"regulation of molecular function" branch

ValWood commented 2 years ago

Please provide as much information as you can:

GO term ID and Label

GO:0065009 "regulation of molecular function"

Reason for deprecation

We have discussed that this term and it's children would be deprecated, but I don't see any ticket for this.

There are currently ~9000 annotations so it will need to be stepwise (with most probably moving to the molecular function regulator term, or removing)

In the interim, is it worth labelling this branch as 'pending obsoletion' and 'not for direct annotation', and alerting people so that further annotations don't accumulate?

ValWood commented 2 years ago

Is there a plan for this? I just finished removing the PomBase annotations to the BP terms "regulation of MF" but annotations are still accumulating (there are still 6313 annotations if I filter on aspect P and experimental evidence).

The label says "automation".

pgaudet commented 1 year ago

Hi,

There are 866 children of 'regulation of molecular function. We can at least start by obsoleting the terms with no annotations - looks like there are 2-300. I'll make the list.

pgaudet commented 1 year ago

Dear all,

The proposal has been made to obsolete 'regulation of molecular function' and all children. The reason for obsoletion is that these represent molecular functions. Please follow the ontology ticket https://github.com/geneontology/go-ontology/issues/22455 if you want to be notified of all obsoletions. We will send annotation review notices for all terms having direct annotations.

Thanks, Pascale

pgaudet commented 1 year ago

These have no annotations:

[x] activation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
[x] activation of protein histidine kinase activity
[x] activation of tryptophan 5-monooxygenase activity

pgaudet commented 1 year ago

Negative regulation terms with no annotations (got the list from AmiGO and re-checked in QuickGO)

[x] negative regulation of 1-phosphatidylinositol 4-kinase activity
[x] negative regulation of 1-phosphatidylinositol-3-kinase activity
[ ] negative regulation of actin binding
[ ] negative regulation of alpha-(1->3)-fucosyltransferase activity
[ ] negative regulation of aminoacyl-tRNA ligase activity
[ ] negative regulation of arginase activity
[x] negative regulation of aspartic endopeptidase activity, intramembrane cleaving
[ ] negative regulation of ATP:ADP antiporter activity
[x] negative regulation of beta1-adrenergic receptor activity
[ ] negative regulation of catalase activity
[ ] negative regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity
[ ] negative regulation of chemorepellent activity
[ ] negative regulation of choline O-acetyltransferase activity
[ ] negative regulation of cohesin unloading
[x] negative regulation of coreceptor activity involved in epidermal growth factor receptor signaling pathway
[ ] negative regulation of cytochrome-c oxidase activity
[ ] negative regulation of diacylglycerol kinase activity
[x] negative regulation of DNA N-glycosylase activity
[x] negative regulation of DNA nucleotidylexotransferase activity
[ ] negative regulation of DNA primase activity
[ ] negative regulation of DNA-directed DNA polymerase activity
[x] negative regulation of dUTP diphosphatase activity
[x] negative regulation of endo-1,4-beta-xylanase activity
[ ] negative regulation of euchromatin binding
[ ] negative regulation of exodeoxyribonuclease activity
[ ] negative regulation of ferrous iron binding
[ ] negative regulation of G-quadruplex DNA binding
[ ] negative regulation of GABA-A receptor activity
[ ] negative regulation of glucuronosyltransferase activity
[ ] negative regulation of glutamate-cysteine ligase activity
[ ] negative regulation of glutathione peroxidase activity
[ ] negative regulation of growth hormone activity
[ ] negative regulation of heme oxygenase activity
[ ] negative regulation of heparan sulfate binding
[ ] negative regulation of heparan sulfate proteoglycan binding
[x] negative regulation of histone demethylase activity (H3-K4 specific)
[ ] negative regulation of iron ion transmembrane transporter activity
[ ] negative regulation of isoleucine-tRNA ligase activity
[ ] negative regulation of L-dopa decarboxylase activity
[ ] negative regulation of ligase activity
[ ] negative regulation of light-activated channel activity
[ ] negative regulation of malate dehydrogenase (decarboxylating) (NADP+) activity
[x] negative regulation of methionine-tRNA ligase activity
[ ] negative regulation of microtubule plus-end binding
[ ] negative regulation of mRNA 3-UTR binding
[ ] negative regulation of mRNA cap binding
[ ] negative regulation of myosin light chain kinase activity
[ ] negative regulation of NAD+ ADP-ribosyltransferase activity
[ ] negative regulation of NAD+ kinase activity
[ ] negative regulation of nerve growth factor receptor activity
[ ] negative regulation of osmolarity-sensing cation channel activity
[ ] negative regulation of phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity
[ ] negative regulation of phospholipid scramblase activity
[ ] negative regulation of poly(A)-specific ribonuclease activity
[ ] negative regulation of polysome binding
[ ] negative regulation of potassium:proton exchanging ATPase activity
[ ] negative regulation of prostaglandin-E synthase activity
[ ] negative regulation of protein histidine kinase activity
[ ] negative regulation of protein-glutamine gamma-glutamyltransferase activity
[ ] negative regulation of proteinase activated receptor activity
[ ] negative regulation of proton-transporting ATP synthase activity, rotational mechanism
[ ] negative regulation of pyruvate kinase activity
[ ] negative regulation of restriction endodeoxyribonuclease activity
[ ] negative regulation of RNA binding transcription factor activity
[ ] negative regulation of RNA polymerase III activity
[ ] negative regulation of small GTPase binding
[ ] negative regulation of substance P receptor binding
[ ] negative regulation of succinate dehydrogenase activity
[ ] negative regulation of SUMO transferase activity
[x] negative regulation of threonine-tRNA ligase activity
[ ] negative regulation of transferrin receptor binding
[ ] negative regulation of triplex DNA binding
[ ] negative regulation of tubulin deacetylase activity
[ ] negative regulation of type I site-specific deoxyribonuclease activity
[ ] negative regulation of type II site-specific deoxyribonuclease activity
[ ] negative regulation of type III site-specific deoxyribonuclease activity
[ ] negative regulation of type IV site-specific deoxyribonuclease activity
[ ] negative regulation of tyrosinase activity
[ ] negative regulation of tyrosine 3-monooxygenase activity
[ ] negative regulation of voltage-gated chloride channel activity
[ ] negative regulation of voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization
[ ] negative regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization
[ ] negative regulation of water channel activity

