receptor, diffusing freely within the plasma membrane, becomes trapped in some plasma membrane region. This can happen when a receptor bind, directly or indirectly, to some component of the underlying matrix." [PMID:18832033]
is_a: GO:0051668 ! localization within membrane
relationship: occurs_in GO:0005886 ! plasma membrane
@@ -456803,7 +457166,7 @@
id: GO:0099049
name: clathrin coat assembly involved in endocytosis
namespace: biological_process
-def: "The process that results in the assembly of clathrin triskelia into a clathrin cage during endocytosis. Clathrin is recruited to the plasma membrane via interaction with scaffolding proteins that bridge between clathtin and cell surface receptors. Clathrin coat formation is concomittant with coated pit formation leading to endocytic vesicle formation." [PMID:21779028]
+def: "The process that results in the assembly of clathrin triskelia into a clathrin cage during endocytosis. Clathrin is recruited to the plasma membrane via interaction with scaffolding proteins that bridge between clathrin and cell surface receptors. Clathrin coat formation is concomitant with coated pit formation leading to endocytic vesicle formation." [PMID:21779028]
is_a: GO:0048268 ! clathrin coat assembly
relationship: part_of GO:0072583 ! clathrin-dependent endocytosis
@@ -458788,6 +459151,7 @@
def: "Cell-cell signaling in either direction across the synaptic cleft, mediated by an endocannabinoid ligand." [GOC:dos]
subset: goslim_synapse
is_a: GO:0099541 ! trans-synaptic signaling by lipid
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0099543
@@ -458898,6 +459262,7 @@
subset: goslim_synapse
is_a: GO:0099542 ! trans-synaptic signaling by endocannabinoid
is_a: GO:0099552 ! trans-synaptic signaling by lipid, modulating synaptic transmission
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20574" xsd:anyURI
[Term]
id: GO:0099554
@@ -460883,7 +461248,7 @@
[Term]
id: GO:0102013
-name: ATPase-coupled L-glutamate tranmembrane transporter activity
+name: ATPase-coupled L-glutamate transmembrane transporter 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: L-glutamate(out) + ATP + H2O = L-glutamate(in) + ADP + phosphate + H+." [RHEA:29035]
synonym: "L-glutamate-importing ATPase activity" RELATED []
@@ -460991,7 +461356,10 @@
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-hydroxylase activity" RELATED []
xref: EC:1.14.14.80
+xref: KEGG_REACTION:R07041
xref: MetaCyc:RXN-16394
+xref: MetaCyc:RXN-19677
+xref: RHEA:39755
xref: RHEA:40199
xref: RHEA:40203
xref: RHEA:41728
@@ -461003,6 +461371,9 @@
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 KEGG_REACTION:R07041
+property_value: skos:narrowMatch MetaCyc:RXN-19677
+property_value: skos:narrowMatch RHEA:39755
property_value: skos:narrowMatch RHEA:40199
property_value: skos:narrowMatch RHEA:40203
property_value: skos:narrowMatch RHEA:41728
@@ -461013,6 +461384,7 @@
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32503" xsd:anyURI
[Term]
id: GO:0102035
@@ -461066,10 +461438,11 @@
xref: MetaCyc:R4-RXN
xref: Reactome:R-HSA-1222526 "AhpC reduces peroxidated lipids"
xref: RHEA:62628
-is_a: GO:0051920 ! peroxiredoxin activity
+is_a: GO:0004601 ! peroxidase activity
property_value: skos:exactMatch EC:1.11.1.26
property_value: skos:exactMatch RHEA:62628
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/32372" xsd:anyURI
[Term]
id: GO:0102040
@@ -462097,7 +462470,7 @@
[Term]
id: GO:0102146
-name: tricetin O-methytransferase activity
+name: tricetin O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: tricetin + S-adenosyl-L-methionine = H+ + 3'-O-methyltricetin + S-adenosyl-L-homocysteine." [GOC:pz, RHEA:27493]
xref: MetaCyc:RXN-11582
@@ -466211,7 +466584,7 @@
id: GO:0102545
name: B-type glycerophospholipase activity
namespace: molecular_function
-def: "A glycerophospholipase activity that cleaves both fatty acisd attached to the sn-1 and the sn-2 position of the glycerol group of a glycerophospholipid. Substrates include phosphatidylcholine and phosphatidylethanolamine." [PMID:30109646]
+def: "A glycerophospholipase activity that cleaves both fatty acids attached to the sn-1 and the sn-2 position of the glycerol group of a glycerophospholipid. Substrates include phosphatidylcholine and phosphatidylethanolamine." [PMID:30109646]
synonym: "B-type phospholipase activity" EXACT []
synonym: "phosphatidyl phospholipase B activity" EXACT []
synonym: "phospholipase B activity" EXACT []
@@ -470428,7 +470801,6 @@
xref: RHEA:25367
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.295
-property_value: skos:exactMatch RHEA:25363
property_value: skos:narrowMatch RHEA:25363
property_value: skos:narrowMatch RHEA:25367
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19648" xsd:anyURI
@@ -472560,7 +472932,7 @@
id: GO:0106055
name: mannosyl-oligosaccharide 1,2-alpha-mannosidase complex
namespace: cellular_component
-def: "A protein complex capable of catalysing the hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in an oligo-mannose oligosaccharide." [GOC:bhm, PMID:21700223]
+def: "A protein complex capable of catalyzing the hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in an oligo-mannose oligosaccharide." [GOC:bhm, PMID:21700223]
comment: An example is MNL1 (P38888) in Saccharomyces cerevisiae. PMID:19124653 (by physical interaction evidence).
is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
is_a: GO:1902494 ! catalytic complex
@@ -472988,7 +473360,7 @@
id: GO:0106098
name: NAGS/NAGK complex
namespace: cellular_component
-def: "A protein complex that acts both as N-acetylglutamate synthase (NAGS) catalysing the production of N-Acetylglutamate from glutamate and acetyl-CoA, and as N-acetylglutamate kinase (NAGK) catalysing the reaction ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate." [GOC:lnp, PMID:11553611]
+def: "A protein complex that acts both as N-acetylglutamate synthase (NAGS) catalyzing the production of N-Acetylglutamate from glutamate and acetyl-CoA, and as N-acetylglutamate kinase (NAGK) catalyzing the reaction ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamyl 5-phosphate." [GOC:lnp, PMID:11553611]
is_a: GO:0031248 ! protein acetyltransferase complex
is_a: GO:0061695 ! transferase complex, transferring phosphorus-containing groups
is_a: GO:0098798 ! mitochondrial protein-containing complex
@@ -473818,11 +474190,13 @@
[Term]
id: GO:0106175
-name: phagolysosome vesicle membrane
+name: obsolete phagolysosome vesicle membrane
namespace: cellular_component
-def: "The lipid bylayer surrounding a phagolysosome." [GOC:pde, PMID:29471269]
-is_a: GO:0030659 ! cytoplasmic vesicle membrane
-relationship: part_of GO:0032010 ! phagolysosome
+def: "OBSOLETE. The lipid bilayer surrounding a phagolysosome." [GOC:pde, PMID:29471269]
+comment: This term was obsoleted because it was created by error. It is identical to phagolysosome membrane ; GO:0061474.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32571" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061474
created_by: hjd
creation_date: 2019-02-11T19:12:53Z
@@ -474178,7 +474552,7 @@
id: GO:0106215
name: negative regulation of vesicle fusion with Golgi apparatus
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus." [GOC:se, PMID:26195667]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fusion with Golgi apparatus." [GOC:se, PMID:26195667]
is_a: GO:0031339 ! negative regulation of vesicle fusion
is_a: GO:0106214 ! regulation of vesicle fusion with Golgi apparatus
intersection_of: GO:0065007 ! biological regulation
@@ -474907,7 +475281,7 @@
id: GO:0106273
name: cytosol to ERGIC protein transport
namespace: biological_process
-def: "The directed movement of proteins from the cystosol to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC)." [PMID:32272059]
+def: "The directed movement of proteins from the cytosol to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC)." [PMID:32272059]
is_a: GO:0015031 ! protein transport
created_by: hjd
creation_date: 2020-07-01T17:28:07Z
@@ -474932,12 +475306,15 @@
xref: EC:2.4.2.31
xref: MetaCyc:2.4.2.31-RXN
xref: Reactome:R-HSA-1972385 "ADP-Ribosylation of HNP-1"
+xref: RHEA:18077
xref: RHEA:19149
is_a: GO:1990404 ! NAD+-protein mono-ADP-ribosyltransferase activity
property_value: skos:exactMatch EC:2.4.2.31
property_value: skos:exactMatch RHEA:19149
+property_value: skos:narrowMatch RHEA:18077
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22874" 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/32503" xsd:anyURI
created_by: hjd
creation_date: 2020-07-02T01:37:02Z
@@ -475549,7 +475926,7 @@
[Term]
id: GO:0106329
-name: L-phenylalaine oxidase activity
+name: L-phenylalanine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + L-phenylalanine + O2 = 3-phenylpyruvate + H2O2 + NH4+." [RHEA:61240]
xref: RHEA:61240
@@ -475811,6 +476188,7 @@
synonym: "U2 snRNA adenosine m6 methyltransferase activity" EXACT []
synonym: "U2 snRNA adenosine N6 methyltransferase activity" EXACT []
is_a: GO:0106346 ! snRNA methyltransferase activity
+is_a: GO:7770107 ! RNA (adenine-N6)-methyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27392" xsd:anyURI
created_by: hjd
creation_date: 2020-12-18T15:12:57Z
@@ -476408,7 +476786,7 @@
id: GO:0106391
name: bI4 intron splicing complex
namespace: cellular_component
-def: "A protein complex required for the splicing of intron 4 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI4 (which derives from one of the products of the splicing), Leucyl-tRNA synthetase NAM2 and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autoctalyse a group I intron splicing." [GOC:lnp, PMID:19622748]
+def: "A protein complex required for the splicing of intron 4 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI4 (which derives from one of the products of the splicing), Leucyl-tRNA synthetase NAM2 and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autocatalyze a group I intron splicing." [GOC:lnp, PMID:19622748]
xref: Intact:EBI-16420264
is_a: GO:1902555 ! endoribonuclease complex
created_by: hjd
@@ -476418,7 +476796,7 @@
id: GO:0106392
name: bI3 intron splicing complex
namespace: cellular_component
-def: "Aprotein complex required for the splicing of intron 3 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI3 (which derives from one of the products of the splicing), the MRS1 cofactor and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autoctalyse a group I intron splicing." [GOC:lnp, PMID:11773622]
+def: "A protein complex required for the splicing of intron 3 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI3 (which derives from one of the products of the splicing), the MRS1 cofactor and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autocatalyze a group I intron splicing." [GOC:lnp, PMID:11773622]
xref: Intact:EBI-16426213
is_a: GO:1902555 ! endoribonuclease complex
created_by: hjd
@@ -478787,7 +479165,7 @@
id: GO:0110155
name: NAD-cap decapping
namespace: biological_process
-def: "Cleavage of the 5'-NAD-cap of an RNA. The NAD-cap is present at the 5'-end of some RNAs in both bacetria and eukaryotes. While it promotes RNA stability in bacteria, it promotes RNA decay in eukaryotes." [GOC:sp, PMID:25533955, PMID:28283058, PMID:31101919]
+def: "Cleavage of the 5'-NAD-cap of an RNA. The NAD-cap is present at the 5'-end of some RNAs in both bacteria and eukaryotes. While it promotes RNA stability in bacteria, it promotes RNA decay in eukaryotes." [GOC:sp, PMID:25533955, PMID:28283058, PMID:31101919]
is_a: GO:0110154 ! RNA decapping
created_by: kmv
creation_date: 2019-07-08T17:27:56Z
@@ -479500,6 +479878,7 @@
xref: MetaCyc:RXN-18779
xref: RHEA:52808
is_a: GO:0106346 ! snRNA methyltransferase activity
+is_a: GO:7770107 ! RNA (adenine-N6)-methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.346
property_value: skos:exactMatch RHEA:52808
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13569" xsd:anyURI
@@ -481781,7 +482160,7 @@
id: GO:0120231
name: DNA recombinase auxiliary factor complex
namespace: cellular_component
-def: "A protein complex that binds to a recombinase and incrseases its activity." [PMID:32414915]
+def: "A protein complex that binds to a recombinase and increases its activity." [PMID:32414915]
synonym: "DNA recombinase accessory factor complex" EXACT [PMID:32414915]
synonym: "DNA recombinase activator complex" EXACT [PMID:32414915]
is_a: GO:0150005 ! enzyme activator complex
@@ -483526,7 +483905,7 @@
id: GO:0120513
name: 2-(3-amino-3-carboxypropyl)histidine synthase complex
namespace: cellular_component
-def: "A protein complex capable of catalysing the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the histidine residue of translation elongation factor 2 (EF2), which is the first step in the biosynthesis of diphthamide. The complex is a Dph2 homodimer in archaea and a Dph1-Dph2 heterodimer in eukaryotes." [GOC:sjm, PMID:24422557, PMID:31463593]
+def: "A protein complex capable of catalyzing the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-L-methionine (SAM) to the histidine residue of translation elongation factor 2 (EF2), which is the first step in the biosynthesis of diphthamide. The complex is a Dph2 homodimer in archaea and a Dph1-Dph2 heterodimer in eukaryotes." [GOC:sjm, PMID:24422557, PMID:31463593]
synonym: "Dph1-Dph2 complex" EXACT []
is_a: GO:1990234 ! transferase complex
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27957" xsd:anyURI
@@ -484207,7 +484586,7 @@
id: GO:0120547
name: heme A synthase activity
namespace: molecular_function
-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]
+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 occurs 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"
@@ -484559,7 +484938,10 @@
def: "Catalysis of the reaction: N6-[(R)-dihydrolipoyl]-L-lysyl-[protein] + glutaryl-CoA = CoA + N6-[(R)-S8-glutaryldihydrolipoyl]-L-lysyl-[protein]." [PMID:29191460, RHEA:86675]
xref: RHEA:86675
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+property_value: skos:broadMatch RHEA:30795
+property_value: skos:exactMatch RHEA:86675
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31280" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32557" xsd:anyURI
created_by: sjm
creation_date: 2026-01-07T15:48:37Z
@@ -484616,7 +484998,7 @@
[Term]
id: GO:0120574
-name: GPI anchor remodelling
+name: GPI anchor remodeling
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
