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Plant Physiol, December 2002, Vol. 130, pp. 1606-1613

UPDATE
Gramene, a Tool for Grass Genomics

Doreen H. Ware,2 Pankaj Jaiswal,2 Junjian Ni, Immanuel V. Yap, Xioakang Pan, Ken Y. Clark, Leonid Teytelman, Steven C. Schmidt, Wei Zhao, Kuan Chang, Sam Cartinhour, Lincoln D. Stein, and Susan R. McCouch*

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 (D.H.W., X.P., K.Y.C., L.T., S.C.S., W.Z., K.C., L.D.S.); Department of Plant Breeding, Cornell University, Ithaca, New York 14853-1901 (P.J., J.N., I.V.Y., S.R.M.); and United States Department of Agriculture-Agricultural Research Service Center for Agricultural Bioinformatics, 626 Rhodes Hall, Cornell Theory Center, Ithaca, New York 14853 (S.C.)

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.

2 These authors contributed equally to the paper.

* Corresponding author; e-mail SRM4{at}cornell.edu; fax 607-255-6683.

© 2002 American Society of Plant Biologists


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