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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Missing parent: should protein folding chaperone and RNA folding chaperone have a common parent? #26296

Closed ValWood closed 8 months ago

ValWood commented 1 year ago

See

Screenshot 2023-10-20 at 13 41 11

both are directly under molecular function

pgaudet commented 1 year ago

How about 'macromolecule folding chaperone' ?

ValWood commented 1 year ago

that would work.

raymond91125 commented 1 year ago

I have trouble defining macromolecular folding chaperone. Perhaps what you want is a term like 'protein/RNA folding chaperone'? I am not sure what should be the limit of macromolecules. CHEBI:33839 A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. I don't think the types of proteins (or RNAs PMID: 27791471) are similar between RNA folding chaperones and protein folding chaperones thus this grouping class may not be very useful.

ValWood commented 1 year ago

Hi @raymond91125

The term GO:0140691 RNA folding chaperone Binding to an RNA or an RNA-containing complex to assist the folding process. PMID:31165735

is describing proteins which act as chaperones for correct RNA folding, not for RNA's acting as chaperones for protein folding (as in PMID: 27791471) .

I'm not sure that my thinking is correct here, but I think what we are trying to group is "activity" not mechanism, and the 'activity' of an "RNA folding chaperone" and a "protein folding chaperone" are broadly aligned as they are both binding the protein (or RNA) to stabilize various folding intermediates ensure correct folding by preventing non specific binding or aggregation.

That said, I also cannot easily think of a suitable grouping term, which might be why they were never grouped. They may be different enough to keep separate, and they are relatively easy to locate as they are both direct children of molecular function.

I'm happy for this to close, as it isn't critical.

raymond91125 commented 8 months ago

Closed for now. Thanks.