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oncokb / oncokb-annotator

Annotates variants in MAF with OncoKB annotation.
GNU Affero General Public License v3.0
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Search specific data version of OncoKB #198

Open asmmhossain opened 1 year ago

asmmhossain commented 1 year ago

Hi, I am using oncokb-annotator to annotate somatic mutations from a large cohort of patient samples. I am aware that OncoKB database is regularly updated. I was wondering if there is a way of running oncokb-annotator to search and annotate against a specific version of the database? That could be very helpful to be consistent especially when a project runs for many months. Thanks

calvinlu3 commented 1 year ago

Hi @asmmhossain, thanks reaching out! Currently, we don't have a way for users to annotate using a specific data version since the OncoKB API always uses the most recent data version. We are currently making a plan to support this, but I don't have a definitive timeline for when this will be available. I will keep you posted if we made any progress on this.

I will also let @zhx828 chime if he has anything to add.

juliawiggeshoff commented 4 months ago

Just chiming in to support @asmmhossain's request. It would be great to be able to report exactly which data version was used in the process of annotation :)

@calvinlu3 and @zhx828: As it might not be an option for now to select a version for the data release, can the output file (e.g. from MafAnnotator.py) include said information as a column? e.g. ONCOKB_DATA_VERSION

calvinlu3 commented 4 months ago

@juliawiggeshoff The original request is still on our board. As for the oncokb data version, you can generate a README using GenerateReadMe.py, which will return the following:

Files annotated on 04/10/2024
OncoKB API URL: https://www.oncokb.org/api/v1
OncoKB data version: v4.15, released on 03/21/2024
juliawiggeshoff commented 4 months ago

Great! Thanks a lot. I should have read the documentation better ;)