@@ -484671,6 +485053,18 @@
creation_date: 2026-05-07T08:02:58Z
[Term]
+id: GO:0120578
+name: 2-oxoadipate decarboxylation to glutaryl-CoA
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of glutaryl-CoA from 2-oxoadipate. In most organisms, this pathway is part of L-lysine, L-hydroxylysine and L-tryptophan degradation and comprises a series of three reactions carried out by a multisubunit complex called the '2-oxoadipate dehydrogenase complex', even though 2-oxoadipate dehydrogenase activity describes only one of those reactions. The combination of the three reactions can be summarized as: 2-oxoadipate + coenzyme A + NAD+ -> glutaryl-CoA + CO2 + NADH." [PMID:29191460]
+is_a: GO:0043648 ! dicarboxylic acid metabolic process
+is_a: GO:0071616 ! acyl-CoA biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32557" xsd:anyURI
+created_by: sjm
+creation_date: 2026-09-03T06:52:01Z
+
+[Term]
id: GO:0140001
name: morula formation
namespace: biological_process
@@ -485506,7 +485900,7 @@
id: GO:0140073
name: bioadhesive activity
namespace: molecular_function
-def: "A structural molecule ativity that mediates an organism's attachment to an environmental substrate via stable, non-selective binding by a protein to an external surface. Examples includes proteins used by insects to anchor pupae to surfaces." [PMID:39370426]
+def: "A structural molecule activity that mediates an organism's attachment to an environmental substrate via stable, non-selective binding by a protein to an external surface. Examples includes proteins used by insects to anchor pupae to surfaces." [PMID:39370426]
is_a: GO:0005198 ! structural molecule activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29499" xsd:anyURI
created_by: pg
@@ -486005,7 +486399,7 @@
id: GO:0140112
name: extracellular vesicle biogenesis
namespace: biological_process
-def: "The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content." [PMID:28736435]
+def: "The assembly and secretion of a set of components to form an extracellular vesicle, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content." [PMID:28736435]
synonym: "extracellular vesicle assembly" EXACT []
is_a: GO:0044085 ! cellular component biogenesis
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI
@@ -486016,7 +486410,7 @@
id: GO:0140113
name: extracellular microvesicle biogenesis
namespace: biological_process
-def: "The assembly and secretion of a set of components to form an extracellular microvesicule, a membrane-bounded vesicle that ranges in size 100 nm to 1 micron in size) and exits the cell by budding." [PMID:28736435]
+def: "The assembly and secretion of a set of components to form an extracellular microvesicle, a membrane-bounded vesicle that ranges from 100 nm to 1 micron in size and exits the cell by budding." [PMID:28736435]
synonym: "extracellular microvesicle assembly" RELATED []
is_a: GO:0140112 ! extracellular vesicle biogenesis
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14256" xsd:anyURI
@@ -486580,7 +486974,7 @@
id: GO:0140162
name: venom-mediated vasodilation by activation of bradykinin receptor signaling pathway
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that activates bradykinin-dependent signaling, concomittantly reducing blood pressure in the bitten/stung organism. This can take place via several mechanisms that affect endogenous bradykinin: either increasing its release by kallikrein-like proteases, increasing bradykinin action by potentiation, or inhibiting bradykinin degradation." [PMID:31370142]
+def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that activates bradykinin-dependent signaling, concomitantly reducing blood pressure in the bitten/stung organism. This can take place via several mechanisms that affect endogenous bradykinin: either increasing its release by kallikrein-like proteases, increasing bradykinin action by potentiation, or inhibiting bradykinin degradation." [PMID:31370142]
synonym: "venom-mediated vasodilation by activation of bradykinin-dependent signaling" EXACT []
synonym: "venom-mediated vasodilation through activity of bradykinin" EXACT []
is_a: GO:0044513 ! venom-mediated perturbation of G protein-coupled receptor signaling pathway
@@ -486617,7 +487011,7 @@
id: GO:0140165
name: venom-mediated vasodilation by activation of nitric oxide-cGMP-mediated signaling
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that activates nitric oxide-cGMP-mediated signaling, concomittantly reducing blood pressure in the bitten/stung organism." [PMID:10512636]
+def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that activates nitric oxide-cGMP-mediated signaling, concomitantly reducing blood pressure in the bitten/stung organism." [PMID:10512636]
synonym: "venom-mediated vasodilation induced by nitric oxide activity" EXACT []
is_a: GO:0044509 ! venom-mediated perturbation of signal transduction
is_a: GO:0044551 ! venom-mediated vasodilation
@@ -486629,7 +487023,7 @@
id: GO:0140166
name: venom-mediated vasodilation via suppression of angiotensin maturation
namespace: biological_process
-def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that prevents angiotensin maturation, concomittantly reducing blood pressure in the bitten/stung organism." [PMID:31370142]
+def: "A process in which an organism initiates, promotes, or enhances vasodilation via the action of a venom that prevents angiotensin maturation, concomitantly reducing blood pressure in the bitten/stung organism." [PMID:31370142]
synonym: "venom-mediated vasodilation mediated by inhibition of angiotensin-converting enzyme" EXACT []
synonym: "venom-mediated vasodilation through perturbation of angiotensin maturation" EXACT []
is_a: GO:0044509 ! venom-mediated perturbation of signal transduction
@@ -486709,8 +487103,10 @@
def: "Catalysis of the reaction: (R)-lactate + FAD + H+ = FADH2 + pyruvate." [RHEA:82479]
xref: RHEA:82479
is_a: GO:0047809 ! D-lactate dehydrogenase activity
+is_a: GO:0140174 ! (2R)-2-hydroxycarboxylate dehydrogenase (FAD) activity
property_value: skos:exactMatch RHEA:82479
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/32501" xsd:anyURI
created_by: pg
creation_date: 2025-04-17T08:20:22Z
@@ -486753,9 +487149,10 @@
[Term]
id: GO:0140174
-name: (2R)-2-hydroxycarboxylate dehydrogenase activity
+name: (2R)-2-hydroxycarboxylate dehydrogenase (FAD) activity
namespace: molecular_function
def: "Catalysis of the activity: a (2R)-2-hydroxycarboxylate + FAD + H+ = a 2-oxocarboxylate + FADH2." [PMID:37863926, RHEA:82511]
+synonym: "(2R)-2-hydroxycarboxylate dehydrogenase activity" BROAD []
xref: RHEA:82483
xref: RHEA:82487
xref: RHEA:82491
@@ -486889,7 +487286,7 @@
id: GO:0140183
name: venom-mediated vasoconstriction via activation of endothelin receptor signaling pathway
namespace: biological_process
-def: "A process in which an organism promotes the narrowing (constriction) of blood vessels, by inhibiting the widening (dilation) of blood vessels in another organism via the action of a venom that activates endothelin receptor signaling pathway, concomittantly increasing blood pressure in the bitten/stung organism." [PMID:16277978]
+def: "A process in which an organism promotes the narrowing (constriction) of blood vessels, by inhibiting the widening (dilation) of blood vessels in another organism via the action of a venom that activates endothelin receptor signaling pathway, concomitantly increasing blood pressure in the bitten/stung organism." [PMID:16277978]
synonym: "venom-mediated vasoconstriction via activation of endothelin signaling pathway" EXACT []
synonym: "venom-mediated vasoconstriction via activation of endothelin-dependent signaling" EXACT []
synonym: "venom-mediated vasoconstriction via endothelin receptor agonism" EXACT []
@@ -487428,7 +487825,7 @@
id: GO:0140227
name: serotonin-gated cation-selective signaling pathway
namespace: biological_process
-def: "The series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25392484, PMID:27764665]
+def: "The series of molecular signals initiated by serotonin binding to a serotonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:bhm, PMID:25392484, PMID:27764665]
synonym: "5-HT-gated cation-selective signaling pathway" EXACT []
synonym: "5-HT-gated cation-selective signalling pathway" EXACT []
synonym: "5-hydroxytryptamine-gated cation-selective signaling pathway" EXACT []
@@ -487600,7 +487997,7 @@
[Term]
id: GO:0140240
-name: perforant pathway to dendrate granule cell synapse
+name: perforant pathway to dentate granule cell synapse
namespace: cellular_component
def: "A neuron to neuron synapse of a pyramidal neuron in the entorhinal cortex onto a granule cell in the dentate gyrus of the hippocampus." [PMID:22727665, PMID:29199135]
subset: goslim_synapse
@@ -488262,26 +488659,33 @@
def: "OBSOLETE. The transfer, from NAD, of a single (mono) ADP-ribose molecule to protein amino acids." [PMID:25043379]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23249" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
is_obsolete: true
-consider: GO:0003950
+consider: GO:1990404
created_by: pg
creation_date: 2018-11-22T13:52:54Z
[Term]
id: GO:0140290
-name: peptidyl-serine ADP-deribosylation
+name: obsolete peptidyl-serine ADP-deribosylation
namespace: biological_process
-def: "The removal of ADP-ribose from ADP-ribosylserine." [PMID:28650317, PMID:29234005]
-is_a: GO:0051725 ! protein de-ADP-ribosylation
+def: "OBSOLETE. The removal of ADP-ribose from ADP-ribosylserine." [PMID:28650317, PMID:29234005]
+comment: This term was obsoleted because it represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
+is_obsolete: true
+consider: GO:0140292
created_by: pg
creation_date: 2018-11-22T14:32:30Z
[Term]
id: GO:0140291
-name: peptidyl-glutamate ADP-deribosylation
+name: obsolete peptidyl-glutamate ADP-deribosylation
namespace: biological_process
-def: "The removal of ADP-ribose from ADP-ribosylglutamate." [PMID:23481255]
-is_a: GO:0051725 ! protein de-ADP-ribosylation
+def: "OBSOLETE. The removal of ADP-ribose from ADP-ribosylglutamate." [PMID:23481255]
+comment: This term was obsoleted because it represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32538" xsd:anyURI
+is_obsolete: true
+consider: GO:0140293
created_by: pg
creation_date: 2018-11-22T14:34:24Z
@@ -488509,10 +488913,12 @@
id: GO:0140309
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 to an acceptor molecule or to a specific location. The unfolded protein carrier prevents aggregation of the target protein while its being delivers to its final destination." [PMID:39488384]
+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 until it is delivered 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: "carbohydrate-binding holdase" NARROW []
synonym: "holdase" EXACT []
synonym: "holdase-carrier chaperone" EXACT []
+synonym: "lectin chaperone" NARROW []
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
@@ -489129,12 +489535,13 @@
[Term]
id: GO:0140357
-name: heme export from vacuole to cytoplasm
+name: heme export from vacuole to cytosol
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: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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32419" xsd:anyURI
created_by: pg
creation_date: 2019-05-28T07:40:48Z
@@ -489882,7 +490289,7 @@
id: GO:0140414
name: phosphopantetheine-dependent carrier activity
namespace: molecular_function
-def: "Binding a substrate via a thioester at the terminal thiol of a covalentely linked phosphopantetheine prosthetic group and mediating protein-protein interactions with cognate enzymes for processing or offloading of the thiol-bound substrate." [PMID:17502372]
+def: "Binding a substrate via a thioester at the terminal thiol of a covalently linked phosphopantetheine prosthetic group and mediating protein-protein interactions with cognate enzymes for processing or offloading of the thiol-bound substrate." [PMID:17502372]
synonym: "carrier protein activity" EXACT []
is_a: GO:0140104 ! molecular carrier activity
created_by: pg
@@ -490404,9 +490811,11 @@
id: GO:0140455
name: cytoplasm protein quality control
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the cytoplasm, which are either targeted to cytoplasmic proteasomes for degradation or protected by chaperones to shield thermosensitive proteins from degradation until conditions allow disaggregation and refolding." [PMID:32075773]
-is_a: GO:0006515 ! protein quality control for misfolded or incompletely synthesized proteins
+def: "The chemical reactions and pathways resulting in the breakdown or refolding of aberrant proteins in the cytoplasm, including misfolded proteins and orphan subunits that fail to assemble into their cognate protein complex, in which the substrates are either targeted to cytoplasmic proteasomes for degradation or protected by chaperones to shield thermosensitive proteins from degradation until conditions allow disaggregation and refolding." [PMID:30075143, PMID:32075773, PMID:35316660]
+is_a: GO:0006515 ! protein quality control
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19172" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32274" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32442" xsd:anyURI
created_by: pg
creation_date: 2020-04-20T15:46:20Z
@@ -490661,6 +491070,16 @@
creation_date: 2026-06-30T13:02:54Z
[Term]
+id: GO:0140477
+name: coenzyme A phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: CoA + H2O = 3'-dephospho-CoA + phosphate." [PMID:42033660]
+is_a: GO:0016791 ! phosphatase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32572" xsd:anyURI
+created_by: pg
+creation_date: 2026-09-08T11:43:30Z
+
+[Term]
id: GO:0140479
name: obsolete ergothioneine biosynthesis from histidine via hercynylcysteine sulfoxide synthase
namespace: biological_process
@@ -490818,13 +491237,15 @@
[Term]
id: GO:0140493
-name: very long-chain fatty acid beta-oxidation
+name: obsolete very long-chain fatty acid beta-oxidation
namespace: biological_process
-def: "A fatty acid beta-oxidation pathway acting on a very long-chain fatty acid. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons. The partway stars with the conversion of an acyl-CoA to a trans-2-enoyl-CoA, catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC:ha, PMID:17028011, PMID:32169171]
-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).
