Literature DB >> 9697222

DBGET/LinkDB: an integrated database retrieval system.

W Fujibuchi1, S Goto, H Migimatsu, I Uchiyama, A Ogiwara, Y Akiyama, M Kanehisa.   

Abstract

The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese GenomeNet service. DBGET is used to search and extract entries from a wide range of molecular biology databases, while LinkDB is used to search and compute links between entries in different databases. DBGET/LinkDB is designed to be a network distributed database system with an open architecture, which is suitable for incorporating local databases or establishing a specialized server environment. It also has an advantage of simple architecture allowing rapid daily updates of all the major databases. The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools, such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. In addition to factual links between database entries, LinkDB is being extended to included similarity links and biological links toward computerization of logical reasoning processes.

Mesh:

Year:  1998        PMID: 9697222

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  22 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  AAindex: amino acid index database.

Authors:  S Kawashima; M Kanehisa
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  LIGAND: chemical database of enzyme reactions.

Authors:  S Goto; T Nishioka; M Kanehisa
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

4.  PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).

Authors:  T Noguchi; H Matsuda; Y Akiyama
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

5.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  LIGAND: database of chemical compounds and reactions in biological pathways.

Authors:  Susumu Goto; Yasushi Okuno; Masahiro Hattori; Takaaki Nishioka; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags.

Authors:  Takeshi Kawashima; Shuichi Kawashima; Yuji Kohara; Minoru Kanehisa; Kazuhiro W Makabe
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

8.  CyanoBase: the cyanobacteria genome database update 2010.

Authors:  Mitsuteru Nakao; Shinobu Okamoto; Mitsuyo Kohara; Tsunakazu Fujishiro; Takatomo Fujisawa; Shusei Sato; Satoshi Tabata; Takakazu Kaneko; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2009-10-30       Impact factor: 16.971

9.  The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Authors:  Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord Hendrix Barboza; Raoul Jp Bonnal; Richard Bruskiewich; Jan C Bryne; José M Fernández; Akira Funahashi; Paul Mk Gordon; Naohisa Goto; Andreas Groscurth; Alex Gutteridge; Richard Holland; Yoshinobu Kano; Edward A Kawas; Arnaud Kerhornou; Eri Kibukawa; Akira R Kinjo; Michael Kuhn; Hilmar Lapp; Heikki Lehvaslaiho; Hiroyuki Nakamura; Yasukazu Nakamura; Tatsuya Nishizawa; Chikashi Nobata; Tamotsu Noguchi; Thomas M Oinn; Shinobu Okamoto; Stuart Owen; Evangelos Pafilis; Matthew Pocock; Pjotr Prins; René Ranzinger; Florian Reisinger; Lukasz Salwinski; Mark Schreiber; Martin Senger; Yasumasa Shigemoto; Daron M Standley; Hideaki Sugawara; Toshiyuki Tashiro; Oswaldo Trelles; Rutger A Vos; Mark D Wilkinson; William York; Christian M Zmasek; Kiyoshi Asai; Toshihisa Takagi
Journal:  J Biomed Semantics       Date:  2010-08-21

10.  TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

Authors:  Shin Kawano; Tsutomu Watanabe; Sohei Mizuguchi; Norie Araki; Toshiaki Katayama; Atsuko Yamaguchi
Journal:  Nucleic Acids Res       Date:  2014-05-14       Impact factor: 16.971

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