Script to map cBioPortal data to Beacon v2.
Before running the script check basicConfigFile.ini. You must put your Study ID in the field studyId. Then, change your clinical data fields to match the ones in your study. If not, the script will map to the base fields given by cBioPortal.
To map the Individual and Biosample schema it is recommended to use the Beacon v2 schema from the main repository.
- Usage
python3 cBioPortalBeaconMapping.py basicConfigFile.ini
This script create Beacon Friendly Format (BFF) files compatible to the Reference Implementation BeaconV2 API.
For creating a BeaconV2 working instance, you can use the Reference Implementation developed at the Centre for Genomic Regulation (CRG).
- GNU AFFERO GENERAL PUBLIC LICENSE Version 3. Ver
LICENSE.md.
This repo is a discarded work from in the IMPaCT-Data project, with the support of Instituto de Salud Carlos III and the Barcelona SuperComputing Center.
The original on-the-fly work can be found in the IMPaCT-Data repo.