-is_a: GO:0042760 ! very long-chain fatty acid catabolic process
+def: "OBSOLETE. A fatty acid beta-oxidation pathway acting on a very long-chain fatty acid. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons. The partway stars with the conversion of an acyl-CoA to a trans-2-enoyl-CoA, catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively)." [GOC:ha, PMID:17028011, PMID:32169171]
+comment: This term was obsoleted because it represents the same process as very long-chain fatty acid catabolic process ; GO:0042760.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19735" 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/32227" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042760
created_by: pg
creation_date: 2020-07-10T08:39:22Z
@@ -492215,7 +492636,7 @@
name: outward rectifier potassium channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of an outwardly rectifying potassium channel." [PMID:28108814]
-is_a: GO:0019870 ! potassium channel inhibitor activity
+is_a: GO:7770090 ! voltage-gated potassium channel inhibitor activity
relationship: negatively_regulates GO:0015271 ! outward rectifier potassium channel activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21157" xsd:anyURI
created_by: pg
@@ -493975,17 +494396,19 @@
id: GO:0140762
name: glucose dehydrogenase (FAD, quinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: a quinone + D-glucose = a quinol + D-glucono-1,5-lactone." [RHEA:47372]
+def: "Catalysis of the reaction: D-glucose + a quinone = D-glucono-1,5-lactone + a quinol, using FAD as a cofactor." [EC:1.1.5.9]
+synonym: "FAD-dependent glucose dehydrogenase activity" EXACT [EC:1.1.5.9]
xref: EC:1.1.5.9
-xref: MetaCyc:GLUCOSE-DEHYDROGENASE-ACCEPTOR-RXN
-xref: RHEA:47372
is_a: GO:0004344 ! glucose dehydrogenase activity
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
+property_value: skos:broadMatch KEGG_REACTION:R00305
+property_value: skos:broadMatch MetaCyc:GLUCOSE-DEHYDROGENASE-ACCEPTOR-RXN
+property_value: skos:broadMatch RHEA:47372
property_value: skos:exactMatch EC:1.1.5.9
-property_value: skos:exactMatch RHEA:47372
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22585" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25441" 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/32504" xsd:anyURI
created_by: pg
creation_date: 2022-02-04T08:02:40Z
@@ -494862,17 +495285,26 @@
name: thioredoxin-dependent peroxiredoxin activity
namespace: molecular_function
def: "Catalysis of the reaction: [thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O." [PMID:12707274, PMID:19820102, RHEA:62620]
+synonym: "thiol peroxidase activity" RELATED []
+synonym: "thioredoxin peroxidase activity" EXACT []
+synonym: "TPx activity" EXACT []
+synonym: "TrxPx activity" EXACT []
xref: EC:1.11.1.24
+xref: MetaCyc:RXN0-267
xref: RHEA:62620
+xref: RHEA:63528
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 MetaCyc:RXN0-267
+property_value: skos:narrowMatch RHEA:63528
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
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32388" xsd:anyURI
created_by: pg
creation_date: 2022-05-18T14:25:09Z
@@ -497685,7 +498117,7 @@
id: GO:0141032
name: symbiont-mediated perturbation of host actin cytoskeleton via actin filament reorganization
namespace: biological_process
-def: "The process in which an organism effects a change that impairs the structure or function of the host actin cytoskeleton by reorganizing the actin filaments, in a way that keeps the total filementous actin remains approximately constant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:22212282, PMID:31130928]
+def: "The process in which an organism effects a change that impairs the structure or function of the host actin cytoskeleton by reorganizing the actin filaments, in a way that keeps the total filamentous actin approximately constant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:22212282, PMID:31130928]
synonym: "perturbation by symbiont of host actin cytoskeleton via actin filament rearrangement" EXACT []
synonym: "perturbation by symbiont of host actin cytoskeleton via actin filament reorganization" EXACT []
is_a: GO:0141027 ! symbiont-mediated perturbation of host actin cytoskeleton
@@ -499341,9 +499773,11 @@
id: GO:0141164
name: mitochondrial protein quality control
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the mitochondrion, which are targeted for degradation." [PMID:38280230]
-is_a: GO:0006515 ! protein quality control for misfolded or incompletely synthesized proteins
+def: "The chemical reactions and pathways resulting in the breakdown of aberrant proteins in the mitochondrion which are targeted for degradation, including misfolded proteins and orphan subunits that fail to assemble into their cognate complex." [PMID:34436539, PMID:38280230, PMID:7623837]
+is_a: GO:0006515 ! protein quality control
+is_a: GO:0030163 ! protein catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27044" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32546" xsd:anyURI
created_by: pg
creation_date: 2024-02-14T07:11:38Z
@@ -502819,7 +503253,7 @@
id: GO:0160110
name: axonemal microtubule doublet inner sheath
namespace: cellular_component
-def: "A structural network of microtubule inner proteins (MIPs) located inside the lumens of the A and B tubules of the axonemal microtuble doublet that helps stabilize the doublet microtubule." [GOC:krc, PMID:29430673, PMID:37295417]
+def: "A structural network of microtubule inner proteins (MIPs) located inside the lumens of the A and B tubules of the axonemal microtubule doublet that helps stabilize the doublet microtubule." [GOC:krc, PMID:29430673, PMID:37295417]
is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0097545 ! axonemal doublet microtubule
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26148" xsd:anyURI
@@ -502876,7 +503310,7 @@
id: GO:0160115
name: axonemal microtubule doublet ribbon
namespace: cellular_component
-def: "The 3 protofilaments A11, A12, and A13 of the A tubule along with associated inner sheath microtuble inner proteins (MIPs), either in the lumen of the A tubule or of the B tubule, which stabilize these three filiments within the axonemal doublet microtubule. The ribbon protofilaments separate the lumens of the A and B tubules." [GOC:krc, PMID:1262413, PMID:29430673]
+def: "The 3 protofilaments A11, A12, and A13 of the A tubule along with associated inner sheath microtubule inner proteins (MIPs), either in the lumen of the A tubule or of the B tubule, which stabilize these three filaments within the axonemal doublet microtubule. The ribbon protofilaments separate the lumens of the A and B tubules." [GOC:krc, PMID:1262413, PMID:29430673]
is_a: GO:0110165 ! cellular anatomical structure
relationship: part_of GO:0097545 ! axonemal doublet microtubule
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26148" xsd:anyURI
@@ -503532,8 +503966,10 @@
def: "Catalysis of the reaction: 2-oxoadipate + H+ + N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] = CO2 + N(6)-[(R)-S(8)-glutaryldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase]." [PMID:29191460, PMID:32695416, RHEA:69576]
xref: RHEA:69576
is_a: GO:0016624 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
+property_value: skos:broadMatch RHEA:30795
property_value: skos:exactMatch RHEA:69576
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27202" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32557" xsd:anyURI
created_by: rynl
creation_date: 2024-03-06T18:27:05Z
@@ -504537,7 +504973,7 @@
synonym: "autophagy adaptor activity" EXACT []
synonym: "selective autophagy receptor activity" EXACT []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
-relationship: part_of GO:0061753 ! substrate localization to autophagosome
+relationship: part_of GO:0016236 ! macroautophagy
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28283" xsd:anyURI
created_by: rynl
creation_date: 2025-02-10T16:57:01Z
@@ -505274,7 +505710,7 @@
synonym: "protein synthesis" EXACT []
is_a: GO:0009059 ! macromolecule biosynthetic process
is_a: GO:0019538 ! protein metabolic process
-relationship: has_part GO:0043039 ! tRNA aminoacylation
+relationship: has_part GO:0043039 ! tRNA charging
relationship: part_of GO:0010467 ! gene expression
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
created_by: rynl
@@ -506163,13 +506599,14 @@
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
+is_a: GO:0170079 ! peroxisomal protein quality control
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
+name: negative regulation of nuclear-transcribed 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 []
@@ -506186,6 +506623,108 @@
creation_date: 2026-03-23T21:12:37Z
[Term]
+id: GO:0170076
+name: gap endonuclease activity
+namespace: molecular_function
+def: "Specific recognition and catalysis of the internal cleavage of the phosphodiester backbone within single-stranded DNA gaps or looped DNA structures at the junctions of single-stranded and double-stranded DNA. Primarily involved in the resolution of triplet repeat sequences, removal of aberrant secondary structures formed during the maturation of Okazaki fragments, telomeric R-loop resolution and the processing of stalled replication forks, that all involve cleavage at internal or branched DNA structures." [PMID:10330154, PMID:15592449]
+synonym: "Gap specific endonuclease activity" EXACT []
+synonym: "GEN activity" EXACT []
+is_a: GO:0004520 ! DNA endonuclease activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32367" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-10T17:51:18Z
+
+[Term]
+id: GO:0170077
+name: negative regulation of coenzyme A 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 coenzyme A." [PMID:42000723]
+is_a: GO:0080020 ! regulation of coenzyme A biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32390" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-10T18:46:59Z
+
+[Term]
+id: GO:0170078
+name: Sca1 Ras guanyl-nucleotide exchange factor complex
+namespace: cellular_component
+def: "A protein complex found in Dictyostelium, containing the scaffold protein Sca1, the Ras guanine nucleotide exchange factors Aimless (RasGEFA) and RasGEFH, and PP2A components, which promotes RasC activation during chemotaxis." [PMID:20493808]
+synonym: "Sca1 RasGEF complex" BROAD []
+synonym: "Sca1 signaling complex" BROAD []
+synonym: "Sca1-Aimless signaling complex" BROAD []
+synonym: "Sca1-associated Ras guanyl-nucleotide exchange factor complex" BROAD []
+is_a: GO:1905742 ! Ras guanyl-nucleotide exchange factor complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32432" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-11T17:42:26Z
+
+[Term]
+id: GO:0170079
+name: peroxisomal protein quality control
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of dysfunctional peroxisomal proteins, independent of pexophagy." [PMID:19538506, PMID:25305535, PMID:37552037]
+is_a: GO:0006515 ! protein quality control
+is_a: GO:0030163 ! protein catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32442" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-12T16:13:58Z
+
+[Term]
+id: GO:0170080
+name: endoplasmic reticulum protein quality control
+namespace: biological_process
+def: "Any process that monitors and mediates the fidelity of protein folding in the endoplasmic reticulum, or prevents misfolded proteins from accumulating in or transiting the endoplasmic reticulum. Processes result in the export of correctly folded proteins to the Golgi apparatus while retaining, refolding, or targeting terminally misfolded proteins for degradation." [PMID:12612637, PMID:17129784]
+synonym: "ERQC" RELATED []
+is_a: GO:0006515 ! protein quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32495" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-20T16:01:05Z
+
+[Term]
+id: GO:0170081
+name: ribosome-associated chaperone complex
+namespace: cellular_component
+def: "A conserved heterodimeric co-chaperone complex, composed of a J-domain (Hsp40-family) protein and an atypical Hsp70-family protein, that associates with the ribosome and acts on nascent polypeptide chains as they emerge from the exit tunnel to enable their co-translational folding. In Saccharomyces cerevisiae, the complex consists of the J-domain protein Zuo1 (Hsp40) and the non-canonical Hsp70 homolog Ssz1. The mammalian ortholog comprises ZRF1/MPP11 (Hsp40) and HSPA14/HSP70L1 (Hsp70)." [PMID:11274393, PMID:16002468]
+comment: Note that this term does not cover the nascent polypeptide-associated complex (GO:0005854), a distinct ribosome-associated heterodimer that acts in nascent chain sorting rather than folding.
