[Pruthvi] Implement ID Conversion & Protein Function Query Web Service

Context

MSstats output generally contains uniprot IDs or uniprot mnemonic IDs, but not HGNC IDs. In order to query INDRA properly, HGNC IDs are ideal. Fortunately, there are INDRA python client libraries that enable conversion from uniprot to HGNC IDs. Furthermore, there is also a lack of annotation on the protein functions of each protein, e.g. is the protein a kinase? INDRA's python client libraries also enable queries on whether a protein is a kinase, TF, etc.

Since MSstatsBioNet is implemented in R, we need a way to integrate these libraries somehow in R. The best solution at a higher level has been determined to place these libraries behind a web service. Then, MSstatsBioNet will call this web service for ID conversion and protein function queries.

See this python notebook for reference.

Subtasks

Confirm a list of endpoints needed from the INDRA python libraries:
- uniprot_client.get_id_from_mnemonic
- uniprot_client.get_hgnc_id
- hgnc_client.get_hgnc_name
- hgnc_client.is_kinase
- hgnc_client.is_phosphatase
- hgnc_client.is_transcription_factor
Set up time with Ben on where to place this new service and other implementation details. There are 3 options:
- Api.indra.bio
- INDRA Ontology
- Implement as new endpoints in INDRA Cogex
Implement ID conversion and protein function query service
- Enable bulk processing so that if one needs to query for 4000 proteins, it becomes 1 API call rather than 4000.
Add function in MSstatsBioNet to convert IDs and add protein function to MSstats output table.
- Additional consideration: Datasets may have different types of uniprot IDs, e.g. uniprot mnemonic IDs vs uniprot IDs.
PR & merge

Acceptance Criteria

We should be able to perform ID conversions and protein function queries from MSstatsBioNet.

Vitek-Lab / MSstatsBioNet