Work out GPAD output for MF and BP of macromolecular complex members

[vanaukenk]

Hi,

We touched on this issue somewhat in #69 , but I don't think we've quite gotten this sorted out.

The issue here is how individual complex members will be annotated for any associated MF and BP annotations.

I have a simple test model for this here:
http://noctua.berkeleybop.org/editor/graph/gomodel:591f58ab00000003

Right now, in the GPAD, the complex members get a part_of annotation to the CC complex term, but no annotations to the MF enabled by the complex or the associated BP.

We will need to decide if, in the GPAD, the individual members should each get a 'contributes to' qualifier for the MF annotation.

As always, it would probably be worth it to work through a few more examples of macromolecular complexes in Noctua and GO-CAM models to make sure we're satisfied they're being represented properly.

Thanks,
--Kimberly

[balhoff]

Do we want to add a property chain?

part_of o enables -> contributes_to

[vanaukenk]

That's the idea, but I think we may want to model a few different scenarios to make sure we are getting the representation correct. I'm working on another model containing complexes right now.

[ukemi]

Also related to #322

[suzialeksander]

Discussed on pathways call 5 Dec 2023.