facilitate retrieval of Rhea - protein interactions

[andrewsu]

Rhea is a database of "chemical and transport reactions of biological interest". Mappings between chemical compounds and Rhea IDs is available through mychem.info (and will be available to BTE after #123 is complete). However, I don't believe we currently have any resource in SmartAPI that returns links between proteins and Rhea reactions. I see two possible ways to get these mappings.

• We could annotate the EBI Proteins API. For example, given an input UniProt ID, https://www.ebi.ac.uk/proteins/api/proteins/Q93099 will provide links to Rhea under comments.reaction.dbReferences.
• We could incorporate mappings into mygene.info. On the Rhea downloads page, there is a file for rhea2uniprot_sprot.tsv that appears to be regularly updated.

Related to NCATSTranslator/testing#49

[colleenXu]

I've made an attempt here: NCATS-Tangerine/translator-api-registry#64

I've noted in the comments on the PR and in the yaml: I don't know if there will be issues with response-mapping. I notice that the Rhea ID we want is nested in the dbReferences array with CHEBI IDs....(which itself is nested in the comments array where not every element has a "reaction").

[andrewsu]

@colleenXu your PR NCATS-Tangerine/translator-api-registry#64 has been merged and it looks like it is working as expected (biothings/biothings_explorer#172). As you noted on slack, it seems like the last step is to add the EBI Proteins API to the config.js file https://github.com/biothings/BioThings_Explorer_TRAPI/blob/master/src/routes/v1/config.js. Can you create a PR for that please?

[colleenXu]

PR made here biothings/biothings_explorer#187

[colleenXu]

Was done years ago. Can close this issue @NikkiBytes @marcodarko