Database Commons

a catalog of worldwide biological databases

The Arabidopsis Information Resource (TAIR) is a highly sophisticated, extensive, user friendly, Web-based resource for researchers working on the model plant Arabidopsis thaliana. The main gateway to this resource is through TAIR's homepage http://www.arabidopsis.org. It is a repository of large amounts of data including gene, mapping, protein, expression and community data in the form of a relational database. These data can be searched, downloaded and analysed using the tools provided. Here, the simple search (for retrieval of information), Seq Viewer (for the visualization of the five Arabidopsis chromosomes and associated annotations) and AraCyc (database of Arabidopsis biochemical pathways, with a graphical overview onto which large data sets, such as gene expression data, can be overlaid) tools are described with examples.

The Arabidopsis Information Resource (TAIR; http://www.arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene expression, mutant phenotypes, biological materials such as DNA and seed stocks, genetic markers, genetic and physical maps, biochemical pathways, genome organization, images of mutant plants and protein sub-cellular localizations, publications, and the research community Data in TAIR are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes. Gene expression data from microarrays is a recent addition to the database and methods for accessing these data are also described. Two pattern identification programs are described for mining TAIR's unique Arabidopsis sequence data sets. We also describe how to use AraCyc for mining plant metabolic pathways.

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).