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PMDB: a relational database for PubMed

Hughey, Jacob; Schoenbachler, Joshua


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  <identifier identifierType="DOI">10.5281/zenodo.7093972</identifier>
  <creators>
    <creator>
      <creatorName>Hughey, Jacob</creatorName>
      <givenName>Jacob</givenName>
      <familyName>Hughey</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-1558-6089</nameIdentifier>
      <affiliation>Vanderbilt University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Schoenbachler, Joshua</creatorName>
      <givenName>Joshua</givenName>
      <familyName>Schoenbachler</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8544-6359</nameIdentifier>
      <affiliation>Vanderbilt University Medical Center</affiliation>
    </creator>
  </creators>
  <titles>
    <title>PMDB: a relational database for PubMed</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <dates>
    <date dateType="Issued">2022-09-19</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/7093972</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy" resourceTypeGeneral="Preprint">10.1101/2020.09.07.285924</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4008109</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/scholarly-data</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The files constitute a compressed dump of PMDB, which was created in &lt;a href="https://www.postgresql.org/"&gt;PostgreSQL&lt;/a&gt;&amp;nbsp;14&amp;nbsp;using the &lt;a href="https://pmparser.hugheylab.org"&gt;pmparser&lt;/a&gt; R package. Once you have a Postgres server running, you can set up the database as follows:&lt;/p&gt;

&lt;p&gt;1. Untar the file containing the database dump, which will create a folder. Substitute &amp;lt;tar_name&amp;gt; with the name of the tar file.&lt;/p&gt;

&lt;pre&gt;&lt;code class="language-bash"&gt;tar xvf &amp;lt;tar_name&amp;gt; &amp;amp;&amp;amp; rm &amp;lt;tar_name&amp;gt;&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;2.&amp;nbsp;Restore the database onto your Postgres server. Below is one way.&amp;nbsp;Replace &amp;lt;...&amp;gt;&amp;nbsp;as appropriate, substituting&amp;nbsp;&amp;lt;dump_name&amp;gt; with the name of the new folder containing the dump files. This will take some time, so use as many cores as you can spare.&amp;nbsp;Beware the full database is about 136&amp;nbsp;GB.&lt;/p&gt;

&lt;pre&gt;&lt;code class="language-bash"&gt;createdb -h &amp;lt;host_name&amp;gt; -U &amp;lt;user_name&amp;gt; pmdb
pg_restore -j &amp;lt;num_cores&amp;gt; --no-privileges --no-owner -h &amp;lt;host_name&amp;gt; -U &amp;lt;user_name&amp;gt; -d pmdb &amp;lt;dump_name&amp;gt;&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM&amp;#39;s &lt;a href="https://www.nlm.nih.gov/databases/download/terms_and_conditions_pubmed.html"&gt;Terms and Conditions&lt;/a&gt;.&lt;/p&gt;</description>
  </descriptions>
</resource>
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