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Dataset Open Access

PMDB: a relational database for PubMed

Hughey, Jacob; Schoenbachler, Joshua

The files constitute a compressed dump of PMDB, which was created in PostgreSQL 14 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 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.

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.

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