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geneontology / gocamgen

Base repo for constructing GO-CAM model RDF
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Merge imports with existing gene-centric models #47

Open vanaukenk opened 5 years ago

vanaukenk commented 5 years ago

I'm creating some new annotations in Noctua that are just part of gene-by-gene curation, i.e. not part of a larger GO-CAM model.

I've named this model according to our import conventions, i.e. WB:WBGene00003480.

When we actually import the annotations into Noctua, it would be nice if we could merge other annotations to WBGene00003480 into that existing model.

Would that be possible?

Thx.

goodb commented 5 years ago

@vanaukenk this sounds a bit like a one-off, is that right? If not, then we should probably make sure all the curation groups are on the same page with regards to this Noctua naming convention and its expected consequences. If it is a limited, one-time thing, I would suggest keeping the priority down below the completion of the general purpose importer which, if finished, would allow us to get past the need for one-offs like this and move on with the next phase of the project - where I presume you would simply open that model up for editing directly.

vanaukenk commented 5 years ago

@goodb - If it's possible to do this, then yes, I would discuss this with the other curation groups, so that it could be applied more generally upon import. I really just wanted to first gauge whether or not it was even possible.

goodb commented 5 years ago

@vanaukenk anything is possible :). (And I don't think this very hard, but at the same time its work that really shouldn't need to be done at all so would prefer it be avoided if possible.)

dustine32 commented 5 years ago

Hm, that is an interesting question. I suppose we could export this existing model from noctua-dev, then read it into the same python library (rdflib) I use for writing the generated models. We'd then have to compare the annotations in the new GPAD file with the annotations contained in the GO-CAM (hopefully, in their expected "translated-from-GPAD" form) and decide which GPAD annotations should be added to the model.

I could definitely see how this could get messy with deciding whether a GPAD annotation is already in the model.

vanaukenk commented 5 years ago

Hmmmm, I thought I was proposing something much simpler :-). I was only planning to add completely brand new annotations to Noctua to a model entitled WB:WBGenennnnnnnn. What I was thinking was that upon import, the existing annotations would just get added to the model that I created manually with the same name. If this sounds like it would be difficult or problematic, though, let's not worry about it and I'll give the manual models a different name.

dustine32 commented 5 years ago

Oh right, sorry @vanaukenk ! If we don't need to worry about matching up the annotations already in the model then it should be waaay easier.

vanaukenk commented 5 years ago

Thinking longer term, what would happen when we import another group's annotations to a gene that already has a gene-centric model in Noctua? It seems would we also want to merge the annotations in this case, as well.

suzialeksander commented 2 years ago

I was only planning to add completely brand new annotations to Noctua to a model entitled WB:WBGenennnnnnnn. What I was thinking was that upon import, the existing annotations would just get added to the model that I created manually with the same name.

ohh. SGD is very interested in this