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Pathway Databases: A Case Study in Computational Symbolic Theories

A pathway database (DB) is a DB that describes biochemical pathways, reactions, and enzymes. The EcoCyc pathway DB (see http://ecocyc.org) describes the metabolic, transport, and genetic-regulatory networks of Escherichia coli. EcoCyc is an example of a computational symbolic theory, which is a DB that structures a scientific theory within a formal ontology so that it is available for computational analysis. It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively.

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Resource Type: Journal article/Issue
Audience Level: Undergraduate lower division 13-14, Undergraduate upper division 15-16, Graduate, Professional (degree program), Continuing education

Author and Copyright


Authors and Editors: Peter Karp of Bioinformatics Research Group, SRI International
Publisher: AAAS
Format: text/html
Copyright and other restrictions: Yes
Cost: No

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