Question: Best way to obtain list of all drug-variant associations from CIViC
3
gravatar for Malisa
3.0 years ago by
Malisa40
Malisa40 wrote:

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.

civic • 1.5k views
ADD COMMENTlink modified 3.0 years ago by Obi Griffith17k • written 3.0 years ago by Malisa40
4
gravatar for Obi Griffith
3.0 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

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

ADD COMMENTlink written 3.0 years ago by Obi Griffith17k
1

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.

ADD REPLYlink written 3.0 years ago by Malisa40
1

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

ADD REPLYlink written 3.0 years ago by Obi Griffith17k
1

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.

ADD REPLYlink modified 2.6 years ago by Obi Griffith17k • written 2.6 years ago by Malachi Griffith17k
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