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

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:0044845 chain elongation of O-linked mannose residue

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that this term represents a molecular function.

• "Replace by" term (ID and label)
  If all annotations can safely be moved to that term

• "Consider" term(s) (ID and label)
  Suggestions for reannotation

• Are there annotations to this term?

• How many EXP:

2 PomBase EXP, removing today

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• Any other information

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Checklist for ontology editor

Check term usage and metadata in Protégé

• check term usage in the ontology
• check internal mappings: RHEA, EC, MetaCyc
• check subset usage
• check taxon constraints

Check annotations

• create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• find external mappings (via IEAS), include in obsoletion notice
• tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• create obsoletion announcement
• announce to GO friends ([email protected])
• paste the text in the ontology ticket

[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

[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]

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/