PdbAnnotation API dependency

[onursumer]

We cannot completely remove PdbAnnotation API yet, because we fetch PDB header data from there.

[jjgao]

@onursumer is that because we cache the PDB header there? Is performance OK to not use cache?

[onursumer]

@jjgao It is a little slow without the cache since we are querying multiple PDB chains for a single gene. Also if we always hit the PDB web service directly, we may end up having problems similar to the ones we have with PFAM web service. Maybe it is better to add another endpoint in genome nexus for this one too.

[jjgao]

@onursumer good point.

[jjgao]

@onursumer how's going with this one?

[onursumer]

I think this is fully integrated into genome nexus by genome-nexus/genome-nexus#97

[jjgao]

and we are using the genome-nexus end point in portal too?

[onursumer]

@jjgao Looks like we are still using the old endpoint, not genome nexus yet. Do you think it is a good time to switch to genome nexus, or should we do this after releasing 1.11.0?

[jjgao]

as discussed, hotfix later.