Cosmic Counts
Mateusz Marynowski
de Bruijn, Ino
Hi Mateusz,
Thanks for reaching out!
The COSMIC data in cBioPortal is quite old so I would recommend to download this information directly from their website. They have free non-commercial use licenses:
https://cancer.sanger.ac.uk/cosmic/download
The internal API endpoints aren’t really meant for direct API use as they are prone to change. That said for your example you could do something like this to get the COSMIC counts:
curl -X POST "https://www.cbioportal.org/api/cosmic-counts/fetch" -H "accept: application/json" -H "Content-Type: application/json" -d "[ \"TP53 V173 missense\"]"
For downloading the full table, the easiest is to use the download controls in the browser. You can reconstruct the full table through the API as well but you’ll have to download and combine the various data source programmatically. There is some documentation for how to add the annotations from Genome Nexus here:
https://github.com/genome-nexus/genome-nexus/blob/master/notebooks/genome_nexus_python_example.ipynb
Hope that helps!
Best wishes,
Ino
From:
cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Mateusz Marynowski <mateusz.ma...@gmail.com>
Date: Friday, October 6, 2023 at 10:55 AM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Cosmic Counts
Hi, can u please help me with `Cosmic Counts` in internal API? For example how to extract information for TP53 V173L? Or how to get this table with API? Thank you, Mateusz -- You received this message because you are subscribed to the Google
Hi,
can u please help me with `Cosmic Counts` in internal API? For example how to extract information for TP53 V173L?
Or how to get this table with API?
Thank you,
Mateusz
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