A Microbial Biodegradation Database on the World Wide Web

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) first appeared on the World Wide Web (http://dragon.labmed.umn.edu/ ~lynda/index.html) less than one year ago to meet the information needs of microbial biotechnology. It was designed to provide information on specialized, non-intermediary metabolic pathways for the microbial biodegradation of primarily xenobiotic, organic chemical compounds. While microbial catabolism of these types of compounds in nature is more difficult to study than intermediary metabolism, it is important for understanding the cycles of nature, bioremediation of industrial chemicals, and biocatalysis for synthesizing commodity chemicals. The UM-BBD provides locally, or through external links, information on the compounds, the enzymes that metabolize them, the genes that produce the enzymes, and the organisms that contain them. In less than one year of operation, usage has grown to over 20,000 accesses a month from six continents, and over 200 national and international users have joined the UM-BBD e-mail users list. It is well accepted by its peers: Five world-renowned content experts have agreed to join the UM-BBD Scientific Advisory Board. It is or will soon be linked to by six prominent biological databases including Entrez Medline, PIR and GenBank, PUMA, Genobase and Kyoto Encyclopedia of Genes and Genomes. And it has been or will be used instructionally at the University of Minnesota, the University of Connecticut and the Hebrew University in Jerusalem. The UM-BBD's use, users and peer-acceptance within its first year of operation emphasizes a great demand for the information it contains, a design that is attractive to its users, and a desire in ~e scientific community for an accelerated pace of development. The next phase of growth includes increases in depth, breadth, quality and representations of its information; and improved tools to manipulate it; all developed in close consultation with the user community. The number of degradation pathways will be expanded from 8 to 100, the amount of information contained will increase from the present 30 to 300-500 Mbytes; and searching will be allowed not only by compound and enzyme names but by EC codes, CAS numbers, and possibly other ways including compound structure and substructure. The pathways chosen for the expansion will be chosen to represent compounds with the broadest possible set of organic functional groups and biochemical reactions. The UM-BBD will then contain direct information on the most environmentally-relevant organic molecules and a become a knowledge base that can be used to predict the metabolic and environmental fate of the majority of the 8 million known organic compounds, whose microbial metabolism has not yet been studied. The UM-BBD is well-positioned to become a community database, used and useful to scientists at every level and with a wide range of interests. A-l