SRI International (SRI) proposes to expand its electronic encyclopedia of E. coli genes and metabolism. The encyclopedia is encoded as a computer database - EcoCyc - that is accessible to scientists through a user- friendly graphical interface. We propose to complete the description of E. coli intermediary metabolism within the encyclopedia. and to add information on other types of metabolism, including macromolecule metabolism, tRNA metabolism, and cellular processes such as active transport. Data on the regulation of E. coli genes will also be collected. The resulting collection of information will be a nonmammalian model of high connectivity. The graphical user interface will be expanded to provide more sophisticated visualizations of metabolic pathways, and visualizations of genetic regulation, to improve user access to the encyclopedia. We will support the widespread use of EcoCyc in the scientific community through the existing graphical user interface, the World Wide Web, flatfile dumps of the knowledge base (KB), and complex structured queries transported via Internet. The EcoCyc database will describe the reactions of the metabolism of E. coli, listing reaction equations, their EC numbers, cofactors, activators, and inhibitors. EcoCyc will describe the enzymes that catalyze these reactions, listing their molecular weight, subunit composition, and encoding genes. For each gene EcoCyc will list the gene name, the position of the gene within the E. coli chromosome, information on its regulation, and will allow its DNA sequence,to be retrieved. Literature citations will be included in all these items. EcoCyc will be valuable as a reference source for many scientists. Microbial geneticists who work with bacteria other than E. coli may find facile access to E. coli data useful as a point of reference for gene functions, as well as for similarities and differences of gene-enzyme relationships in other organisms. Molecular evolutionists interested in ancestral relationships among genes, enzymes and pathways could use the database to search for examples of duplication and divergence. EcoCyc will also be useful to scientists who perform quantitative simulations of metabolic pathways, and to those who design variants of biochemical pathways for industrial applications.
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