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


JSON-LD (schema.org) Export

{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<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>", 
  "license": "https://opensource.org/licenses/GPL-3.0", 
  "creator": [
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@id": "https://orcid.org/0000-0001-9395-8450", 
      "@type": "Person", 
      "name": "Petr Smirnov"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@id": "https://orcid.org/0000-0001-5849-7337", 
      "@type": "Person", 
      "name": "Victor Kofia"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Alexander Maru"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Mark Freeman"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Chantal Ho"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Nehme El-Hachem"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "George-Alexandru Adam"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Wail Ba-alawi"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@type": "Person", 
      "name": "Zhaleh Safikhani"
    }, 
    {
      "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
      "@id": "https://orcid.org/0000-0002-7684-0079", 
      "@type": "Person", 
      "name": "Benjamin Haibe-Kains"
    }
  ], 
  "url": "https://zenodo.org/record/1038045", 
  "datePublished": "2017-10-09", 
  "keywords": [
    "pharmacodb", 
    "cell-lines", 
    "drug-targets", 
    "drug-dose-response-curves"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/26af9df0-4afa-40be-bcfd-0bb9297782c9/pharmacodb-1.0.0.sql", 
      "encodingFormat": "sql", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/26af9df0-4afa-40be-bcfd-0bb9297782c9/pharmacoDB-1.0.0.sql", 
      "encodingFormat": "sql", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.1038045", 
  "@id": "https://doi.org/10.5281/zenodo.1038045", 
  "@type": "Dataset", 
  "name": "PharmacoDB-1.0.0"
}
162
14
views
downloads
All versions This version
Views 162112
Downloads 1413
Data volume 24.8 GB23.0 GB
Unique views 143103
Unique downloads 1110

Share

Cite as