ValWood
commented
2 years ago Note to self: We also need to consider if this will work for protein A directly inhibits [protein B protein-binding protein C] Maybe not, but I am not convinced there are not better ways to capture/infer this. https://www.pombase.org/gene/SPAC1F5.04c might be a good example to model this (but needs new GO terms).
Cut12 shows a different way of modelling this type of binding dependent pathway choice: https://www.pombase.org/gene/SPBC649.05 although this isn't just competitive binding, it is also modification dependent so it's a bit different, (but I suspect modification will nearly always underlie this differential binding). Anyway I think 'regulating' binding is something we might need to figure out.
continued discussion in https://github.com/pombase/curation/issues/3058
Summary:
Essentially, this additional this will enable us to draw activator -> or inhibitor -| arrows in network diagrams.
for any MF annotation with an has_input(substrate) allow the selection of the appropriate causal relation.
This will be either:
Will also need to a) add to legacy (a log of those without would b e a good idea. I always record if the interaction is inhibitory, so we might be able to default to positive and then just fix the. negative ones b) think about how to display (I will open a coupled website ticket for this)
2. In addition, we also need to specify which MF of the input is regulated. If there is only one existing non-binding MF annotation all existing can default to this term. This is only really an issue for multifunctional proteins (of which there are not so many). More often the problem will be that the same activity is described in 2 different ways. I'm trying to fix these..
a). We will need a log of things where the regulated activity eas not specified b) We probably don't need to display this for our users, but it will be required for the GO-CAM format.
I'd like to move forward with this, can discuss on next call.