MBL scientist Monica Riley, Ph.D., was instrumental in the collection of the descriptions of all the genes and metabolism of E. coli. Pieces of data were sourced and analyzed from more than 50 scientific journals. Once the data were collected, they were encoded into an object-oriented database developed by SRI.

"The E. coli database manages the entry of existing and new data and is accessible over the Internet," said Riley. "The EcoCyc database is intended to save scientists time in looking up facts about genes and metabolism and to provide greater accessibility of the E. coli genome." Through a single interface, the user is able to move rapidly between the DNA gene sequence to information about the protein encoded by that gene and on up to the role of its product enzyme in a biochemical pathway.

One major feature of EcoCyc is that it provides a window on entire metabolic pathways. For example, one could look at the synthesis of a key intermediate in cell wall biosynthesis. EcoCyc organizes the data on all the enzymes that participate in cell wall synthesis, which allows researchers to work back to their DNA sequence. This enables them to clone one of the genes to express large amounts of one critical enzyme as a potential target for a new antibiotic. A compound that inhibits the activity of the enzyme is a good candidate for a drug that will interfere with the synthesis of the key intermediate, ultimately leading to a damaged cell wall and death of the bacteria.

To extend the utility of EcoCyc, SRI developed PathoLogic, an advanced proprietary software package that predicts the metabolic pathways of an organism whose genome has been sequenced, such as H. influenza or H. pylori. PathoLogic uses the EcoCyc database to analyze how the predicted genes of that organism are organized into pathways. It then creates a new database that describes the predicted pathways and enzymes of the organism.

"EcoCyc is the first database to reach such a high level of scientific detail and sophistication," said Ray Perrault, Ph.D., director of SRI's Artificial Intelligence Center. "With our new PathoLogic software, pharmaceutical companies will have easier access to the requisite molecular biology to develop novel antibiotics for many strains of pathogenic microorganisms. The new database and software are important tools for the pharmaceutical industry in their constant search for new and effective antibiotics and other important pharmaceutical products."

SRI and MBL have exclusively licensed the database and software tools to Oakland, Calif.-based Pangea Systems, a major provider of bioinformatic systems to the scientific community. Pangea Systems will further develop and support EcoCyc and derived databases as well as the PathoLogic software, and will provide these products to the pharmaceutical industry as an important tool for the development of new drugs.

The Marine Biological Laboratory is an independent, nonprofit research and educational institution and North America's oldest private marine laboratory. Since the laboratory was established in 1888, MBL summer investigators and advanced students from around the world have used the diverse and abundant marine organisms found in surrounding waters as model systems for exploring fundamental life processes. In addition to serving as the summer home for American biology, the MBL hosts major research programs in cell and developmental biology, ecosystems studies, neurobiology, behavior, sensory biology and molecular evolution.

SRI International is one of the largest research, technology development and consulting firms in the world providing corporations, governments and organizations worldwide with the technology research and resources needed for competing more effectively in today's changing global environment. SRI's Artificial Intelligence Center is a pioneer and major contributor to the development of computer capabilities such as natural language, perception, and representation and reasoning for intelligent behavior in complex situations.