+synonym: "MPP11/Hsp70L1 complex" NARROW []
+synonym: "RAC" RELATED []
+synonym: "ribosome-associated complex" RELATED []
+synonym: "Zuo1/Ssz1 complex" NARROW []
+synonym: "zuotin complex" NARROW []
+is_a: GO:0101031 ! protein folding chaperone complex
+relationship: part_of GO:0005829 ! cytosol
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32185" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-20T20:04:20Z
+
+[Term]
+id: GO:0170082
+name: proteasome substrate carrier activity
+namespace: molecular_function
+def: "A protein carrier activity that recognizes and binds a polyubiquitinated substrate, usually via a UBA or similar ubiquitin-binding domain, and delivers it to the 26S proteasome by docking onto the 19S regulatory particle and releasing the substrate." [PMID:33211406]
+synonym: "proteasome substrate carrier" EXACT []
+synonym: "ubiquitin receptor" BROAD []
+is_a: GO:0140597 ! protein carrier activity
+relationship: has_part GO:0031593 ! polyubiquitin modification-dependent protein binding
+relationship: has_part GO:0070628 ! proteasome binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32506" xsd:anyURI
+created_by: ew
+creation_date: 2026-08-25T15:54:46Z
+
+[Term]
+id: GO:0170085
+name: voltage-driven motor activity
+namespace: molecular_function
+def: "A motor activity that detects and converts a change in transmembrane electrical potential directly into mechanical force or a conformational change, without coupling to ATP hydrolysis, ion transport, or a proton-motive force. As an example, mammalian prestin converts voltage changes into outer hair cell movement which is required for sound amplification in the hearing organ." [PMID:12239568]
+synonym: "electromechanical transducer activity" EXACT []
+synonym: "electromotility activity" RELATED []
+synonym: "voltage-sensitive motor activity" EXACT []
+is_a: GO:0031992 ! energy transducer activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32556" xsd:anyURI
+created_by: ew
+creation_date: 2026-09-02T21:59:45Z
+
+[Term]
id: GO:0180000
name: histone methyltransferase inhibitor activity
namespace: molecular_function
@@ -506469,7 +507008,7 @@
id: GO:0180022
name: RQC-trigger complex
namespace: cellular_component
-def: "A ribosome disassembly complex which dissociates stalled ribsome subunits as part of the ribosome quality control pathway. RQT complex is composed of a RNA helicase-family protein yeast Rqt2 (human ASCC3), a ubiquitin-binding protein yeast Rqt3, (human ASCC2), and Rqt4 (human TRIP4). The human complex has an additional component protein ASCC1 and can act as a transcriptional coactivator by interacting with transcription factors such as NF-kappa B." [PMID:12077347, PMID:28757607, PMID:32099016]
+def: "A ribosome disassembly complex which dissociates stalled ribosome subunits as part of the ribosome quality control pathway. RQT complex is composed of a RNA helicase-family protein yeast Rqt2 (human ASCC3), a ubiquitin-binding protein yeast Rqt3, (human ASCC2), and Rqt4 (human TRIP4). The human complex has an additional component protein ASCC1 and can act as a transcriptional coactivator by interacting with transcription factors such as NF-kappa B." [PMID:12077347, PMID:28757607, PMID:32099016]
synonym: "activating signal cointegrator 1 complex" EXACT []
synonym: "ASC-1 complex" EXACT [PMID:12077347]
synonym: "RQT complex" EXACT []
@@ -506568,12 +507107,16 @@
id: GO:0180031
name: snoRNA 2,2,7-trimethylguanosine (TMG) capping
namespace: biological_process
-def: "The sequence of enzymatic reactions by which a 2,2,7-trimethylguanosine cap structure is added to the 5' end of an snoRNA. The snoRNA capping includes the formation of 7-methyl-G caps found on all RNA polymerase II transcripts, followed by hypermethylation at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. Note that the pol III transcribed snoRNAs are also TMG capped." [GOC:vw, PMID:15590684]
+def: "The sequence of enzymatic reactions by which a 2,2,7-trimethylguanosine (TMG) cap structure is added to the 5' end of an snoRNA. The process begins with the formation of a 7-methylguanosine cap, as found on all RNA polymerase II transcripts, followed by dimethylation at the N2 position of the guanine base to convert the monomethylated cap to a 2,2,7-trimethylguanosine cap structure." [GOC:vw, PMID:11983179, PMID:15590684]
+comment: TMG capped snoRNAs are RNA polymerase II transcripts. Where a snoRNA is transcribed by RNA polymerase III it is not TMG capped: plant U3 snoRNA, which is Pol III transcribed, carries a gamma-monomethyl phosphate cap, whereas the same snoRNA is TMG capped in the animals and fungi where it is Pol II transcribed (PMID:1618872).
synonym: "snoRNA 2,2,7-trimethylguanosine (TMG) cap formation" EXACT []
synonym: "snoRNA capping" EXACT []
is_a: GO:0036260 ! RNA capping
is_a: GO:0043144 ! sno(s)RNA processing
+relationship: has_part GO:0009452 ! 7-methylguanosine RNA capping
+relationship: has_part GO:0036261 ! 7-methylguanosine cap hypermethylation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26940" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27628" xsd:anyURI
created_by: vw
creation_date: 2024-02-07T13:55:54Z
@@ -506877,7 +507420,7 @@
id: GO:0180056
name: citrate:2-oxoglutarate antiporter 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: citrate(out) + 2-oxogluarate(in) = citrate(in) + 2-oxogluarat(out)." [PMID:20371607]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: citrate(out) + 2-oxoglutarate(in) = citrate(in) + 2-oxoglutarate(out)." [PMID:20371607]
is_a: GO:0015139 ! alpha-ketoglutarate transmembrane transporter activity
is_a: GO:0015297 ! antiporter activity
is_a: GO:0071913 ! citrate secondary active transmembrane transporter activity
@@ -508107,6 +508650,7 @@
synonym: "regulation of sulphate assimilation" EXACT [GOC:TermGenie]
synonym: "regulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor" NARROW [GOC:TermGenie]
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:0000103 ! sulfate assimilation
relationship: regulates GO:0000103 ! sulfate assimilation
@@ -508137,7 +508681,7 @@
synonym: "upregulation of sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor" NARROW [GOC:TermGenie]
synonym: "upregulation of sulphate assimilation" EXACT [GOC:TermGenie]
synonym: "upregulation of sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor" NARROW [GOC:TermGenie]
-is_a: GO:0009893 ! positive regulation of metabolic process
+is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900058 ! regulation of sulfate assimilation
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0000103 ! sulfate assimilation
@@ -522522,7 +523066,6 @@
synonym: "regulation of protein insertion into mitochondrion membrane during induction of apoptosis" NARROW [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26245" xsd:anyURI
is_obsolete: true
-consider: GO:1903747
created_by: pr
creation_date: 2012-05-28T02:28:18Z
@@ -522558,7 +523101,6 @@
synonym: "upregulation of protein insertion into mitochondrion membrane during induction of apoptosis" NARROW [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26245" xsd:anyURI
is_obsolete: true
-consider: GO:1903749
created_by: pr
creation_date: 2012-05-28T02:28:40Z
@@ -522848,6 +523390,8 @@
intersection_of: GO:0016485 ! protein processing
intersection_of: occurs_in GO:0045335 ! phagocytic vesicle
relationship: occurs_in GO:0045335 ! phagocytic vesicle
+relationship: part_of GO:0006909 ! phagocytosis
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32152" xsd:anyURI
created_by: rjd
creation_date: 2012-05-29T09:55:14Z
@@ -550711,12 +551255,13 @@
[Term]
id: GO:1902334
-name: fructose export from vacuole to cytoplasm
+name: fructose export from vacuole to cytosol
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:0015755 ! fructose transmembrane transport
is_a: GO:0034486 ! vacuolar transmembrane transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32419" xsd:anyURI
created_by: tb
creation_date: 2013-07-26T22:18:12Z
@@ -555068,7 +555613,8 @@
synonym: "66S preribosome formation" NARROW [GOC:TermGenie]
synonym: "preribosome, large subunit precursor formation" EXACT [GOC:TermGenie]
is_a: GO:0022618 ! protein-RNA complex assembly
-relationship: part_of GO:0000027 ! ribosomal large subunit assembly
+relationship: part_of GO:0180023 ! cytosolic large ribosomal subunit assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32473" xsd:anyURI
created_by: tb
creation_date: 2014-01-16T19:38:05Z
@@ -566544,7 +567090,6 @@
synonym: "regulation of protein-mitochondrial targeting" EXACT [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1903747
created_by: bf
creation_date: 2014-07-24T10:17:13Z
@@ -566585,7 +567130,6 @@
synonym: "negative regulation of protein-mitochondrial targeting" EXACT [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1903748
created_by: bf
creation_date: 2014-07-24T10:17:19Z
@@ -566599,7 +567143,6 @@
synonym: "regulation of mitochondrial protein processing during import" RELATED [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1903747
created_by: bf
creation_date: 2014-07-24T10:20:54Z
@@ -566620,7 +567163,6 @@
synonym: "negative regulation of mitochondrial protein processing during import" RELATED [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1903748
created_by: bf
creation_date: 2014-07-24T10:21:00Z
@@ -574257,14 +574799,16 @@
[Term]
id: GO:1903608
-name: protein localization to cytoplasmic stress granule
+name: obsolete protein localization to cytoplasmic stress granule
namespace: biological_process
-def: "A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule." [GO_REF:0000087, GOC:TermGenie, PMID:24755092]
+def: "OBSOLETE. A process in which a protein is transported to, or maintained in, a location within a cytoplasmic stress granule." [GO_REF:0000087, GOC:TermGenie, PMID:24755092]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. In practice it was applied to proteins observed in stress granules, that is, to a co-localization readout rather than to a process that localizes a protein there. Annotations to this term have been reviewed and removed; see https://github.com/geneontology/go-annotation/issues/6484.
