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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        <foaf:name>Benjamin Haibe-Kains</foaf:name>
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    <dct:title>PharmacoDB-1.0.0</dct:title>
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    <dcat:keyword>pharmacodb</dcat:keyword>
    <dcat:keyword>cell-lines</dcat:keyword>
    <dcat:keyword>drug-targets</dcat:keyword>
    <dcat:keyword>drug-dose-response-curves</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2017-10-09</dct:issued>
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    <dct:description>&lt;p&gt;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.&lt;/p&gt; &lt;p&gt;We&amp;nbsp;are providing full access to the contents of the&amp;nbsp;first stable release of&amp;nbsp;PharmacoDB&amp;nbsp;and are distributing the data&amp;nbsp;as a MySQL&amp;nbsp;dump.&amp;nbsp;Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory.&lt;/p&gt; &lt;p&gt;The existing dump can be made &lt;em&gt;PostgreSQL&lt;/em&gt; compatible by&amp;nbsp;following the instructions below:&lt;/p&gt; &lt;p&gt;Step 1: Install Docker (https://www.docker.com/)&lt;/p&gt; &lt;p&gt;Step 2: Run the commands below&lt;/p&gt; &lt;p&gt;sudo docker pull bhklab/pharmacodb:1.0.0&lt;/p&gt; &lt;p&gt;sudo docker run -d -p 3000:3000 -v ~:/home -it --name pharmacodb_v1.0.0 --entrypoint /bin/bash bhklab/pharmacodb:1.0.0&lt;/p&gt; &lt;p&gt;sudo docker exec -it --user root pharmacodb_v1.0.0 /usr/src/app/data/mysql_to_postgres&lt;/p&gt; &lt;p&gt;The new PostgreSQL compatible dump will be available in your home directory as &amp;#39;pharmacodb_development.psql&amp;#39;.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;em&gt;Update&lt;/em&gt;&lt;/p&gt; &lt;p&gt;&lt;em&gt;Version 1 of this dataset did&amp;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.&lt;/em&gt;&lt;/p&gt; &lt;p&gt;For more information, please visit https://pharmacodb.pmgenomics.ca&lt;/p&gt;</dct:description>
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