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BMC Bioinformatics

, 8:367

First Online: 02 October 2007Received: 02 July 2007Accepted: 02 October 2007


BackgroundTechnological 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.

DescriptionWe 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.

ConclusionBNDB 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

AbbreviationsBN++ Biochemical Network Library

BiNA Biological Network Analysis

DBMS Database Management System

NCBI National Center for Biotechnology Information

BGL Boost Graph Library

SQL Standard Query Language

SBML Systems Biology Markup Language

BioPAX Biological Pathways Exchange

GEO Gene Expression Omnibus database

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-8-367 contains supplementary material, which is available to authorized users.

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Autor: Jan Küntzer - Christina Backes - Torsten Blum - Andreas Gerasch - Michael Kaufmann - Oliver Kohlbacher - Hans-Peter Lenhof


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