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PMDB: a relational database for PubMed

Hughey, Jacob; Schoenbachler, Joshua


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    <dct:description>&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;</dct:description>
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