Mine 2 RDB local install

You can have a local copy of the Mine 2 Relational DataBase by using dump files provided by PDBj. The dump files have been designed to be used with a recent version of PostgreSQL. In the future we will also release a manager script to help install and maintain your copy of the PDBj Mine 2 RDB. For questions, please contact us.

Requirements

• Recent version of PostgreSQL: 12 or higher is recommended. (older versions might work, but have not been tested and are thus not recommended)
• Minimal of 50GB of free hard drive space (75GB+ of hard drive space is recommended for future updates)

Downloading the dump files

The dump files can be found on our data site (https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/). The following files are available:

• PDB data: https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/pdbj.mine2.dump
• chem_comp data: https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/cc.mine2.dump
• CSD integration: https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/ccmodel.mine2.dump
• BIRD data: https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/prd.mine2.dump
• EMDB data: https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/emdb.mine2.dump

Loading the RDB from scratch

First PostgreSQL needs to be prepared for the Mine 2 RDB (in case this has already been done, the following steps can be ommited):

  % createuser -s pdbj
  % createdb mine2

Download the full dump file from the pdbj ftp site (alternatily use the split files instead):

  % wget https://data.pdbjbk1.pdbj.org/pdbjplus/mine2/dump/pdbj.mine2.dump

The database can then be (re-)populated using the pg_restore command. This can be done as follows:

  % pg_restore -d mine2 pdbj.mine2.dump -Updbj -j16

The other schemas can be loaded via pg_restore into the mine2 database in the same manner.

Weekly update

We've developed a new system for upgrading local Mine 2 RDB data, which is described in further detail at our GitLab repository for the new software. This new system has replaced the old delta file system previously in use.

Upgrade dates of the RDB

The RDB is now automatically updated to the latest version of wwPDB dictionary on a weekly basis.