PHI-base needs 'binds' in MF config to have role 'user'

[jseager7]

We have a PHI-Canto curation session where we need to annotate 'pathogen-derived receptor ligand activity' (GO:0140295) with the 'binds' annotation extension (see here). However, the extension is currently admin-only and we want it to be enabled for all users.

@ValWood Does PomBase have a reason to keep this extension admin-only? If so, PHI-base can look into overriding this line with our own configuration instead (unless you think doing that is a bad idea).

[ValWood]

Our extension is admin only because normally protein binding is only "binds" and the option we have under admin is for a "modified form" and this is restricted to admin because we need to request the IDs for modified forms from PRO.

However usually extensions are restricted to the input, and the relationship should be in the direction receptor has_input ligand. Although I do remember a discussion on the GO slack channel about this exact problem (I think Flybase wanted to add the receptor as input for the ligand @hattrill? did I remember that correctly?). I can't find the discussion it so I suspect it has rolled off my 90 day access- but also I never saw a resolution.

You could try adding a row only for
GO:0140295 pathogen-derived receptor ligand activity
because we won't use this term.

We generally treat "binding" a bit differently, because it isn't really a molecular function, it's only an interaction.
But this term has a parentage which is not under "protein binding", so it would be like any other MF extension term. I suspect we never configured the "signalling receptor activator" branch because we never used it.

I probably haven't explained this very well as it's typed in a hurry. I have some deadlines today, but I can provide more detail in a couple of days if this did't maker sense.

CC @kimrutherford

[jseager7]

You could try adding a row only for GO:0140295 pathogen-derived receptor ligand activity because we won't use this term.

We might be able to just add that to our own GO extension configuration file for PHI-Canto, assuming it won't be overridden by the PomBase config (which it probably won't be, due to the different domain ID). That way we won't clutter up your configuration with terms that nobody except PHI-base is using.

[jseager7]

For now we've just enabled the 'binds' extension on GO:0140295 in our own configuration since we needed a fix for this quickly and I'm not sure it would be relevant for PomBase or anyone else.

Maybe when we've sorted out exactly how we want the extension to be used we can revert to using some shared extension configuration.