Poster: Genomic & proteomic resources

Abs # 898: MetaCyc and AraCyc: Metabolic Pathway Databases for Plant Research and Application

Presenter:	Zhang, Peifen , peifenz@acoma.stanford.edu
Authors	Zhang, Peifen  (A)   Krieger, Cynthia J. (B)   Paley, Suzanne  (B)   Karp, Peter D. (B)   Rhee, Seung Yon (A)
Affiliations:	(A): The Arabidopsis Information Resource, Carnegie Institution of Washington (B): Bioinformatics Research Group, SRI International

MetaCyc (http://metacyc.org/) is a literature-based metabolic pathway database. It currently has ca. 500 pathways from over 150 organisms. The goal is to include all experimentally identified pathways and provide a reference metabolism database. Pathways are collected from multiple organisms to ensure that all known pathways and variants are included. Each pathway is associated with the species in which it was curated or is known to occur. A recent enhancement to the database was to include primary metabolism pathways specific to plants. In addition to pathways, other objects in the database include reactions (annotated with EC numbers), compounds (associated with chemical structures), and enzymes (curated with physical and catalytic properties and their coding genes). MetaCyc lists extensive literature citations and curator commentaries to the major data objects. MetaCyc can be used as a reference for predicting the metabolic pathway content of a given set of annotated genes (e.g. a newly sequenced and annotated genome, a set of annotated ESTs). This has been applied to the Arabidopsis genome to generate the Arabidopsis metabolic pathway database AraCyc (http://arabidopsis.org/tools/aracyc/). Manual curation of AraCyc after its initial build is an on-going effort at the Arabidopsis Information Resource (TAIR). The bulk data exchange mechanisms between MetaCyc and all of its derived databases facilitate easy data sharing. We are currently applying an evidence code system to MetaCyc and AraCyc, which provides an assertion for the existence of a pathway or an enzyme activity. The expression overview feature in AraCyc allows overlaying of a list of genes and numeric values onto the pathways, ideal for large-scale Arabidopsis gene expression data or a gene family data.