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Work out GPAD output for MF and BP of macromolecular complex members #110

Open vanaukenk opened 7 years ago

vanaukenk commented 7 years ago

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 commented 7 years ago

Do we want to add a property chain?

part_of o enables -> contributes_to

vanaukenk commented 7 years ago

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 commented 2 years ago

Also related to #322

suzialeksander commented 8 months ago

Discussed on pathways call 5 Dec 2023.