pgaudet commented 1 year ago

Positive regulation with no annotations:

[ ] positive regulation of acid-sensing ion channel activity
[ ] positive regulation of actin binding
[ ] positive regulation of advanced glycation end-product receptor activity
[ ] positive regulation of all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity
[ ] positive regulation of alpha-(1->3)-fucosyltransferase activity
[ ] positive regulation of apolipoprotein binding
[x] positive regulation of argininosuccinate synthase activity
[x] positive regulation of aspartic endopeptidase activity, intramembrane cleaving
[x] positive regulation of beta1-adrenergic receptor activity
[ ] positive regulation of brain-derived neurotrophic factor-activated receptor activity
[ ] positive regulation of C-C chemokine binding
[ ] positive regulation of calcium ion binding
[x] positive regulation of coreceptor activity involved in epidermal growth factor receptor signaling pathway
[ ] positive regulation of corticotropin-releasing hormone receptor activity
[ ] positive regulation of creatine transmembrane transporter activity
[ ] positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in meiotic nuclear division
[ ] positive regulation of cystathionine beta-synthase activity
[ ] positive regulation of D-amino-acid oxidase activity
[ ] positive regulation of D-erythro-sphingosine kinase activity
[x] positive regulation of DNA nucleotidylexotransferase activity
[ ] positive regulation of double-stranded telomeric DNA binding
[ ] positive regulation of electron transfer activity
[ ] positive regulation of euchromatin binding
[ ] positive regulation of G-protein activated inward rectifier potassium channel activity
[ ] positive regulation of G-quadruplex DNA binding
[ ] positive regulation of GABA-A receptor activity
[ ] positive regulation of glucuronosyltransferase activity
[ ] positive regulation of glycogen synthase activity, transferring glucose-1-phosphate
[ ] positive regulation of growth hormone activity
[ ] positive regulation of heme oxygenase activity
[ ] positive regulation of heparan sulfate proteoglycan biosynthesis by positive regulation of epimerase activity
[x] positive regulation of histone demethylase activity (H3-K4 specific)
[ ] positive regulation of IKACh channel activity by G protein-coupled acetylcholine receptor signaling pathway involved in negative regulation of heart rate
[ ] positive regulation of intracellular calcium activated chloride channel activity
[ ] positive regulation of iron ion transmembrane transporter activity
[x] positive regulation of leucine-tRNA ligase activity
[ ] positive regulation of light-activated channel activity
[ ] positive regulation of lipid binding
[ ] positive regulation of m7G(5)pppN diphosphatase activity
[ ] positive regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process
[ ] positive regulation of methylenetetrahydrofolate reductase (NAD(P)H) activity
[ ] positive regulation of microtubule minus-end binding
[ ] positive regulation of mRNA 3-UTR binding
[ ] positive regulation of NAD+ kinase activity
[ ] positive regulation of nerve growth factor receptor activity
[ ] positive regulation of osmolarity-sensing cation channel activity
[ ] positive regulation of phosphodiesterase activity, acting on 3-phosphoglycolate-terminated DNA strands
[ ] positive regulation of poly(A)-specific ribonuclease activity
[ ] positive regulation of proteinase activated receptor activity
[ ] positive regulation of pyruvate kinase activity
[ ] positive regulation of recombination hotspot binding
[ ] positive regulation of RNA binding transcription factor activity
[ ] positive regulation of selenocysteine insertion sequence binding
[ ] positive regulation of small GTPase binding
[ ] positive regulation of substance P receptor binding
[ ] positive regulation of triplex DNA binding
[ ] positive regulation of tubulin deacetylase activity
[ ] positive regulation of water channel activity
[ ] positive regulation of water channel activity involved in maintenance of lens transparency

