Science. 2001 Sep 14;293(5537):2040-4.

Pathway databases: a case study in computational symbolic theories.

Source

Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA. pkarp@ai.sri.com

Abstract

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.

PMID:: 11557880; [PubMed - indexed for MEDLINE]

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Research Support, U.S. Gov't, P.H.S.

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Culture Media

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1-R01-RR07861-01/RR/NCRR NIH HHS/United States

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