Q how to annotate regulation upstream within a process

[ValWood]

@ukemi @vanaukenk would this match what you would do in LEGO?

[ValWood]

then I also see

"indirectly activates" which might be the correct term to use?

The use of the word indirect here worries me a little because in general when biologists say some effect us "indirect" it isn't usually regulatory at all in a normal cell, its just an effect of breaking an upstream process.

[ValWood]

The outcome of the first question will be important for
geneontology/go-ontology#12859
because it will provide the mechanism in traditional annotation to continue to capture some of the information which is currently represented on the the single step process terms (this might be a pombase hack anyway, but if we know which relations to use we can fix).

[dosumis]

It is correct to use regulates for 'unknown steps, incomplete pathway' (although strictly it is the activity of the substrate that is regulated, not the substrate).

then I also see
"indirectly activates" which might be the correct term to use?

This relation should be deprecated.