6573400
doi
10.5281/zenodo.6573400
oai:zenodo.org:6573400
user-scholarly-data
Schoenbachler, Joshua
Vanderbilt University Medical Center
PMDB: a relational database for PubMed
Hughey, Jacob
Vanderbilt University Medical Center
doi:10.1101/2020.09.07.285924
info:eu-repo/semantics/openAccess
Other (Public Domain)
<p>The files constitute a compressed dump of PMDB, which was created in <a href="https://www.postgresql.org/">PostgreSQL</a> 14 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>
<p>1. Untar the file containing the database dump, which will create a folder. Substitute <tar_name> with the name of the tar file.</p>
<pre><code class="language-bash">tar xvf <tar_name> && rm <tar_name></code></pre>
<p>2. Restore the database onto your Postgres server. Below is one way. Replace <...> as appropriate, substituting <dump_name> 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. Beware the full database is about 136 GB.</p>
<pre><code class="language-bash">createdb -h <host_name> -U <user_name> pmdb
pg_restore -j <num_cores> --no-privileges --no-owner -h <host_name> -U <user_name> -d pmdb <dump_name></code></pre>
<p>MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM's <a href="https://www.nlm.nih.gov/databases/download/terms_and_conditions_pubmed.html">Terms and Conditions</a>.</p>
Zenodo
2022-05-23
info:eu-repo/semantics/other
4008109
user-scholarly-data
1692050466.266853
25626265600
md5:fcba674d4bf97435afe8941562ed8ec9
https://zenodo.org/records/6573400/files/pmdb_20220523_084321.tar
public
10.1101/2020.09.07.285924
Is referenced by
doi
10.5281/zenodo.4008109
isVersionOf
doi