DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE

Sri International, Menlo Park CA

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Abstract

DESCRIPTION (provided by applicant): MetaCyc is a general metabolic pathway DB that currently (February 2001) contains 366 pathways from 131 different organisms. MetaCyc describes metabolic pathways, reactions, enzymes, and substrate compounds. The MetaCyc data have been derived from the experimental literature, and the DB contains copious citations to the literature. MetaCyc is accessed using the same query and visualization software as used for EcoCyc, which is called the Pathway Tools. The objectives of the proposed project are to enrich the MetaCyc metabolic DB to serve as a key resource for metabolic engineering. Although MetaCyc contains significant amounts of data at present, by adding additional data on metabolic pathways and enzymes, we can significantly increase its utility to the metabolic-engineering community. Our specific research objectives are to (a) add microbial pathways to MetaCyc through a curation effort at SRI International; (b) add plant pathways to MetaCyc through a curation effort at the Carnegie Institution of Washington; (c) create software to support direct submission to MetaCyc by biological scientists of newly characterized enzymes that are published in the scientific literature; (d) link MetaCyc to the protein-sequence DBs Swiss-Prot and PIR, and to the TAIR DB; and (e) curate the chemical-compound data within MetaCyc to permit automated consistency checking of MetaCyc.