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monarch-initiative / biolink-api

API for linked biological knowledge
https://api.monarchinitiative.org/api/
BSD 3-Clause "New" or "Revised" License
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Add all monarch association types as biolink routes #278

Closed kshefchek closed 5 years ago

kshefchek commented 5 years ago

With the association types and routes.yaml we should be able to determine what routes have yet to be added to biolink from the monarch solr:

https://solr.monarchinitiative.org/solr/golr/select/?facet.field=association_type&q=*%3A*&facet=true&facet.method=enum&facet.limit=3000&rows=0&wt=json&facet.mincount=1&indent=on&facet.sort=count

For exmaple: variant/:id/models, and all case endpoints that would be needed to create our UDP pages, eg: http://monarchinitiative.org/case/:MONARCH:c000017

Note that gene_temporal is bad naming and should be merged with gene interactions (colocalization data)

deepakunni3 commented 5 years ago

@kshefchek I think I was being conservative when adding routes to avoid routes that never returned any associations (and I must have missed a few in the process).

But I saw @DoctorBud mention that certain pages fail to load because it expects routes to be symmetrical.

Do you recommend adding all possible enumeration of routes to the API and then have the API respond with an empty JSON if that route is not yet implemented?

kshefchek commented 5 years ago

Do you recommend adding all possible enumeration of routes to the API and then have the API respond with an empty JSON if that route is not yet implemented?

I don't think we should add routes if we know it will not return any data (in the current db). But I may be misunderstanding. I know there are some nuances with sequence features being treated as models.

deepakunni3 commented 5 years ago

Okay, just making sure. Couple of months back I had pruned many of the routes that never returned any associations.

deepakunni3 commented 5 years ago

After doing the comparison between routes.yaml and facets for association_type, it looks like the following routes are missing:

@kshefchek Do you want me to take a stab at adding these routes or have you started working on this already?

kshefchek commented 5 years ago

go for it!