# Import OncoKB annotations as custom driver annotations

The Annotation Configuration menu in Study View and Group Comparison is available only when custom driver annotations are present in the cBioPortal database for the genes in the study (or studies). In order to use OncoKB annotations to filter mutations and discrete copy number alteration in Study View and Group Comparison, OncoKB annotations can be added to the respective data files of a study prior to import into the database. This page describes how to import OncoKB annotations as custom driver annotations. It assumes the following requirements have been satisfied:

1. The cBioPortal software has been correctly built from source.
2. The user is able to successfully import a study into the database.
3. The study subjected to OncoKB import is confirmed to be valid

OncoKB annotations can be added automatically to the study files when the study is loaded into the database by adding the --import_oncokb parameter to the metaImport.py script like so:

python metaImport.py --import_oncokb -u http://cbioportal:8080 -s study/lgg_ucsf_2014/

This will add OncoKB data to the mutation and discrete CNA files of a study, revalidate the results and load the study into the database.

The addition of mutation and discrete CNA files is explained in detail below.

OncoKB annotations can be added to the MAF file by running importOncokbMutation.py like so:

python importOncokbMutation.py -s study/lgg_ucsf_2014/ -u https://cbioportal.org

Where -s is the path to the directory of the MAF file and -u is the URL to a cBioPortal instance (needed for resolution of gene identifiers).

importOncokbMutation.py will add OncoKB annotations as custom driver annotation columns in the MAF file. The unmodified MAF file will be stored in the study directory with the ONCOKB_IMPORT_BACKUP_ prefix.

OncoKB annotations can be added to the Discrete Copy Number data by running importOncokbDiscreteCNA.py like so:

python importOncokbDiscreteCNA.py -s /tmp/study -u https://cbioportal.org

Where -s is the path to the directory of the iscrete Copy Number data file and -u is the URL to a cBioPortal instance (needed for resolution of gene identifiers).

importOncokbDiscreteCNA.py will create a custom driver annotation file with name data_cna_pd_annotation.txt in the study directory. It will add a field pd_annotations_filename field in the CNA meta file that references the newly created custom driver annotation file. The unmodified CNA meta file will be stored in the study directory with the ONCOKB_IMPORT_BACKUP_ prefix.