Introduction

Using OncoKB does not require a data access token. But the instance you are connecting to only includes biological information by default. If you want to include tumor type summary, therapeutic levels and more, please consider obtaining a license from OncoKB.

How to obtain an OncoKB license

1. Please review OncoKB terms

2. Please request for data access​

3. You can find your token in your Account Settings after login.

Set up cBioPortal to include full OncoKB content

Following properties can be edited in the portal.properties file or set in system variables if you are using docker.

• show.oncokb should be set to true

• oncokb.token should be set to a valid OncoKB access token value

• oncokb.public_api.url should be set to https://www.oncokb.org/api/v1

Thank you for supporting future OncoKB development.

Include MSI-H and TMB-H annotation

If you want to include the MSI-H and TMB-H annotation on patient view, please follow the instruction to import required clinical data. For MSI-H, a clinical attribute MSI_TYPE with value Instable is required. For TMB-H, a clinical attribute TMB_SCORE with value >=10 is required.

Disable OncoKB Service

Please set show.oncokb to false in portal.properties or in system variables if you are using docker.