Document annotation source - CIViC

[rdocking]

Please answer the following questions about the CIViC data source:

• Where is it located online?
• Is there an API?
• Are bulk downloads available?
• In general, what kinds of information are int this data source

The answers should be uploaded to the wiki in an appropriate spot.

[rdocking]

Aha - there are bulk downloads: https://civic.genome.wustl.edu/releases

[rdocking]

• Located online at https://civic.genome.wustl.edu/
• There is a documented API, and bulk downloads are available at https://civic.genome.wustl.edu/releases

[rdocking]

Downloaded the September 2017 release:

[2017-10-20 20:51:10]{rdocking_hs@orca01}/home/projects/hackseq17_3/annotation_sources/civic/> ls -lh
total 2.8M
-rw-r--r-- 1 rdocking_hs hackseq17_3 2.3M Oct  1 05:00 01-Sep-2017-ClinicalEvidenceSummaries.tsv
-rw-r--r-- 1 rdocking_hs hackseq17_3  68K Oct  1 04:59 01-Sep-2017-GeneSummaries.tsv
-rw-r--r-- 1 rdocking_hs hackseq17_3 7.8K Oct  1 05:00 01-Sep-2017-VariantGroupSummaries.tsv
-rw-r--r-- 1 rdocking_hs hackseq17_3 390K Oct  1 05:00 01-Sep-2017-VariantSummaries.tsv

[rdocking]

GeneSummaries.tsv: 332 x 6, with gene name, entrez id, brief description, and review date
VariantGroupSummaries.tsv: 20 x 5, descriptions of 'variant groups'
VariantSummaries: 1,716 x 22, actual descriptions of variants. Only ~85 look to be annotated fusions
ClinicalEvidenceSummaries.tsv: 2,238 clinical evidence entries

[rdocking]

Update wiki with a summary here