BMRB Relational DB Snapshot

Snapshot of BMRB Relational DB is available for intensive search on local environment. The snapshot is updated every week (mostly scheduled on Friday) and provided as compressed PostgreSQL dump files using rsync protocol. Data is fully compatible with BMRB/XML (noatom) version. It is possible to reduce latency as much as you want by additional optimization.

Download

Initial setup

% createdb -d $DB_NAME -U $DB_USER

Update

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-pg-dump .
% pg_restore -c -d $DB_NAME -U $DB_USER bmrb_clone.sql

where $DB_NAME is database name and $DB_USER is user name.

References

  1. Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura, Protein Science, 27(1), 95-102 (2018)
  2. Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Linvy, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara, J. Biomed. Semantics, 7(1), 16 (2016).
  3. Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley, Nucleic Acids Research, 36, D402-D408 (2008).