synonym: "protein localisation in cytoplasmic stress granule" EXACT [GOC:TermGenie]
synonym: "protein localisation to cytoplasmic stress granule" EXACT [GOC:TermGenie]
synonym: "protein localization in cytoplasmic stress granule" EXACT [GOC:TermGenie]
synonym: "protein localization to stress granule" BROAD []
-is_a: GO:0033365 ! protein localization to organelle
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32318" xsd:anyURI
+is_obsolete: true
created_by: mah
creation_date: 2014-11-14T16:20:32Z
@@ -576858,44 +577402,36 @@
[Term]
id: GO:1903747
-name: regulation of protein localization to mitochondrion
+name: obsolete regulation of protein localization to mitochondrion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
-is_a: GO:0032880 ! regulation of protein localization
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0070585 ! protein localization to mitochondrion
-relationship: regulates GO:0070585 ! protein localization to mitochondrion
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
+comment: The reason for obsoletion is that this term represents a phenotype and was added in error. Consider annotating to regulation of the specific process being regulated (e.g. regulation of mitophagy) or to a specific mitochondrial protein import pathway; if the underlying evidence is a readout or a phenotype, or the mechanism is unclear, consider removal rather than re-annotation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32107" xsd:anyURI
+is_obsolete: true
created_by: krc
creation_date: 2014-12-12T22:18:09Z
[Term]
id: GO:1903748
-name: negative regulation of protein localization to mitochondrion
+name: obsolete negative regulation of protein localization to mitochondrion
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
-is_a: GO:1903747 ! regulation of protein localization to mitochondrion
-is_a: GO:1903828 ! negative regulation of protein localization
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0070585 ! protein localization to mitochondrion
-relationship: negatively_regulates GO:0070585 ! protein localization to mitochondrion
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
+comment: The reason for obsoletion is that this term represents a phenotype and was added in error. Consider annotating to negative regulation of the specific process being regulated (e.g. negative regulation of mitophagy) or to a specific mitochondrial protein import pathway; if the underlying evidence is a readout or a phenotype, or the mechanism is unclear, consider removal rather than re-annotation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32107" xsd:anyURI
+is_obsolete: true
created_by: krc
creation_date: 2014-12-12T22:18:18Z
[Term]
id: GO:1903749
-name: positive regulation of protein localization to mitochondrion
+name: obsolete positive regulation of protein localization to mitochondrion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
+comment: The reason for obsoletion is that this term represents a phenotype and was added in error. Consider annotating to positive regulation of the specific process being regulated (e.g. positive regulation of mitophagy) or to a specific mitochondrial protein import pathway; if the underlying evidence is a readout or a phenotype, or the mechanism is unclear, consider removal rather than re-annotation.
xref: Reactome:R-HSA-114452 "Activation of BH3-only proteins"
xref: Reactome:R-HSA-75108 "Activation, myristolyation of BID and translocation to mitochondria"
-is_a: GO:1903747 ! regulation of protein localization to mitochondrion
-is_a: GO:1903829 ! positive regulation of protein localization
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0070585 ! protein localization to mitochondrion
-relationship: positively_regulates GO:0070585 ! protein localization to mitochondrion
-property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32107" xsd:anyURI
+is_obsolete: true
created_by: krc
creation_date: 2014-12-12T22:18:26Z
@@ -578736,7 +579272,7 @@
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cristae formation." [GO_REF:0000058, GOC:pad, GOC:PARL, GOC:TermGenie, PMID:19279012]
comment: AN example of this is PINK1 in human (Q9BXM7) in PMID:19279012 inferred from mutant phenotype
-is_a: GO:0010821 ! regulation of mitochondrion organization
+is_a: GO:0051128 ! regulation of cellular component organization
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042407 ! cristae formation
relationship: regulates GO:0042407 ! cristae formation
@@ -578753,7 +579289,7 @@
synonym: "down-regulation of cristae formation" EXACT [GOC:TermGenie]
synonym: "downregulation of cristae formation" EXACT [GOC:TermGenie]
synonym: "inhibition of cristae formation" NARROW [GOC:TermGenie]
-is_a: GO:0010639 ! negative regulation of organelle organization
+is_a: GO:0051129 ! negative regulation of cellular component organization
is_a: GO:1903850 ! regulation of cristae formation
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0042407 ! cristae formation
@@ -578771,7 +579307,7 @@
synonym: "up regulation of cristae formation" EXACT [GOC:TermGenie]
synonym: "up-regulation of cristae formation" EXACT [GOC:TermGenie]
synonym: "upregulation of cristae formation" EXACT [GOC:TermGenie]
-is_a: GO:0010638 ! positive regulation of organelle organization
+is_a: GO:0051130 ! positive regulation of cellular component organization
is_a: GO:1903850 ! regulation of cristae formation
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0042407 ! cristae formation
@@ -581223,7 +581759,6 @@
synonym: "upregulation of protein-mitochondrial targeting" EXACT [GOC:TermGenie]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30349" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1903749
created_by: pad
creation_date: 2015-02-24T16:58:21Z
@@ -584866,24 +585401,25 @@
[Term]
id: GO:1904152
-name: regulation of retrograde protein transport, ER to cytosol
+name: obsolete regulation of retrograde protein transport, ER to cytosol
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent, the data from the paper for which the term was requested can be accurately described using reguation of ERAD pathway terms, and this term was added in error.
synonym: "regulation of protein dislocation from ER" EXACT [GOC:TermGenie]
synonym: "regulation of protein retrotranslocation from ER" EXACT [GOC:bf]
synonym: "regulation of retrograde protein transport, endoplasmic reticulum to cytosol" EXACT [GOC:TermGenie]
-is_a: GO:0051223 ! regulation of protein transport
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0030970 ! retrograde protein transport, ER to cytosol
-relationship: regulates GO:0030970 ! retrograde protein transport, ER to cytosol
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0036503
created_by: bf
creation_date: 2015-04-15T09:23:06Z
[Term]
id: GO:1904153
-name: negative regulation of retrograde protein transport, ER to cytosol
+name: obsolete negative regulation of retrograde protein transport, ER to cytosol
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent, the data from the paper for which the term was requested can be accurately described using reguation of ERAD pathway terms, and this term was added in error.
synonym: "down regulation of protein dislocation from ER" EXACT [GOC:TermGenie]
synonym: "down regulation of retrograde protein transport, endoplasmic reticulum to cytosol" EXACT [GOC:TermGenie]
synonym: "down regulation of retrograde protein transport, ER to cytosol" EXACT [GOC:TermGenie]
@@ -584899,19 +585435,18 @@
synonym: "negative regulation of protein dislocation from ER" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein retrotranslocation from ER" EXACT [GOC:bf]
synonym: "negative regulation of retrograde protein transport, endoplasmic reticulum to cytosol" EXACT [GOC:TermGenie]
-is_a: GO:0051224 ! negative regulation of protein transport
-is_a: GO:1904152 ! regulation of retrograde protein transport, ER to cytosol
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0030970 ! retrograde protein transport, ER to cytosol
-relationship: negatively_regulates GO:0030970 ! retrograde protein transport, ER to cytosol
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:1904293
created_by: bf
creation_date: 2015-04-15T09:23:13Z
[Term]
id: GO:1904154
-name: positive regulation of retrograde protein transport, ER to cytosol
+name: obsolete positive regulation of retrograde protein transport, ER to cytosol
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of retrograde protein transport, ER to cytosol." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18555783]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent, the data from the paper for which the term was requested can be accurately described using reguation of ERAD pathway terms, and this term was added in error.
synonym: "activation of protein dislocation from ER" NARROW [GOC:TermGenie]
synonym: "activation of retrograde protein transport, endoplasmic reticulum to cytosol" NARROW [GOC:TermGenie]
synonym: "activation of retrograde protein transport, ER to cytosol" NARROW [GOC:TermGenie]
@@ -584928,11 +585463,9 @@
synonym: "upregulation of protein dislocation from ER" EXACT [GOC:TermGenie]
synonym: "upregulation of retrograde protein transport, endoplasmic reticulum to cytosol" EXACT [GOC:TermGenie]
synonym: "upregulation of retrograde protein transport, ER to cytosol" EXACT [GOC:TermGenie]
-is_a: GO:0051222 ! positive regulation of protein transport
-is_a: GO:1904152 ! regulation of retrograde protein transport, ER to cytosol
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0030970 ! retrograde protein transport, ER to cytosol
-relationship: positively_regulates GO:0030970 ! retrograde protein transport, ER to cytosol
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32525" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:1904294
created_by: bf
creation_date: 2015-04-15T09:23:19Z
@@ -588352,10 +588885,9 @@
synonym: "regulation of endoplasmic reticulum-associated protein degradation pathway" RELATED [GOC:TermGenie]
synonym: "regulation of ER-associated degradation pathway" RELATED [GOC:TermGenie]
is_a: GO:0061136 ! regulation of proteasomal protein catabolic process
-is_a: GO:1905897 ! regulation of response to endoplasmic reticulum stress
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0036503 ! ERAD pathway
-relationship: regulates GO:0036503 ! ERAD pathway
+intersection_of: regulates GO:0036503 ! ERAD quality control pathway
+relationship: regulates GO:0036503 ! ERAD quality control pathway
created_by: bf
creation_date: 2015-06-09T14:44:27Z
@@ -588384,11 +588916,10 @@
synonym: "negative regulation of endoplasmic reticulum-associated protein degradation pathway" RELATED [GOC:TermGenie]
synonym: "negative regulation of ER-associated degradation pathway" RELATED [GOC:TermGenie]
is_a: GO:1901799 ! negative regulation of proteasomal protein catabolic process
-is_a: GO:1903573 ! negative regulation of response to endoplasmic reticulum stress
is_a: GO:1904292 ! regulation of ERAD pathway
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0036503 ! ERAD pathway
-relationship: negatively_regulates GO:0036503 ! ERAD pathway
+intersection_of: negatively_regulates GO:0036503 ! ERAD quality control pathway
+relationship: negatively_regulates GO:0036503 ! ERAD quality control pathway
created_by: bf
creation_date: 2015-06-09T14:44:33Z
@@ -588418,10 +588949,9 @@
synonym: "upregulation of ERAD pathway" EXACT [GOC:TermGenie]
is_a: GO:1901800 ! positive regulation of proteasomal protein catabolic process
is_a: GO:1904292 ! regulation of ERAD pathway
-is_a: GO:1905898 ! positive regulation of response to endoplasmic reticulum stress
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0036503 ! ERAD pathway
-relationship: positively_regulates GO:0036503 ! ERAD pathway
+intersection_of: positively_regulates GO:0036503 ! ERAD quality control pathway
+relationship: positively_regulates GO:0036503 ! ERAD quality control pathway
created_by: bf
creation_date: 2015-06-09T14:44:39Z
@@ -592740,9 +593270,10 @@
[Term]
id: GO:1904539
-name: negative regulation of glycolytic process through fructose-6-phosphate
+name: obsolete negative regulation of glycolytic process through fructose-6-phosphate
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of glycolytic process through fructose-6-phosphate." [GO_REF:0000058, GOC:dph, GOC:TermGenie, ISBN:0201090910, ISBN:0879010479]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of glycolytic process through fructose-6-phosphate." [GO_REF:0000058, GOC:dph, GOC:TermGenie, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "down regulation of glycolysis through fructose-6-phosphate" EXACT [GOC:TermGenie]
synonym: "down regulation of glycolytic process through fructose-6-phosphate" EXACT [GOC:TermGenie]
synonym: "down-regulation of glycolysis through fructose-6-phosphate" EXACT [GOC:TermGenie]
@@ -592752,18 +593283,18 @@
synonym: "inhibition of glycolysis through fructose-6-phosphate" NARROW [GOC:TermGenie]
synonym: "inhibition of glycolytic process through fructose-6-phosphate" NARROW [GOC:TermGenie]
synonym: "negative regulation of glycolysis through fructose-6-phosphate" EXACT [GOC:TermGenie]
-is_a: GO:0045820 ! negative regulation of glycolytic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0061615 ! glycolytic process through fructose-6-phosphate
-relationship: negatively_regulates GO:0061615 ! glycolytic process through fructose-6-phosphate
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0045820
created_by: dph
creation_date: 2015-08-07T11:35:16Z
[Term]
id: GO:1904540
-name: positive regulation of glycolytic process through fructose-6-phosphate
+name: obsolete positive regulation of glycolytic process through fructose-6-phosphate
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of glycolytic process through fructose-6-phosphate." [GO_REF:0000058, GOC:dph, GOC:TermGenie, ISBN:0201090910, ISBN:0879010479]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of glycolytic process through fructose-6-phosphate." [GO_REF:0000058, GOC:dph, GOC:TermGenie, ISBN:0201090910, ISBN:0879010479]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "activation of glycolysis through fructose-6-phosphate" NARROW [GOC:TermGenie]
synonym: "activation of glycolytic process through fructose-6-phosphate" NARROW [GOC:TermGenie]
synonym: "positive regulation of glycolysis through fructose-6-phosphate" EXACT [GOC:TermGenie]
@@ -592773,10 +593304,9 @@
synonym: "up-regulation of glycolytic process through fructose-6-phosphate" EXACT [GOC:TermGenie]
synonym: "upregulation of glycolysis through fructose-6-phosphate" EXACT [GOC:TermGenie]
synonym: "upregulation of glycolytic process through fructose-6-phosphate" EXACT [GOC:TermGenie]
-is_a: GO:0045821 ! positive regulation of glycolytic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0061615 ! glycolytic process through fructose-6-phosphate
-relationship: positively_regulates GO:0061615 ! glycolytic process through fructose-6-phosphate
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32471" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0045821
created_by: dph
creation_date: 2015-08-07T11:35:22Z
@@ -622662,6 +623192,8 @@
synonym: "ribosome-associated ubiquitin-dependent protein catabolism" EXACT []
synonym: "ribosome-associated ubiquitin-dependent protein degradation" EXACT []
is_a: GO:0043161 ! proteasome-mediated ubiquitin-dependent protein catabolic process
+relationship: part_of GO:7770112 ! ribosome-associated quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26238" xsd:anyURI
created_by: pr
creation_date: 2013-06-05T11:46:01Z
@@ -624414,14 +624946,18 @@
id: GO:1990273
name: snRNA 2,2,7-trimethylguanosine (TMG) capping
namespace: biological_process
-def: "The sequence of enzymatic reactions by which a 2,2,7-trimethylguanosine cap structure is added to the 5' end of an snRNA. The snRNA capping process includes the formation of 7-methyl-G caps found on all RNA polymerase II transcripts, followed by hypermethylation at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. Note that the pol III transcribed U6 snRNA is also TMG capped." [GOC:vw, PMID:15590684]
+def: "The sequence of enzymatic reactions by which a 2,2,7-trimethylguanosine (TMG) cap structure is added to the 5' end of an snRNA. The process begins with the formation of a 7-methylguanosine cap, as found on all RNA polymerase II transcripts, followed by dimethylation at the N2 position of the guanine base to convert the monomethylated cap to a 2,2,7-trimethylguanosine cap structure." [GOC:vw, PMID:11142384, PMID:15590684]
+comment: TMG capped snRNAs are RNA polymerase II transcripts. The RNA polymerase III transcribed U6 snRNA is not TMG capped; it carries a gamma-monomethyl phosphate cap added by the Bin3/MePCE family of methylphosphate capping enzymes (PMID:2229067, PMID:37403782). TMG capping of a Pol III transcript has been reported only for engineered U6 variants in which disruption of the 5' stem-loop exposes the 5'-triphosphate to the normal methylguanosine capping machinery (PMID:11142384).
