METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database.
The table of 'biochemical pathways' published by Boehringer is considered as the most exhaustive document dealing with intermediary metabolism. The present work consisted of constructing a database in which is collected everything known to date about intermediary metabolism: metabolic pathways, bioreactions, metabolites, enzymatic activities, genes and regulation. Data on genes make it possible to establish a link with existing computer structures specialized for genomic sequences. The present structure of the database presented here consists of three environments. The first environment is graphic; it is modeled upon the Boehringer table, but is more convenient to use. The second environment provides the user with all kinds of manipulations of data (entries, corrections, deletions, consistency, limiting redundancy, etc.). These operations either are automatic or depend on a user-friendly interface (menus selected with the mouse) and so allow biologists at all levels to use the database and to develop it for their own particular needs. Finally, the third environment offers various procedures that make it possible to carry out multicriteria research on all the data in the database at once. This database can thus be substituted for the Boehringer table as a standard reference. It is also a tool that can be used to develop information systems not only in the domain of metabolism but also in the study of genomes (modeling, analysis of data, predictions, etc.).
Rouxel
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Centre de Génétique Moléculaire du CNRS, Gif-sur-Yvette, France.
Danchin
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Henaut
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D003196:Computer Graphics; D001330:Electronic Data Processing; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D012984:Software; D014584:User-Computer Interface