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Dataset Open Access

PMDB: a relational database for PubMed

Hughey, Jacob; Schoenbachler, Joshua


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.7093972", 
  "author": [
    {
      "family": "Hughey, Jacob"
    }, 
    {
      "family": "Schoenbachler, Joshua"
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2022, 
        9, 
        19
      ]
    ]
  }, 
  "abstract": "<p>The files constitute a compressed dump of PMDB, which was created in <a href=\"https://www.postgresql.org/\">PostgreSQL</a>&nbsp;14&nbsp;using the <a href=\"https://pmparser.hugheylab.org\">pmparser</a> R package. Once you have a Postgres server running, you can set up the database as follows:</p>\n\n<p>1. Untar the file containing the database dump, which will create a folder. Substitute &lt;tar_name&gt; with the name of the tar file.</p>\n\n<pre><code class=\"language-bash\">tar xvf &lt;tar_name&gt; &amp;&amp; rm &lt;tar_name&gt;</code></pre>\n\n<p>2.&nbsp;Restore the database onto your Postgres server. Below is one way.&nbsp;Replace &lt;...&gt;&nbsp;as appropriate, substituting&nbsp;&lt;dump_name&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.&nbsp;Beware the full database is about 136&nbsp;GB.</p>\n\n<pre><code class=\"language-bash\">createdb -h &lt;host_name&gt; -U &lt;user_name&gt; pmdb\npg_restore -j &lt;num_cores&gt; --no-privileges --no-owner -h &lt;host_name&gt; -U &lt;user_name&gt; -d pmdb &lt;dump_name&gt;</code></pre>\n\n<p>MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM&#39;s <a href=\"https://www.nlm.nih.gov/databases/download/terms_and_conditions_pubmed.html\">Terms and Conditions</a>.</p>", 
  "title": "PMDB: a relational database for PubMed", 
  "type": "dataset", 
  "id": "7093972"
}
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