TPV GO:0006506 GPI anchor biosynthetic process should not be GO:0006661 (phosphatidylinositol biosynthetic process)

[ValWood]

GO:0006506 GPI anchor biosynthetic process should not be GO:0006661 phosphatidylinositol biosynthetic process

phosphatidylinositol forms part of the GPI anchor, therefore phosphatidylinositol biosynthetic process precedes GO:0006506 GPI anchor biosynthetic process and GPI anchor biosynthetic process is not part of GO:0006661 phosphatidylinositol biosynthetic process

(because it has other parts)

[pgaudet]

It looks like the problem is that the logical definition is

'biosynthetic process' and ('has primary output' some glycosylphosphatidylinositol), ie CHEBI:24410

According to ChEBI this is correct:

[ValWood]

Of couse, glyco-phosphoinositols are phosphoinositols.

But the phosphoinositol part already exists when the glyco part is formed.

It's a bit unsatisfactory that there is no grouping term for inositol phosphate IP and phosphatidyl inositol phosphate PIP etc which are a much smaller class than the glyco part. We would be unlikely to see enrichment for the PI/PIP/ etc pathways

i.e.

because of the larger number of genes involved in building the GPI part of of a GPI anchor.

A GPI is a phospholipid, but really the glyco part is a modification to an existing phospholipid.

It is impossible to access the list of phospholipid synthesis pathways in GO without pulling in all of the 31 genes involved in the 'glyco- part

[ValWood]

@pgaudet So should I ask CHEBI to remove glycosylphosphatidylinositol (CHEBI:24410) is a phosphatidylinositol (CHEBI:28874)

glycophosphatidylinositol includes a phosphatidylinositol core but has additional sugars and other molecules attached, so it isn't a phosphatidylinositol.

[deustp01]

glycophosphatidylinositol includes a phosphatidylinositol core but has additional sugars and other molecules attached, so it isn't a phosphatidylinositol.

But the definition of phosphatidylinositol in ChBI is "Any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol." That definition appears to put no restriction on what else may be attached, so, unless I'm missing something (quite possible) glycophosphatidylinositol fits the definition. Check with someone with a good knowledge of this chemistry?

[pgaudet]

@deustp01 glycerophosphoinositol (CHEBI:36315) is the parent - it does contain glycerol.

The problematic chemical is the child, glycosylphosphatidylinositol (CHEBI:24410)

Maybe ChEBI would agree that glycosylphosphatidylinositol (CHEBI:24410) is a derivative of CHEBI:28874 phosphatidylinositol.

@deustp01 Does this seems correct ?

Thanks, Pascale

[deustp01]

@deustp01 Does this seems correct ?

For what it's worth, yes, but could we get some expert advice on from, say, Kristian Axelsen or Steven Marygold, who are better at biochemical nomenclature and classification and who (at least Kristian) have a direct stake in the outcome?

[pgaudet]

@kaxelsen @sjm41 We'd like your inout on the suggestion above: https://github.com/geneontology/go-ontology/issues/27954#issuecomment-2437851113

[sjm41]

I think this is in @kaxelsen's domain more than mine!

[ValWood]

OK I also mailed lipid maps