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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    "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>", 
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    "title": "PharmacoDB-1.0.0", 
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    "publication_date": "2017-10-09", 
    "creators": [
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        "orcid": "0000-0001-9395-8450", 
        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
        "name": "Petr Smirnov"
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
        "name": "Nehme El-Hachem"
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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        "name": "Wail Ba-alawi"
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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        "affiliation": "Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada", 
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Data volume 24.8 GB23.0 GB
Unique views 143103
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