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BNDB – The Biochemical Network Database

Jan Küntzer1*, Christina Backes1, Torsten Blum2, Andreas Gerasch2, Michael Kaufmann2, Oliver Kohlbacher2 and Hans-Peter Lenhof1

Author Affiliations

1 Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Germany

2 Center for Bioinformatics/Wilhelm Schickard Institute for Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Germany

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BMC Bioinformatics 2007, 8:367  doi:10.1186/1471-2105-8-367

Published: 2 October 2007



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.


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.


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 webcite.