pgaudet commented 1 year ago

Regulation with no annotations (and children not annotated):

[ ] regulation of advanced glycation end-product receptor activity 1 NAS @RLovering
[x] regulation of apurinic/apyrimidinic endodeoxyribonuclease activity
[x] regulation of argininosuccinate synthase activity
[x] regulation of aspartic endopeptidase activity, intramembrane cleaving
[x] regulation of beta1-adrenergic receptor activity
[x] regulation of coreceptor activity involved in epidermal growth factor receptor signaling pathway
[x] regulation of DNA nucleotidylexotransferase activity
[x] regulation of histone demethylase activity (H3-K4 specific)
[ ] regulation of NAD+ kinase activity
[ ] regulation of osmolarity-sensing cation channel activity
[ ] regulation of poly(A)-specific ribonuclease activity
[ ] regulation of tubulin deacetylase activity
[ ] regulation of type I site-specific deoxyribonuclease activity
[ ] regulation of type II site-specific deoxyribonuclease activity
[ ] regulation of type III site-specific deoxyribonuclease activity
[ ] regulation of type IV site-specific deoxyribonuclease activity
[ ] regulation of tyrosinase activity
[ ] regulation of tyrosine 3-monooxygenase activity
[ ] regulation of urease activity
[ ] regulation of water channel activity

pfey03 commented 1 year ago

@pgaudet @ValWood - I just now came across this. There are many children under this top term GO:0065009. are all the children that are positive regulation of MF obsoleted? Some children are activation of MF those stay I hope. But what about 'GO:1903669 positive regulation of chemorepellent activity' for example. Why can't MF be regulated? We have, including the activation terms 126 annotations. Need clarification before going into this and this will be hard.

We have 86 regulation , positive , negative of MF, of which 3 ISS, 1 TAS rest EXP, and 39 activation of MF with 1 TAS. ISS and maybe TAS I may delete but the rest will be tough.

pgaudet commented 1 year ago

Hi @pfey03

These will also be obsoleted. 'activation of' should be moved to 'x regulator activity'. Unfortunately these need to be manually reannotated as we cannot safely move a BP to a MF.

Thanks, Pascale

jlewsmith commented 1 year ago

CGD done

pfey03 commented 1 year ago

Dicty done and filled the Google table

pgaudet commented 2 months ago

These have no remaining annotations, see https://github.com/geneontology/go-annotation/issues/5450

[x] GO:0031552 negative regulation of brain-derived neurotrophic factor-activated receptor activity
[x] GO:0031586 negative regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity
[x] GO:0090073 positive regulation of protein homodimerization activity
[x] GO:1900261 positive regulation of RNA-dependent RNA polymerase activity
[x] GO:1902160 negative regulation of cyclic nucleotide-gated ion channel activity
[x] GO:1902963 negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process
[x] GO:1903280 negative regulation of calcium:sodium antiporter activity
[x] GO:1903591 negative regulation of lysozyme activity
[x] GO:1903869 negative regulation of methylenetetrahydrofolate reductase (NAD(P)H) activity
[x] GO:1903954 positive regulation of voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization
[x] GO:1904219 positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity
[x] GO:1904255 negative regulation of iron ion transmembrane transporter activity
[x] GO:1904605 positive regulation of advanced glycation end-product receptor activity
[x] GO:1904876 negative regulation of DNA ligase activity
[x] GO:1905775 negative regulation of DNA helicase activity
[x] GO:0010578 regulation of adenylate cyclase activity involved in G protein-coupled receptor signaling pathway

geneontology / go-ontology

"regulation of molecular function" branch #22455