PharmacoDB-1.0.0

PharmacoDB allows scientists to search across publicly available datasets to find instances where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair from any of the studies included in the database.

We are providing full access to the contents of the first stable release of PharmacoDB and are distributing the data as a MySQL dump. Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory.

The existing dump can be made PostgreSQL compatible by following the instructions below:

Step 1: Install Docker (https://www.docker.com/)

Step 2: Run the commands below

sudo docker pull bhklab/pharmacodb:1.0.0

sudo docker run -d -p 3000:3000 -v ~:/home -it --name pharmacodb_v1.0.0 --entrypoint /bin/bash bhklab/pharmacodb:1.0.0

sudo docker exec -it --user root pharmacodb_v1.0.0 /usr/src/app/data/mysql_to_postgres

The new PostgreSQL compatible dump will be available in your home directory as 'pharmacodb_development.psql'. 

Update

Version 1 of this dataset did not contain the HARA cell-line annotation correction (tissue type is lung and not breast). Our apologies for any inconvenience. Please use and cite Version 2 instead.

For more information, please visit https://pharmacodb.pmgenomics.ca