Pathway Databases: A Case Study in Computational Symbolic Theories
Peter D. Karp
Bioinformatics Research Group
pkarp @ ai.sri.com
Science 293:2040-4 (2001).
A pathway database (DB) is a DB that describes biochemical pathways,
reactions, and enzymes. The EcoCyc pathway DB (see
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
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