Best way to obtain list of all drug-variant associations from CIViC

Question

[Malisa]

I would like a list of drug-variant interactions (i.e. a variant for which its mutational status affects the efficacy of a particular drug).

I noticed that nightly-ClinicalEvidenceSummaries.tsv currently contains 593 drug-variant interactions (as of March 22, 2016). Is this the full list of all drug-variant interactions currently contained in the CIViC database?

If so, great! Otherwise, it seems like the alternative is to use the API to obtain variant/evidence information and then parse the resulting JSON. Thanks.

Answer 1

[Obi Griffith]

That sound right. The nightly TSV file should be a complete representation of the total number of evidence statements in CIViC. However, the level of detail is reduced compared to what you could get from the API. Also, I see that there are some formatting issues still occurring with the TSV file. We are working to fix this. However, the API is definitely recommended.

Check out this set of python tools (under active development) that pulls CIViC data via the API in various ways. https://github.com/griffithlab/civic-api-client

[Malisa]

Thank you for the helpful response.

I'm just looking for a lists of gene, drugs, evidence_direction, and clinical_significance combinations for each association, so I think the nightly summaries should be enough -- but I'll keep the API in mind. It looks like I would need to loop through the variants using the https://civic.genome.wustl.edu/api/variants/497 call in order to obtain most of the information I'm interested in.

[Obi Griffith]

Yup. That should work. If there are details of the evidence items not there you can dig further with something like: https://civic.genome.wustl.edu/api/evidence_items/1179

[Malachi Griffith]

Please note that both the Data Releases section and API documentation of www.civicdb.org have been substantially updated! Please let us know if you have any issues.