geneontology/pathways2GO

Complexes & Sets - info needed for PRO

Opened this issue · 0 comments

I propose the following fields for Complexes and Sets, which can be handled in the same file as far as I'm concerned. Listed below are the columns I'd like, with content indicated, in tab-delimited format.

Type                    'Complex' or 'Set'
Identifier              (for the complex or set)
Location                (for the complex or set)
Accession               (for the complex or set)
Components/Members           *see below*
Display Name            (for the complex or set)
Free Text               (empty for now)

For the components/members column, I'd like it to be like so:
Type:Component/Member_identifier(stoichiometry); Type:Component/Member_identifier(stoichiometry); etc...

For example, for complex R-HSA-140976, that field should be:

EWAS:R-HSA-57031(1); Complex:R-HSA-140977(1)

For R-HSA-140977 (the subcomplex given above):

EWAS:R-HSA-54639(2); Complex:R-HSA-140935(1)

...and so on. HOWEVER! If possible, I'd like the components spelled out fully for each complex instead of referencing a subcomplex. If that is possible, then for complex R-HSA-140976 we'd have:

EWAS:R-HSA-57031(1); EWAS:R-HSA-54639(2); EWAS:R-HSA-168651(1); EWAS:R-HSA-66376(3); EWAS:R-HSA-66370(3);

Sets should be treated the same way. If I understand the way stoichiometry is handled for complexes in Reactome, the default is '1', so that should work for Sets as well. In other words, this column should look the same as for complexes (though all stoichiometries would be '1').