--- go-lastrelease.obo 2026-08-18 05:38:49.942317460 +0000
+++ go.obo 2026-08-18 05:52:54.152974348 +0000
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2026-07-26
+data-version: releases/2026-08-18
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
@@ -44,7 +44,7 @@
property_value: has_ontology_root_term GO:0003674
property_value: has_ontology_root_term GO:0005575
property_value: has_ontology_root_term GO:0008150
-property_value: owl:versionInfo "2026-07-26" xsd:string
+property_value: owl:versionInfo "2026-08-18" xsd:string
property_value: terms:license http://creativecommons.org/licenses/by/4.0/
[Term]
@@ -1071,8 +1071,10 @@
xref: MetaCyc:SO4ASSIM-PWY
xref: MetaCyc:SULFMETII-PWY
is_a: GO:0006790 ! sulfur compound 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/32376" xsd:anyURI
[Term]
id: GO:0000104
@@ -10748,6 +10750,7 @@
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 +12204,7 @@
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
@@ -16017,13 +16021,13 @@
[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
@@ -34490,7 +34494,7 @@
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 +34514,7 @@
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 +36663,6 @@
xref: RHEA:10736
xref: RHEA:10740
xref: RHEA:12216
-xref: RHEA:12785
xref: RHEA:13221
xref: RHEA:15757
xref: RHEA:16317
@@ -36731,7 +36735,6 @@
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 +37089,32 @@
[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
@@ -61237,11 +61246,13 @@
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
@@ -66958,6 +66969,7 @@
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
@@ -71811,17 +71823,19 @@
[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: "The chemical reactions and pathways resulting in the breakdown or refolding of misfolded, dysfunctional, or incompletely synthesized proteins." [PMID:21746797]
+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/32442" xsd:anyURI
[Term]
id: GO:0006516
@@ -73107,6 +73121,7 @@
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 +73163,7 @@
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
@@ -77490,11 +77506,9 @@
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 +81079,19 @@
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 +81118,27 @@
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 +81158,9 @@
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 +81168,11 @@
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 +81193,7 @@
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 +81202,10 @@
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 +81225,7 @@
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 +81243,18 @@
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 +81343,10 @@
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 +81401,27 @@
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 +82075,10 @@
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
@@ -84132,9 +84161,10 @@
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 +84180,14 @@
[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 +87903,9 @@
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 +88104,24 @@
[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 +90322,7 @@
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 +90338,7 @@
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 +90581,7 @@
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 +90590,12 @@
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
@@ -90754,19 +90789,17 @@
[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 +91099,7 @@
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
@@ -97203,7 +97236,8 @@
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 +97357,8 @@
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
@@ -100802,19 +100836,20 @@
[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
@@ -125811,6 +125846,7 @@
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 +125856,9 @@
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]
@@ -159257,7 +159295,7 @@
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 +159810,12 @@
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 +161809,6 @@
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 +161924,12 @@
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 +162058,7 @@
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 +162450,13 @@
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
@@ -164637,14 +164680,14 @@
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
@@ -188877,12 +188920,12 @@
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
@@ -203927,11 +203970,13 @@
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 +203991,11 @@
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 +205401,9 @@
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
@@ -209095,11 +209142,14 @@
[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 +209162,6 @@
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 +209360,7 @@
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 +209368,7 @@
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 +209376,7 @@
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 +211353,11 @@
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
@@ -222163,6 +222216,7 @@
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
@@ -239543,11 +239597,13 @@
[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 +239614,7 @@
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 +241004,6 @@
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]
@@ -246714,6 +246770,7 @@
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 +248141,7 @@
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 +253234,7 @@
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 +253243,7 @@
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
@@ -259024,11 +259084,10 @@
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
@@ -260158,7 +260217,7 @@
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 []
@@ -278118,66 +278177,81 @@
[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 +278454,47 @@
[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
@@ -279221,28 +279304,33 @@
[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 +279349,16 @@
[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 +279372,6 @@
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 +279384,6 @@
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 +281133,58 @@
[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
@@ -287032,8 +287130,9 @@
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
@@ -298885,23 +298984,27 @@
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 +299493,13 @@
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
@@ -304916,16 +305021,18 @@
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
@@ -331504,11 +331611,12 @@
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
@@ -350108,7 +350216,6 @@
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 +358628,7 @@
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 +358636,13 @@
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
@@ -383918,22 +384022,25 @@
[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 +384974,13 @@
[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 +385637,13 @@
[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 +386315,25 @@
[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
@@ -390717,13 +390831,14 @@
[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 +391333,13 @@
[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 +391508,14 @@
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 +391545,16 @@
[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
@@ -395986,10 +396104,12 @@
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
@@ -399284,7 +399404,7 @@
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]
@@ -414502,7 +414622,7 @@
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
@@ -424177,7 +424297,7 @@
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 +438959,8 @@
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: has_part GO:0006897 ! endocytosis
+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
@@ -439115,8 +439236,10 @@
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 +440823,8 @@
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
@@ -452278,7 +452402,6 @@
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
@@ -453703,10 +453826,14 @@
[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
@@ -461066,10 +461193,11 @@
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
@@ -470428,7 +470556,6 @@
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
@@ -475811,6 +475938,7 @@
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
@@ -479500,6 +479628,7 @@
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
@@ -489129,12 +489258,13 @@
[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
@@ -490404,9 +490534,10 @@
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 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
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/32442" xsd:anyURI
created_by: pg
creation_date: 2020-04-20T15:46:20Z
@@ -490818,13 +490949,15 @@
[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 +492348,7 @@
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
@@ -494862,17 +494995,26 @@
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
@@ -499342,7 +499484,8 @@
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
+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
created_by: pg
creation_date: 2024-02-14T07:11:38Z
@@ -504537,7 +504680,7 @@
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
@@ -506163,6 +506306,7 @@
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
@@ -506186,6 +506330,53 @@
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:0180000
name: histone methyltransferase inhibitor activity
namespace: molecular_function
@@ -550711,12 +550902,13 @@
[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
@@ -578736,7 +578928,7 @@
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 +578945,7 @@
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 +578963,7 @@
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
@@ -633383,14 +633575,13 @@
[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 +633796,13 @@
[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 +635671,13 @@
[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 +642813,13 @@
[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
@@ -650961,8 +651150,8 @@
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 +651609,344 @@
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
+
[Typedef]
id: ends_during
name: ends during