Question: Public Api For Sanger'S Cosmic Databases
gravatar for woemler
6.4 years ago by
Boston, MA
woemler150 wrote:

Does there exist a public API for retrieving records from Sanger's COSMIC databases? I have a data set which has thousands of samples annotated only by cell line name and COSMIC sample ID, I'd like to look up the sample annotations, but don't want to spend all day copy-and-paste-ing with their web interface. I know you can download the COSMIC data sets and databases through their FTP site, but I do not see any reference to the COSMIC cell line sample annotations.

EDIT: Thanks, everyone for the suggestions. Unfortunately, it looks like the web service or API I am looking for does not exist. I created a quick script for scraping the basic cell line information I need from COSMIC.

sanger api database • 4.1k views
ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by woemler150
gravatar for Arnaud Ceol
6.4 years ago by
Arnaud Ceol850
Milan, Italy
Arnaud Ceol850 wrote:

You may have a look at Ensembl's Biomart: If you choose as dataset "ensembl variations" and then "Short Variation (SNPs and indels)" you have the possibility to select only entries from COSMIC. Have a look at the attribute available in output, maybe the ones you're interested in are there.

ADD COMMENTlink written 6.4 years ago by Arnaud Ceol850
gravatar for Emily_Ensembl
6.4 years ago by
Emily_Ensembl20k wrote:

We import COSMIC variants into Ensembl. You can access them via our API.

ADD COMMENTlink written 6.4 years ago by Emily_Ensembl20k
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