T. Rouxel et al., METALGEN DB - METABOLISM LINKED TO THE GENOME OF ESCHERICHIA-COLI, A GRAPHICS-ORIENTED DATABASE, Computer applications in the biosciences, 9(3), 1993, pp. 315-324
The table of 'biochemical pathways' published by Boehringer is conside
red as the most exhaustive document dealing with intermediary metaboli
sm. The present work consisted of constructing a database in which is
collected everything known to date about intermediary metabolism: meta
bolic pathways, bioreactions, metabolites, enzymatic activities, genes
and regulation. Data on genes make it possible to establish a link wi
th existing computer structures specialized for genomic sequences. The
present structure of the database presented here consists of three en
vironments. The first environment is graphic; it is modeled upon the B
oehringer table, but is more convenient to use. The second environment
provides the user with all kinds of manipulations of data (entries, c
orrections, 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 d
atabase at once. This database can thus be substituted for the Boehrin
ger 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 bu
t also in the study of genomes (modeling, analysis of data, prediction
s, etc.).