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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 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 (~ 1.5GB as of 2014-03-05)
  • /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
Alternatively, if you have downloaded the split dump files, do as:
  % cat mine2.* | pg_restore -d mine2 -Updbj

Weekly update

The download size of the weekly updates varies between 5-10MB, 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).
2014-03-10 (last edited: 10 months ago)2016-06-21
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