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Publication Details
The Pathway Tools Software
by Karp, P.D. and Paley, S. and Romero, P.
Bioinformatics, vol. 18, pp. S225-S232, 2002.
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Motivation: Bioinformatics requires reusable software tools for creating model-organism databases (MODs). Results: The
Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a
Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving
understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an
overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new
PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and
Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway
Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for
data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI
and by external users. Availability: The software is freely available to academics and is available for a fee to commercial
institutions.
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Pathway Tools
Pathway Tools consists of two sets of tools: the Editors and Pathologic. The Editors are specialized for editing a pathway/genome database. Pathologic helps create a new pathway/genome database containing pathways predicted from an annotated genome (typically as a Genbank entry) and the MetaCyc database.
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