synonym: "snRNA 2,2,7-trimethylguanosine (TMG) cap formation" EXACT []
synonym: "snRNA 5'-end processing" BROAD []
synonym: "snRNA capping" EXACT []
is_a: GO:0016180 ! snRNA processing
is_a: GO:0036260 ! RNA capping
+relationship: has_part GO:0009452 ! 7-methylguanosine RNA capping
+relationship: has_part GO:0036261 ! 7-methylguanosine cap hypermethylation
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23084" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26940" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27628" xsd:anyURI
created_by: al
creation_date: 2014-01-15T15:32:06Z
@@ -624994,12 +625530,14 @@
[Term]
id: GO:1990343
-name: heterochromatin domain
+name: obsolete heterochromatin domain
namespace: cellular_component
-def: "A region of heterochromatin that is formed dynamically under specific growth conditions by a process that requires RNAi, and is enriched in histone H3 methylated on lysine 9 (H3K9me)." [PMID:23151475, PMID:24210919]
-comment: An example of this type of heterochromatin is found in Schizosaccharomyces pombe, where heterochromatin domains preferentially assemble at sexual differentiation genes and retrotransposons.
+def: "OBSOLETE. A region of heterochromatin that is formed dynamically under specific growth conditions by a process that requires RNAi, and is enriched in histone H3 methylated on lysine 9 (H3K9me)." [PMID:23151475, PMID:24210919]
+comment: The reason for obsoletion is that this term was added in error.
synonym: "HOOD" EXACT [PMID:23151475]
-is_a: GO:0000792 ! heterochromatin
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26839" xsd:anyURI
+is_obsolete: true
+consider: GO:0000792
created_by: mah
creation_date: 2014-03-21T15:40:48Z
@@ -629552,11 +630090,13 @@
[Term]
id: GO:1990762
-name: cytoplasmic alanyl-tRNA aminoacylation
+name: obsolete cytoplasmic alanyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase involved in cytoplasmic translation." [GOC:vw]
-is_a: GO:0006419 ! alanyl-tRNA aminoacylation
-relationship: part_of GO:0002181 ! cytoplasmic translation
+def: "OBSOLETE. The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase involved in cytoplasmic translation." [GOC:vw]
+comment: The reason for obsoletion is that this term restates an existing molecular function, GO:0004813 alanine-tRNA ligase activity, and adds nothing beyond it. Gene products should be annotated to that molecular function; the biological process is covered by GO:0006418 tRNA aminoacylation for protein translation.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15375" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0006418
created_by: vw
creation_date: 2015-06-08T15:56:51Z
@@ -631100,7 +631640,7 @@
id: GO:1990905
name: dinoflagellate peduncle
namespace: cellular_component
-def: "A small, flexible, finger-like projection of cytoplasm containing an array of microtubles and located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy)." [GOC:at, PMID:1480107, Wikipedia:Dinoflagellate]
+def: "A small, flexible, finger-like projection of cytoplasm containing an array of microtubules and located near the flagellar pores in some photosynthetic as well as nonphotosynthetic dinoflagellate species. Its functions are not fully understood, but it has been associated with feeding behavior (phagotrophy)." [GOC:at, PMID:1480107, Wikipedia:Dinoflagellate]
comment: The term name refers to a taxonomic group to make the label unique with respect to similarly-named anatomical structures.
is_a: GO:0120025 ! plasma membrane bounded cell projection
created_by: pr
@@ -633383,14 +633923,13 @@
[Term]
id: GO:2000100
-name: regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
+name: obsolete regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:obol]
-is_a: GO:2000099 ! regulation of establishment or maintenance of bipolar cell polarity
-is_a: GO:2000769 ! regulation of establishment or maintenance of cell polarity regulating cell shape
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
-relationship: regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:obol]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-09-14T04:44:57Z
@@ -633605,13 +634144,13 @@
[Term]
id: GO:2000115
-name: regulation of maintenance of bipolar cell polarity regulating cell shape
+name: obsolete regulation of maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of maintenance of bipolar cell polarity regulating in cell shape." [GOC:obol]
-is_a: GO:2000100 ! regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0061305 ! maintenance of bipolar cell polarity regulating cell shape
-relationship: regulates GO:0061305 ! maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of maintenance of bipolar cell polarity regulating in cell shape." [GOC:obol]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: dph
creation_date: 2010-09-21T06:33:26Z
@@ -635480,14 +636019,13 @@
[Term]
id: GO:2000247
-name: positive regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
+name: obsolete positive regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:obol]
-is_a: GO:2000100 ! regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
-is_a: GO:2000771 ! positive regulation of establishment or maintenance of cell polarity regulating cell shape
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
-relationship: positively_regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:obol]
+comment: The reason for obsoletion is that these terms were added in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: vw
creation_date: 2010-11-11T11:39:34Z
@@ -642623,14 +643161,13 @@
[Term]
id: GO:2000750
-name: negative regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
+name: obsolete negative regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:mah]
-is_a: GO:2000100 ! regulation of establishment or maintenance of bipolar cell polarity regulating cell shape
-is_a: GO:2000770 ! negative regulation of establishment or maintenance of cell polarity regulating cell shape
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
-relationship: negatively_regulates GO:0061246 ! establishment or maintenance of bipolar cell polarity regulating cell shape
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of establishment or maintenance of bipolar cell polarity regulating cell shape." [GOC:mah]
+comment: The reason for obsoletion is that this term was made in error.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21217" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0061245
created_by: mah
creation_date: 2011-06-16T11:51:49Z
@@ -649884,9 +650421,10 @@
[Term]
id: GO:2001289
-name: lipid X metabolic process
+name: obsolete lipid X metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving lipid X, 2,3-diacylglucosamine 1-phosphate." [GOC:obol]
+def: "OBSOLETE. The chemical reactions and pathways involving lipid X, 2,3-diacylglucosamine 1-phosphate." [GOC:obol]
+comment: The reason for obsoletion is that this term was made in error and is an unnecessary grouping term.
synonym: "2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate metabolic process" RELATED [GOC:obol]
synonym: "2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate metabolism" RELATED [GOC:obol]
synonym: "2,3-Bis(beta-hydoroxymyristoyl)-beta-D-glucosaminyl 1-phosphate metabolic process" RELATED [GOC:obol]
@@ -649894,8 +650432,8 @@
synonym: "2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose metabolic process" EXACT [GOC:obol]
synonym: "2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose metabolism" EXACT [GOC:obol]
synonym: "lipid X metabolism" EXACT [GOC:obol]
-is_a: GO:0006040 ! amino sugar metabolic process
-is_a: GO:0019637 ! organophosphate metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32273" xsd:anyURI
+is_obsolete: true
created_by: tb
creation_date: 2012-01-13T11:28:58Z
@@ -650514,8 +651052,9 @@
name: rescue of stalled mitochondrial ribosome
namespace: biological_process
def: "A process of mitochondrial translational elongation that takes place when a mitochondrial ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex." [PMID:33243891]
+is_a: GO:0032790 ! ribosome disassembly
is_a: GO:0070125 ! mitochondrial translational elongation
-is_a: GO:0072344 ! rescue of stalled cytosolic ribosome
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26238" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30547" xsd:anyURI
created_by: dragon-ai-agent
@@ -650961,8 +651500,8 @@
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
+is_a: GO:7770107 ! RNA (adenine-N6)-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
@@ -651420,6 +651959,490 @@
created_by: dragon-ai-agent
creation_date: 2026-07-22T21:20:31Z
+[Term]
+id: GO:7770089
+name: large conductance calcium-activated potassium channel inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents, or reduces the activity of a large conductance calcium-activated potassium channel." [PMID:17591990, PMID:39971906]
+synonym: "BK calcium-activated potassium channel inhibitor activity" EXACT []
+synonym: "BK channel inhibitor activity" RELATED []
+synonym: "BK KCa channel inhibitor activity" EXACT []
+synonym: "large conductance KCa channel inhibitor activity" EXACT []
+is_a: GO:0019870 ! potassium channel inhibitor activity
+relationship: negatively_regulates GO:0060072 ! large conductance calcium-activated potassium channel activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32358" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-28T00:46:41Z
+
+[Term]
+id: GO:7770090
+name: voltage-gated potassium channel inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents, or reduces the activity of a voltage-gated potassium channel." [PMID:35797055]
+synonym: "Kv channel inhibitor activity" EXACT []
+synonym: "Kv inhibitor activity" EXACT []
+synonym: "voltage-gated potassium channel (Kv) inhibitor activity" EXACT []
+is_a: GO:0019870 ! potassium channel inhibitor activity
+relationship: negatively_regulates GO:0005249 ! voltage-gated potassium channel activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32371" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-28T16:49:43Z
+
+[Term]
+id: GO:7770091
+name: lipoyl-GcvH:protein N-lipoyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N6-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + L-lysyl-[lipoyl-carrier protein] = L-lysyl-[glycine-cleavage complex H protein] + N6-[(R)-lipoyl]-L-lysyl-[lipoyl-carrier protein]." [EC:2.3.1.204, PMID:38624243]
+comment: The enzyme also transfers the biosynthetic precursor octanoyl group, and relays the acyl group from GcvH onto the E2 subunits of the pyruvate, 2-oxoglutarate, branched-chain 2-oxoacid and acetoin dehydrogenase complexes.
