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Plant Physiology 132:453-460 (2003)
© 2003 American Society of Plant Biologists

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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

AraCyc: A Biochemical Pathway Database for Arabidopsis1

Lukas A. Mueller*, Peifen Zhang and Seung Y. Rhee

The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, California 94305

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.102.017236.

1 This work was supported by the National Science Foundation (grant no. DBI–9978564) and by the National Institutes of Health (grant no. R01–GM65466–01).

* Corresponding author; e-mail mueller{at}acoma.stanford.edu; fax 650–325–6857.

Received November 5, 2002; returned for revision December 11, 2002; accepted February 7, 2003.




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