PMDB: a relational database for PubMed

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 with the name of the tar file.

tar xvf && rm

2. Restore the database onto your Postgres server. Below is one way. Replace <...> as appropriate, substituting  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 -U pmdb
pg_restore -j --no-privileges --no-owner -h -U -d pmdb

MEDLINE/PubMed data are courtesy of the U.S. National Library of Medicine. See NLM's Terms and Conditions.

本文件集为PMDB的压缩备份数据集，该数据库基于PostgreSQL 14版本构建，构建过程使用了pmparser R包。当您的Postgres服务器已正常运行后，可按照以下步骤完成数据库搭建：

1. 解压包含数据库备份的压缩包，解压后将生成一个专属文件夹。请将<archive>替换为该tar压缩包的文件名：
tar xvf <archive> && rm <archive>

2. 将备份数据恢复至您的Postgres服务器。以下为其中一种恢复方案，请按需替换<...>占位符，将<dump_folder>替换为存放备份文件的新文件夹名称。该恢复过程耗时较长，建议使用可分配的全部CPU核心以加速流程。请注意，完整数据库体量约为136 GB。
createdb -h <host> -U <username> pmdb
pg_restore -j <num_cores> --no-privileges --no-owner -h <host> -U <username> -d pmdb <dump_folder>

本数据集所用的MEDLINE/PubMed数据由美国国家医学图书馆（U.S. National Library of Medicine）提供，相关使用规范请参阅NLM的条款与条件。