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Nucleic Acids Research, 2003, Vol. 31, No. 1 224-228
© 2003 Oxford University Press

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

Seung Yon Rhee*, William Beavis1, Tanya Z. Berardini, Guanghong Chen1, David Dixon1, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya1, Neil Miller1, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems1, Yihe Wu1, Iris Xu, Daniel Yoo, Jungwon Yoon and Peifen Zhang

Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA 1 National Center for Genome Resources, 2939 Rodeo Park Dr. East, Santa Fe, NM 87505, USA

*To whom correspondence should be addressed. Email: rhee{at}acoma.stanford.edu

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.


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Plant Cell Physiol., April 1, 2006; 47(4): 481 - 492.
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J.-B. Lee, J.-j. Kim, and J. C. Park
Automatic extension of Gene Ontology with flexible identification of candidate terms
Bioinformatics, March 15, 2006; 22(6): 665 - 670.
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S. K. Palaniswamy, S. James, H. Sun, R. S. Lamb, R. V. Davuluri, and E. Grotewold
AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks
Plant Physiology, March 1, 2006; 140(3): 818 - 829.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
C. H. Wu, R. Apweiler, A. Bairoch, D. A. Natale, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, et al.
The Universal Protein Resource (UniProt): an expanding universe of protein information
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D187 - D191.
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