+synonym: "lipoyl amidotransferase activity" BROAD []
+synonym: "lipoyl relay activity" RELATED []
+synonym: "octanoyl-[GcvH]:protein N-octanoyltransferase activity" RELATED []
+xref: EC:2.3.1.204
+xref: RHEA:16413
+xref: RHEA:20213
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+is_a: GO:0140096 ! catalytic activity, acting on a protein
+property_value: skos:exactMatch EC:2.3.1.204
+property_value: skos:narrowMatch RHEA:16413
+property_value: skos:narrowMatch RHEA:20213
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32361" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-28T20:08:06Z
+
+[Term]
+id: GO:7770092
+name: Sec body
+namespace: cellular_component
+def: "A condensate that forms reversibly in the cytoplasm under stress, notably amino acid starvation or salt stress, by coalescence of endoplasmic reticulum exit site (ERES) components including the scaffold protein Sec16 and COPII coat subunits. Sec bodies form through liquid-liquid phase separation and act as a protective reservoir for ERES components, permitting reversible shutdown of the early secretory pathway and promoting cell survival during stress." [PMID:25386913, PMID:31152627, PMID:36325988]
+comment: A Sec body forms from components of an endoplasmic reticulum exit site (GO:0070971), which is progressively depleted as the Sec body grows; a Sec body is a distinct structure and is not part of an ER exit site.
+synonym: "sec-body" EXACT []
+is_a: GO:0043232 ! intracellular membraneless organelle
+relationship: part_of GO:0005737 ! cytoplasm
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32313" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-28T23:40:49Z
+
+[Term]
+id: GO:7770093
+name: Sec body assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a Sec body." [PMID:25386913, PMID:27874829]
+synonym: "Sec body formation" EXACT []
+synonym: "sec-body assembly" EXACT []
+is_a: GO:0140694 ! membraneless organelle assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32314" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-28T23:40:49Z
+
+[Term]
+id: GO:7770094
+name: ER membrane protein retrieval receptor activity
+namespace: molecular_function
+def: "Binding to a retrieval signal, such as a C-terminal KKXX/KXKX-type dilysine motif or an exposed transmembrane domain determinant, present on integral membrane proteins that have escaped from the endoplasmic reticulum (ER) to the Golgi, and mediating their return to the ER." [PMID:12972550]
+synonym: "dilysine motif binding" NARROW []
+synonym: "endoplasmic reticulum membrane protein retrieval receptor activity" EXACT []
+synonym: "KKXX motif binding" NARROW []
+synonym: "KKXX signal receptor activity" NARROW []
+is_a: GO:0038024 ! cargo receptor activity
+relationship: part_of GO:0006890 ! retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32307" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-29T19:05:05Z
+
+[Term]
+id: GO:7770095
+name: 4'-phosphopantetheine phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: (R)-4'-phosphopantetheine + H2O = (R)-pantetheine + phosphate." [EC:3.1.3.110, PMID:18678912, PMID:27322068, PMID:35896750, RHEA:68328]
+synonym: "pantetheine-4'-phosphate phosphatase activity" EXACT []
+synonym: "phosphopantetheine phosphatase activity" EXACT []
+xref: EC:3.1.3.110
+xref: KEGG_REACTION:R10748
+xref: MetaCyc:RXN-24222
+xref: RHEA:68328
+is_a: GO:0016791 ! phosphatase activity
+property_value: skos:exactMatch EC:3.1.3.110
+property_value: skos:exactMatch MetaCyc:RXN-24222
+property_value: skos:exactMatch RHEA:68328
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32389" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-30T17:40:49Z
+
+[Term]
+id: GO:7770096
+name: FAD regeneration via ETF:ETFQO system
+namespace: biological_process
+def: "A metabolic process that transfers electrons produced by FAD-dependent dehydrogenases involved in amino acid and lipid catabolism to the electron transport chain. Electrons released during FADH2 oxidation are transferred by electron-transfer flavoprotein (ETF) to ETF-ubiquinone oxidoreductase (ETF-QO), which in turn transfers them to ubiquinone and then to complex III of the electron transport chain." [PMID:28808132, PMID:33450351]
+comment: In eukaryotes, FAD regeneration via the ETF:ETFQO system occurs in the mitochondrion, with ETF in the matrix and ETF-QO in the inner membrane. Some bacteria and archaea have a similar system, so no taxon constraint applies to this term. This term covers the ETF/ETF-QO route specifically; do not use it for flavoprotein dehydrogenases that reduce the quinone pool directly without ETF (for example succinate dehydrogenase, see GO:0006121), or for reoxidation of flavin by molecular oxygen in peroxisomes or the endoplasmic reticulum.
+synonym: "ETF-ETFQO system" EXACT []
+synonym: "FAD regeneration via ETF-ETFQO system" EXACT []
+synonym: "reoxidation of reduced electron transfer flavoprotein" EXACT []
+is_a: GO:0022904 ! respiratory electron transport chain
+is_a: GO:0046443 ! FAD metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32355" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-30T22:03:00Z
+
+[Term]
+id: GO:7770097
+name: nutrient assimilation
+namespace: biological_process
+def: "The chemical reactions and pathways by which a cell or organism takes up a nutrient from its environment and incorporates it into cellular constituents, characteristically converting a simple, usually inorganic, nutrient source such as nitrate, sulfate, ammonia or a one-carbon compound into organic constituents of the cell." [PMID:22103536, PMID:27572125, PMID:34973427]
+subset: gocheck_do_not_annotate
+synonym: "assimilation of nutrients" EXACT []
+is_a: GO:0008152 ! metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32376" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-07-29T05:36:39Z
+
+[Term]
+id: GO:7770098
+name: ATP-dependent folded protein transmembrane transporter activity
+namespace: molecular_function
+def: "Enables the transfer of a protein in its native, folded conformation from one side of a membrane to the other, coupled to the hydrolysis of ATP and without unfolding of the substrate, according to the reaction: ATP + H2O + protein[side 1] = ADP + phosphate + protein[side 2]." [PMID:31988523, PMID:32042153, PMID:40410623]
+comment: This activity is exemplified by the mitochondrial inner membrane AAA-ATPase Bcs1 (BCS1L in mammals), which translocates the folded, 2Fe-2S-loaded Rieske iron-sulfur protein from the mitochondrial matrix across the inner membrane during respiratory complex III assembly. Unlike most AAA+ protein translocases, the substrate is not threaded through an axial pore in an extended conformation; in Bcs1 it passes between two aqueous vestibules separated by a seal, in an airlock-like mechanism that preserves the membrane permeability barrier. Do not use this term for the separable channel and motor activities of multi-subunit translocases; for those, consider 'transmembrane protein transporter activity ; GO:0008320' and 'protein translocation chaperone activity ; GO:0140388'.
+synonym: "ATPase-coupled folded protein transmembrane transporter activity" EXACT []
+synonym: "folded protein translocase activity" RELATED []
+synonym: "folded protein-transporting ATPase activity" EXACT []
+is_a: GO:0015450 ! protein-transporting ATPase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32394" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T00:40:41Z
+
+[Term]
+id: GO:7770099
+name: glutaredoxin-dependent peroxiredoxin activity
+namespace: molecular_function
+def: "Catalysis of the reaction: [glutaredoxin]-dithiol + a hydroperoxide = [glutaredoxin]-disulfide + an alcohol + H2O." [PMID:11832487, PMID:12517450, RHEA:62624]
+synonym: "GrxPx activity" EXACT []
+synonym: "thiol peroxidase activity" RELATED []
+xref: EC:1.11.1.25
+xref: RHEA:62624
+is_a: GO:0051920 ! peroxiredoxin activity
+property_value: skos:exactMatch EC:1.11.1.25
+property_value: skos:exactMatch RHEA:62624
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32405" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T17:43:33Z
+
+[Term]
+id: GO:7770100
+name: mycoredoxin-dependent peroxiredoxin activity
+namespace: molecular_function
+def: "Catalysis of the reaction: [mycoredoxin]-dithiol + a hydroperoxide = [mycoredoxin]-disulfide + an alcohol + H2O." [PMID:19737009, PMID:24379404, RHEA:62640]
+synonym: "thiol peroxidase activity" RELATED []
+xref: EC:1.11.1.29
+xref: RHEA:62640
+is_a: GO:0051920 ! peroxiredoxin activity
+property_value: skos:exactMatch EC:1.11.1.29
+property_value: skos:exactMatch RHEA:62640
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32405" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T17:43:33Z
+
+[Term]
+id: GO:7770101
+name: glutathione-dependent peroxiredoxin activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a hydroperoxide + 2 glutathione = an alcohol + glutathione disulfide + H2O." [PMID:12606554, PMID:15004285, RHEA:62632]
+synonym: "thiol peroxidase activity" RELATED []
+xref: EC:1.11.1.27
+xref: RHEA:62632
+xref: RHEA:69412
+xref: RHEA:69651
+xref: RHEA:76731
+is_a: GO:0004601 ! peroxidase activity
+property_value: skos:exactMatch EC:1.11.1.27
+property_value: skos:exactMatch RHEA:62632
+property_value: skos:narrowMatch RHEA:69412
+property_value: skos:narrowMatch RHEA:69651
+property_value: skos:narrowMatch RHEA:76731
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32405" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T17:43:33Z
+
+[Term]
+id: GO:7770102
+name: response to interleukin-5
+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 interleukin-5 stimulus." [PMID:41207640]
+synonym: "response to IL-5" EXACT []
+is_a: GO:0034097 ! response to cytokine
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32411" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T23:16:15Z
+
+[Term]
+id: GO:7770103
+name: cellular response to interleukin-5
+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 an interleukin-5 stimulus." [PMID:41207640]
+synonym: "cellular response to IL-5" EXACT []
+is_a: GO:0071345 ! cellular response to cytokine stimulus
+is_a: GO:7770102 ! response to interleukin-5
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32411" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-04T23:16:15Z
+
+[Term]
+id: GO:7770104
+name: Tim8-Tim13 complex
+namespace: cellular_component
+def: "A chaperone complex located in the mitochondrial intermembrane space, composed of the small TIM proteins Tim8 and Tim13." [PMID:11101512, PMID:33355130]
+synonym: "TIM8-13 complex" EXACT []
+is_a: GO:0042719 ! mitochondrial intermembrane space chaperone complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32408" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-07T16:51:54Z
+
+[Term]
+id: GO:7770105
+name: Tim9-Tim10 complex
+namespace: cellular_component
+def: "A chaperone complex located in the mitochondrial intermembrane space, composed of the small TIM proteins Tim9 and Tim10." [PMID:16387659, PMID:33355130]
+synonym: "TIM9-10 complex" EXACT []
+is_a: GO:0042719 ! mitochondrial intermembrane space chaperone complex
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32408" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-07T16:51:54Z
+
+[Term]
+id: GO:7770106
+name: ATP-dependent protein-RNA complex displacement activity
+namespace: molecular_function
+def: "An activity that displaces a protein or protein complex from RNA in a ribonucleoprotein (RNP) complex, driven by ATP hydrolysis." [PMID:11175897, PMID:15118161, PMID:28864812, PMID:39122693]
+comment: Analogous to the DNA-side activity GO:0061995 (ATP-dependent protein-DNA complex displacement activity). The community-used term "RNPase" refers to this activity.
