missing annotations

[hariszaf]

In the gapfilled model, the annotations are most of the times missing.
Here is the SBO checks from MEMOTE in the originally modelSEEDpy built GEM and after gapfilling it with DNNGIOR:

I suggest a post-annotation step based on the non-gapfilled model.

[Biomerene]

As far as I know it should be done in the model_refinement function (in dnngior/build_model.py) where it uses the aliases assign all relevant annotations. We could add

 if hasattr(reaction, 'annotation'):
                    mc.reactions.get_by_id(reaction.id).annotation = reaction.annotation

at line 113 (where it copies the gpr) but that could be a less clean option.
I am working on some things in the develop branch where I can add this so it would be fixed when we merge my new features.

[hariszaf]

Sounds good to me since that way it would just inherit the annotations of the draft model.

Let me know if I could do anything to help. 🛩️