Molecular Biology Database
Bionemo stores manually curated information about proteins and genes directly implicated in biodegradation metabolism. The database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes.
Bionemo complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus on the biochemical aspects of biodegradation.
Bionemo has been built by manually associating sequences databases entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network.
The information in the Bionemo database can be downloaded as a PostgresSQL dump. To facilitate the programmatic use of the information contained in the database an object-oriented Perl API is also provided.