Currently we are experiencing a rapidly increasing rate of production of large-scale data such as genome sequences, genome-wide gene expression profiles, proteomics and metabolomics data. The necessity to organize all of these data into a biological framework has been, in part, the motivation for the work described in this review. While we have created a comprehensive database that describes the metabolic network of a model plant species, Arabidopsis thaliana, the database is far from being either complete or error-free. Many of the pathways are in need of manual curation using the current literature and many more pathways, particularly those for secondary metabolism and those that include transport reactions, need to be brought into the database. As with any other database project, the content of the AraCyc database is dynamic and will continue to undergo enhancement, additions, and modifications to make it more useful.