There is a newer version of this record available.

Dataset Open Access

PMDB: a relational database for PubMed

Hughey, Jacob; Schoenbachler, Joshua


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/2b2683d0-c130-4ea9-ba17-21879172c909/pmdb_20220919_124740.tar"
      }, 
      "checksum": "md5:388e128c0cad064cc024c3b25203b9fa", 
      "bucket": "2b2683d0-c130-4ea9-ba17-21879172c909", 
      "key": "pmdb_20220919_124740.tar", 
      "type": "tar", 
      "size": 26259660800
    }
  ], 
  "owners": [
    10752
  ], 
  "doi": "10.5281/zenodo.7093972", 
  "stats": {
    "version_unique_downloads": 265.0, 
    "unique_views": 10.0, 
    "views": 12.0, 
    "version_views": 1278.0, 
    "unique_downloads": 0.0, 
    "version_unique_views": 1075.0, 
    "volume": 0.0, 
    "version_downloads": 604.0, 
    "downloads": 0.0, 
    "version_volume": 7449433321929.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.7093972", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.4008109", 
    "bucket": "https://zenodo.org/api/files/2b2683d0-c130-4ea9-ba17-21879172c909", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.4008109.svg", 
    "html": "https://zenodo.org/record/7093972", 
    "latest_html": "https://zenodo.org/record/7328849", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.7093972.svg", 
    "latest": "https://zenodo.org/api/records/7328849"
  }, 
  "conceptdoi": "10.5281/zenodo.4008109", 
  "created": "2022-09-20T17:20:52.004641+00:00", 
  "updated": "2022-11-17T21:13:06.397696+00:00", 
  "conceptrecid": "4008109", 
  "revision": 4, 
  "id": 7093972, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.7093972", 
    "description": "<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>", 
    "license": {
      "id": "other-pd"
    }, 
    "title": "PMDB: a relational database for PubMed", 
    "relations": {
      "version": [
        {
          "count": 23, 
          "index": 20, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "4008109"
          }, 
          "is_last": false, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "7328849"
          }
        }
      ]
    }, 
    "communities": [
      {
        "id": "scholarly-data"
      }
    ], 
    "publication_date": "2022-09-19", 
    "creators": [
      {
        "orcid": "0000-0002-1558-6089", 
        "affiliation": "Vanderbilt University Medical Center", 
        "name": "Hughey, Jacob"
      }, 
      {
        "orcid": "0000-0001-8544-6359", 
        "affiliation": "Vanderbilt University Medical Center", 
        "name": "Schoenbachler, Joshua"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.1101/2020.09.07.285924", 
        "relation": "isReferencedBy", 
        "resource_type": "publication-preprint"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.4008109", 
        "relation": "isVersionOf"
      }
    ]
  }
}
1,278
604
views
downloads
All versions This version
Views 1,27812
Downloads 6040
Data volume 7.4 TB0 Bytes
Unique views 1,07510
Unique downloads 2650

Share

Cite as