Obsoletion request: GO:0016254 preassembly of GPI anchor in ER membrane about go-ontology

[deustp01]

I don't know how it is differentiated from the parent GPI anchor biosynthesis?

In humans (and I think in yeasts), the overall process can be divided into distinct steps - see R-HSA-163125 " Post-translational modification: synthesis of GPI-anchored proteins", and the reaction sequence covered by GO:0016254 "preassembly ..." is one of them. It wouldn't destroy our annotations to lose this term and annotations were all to the overall parent process, but a useful biological distinction would be lost.

[ValWood]

But do we have the other 2 steps? It's a linear pathway so it adds an extra level of unnecessary complication to add this grouping. If we keep it we should make connections between the MF terms and t this BP because I'm not sure which BPs go under here from the existing annotation PIG-N, PIG-L and PIG-A

Also the definitions should be better to say which part of the pathway it refers to (steps X to Y). DO you know which steps it is?

[deustp01]

Subpathway R-HSA-162710 "Synthesis of glycosylphosphatidylinositol (GPI)" lays out the steps that we grouped under GO:0016524 "preassembly of GPI anchor in ER membrane", and the next subpathway R-HSA-162791 "Attachment of GPI anchor to uPAR" lays out the steps that we grouped under GO:016255 "attachment of GPI anchor to protein"

[ValWood]

GO:016255 "attachment of GPI anchor to protein"
is defined
A transamidation reaction that results in the cleavage of the polypeptide chain and the concomitant transfer of the GPI anchor to the newly formed carboxy-terminal amino acid of the anchored protein. The cleaved C-terminal contains the C-terminal GPI signal sequence of the newly synthesized polypeptide chain.

so it seems to be single step (even though it is a 6 subunit complex, its only a single reaction)

[ValWood]

@pgaudet Maybe we can discuss this on a call?