Kanehisa Laboratories

Fukuoka - Kyoto - Tokyo


DBGET is a simple database retrieval system developed by Kanehisa Laboratories, which is used as the backbone retrieval system for all GenomeNet databases including KEGG. DBGET is based on a flat-file view of molecular biology databases, where the database is considered as a collection of entries. Because each entry is given a unique entry name (or an accession number) within a database, the molecular biology databases in the world can be retrieved uniformly by the combination of the database name and the entry name:
The gene catalog for each organism in the KEGG GENES database is treated like a flat-file database. Any gene or gene product (protein or RNA) in KEGG can thus be specified by the combination of the organism name and the gene name:
When two data entries are related in any way, it is customary to incorporate cross-reference information in the molecular biology databases. The link information between two entries is a binary relation represented by:
database1:entry1 --> database2:entry2
LinkDB is a collection of all such links among the GenomeNet databases as well as to many outside databases, especially from KEGG.

Brief History of DBGET and LinkDB

  • 1980, Los Alamos Sequence Analysis System for CDC7600 in the pre-GenBank project (by Minoru Kanehisa in Los Alamos)
  • 1983, IDEAS: Integrated Database and Extended Analysis System for nucleic acids and protein for VAX (by Minoru Kanehisa in NIH)
  • 1986, IDEAS ported from VAX to FACOM (by Minoru Kanehisa in Kyoto)
  • 1989, A portion of SEQMAN program in IDEAS ported to UNIX and named DBGET (by Atsushi Ogiwara)
  • 1991, Database update program SEQNEW ported to UNIX (by Ikuo Uchiyama)
  • 1992, GenomeNet Database Service initiated (by Kanehisa Laboratory)
  • 1993, Client version of DBGET (by Atsushi Ogiwara)
  • 1994, WWW version of DBGET (by Yutaka Akiyama)
  • 1994, LinkDB implementation (by Susumu Goto)
  • 1995, KEGG Project initiated (by Kanehisa Laboratory)
  • 1996, New version of DBGET for KEGG (by Hiroshi Migimatsu)
  • Since 2000, Further development and maintenance of DBGET (by Koichi Ohkubo)
  • Since 2007, Further development and maintenance of LinkDB (by Kentaro Ozawa)
  • 2012, REST-style implementation of DBGET/LinkDB (by Masayuki Kawasima)

  1. Kanehisa, M.I.; Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res. 10, 183-196 (1982). [pubmed] [pdf]
  2. Kanehisa, M., Klein, P., Greif, P., and DeLisi, C.; Computer analysis and structure prediction of nucleic acids and proteins. Nucleic Acids Res. 12, 417-428 (1984). [pubmed] [pdf]
  3. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an integrated database retrieval system. Pacific Symp. Biocomputing 1998, 683-694 (1997). [pubmed] [pdf]
  4. Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997). [pubmed]