B-Net : A Biochemical Network database

Search B-Net

Introduction to B-NET:

Functional genomic studies are beginning to combine microarray, proteomic and metabolomic data. While genes and proteins can be related by their sequence similarity, metabolites cannot easily be related with genes or proteins. So far, the most effective way to do this is through reference databases that collect the known information about metabolic reactions, i.e. their substrates, products, and enzymes. While several such biochemical databases already exist, not one of them combined all the features necessary for interpretation of metabolomics data. We have developed B-NET (for Biochemical Network), a relational database to serve as a reference for the functional genomic studies. B-NET follows a simple schema that, nevertheless, reflects the relevant intricacies of biochemistry. Unlike most metabolic databases, B-NET is specific for each molecular species in each organism.

B-NET is organized based on four important concepts: genes, protein, compound (metabolite), and reaction. These concepts act as logical organizers for the data to be entered and viewed. We have followed a policy that each specific fact supporting the information in the database is stored in an "evidence" table. Evidence is classified with the codes defined in the Gene OntologyTM (Consortium, 2001). Our policy is to archive each single piece of evidence known for the data represented in the database. This allows users to have more or less credibility in the information. Each piece of evidence is also associated with a bibliographic reference, or alternatively with a web site.

Currently we have used B-NET for Medicago truncatula

Summary of current information stored in B-NET for Medicago truncatula (Release 2) are:

EntityCountData
References142HTML
Genes43298HTML, XML
Proteins308HTML, XML
Metabolites1493HTML, XML