Obsoletion request: GO:0044845 chain elongation of O-linked mannose residue about go-ontology

[ValWood]

Yes I now think that most of the branch can go. I have been holding off because I am not sure about the
N-linked, O-linked etc.

So far I have only done the N-linked GO:0006488 dolichol-linked oligosaccharide biosynthetic process
so I noted any terms that were clearly MF terms during that work

Lets discuss this one on Monday

[pgaudet]

There are other siblings:

GO:0035269    protein O-linked mannosylation | is_a
GO:0018406    protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan

I think these should also be obsoleted?

Also, can you suggest which MF the terms correspond to?

Thanks!

Pascale

[ValWood]

I don't think there is a direct mapping for these, they are only describing the type of linakge.

For GO:0035269 protein O-linked mannosylation
they can be GPI anchor biosynthetic process (pombe dpm1,2,3,4 )

or ogm2,4 omh3
call wall mannoprotein biosynthetic process

and I think some could be
GO:0006488 | dolichol-linked oligosaccharide biosynthetic process
although I only have these with MF mannosyltransferases

[ValWood]

I realise you asked about MF. These are multiple.

dolichyl-phosphate-mannose-protein mannosyltransferase activity
dolichyl-phosphate beta-D-mannosyltransferase activity
alpha-1,2-mannosyltransferase activity
enzyme regulator activity

[ValWood]

@pgaudet should I still go ahead with these obsoletions. I can't suggest precise replacements, but I can suggest that
MF & BP are reviewed.

[ValWood]

@pgaudet let me know if I can go ahead with this one.

[pgaudet]

Hi Val,

How do you plan for the glycosylation branch to be re-organized? I have a hard time making comments if we obsolete some terms, in isolation from the rest of the branch.

Do you want to merge all into GO:0006486 protein glycosylation ?

We could discuss this on Monday's ontology call.

Thanks, Pascale

[pgaudet]

It would be clearer and possibly more efficient if you did a large tickets with all the terms that should be obsoleted, so we have a better idea of the work involved.

Thanks, Pascale

[pgaudet]

Nice review: https://academic.oup.com/glycob/article/19/8/816/1988198

[pgaudet]

See also https://pubmed.ncbi.nlm.nih.gov/37565810/