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Representing metabolic pathway information: an object-oriented approach
L B Ellis1, S M Speedie, R McLeish
1Center for Biodegradation Research and Informatics and Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Box 609 Mayo Building, 420 SE Delaware Street, Minneapolis, MN 55455, USA. lynda@email.labmed.umn.edu
Motivation:
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information.
Results:
CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction.
Availability:
CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.