PMDB: a relational database for PubMed

The tar file contains a compressed dump of PMDB, which was created in PostgreSQL 12 using 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, substituting <dump_name> with the name of the dump folder. This will take some time, so use as many cores as you can spare. Beware the full database is about 113 GiB.

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 NLM's Terms and Conditions.