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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 a configurable service specific identifier converter #322

Closed deepakunni3 closed 5 years ago

deepakunni3 commented 5 years ago

This PR adds two identifier converter classes, one for SciGraph and another for MyGene. Both these classes have convert_gene_to_proteins and convert_protein_to_gene methods.

Which identifier converter to use is determined by conf/config.yaml.

The purpose of doing this is to allow flexibility in service that each implementation uses.

For Monarch, the conversion is done via SciGraph. For GO, the conversion is done via MyGene.

If there is a new implementation of the BioLink API that needs to use another service, then one can add a new class and refer to that in config.yaml.

@cmungall @kshefchek Would like your feedback on the approach used

cmungall commented 5 years ago

Have not looked yet, but the basic concept seems v sound and useful

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322 https://github.com/biolink/biolink-api/pull/322 Add a configurable

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deepakunni3 commented 5 years ago

@kshefchek If this looks like the right approach and will not break anything in particular, please feel free to merge.

The behave tests are failing on Travis due to change in the data. I can tidy that as a separate PR