Document annotation source: COSMIC

[rdocking]

Please answer the following questions about the COSMIC data source:

• Where is it located online?
• Is there an API?
• Are bulk downloads available?

In general, what kinds of information are in this data source?
The answers should be uploaded to the wiki in an appropriate spot.

[wilcas]

I'll try to answer at least one of these questions in around 10 minutes, but anyone should feel free to take it over when I have to step out for my test.

[wilcas]

Online Location

COSMIC
Cell Lines Database

##API
It looks like you can submit HTML GET requests to COSMIC of the form

http://cancer.sanger.ac.uk/api/ga4gh/beacon?format=json&ref=?&dataset=cosmic&allele=?&pos=?&chrom=?

You specify a response format, the reference genome by number (for example GrCH38 would be specified with ref=38), the dataset (i.e. dataset=cosmic), the allele, position, and chrom. Essentially just replace the question marks above. More information about querying the COSMIC database can be found at their BEACON Project page.

Given that you can specify output as a JSON, this should be pretty straightforward to work with in python using the requests and json modules, both of which are in the "standard" library.

##Bulk Download
See Complete Fusion Export

[rdocking]

I've summarized these comments on the 'Data Sets' page of the wiki - thanks @wilcas !