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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  <identifier identifierType="DOI">10.5281/zenodo.1038045</identifier>
  <creators>
    <creator>
      <creatorName>Petr Smirnov</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-9395-8450</nameIdentifier>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Victor Kofia</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5849-7337</nameIdentifier>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Alexander Maru</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Mark Freeman</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Chantal Ho</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Nehme El-Hachem</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>George-Alexandru Adam</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Wail Ba-alawi</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Zhaleh Safikhani</creatorName>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
    <creator>
      <creatorName>Benjamin Haibe-Kains</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7684-0079</nameIdentifier>
      <affiliation>Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada</affiliation>
    </creator>
  </creators>
  <titles>
    <title>PharmacoDB-1.0.0</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <subjects>
    <subject>pharmacodb</subject>
    <subject>cell-lines</subject>
    <subject>drug-targets</subject>
    <subject>drug-dose-response-curves</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2017-10-09</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1038045</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1027720</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/GPL-3.0">GNU General Public License v3.0 only</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
</resource>
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