Abstract
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 .
Highlights
Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data
BNDB is a representative of this category, as are other systems like GUS [11], ONDEX [12], cPath [13], and Biozon [14]
With BNDB we present a data warehouse system integrating a large number of different biological databases
Summary
With BNDB we present a data warehouse system integrating a large number of different biological databases. Researchers can adapt it to their own needs and build customized databases Another benefit is the full integration of BNDB into the visualizer BiNA. We have developed several applications based on BNDB that show the usefulness of the approach, e.g. an efficient gene set analysis tool, GeneTrail [36], which enables the user to identify enriched functional categories in protein or gene sets. The edge labels are colored by the expression value of the enzyme-coding genes In this example we use expression values for the normal control of the GDS820 data set from the GEO database.
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