PMDB: a relational database for PubMed

DOI10.5281/zenodo.14616021Zenodo14616021MaRDI QIDQ6676725FDOQ6676725

Dataset published at Zenodo repository.

Joshua Schoenbachler, Jacob Joseph Hughey

Publication date: 8 January 2025

Description

The files constitute a compressed dump of PMDB, which was created in PostgreSQL14using the pmparser R package. Once you have a Postgres server running, you can set up the database as follows: 1. Untar the file containing the database dump, which will create a folder. Substitute tar_name with the name of the tar file. tar xvf tar_name rm tar_name 2.Restore the database onto your Postgres server. Below is one way.Replace ...as appropriate, substitutingdump_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 136GB. 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 MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLMs Terms and Conditions.

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