Dataset Open Access

PharmacoDB-1.0.0

Petr Smirnov; Victor Kofia; Alexander Maru; Mark Freeman; Chantal Ho; Nehme El-Hachem; George-Alexandru Adam; Wail Ba-alawi; Zhaleh Safikhani; Benjamin Haibe-Kains


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1038045", 
  "language": "eng", 
  "title": "PharmacoDB-1.0.0", 
  "issued": {
    "date-parts": [
      [
        2017, 
        10, 
        9
      ]
    ]
  }, 
  "abstract": "<p>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.</p>\n\n<p>We&nbsp;are providing full access to the contents of the&nbsp;first stable release of&nbsp;PharmacoDB&nbsp;and are distributing the data&nbsp;as a MySQL&nbsp;dump.&nbsp;Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory.</p>\n\n<p>The existing dump can be made <em>PostgreSQL</em> compatible by&nbsp;following the instructions below:</p>\n\n<p>Step 1: Install Docker (https://www.docker.com/)</p>\n\n<p>Step 2: Run the commands below</p>\n\n<p>sudo docker pull bhklab/pharmacodb:1.0.0</p>\n\n<p>sudo docker run -d -p 3000:3000 -v ~:/home -it --name pharmacodb_v1.0.0 --entrypoint /bin/bash bhklab/pharmacodb:1.0.0</p>\n\n<p>sudo docker exec -it --user root pharmacodb_v1.0.0 /usr/src/app/data/mysql_to_postgres</p>\n\n<p>The new PostgreSQL compatible dump will be available in your home directory as &#39;pharmacodb_development.psql&#39;.&nbsp;</p>\n\n<p><em>Update</em></p>\n\n<p><em>Version 1 of this dataset did&nbsp;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.</em></p>\n\n<p>For more information, please visit https://pharmacodb.pmgenomics.ca</p>", 
  "author": [
    {
      "family": "Petr Smirnov"
    }, 
    {
      "family": "Victor Kofia"
    }, 
    {
      "family": "Alexander Maru"
    }, 
    {
      "family": "Mark Freeman"
    }, 
    {
      "family": "Chantal Ho"
    }, 
    {
      "family": "Nehme El-Hachem"
    }, 
    {
      "family": "George-Alexandru Adam"
    }, 
    {
      "family": "Wail Ba-alawi"
    }, 
    {
      "family": "Zhaleh Safikhani"
    }, 
    {
      "family": "Benjamin Haibe-Kains"
    }
  ], 
  "type": "dataset", 
  "id": "1038045"
}
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