Import the Seed Database

The next step is to populate your cBioPortal instance with all the required background data sets. This includes, for example: gene data, ID mappings, and network interactions. Rather than importing each of these data sets individually, we have provided a simpler "seed" database that you can import directly.

Download the cBioPortal Database

A cBioPortal seed database can be found on the Downloads page.

After download, this file can be unzipped by entering the following command:

gunzip cbioportal-seed.sql.gz

Import the cBioPortal Database

Important: Before importing, make sure that you have followed the pre-build steps for creating the cbioportal database.

Then import the seed database via the mysql command:

> mysql --user=cbio_user --password=somepassword cbioportal  < cbioportal-seed.sql

Drug-target and Clinical Trial Data

Due to data provider specific restrictions on data re-distribution, the database setup, as outlined above, will lack some of the drug-gene relationships from specific data-resources and also all clinical trial information. If you would like to obtain the complete the data sets from these resources, we encourage you to take advantage of PiHelper for aggregating drug-target associations and NCI's Data Dissemination Program, PDQ, for clinical trials data; and use the corresponding data importers, importPiHelperData.sh and importClinicalTrialData.pl, that are distributed as part of cBioPortal.