Proton-transporting ATP synthase complex terms

[ValWood]

I wasn't sure where to put this ticket. It is about GO-CAM modelling but overlaps with the ontology representation

I am building a CO-CAM for the respiratory chain/oxidative phosphorylation

For the ATP synthase complex we have a number of terms:

https://www.pombase.org/term/GO:0045259

The complex and its various parts.

1. catalytic core
2. coupling factor
3. central stalk
4. stator stalk

Are these 'sub parts' too granular for GO (I am wondering what activities we could attach to these )

All 17 subunits have
proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)

Didn't we have a rule that we would only add complexes that were functional units?

[ValWood]

I guess all of the complex sub parts could be connected and have the same MF term, or for the model I could just ignore the sub parts

@hattrill
@gantonazzo
@vanaukenk

[hattrill]

When we discussed the use of contributes_to this was definitely the case - a complex should be the functional unit not just sub-complexes. I think the reason those terms weren't obsoleted is some nervousness about whether people found the sub-complex labels useful or not. We should really get rid of them to be consistent with the policy.

In terms of conventional annotation guidelines - all the SUs should have contributes_to "proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)"

In terms of modelling, use the GO:0045259 proton-transporting ATP synthase complex term and not the sub-complexes as they cannot do proton-transporting ATP synthase activity, rotational mechanism (GO:0046933) individually.

Are you going to make a complex in the VPE and add all the subunits to that and attach the MF to the complex unit?

[ValWood]

Yes, I started the model (I have added complex II, III and iv).
http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A663d668500000596
(all of the evidence is currently NAS because it isn't possible to import existing annotations onto a complex and I didn't want to remake them).
I also had to manually add all of the has_parts, even though they are in the GPI file, so this is also a pain (so to make the model exportable I added NAS to these too, even though there is IDA,IBA or ISO evidence for all of these, life is too short to add them all again)

[sjm41]

@ValWood Complex V terms are simpler than they used to be! See #27253

As you say, the branch now looks like this:

|__proton-transporting ATP synthase complex
    |__proton-transporting ATP synthase complex, catalytic core F(1)
        |__proton-transporting ATP synthase, catalytic core
        |__proton-transporting ATP synthase, central stalk
    |__proton-transporting ATP synthase complex, coupling factor F(o)
        |__proton-transporting ATP synthase, stator stalk

At the time of making all the obsoletions in the other ticket, we did stop short of obsoleting these complex V subcomplexes - yes, partly because of nervousness of obsoleting even more, especially since these these subcomplexes are well characterized/defined and the terms are heavily used:
proton-transporting ATP synthase complex, catalytic core F(1) - 750K annotations, 35 EXP
proton-transporting ATP synthase complex, coupling factor F(o) - 615K annotations, 31 EXP

That said, the GO guidelines for complexes do say that subcomplexes are out of scope.

I'd be happy to see these subcomplex terms disappear from the GO.

[sjm41]

I can't remember - does PomBase not have Complex Portal IDs?

[sjm41]

@rozaru

[sandraorchard]

CPX-25764

[ValWood]

Action
Obsolete
proton-transporting ATP synthase complex, catalytic core F(1)
|__proton-transporting ATP synthase, catalytic core
|__proton-transporting ATP synthase, central stalk
|__proton-transporting ATP synthase complex, coupling factor F(o)
|__proton-transporting ATP synthase, stator stalk