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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: 9.3 or higher is recommended. (9.0/9.1/9.2 might work, but have not been tested and are thus not recommended)
  • Minimal of 25GB of free hard drive space (50GB+ of hard drive space is recommended for future updates)

Downloading the dump files

The dump files can be found on our ftp site (ftp://ftp.pdbj.org/mine2/). The following files are available:
  • /mine2/mine2.dump -- The full dump file (~ 2.3GB as of 2017-04-19)
  • /mine2/split/mine2.** -- Split file version of the full dump file in 100MB chunks
  • /mine2/weekly/mine2_update_yyyymmdd.sql.gz -- Incremental update to the RDB compared to the preceeding release. yyyymmdd is the date of the update
  • /mine2/weekly/mine2_weekly.latest.gz -- Latest incremental update to the RDB compared to the preceeding release.

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 ftp://ftp.pdbj.org/mine2/mine2.dump
The database can then be (re-)populated using the pg_restore command. This can be done as follows:
  % pg_restore -d mine2 mine2.dump -Updbj -j8
Alternatively, if you have downloaded the split dump files, do as:
  % cat mine2.* | pg_restore -d mine2 -Updbj -j8

Weekly update

The download size of the weekly updates varies between 5-30MB, but can sometimes be larger in case for many entries the addional PDBj annotations (pdbmlplus) have been updated. The weekly updates can be downloaded via the following commands:
  % wget -r ftp://ftp.pdbj.org/mine2/weekly/mine2_weekly.latest.gz
  % gunzip -c mine2_weekly.latest.gz | psql mine2 -Updbj  
Alternatively, these commands can be added to a bash script and using a cronjob these can be automatically downloaded on release day (Wednesday after 09:00 JST, or Wednesday after 00:00 UTC).

Troubles updating using the delta file

In case you notice any issues with the delta file, such as after the RDB has been upgraded, please delete the RDB and reload it using the mine2.dump file.
  psql> drop schema pdbj cascade;
  % wget ftp://ftp.pdbj.org/mine2/mine2.dump
  % pg_restore -d mine2 mine2.dump -Updbj -j8

Upgrade dates of the RDB

2017-04-19 pdbx-v42-v4.069

Notes for Weekly update

2017-05-24 The update sql file mine2_update_20170524.sql is incomplete. Please apply mine2_update_20170524b.sql after applying the aforementioned file.
2014-03-10 (last edited: 1 month ago)2017-05-25
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