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Science 14 September 2001:
Vol. 293. no. 5537, pp. 2040 - 2044
DOI: 10.1126/science.1064621
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Pathway Databases: A Case Study in Computational Symbolic Theories
Peter D. Karp
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.
Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA. E-mail:
pkarp{at}ai.sri.com
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