+synonym: "ATP-dependent RNA-protein complex displacement activity" EXACT []
+synonym: "RNP remodeling ATPase activity" BROAD []
+synonym: "RNPase activity" EXACT []
+is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32232" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-07T16:59:22Z
+
+[Term]
+id: GO:7770107
+name: RNA (adenine-N6)-methyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an adenosine in RNA + S-adenosyl-L-methionine = an N(6)-methyladenosine in RNA + S-adenosyl-L-homocysteine + H+." [PMID:34023900, PMID:36736310]
+synonym: "RNA (N6-adenosine)-methyltransferase activity" EXACT []
+synonym: "RNA m6A methyltransferase activity" EXACT []
+is_a: GO:0008170 ! N-methyltransferase activity
+is_a: GO:0008173 ! RNA methyltransferase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27200" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-07T23:44:01Z
+
+[Term]
+id: GO:7770108
+name: citrate-malate shuttle
+namespace: biological_process
+def: "The process of transferring acetyl-CoA from the mitochondrion to the cytosol via citrate. Acetyl-CoA and oxaloacetate produced in the mitochondrion are condensed to citrate by citrate synthase; the citrate is exported to the cytosol by the mitochondrial citrate/malate antiporter in exchange for malate; in the cytosol, ATP citrate lyase cleaves the citrate back to acetyl-CoA and oxaloacetate; the oxaloacetate is then reduced to malate by cytosolic malate dehydrogenase, and the malate is imported back into the mitochondrion to complete the cycle." [PMID:32414018, PMID:35264789]
+synonym: "acetyl-CoA biosynthesis from citrate" NARROW []
+synonym: "citrate-malate cycle" EXACT []
+synonym: "malate-citrate shuttle" EXACT []
+synonym: "non-canonical TCA cycle" RELATED []
+xref: Wikipedia:Citrate-malate_shuttle
+is_a: GO:0006084 ! acetyl-CoA metabolic process
+is_a: GO:0006101 ! citrate metabolic process
+intersection_of: GO:0008152 ! metabolic process
+intersection_of: has_part GO:0003878 ! ATP citrate synthase activity
+intersection_of: has_part GO:0030060 ! L-malate dehydrogenase (NAD+) activity
+relationship: has_part GO:0003878 ! ATP citrate synthase activity
+relationship: has_part GO:0006843 ! mitochondrial citrate transmembrane transport
+relationship: has_part GO:0030060 ! L-malate dehydrogenase (NAD+) activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32353" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-12T10:08:31Z
+
+[Term]
+id: GO:7770109
+name: myo-inositol export across plasma membrane
+namespace: biological_process
+def: "The directed movement of myo-inositol from inside of a cell, across the plasma membrane and into the extracellular region." [PMID:42567923]
+synonym: "inositol export" BROAD []
+synonym: "myo-inositol export" BROAD []
+synonym: "myo-inositol export from cell" EXACT []
+is_a: GO:0015791 ! polyol transmembrane transport
+is_a: GO:0015798 ! myo-inositol transport
+is_a: GO:0140115 ! export across plasma membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32460" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-14T19:33:20Z
+
+[Term]
+id: GO:7770110
+name: exit from cytosolic ribosome hibernation
+namespace: biological_process
+def: "A cellular process that results in the reactivation of hibernating cytosolic ribosomes, enabling them to resume translation. Upon reversal of unfavorable conditions such as nutrient limitation, dedicated molecular machinery reactivates hibernating ribosomes and promotes recovery of active translation." [PMID:32687489, PMID:42129552]
+synonym: "ribosome hibernation exit" EXACT []
+synonym: "ribosome reactivation" RELATED []
+synonym: "translational restart after ribosome hibernation" EXACT []
+is_a: GO:2000767 ! positive regulation of cytoplasmic translation
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32461" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-14T22:52:06Z
+
+[Term]
+id: GO:7770111
+name: group translocator activity
+namespace: molecular_function
+def: "Enables the transfer of a substance from one side of a membrane to the other, where the substance is chemically modified as an integral part of the translocation process, so that the species released on the far side of the membrane is not the species that was bound on the near side. This differs from primary and secondary active transport, in which the transported substance is unchanged." [PMID:31214989, PMID:33170213]
+synonym: "group translocation activity" EXACT []
+synonym: "group translocator" RELATED []
+xref: TC:4
+is_a: GO:0022857 ! transmembrane transporter activity
+relationship: has_part GO:0003824 ! catalytic activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27496" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-18T00:41:26Z
+
+[Term]
+id: GO:7770112
+name: ribosome-associated quality control
+namespace: biological_process
+def: "A protein quality control pathway that acts on ribosomes stalled during translation to target the incomplete nascent polypeptide chain for degradation." [PMID:32569528, PMID:34233554, PMID:35452614]
+comment: The core RQC machinery (NEMF/Rqc2/RqcH and the associated untemplated C-terminal chain elongation) is conserved from bacteria to humans, so this term is not restricted to eukaryotes.
+synonym: "ribosome quality control" EXACT []
+synonym: "ribosome-associated protein quality control" EXACT [PMID:26733220]
+synonym: "RQC" EXACT []
+is_a: GO:0006515 ! protein quality control
+relationship: has_part GO:0030163 ! protein catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18610" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26238" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32546" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-18T05:06:46Z
+
+[Term]
+id: GO:7770113
+name: RQC-specific ribosome subunit dissociation
+namespace: biological_process
+def: "The disaggregation of a stalled ribosome into its constituent large and small ribosomal subunits as part of ribosome-associated quality control (RQC), releasing the large subunit with the incomplete nascent polypeptide chain still attached via peptidyl-tRNA for downstream RQC processing." [PMID:32203490, PMID:32579943, PMID:35452614]
+comment: In eukaryotes, this step is carried out by the yeast RQT complex (Rqt2/Slh1, Rqt3/Cue3, Rqt4) or the metazoan ASCC complex, acting on Hel2/ZNF598-ubiquitinated collided ribosomes. In bacteria, MutS2 splits stalled collided ribosomes; this term is not restricted to eukaryotes.
+synonym: "ASCC-dependent ribosome subunit dissociation" NARROW []
+synonym: "ribosome disassembly involved in ribosome-associated quality control" EXACT []
+synonym: "RQT-dependent ribosome subunit dissociation" NARROW []
+is_a: GO:0032790 ! ribosome disassembly
+intersection_of: GO:0032790 ! ribosome disassembly
+intersection_of: part_of GO:7770112 ! ribosome-associated quality control
+relationship: part_of GO:7770112 ! ribosome-associated quality control
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32478" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-18T18:06:47Z
+
+[Term]
+id: GO:7770114
+name: phagophore membrane
+namespace: cellular_component
+def: "A membrane that is part of a phagophore." [PMID:23217709, PMID:33773106]
+comment: Covers the membrane of the nascent phagophore, including membrane contributed by Atg9/ATG9A-containing vesicles once they have been incorporated into the phagophore, and the membrane of the expanding cup-shaped structure. After the structure has closed, annotate to autophagosome membrane (GO:0000421) instead. Do not use for Atg9/ATG9A-containing vesicles themselves, either before or after their recruitment to the phagophore assembly site: a vesicle is a membrane-bounded structure, not a membrane.
+is_a: GO:0016020 ! membrane
+relationship: part_of GO:0061908 ! phagophore
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29437" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-19T23:59:26Z
+
+[Term]
+id: GO:7770115
+name: Atg9-containing vesicle
+namespace: cellular_component
+def: "A small, single-membrane cytoplasmic vesicle that carries the transmembrane autophagy protein Atg9 (ATG9A in mammals). Vesicles of this type are derived from the Golgi apparatus and from endosomal compartments, and can be delivered to the phagophore assembly site, where they contribute membrane to the nascent phagophore." [PMID:20855505, PMID:22826123, PMID:24034251, PMID:32883836]
+comment: In Saccharomyces cerevisiae these vesicles are 30-60 nm in diameter and approximately three are consumed per autophagosome. In mammals ATG9A vesicles traffic via the trans-Golgi network and recycling endosomes, and a substantial part of the pool is not engaged in autophagosome formation at any given time. Use this term for the vesicle itself, at any stage of its itinerary. Membrane that has been incorporated into the phagophore is phagophore membrane (GO:7770114) rather than a vesicle. The Atg9-containing compartment/reservoir described by Mari et al. (PMID:20855505) is a cluster of these vesicles and tubules rather than a single vesicle; use this term for the individual vesicles that make up such clusters.
+synonym: "Atg9 vesicle" EXACT []
+synonym: "Atg9-containing compartment" RELATED [PMID:20855505]
+synonym: "ATG9A vesicle" NARROW []
+is_a: GO:0031410 ! cytoplasmic vesicle
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29437" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-20T23:57:41Z
+
+[Term]
+id: GO:7770116
+name: obsolete lectin-type holdase activity
+namespace: molecular_function
+def: "OBSOLETE. A holdase activity that additionally recognizes a specific glycan structure on a protein via a lectin domain, and prevents aggregation of the protein until it is correctly folded." [PMID:16467570]
+comment: The reason for obsoletion is that this term was added in error.
+synonym: "carbohydrate-binding holdase" EXACT []
+synonym: "lectin chaperone" RELATED []
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32494" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0140309
+created_by: ai4c-agent
+creation_date: 2026-08-26T21:57:40Z
+
+[Term]
+id: GO:7770117
+name: proteasomal degradation of multi-protein complex orphan subunits
+namespace: biological_process
+def: "A protein quality control pathway that results in the ubiquitin-dependent, proteasome-mediated breakdown of orphan subunits of a multi-protein complex (including complexes that also contain non-protein components, such as the ribosome), i.e. subunits that have failed to assemble into their cognate complex, for example as a result of imbalanced subunit synthesis. This process eliminates unassembled subunits and thereby maintains protein complex stoichiometry." [PMID:28774922, PMID:35316660, PMID:37480851]
+synonym: "degradation of orphan subunits of multi-protein complexes" BROAD []
+synonym: "orphan subunit degradation" BROAD []
+is_a: GO:0006515 ! protein quality control
+is_a: GO:0043161 ! proteasome-mediated ubiquitin-dependent protein catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32274" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-08-27T23:33:52Z
+
+[Term]
+id: GO:7770118
+name: amino acid--[peptidyl-carrier protein] ligase activity
+namespace: molecular_function
+def: "Catalysis of the ATP-dependent activation of an amino acid and its transfer as a thiol ester to the phosphopantetheine prosthetic group of a peptidyl-carrier protein, according to the reaction: an amino acid + ATP + holo-[peptidyl-carrier protein] = an aminoacyl-[peptidyl-carrier protein] + AMP + diphosphate. This is the reaction carried out by adenylation (A) domains of nonribosomal peptide synthetases, and by the standalone type II adenylation enzymes that load amino acids onto peptidyl-carrier proteins in related assembly lines." [PMID:17502372, PMID:9250661]
+synonym: "amino acid adenylylation by nonribosomal peptide synthase" RELATED []
+synonym: "NRPS adenylation domain activity" RELATED []
+xref: RHEA:11656
+xref: RHEA:59436
+xref: RHEA:61680
+xref: RHEA:61688
+xref: RHEA:61696
+xref: RHEA:61704
+xref: RHEA:61788
+xref: RHEA:61800
+xref: RHEA:62452
+xref: RHEA:62492
+is_a: GO:0016878 ! acid-thiol ligase activity
+property_value: skos:narrowMatch RHEA:11656
+property_value: skos:narrowMatch RHEA:59436
+property_value: skos:narrowMatch RHEA:61680
+property_value: skos:narrowMatch RHEA:61688
+property_value: skos:narrowMatch RHEA:61696
+property_value: skos:narrowMatch RHEA:61704
+property_value: skos:narrowMatch RHEA:61788
+property_value: skos:narrowMatch RHEA:61800
+property_value: skos:narrowMatch RHEA:62452
+property_value: skos:narrowMatch RHEA:62492
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30872" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-09-03T23:34:51Z
+
+[Term]
+id: GO:7770119
+name: regulation of mitochondrial respiratory chain complex I assembly
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of mitochondrial respiratory chain complex I assembly." [PMID:42361792]
+is_a: GO:0043254 ! regulation of protein-containing complex assembly
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: regulates GO:0032981 ! mitochondrial respiratory chain complex I assembly
+relationship: regulates GO:0032981 ! mitochondrial respiratory chain complex I assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32577" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-09-11T00:23:26Z
+
+[Term]
+id: GO:7770120
+name: negative regulation of mitochondrial respiratory chain complex I assembly
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of mitochondrial respiratory chain complex I assembly." [PMID:42361792]
+is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
+is_a: GO:7770119 ! regulation of mitochondrial respiratory chain complex I assembly
+intersection_of: GO:0065007 ! biological regulation
+intersection_of: negatively_regulates GO:0032981 ! mitochondrial respiratory chain complex I assembly
+relationship: negatively_regulates GO:0032981 ! mitochondrial respiratory chain complex I assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/32577" xsd:anyURI
+created_by: ai4c-agent
+creation_date: 2026-09-11T00:23:26Z
+
[Typedef]
id: ends_during
name: ends during