The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community

Abstract

Arabidopsis thaliana is the most widely-studied plant today. The concerted efforts of over 11 000 researchers and 4000 organizations around the world are generating a rich diversity and quantity of information and materials. This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers and can be searched and downloaded in a number of ways. In the last two years, efforts have been focused on increasing data content and diversity, functionally annotating genes and gene products with controlled vocabularies, and improving data retrieval, analysis and visualization tools. New information include sequence polymorphisms including alleles, germplasms and phenotypes, Gene Ontology annotations, gene families, protein information, metabolic pathways, gene expression data from microarray experiments and seed and DNA stocks. New data visualization and analysis tools include SeqViewer, which interactively displays the genome from the whole chromosome down to 10 kb of nucleotide sequence and AraCyc, a metabolic pathway database and map tool that allows overlaying expression data onto the pathway diagrams. Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system.

Figure 1

TAIRs SeqViewer. (A) Nucleotide view showing 10 kb of sequence with genes indicated as colored letters (UTRs in red, exons in gold, introns in purple) with translational starts and stops highlighted in blue and mutated nucleotides highlighted in gray. (B) Close up view showing a 40 kb region surrounding the gene visible in A, with mutations and polymorphisms shown at top (poly band), genes shown in center (gene band) and EST matches shown at bottom (transcript band). (C) Genome view showing the five Arabidopsis chromosomes in green with the positions of genes matching a name search indicated as vertical red lines.