BNDB - the Biochemical Network Database.
BACKGROUND
Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources.


METHODS
We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB.


CONCLUSIONS
BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.
Küntzer
Jan
J
Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany. kuentzer@bioinf.uni-sb.de
Backes
Christina
C
Blum
Torsten
T
Gerasch
Andreas
A
Kaufmann
Michael
M
Kohlbacher
Oliver
O
Lenhof
Hans-Peter
HP
D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000737:chemistry / Q000502:physiology*; D015398:Signal Transduction / Q000502:physiology*; D018511:Systems Integration; D014157:Transcription Factors / Q000502:physiology; D014584:User-Computer Interface
D020543:Proteome; D014157:Transcription Factors