Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
           Computer: Poster and Demo

GRAMENE: COMPARATIVE GENOMICS FOR RICE AND OTHER CEREALS

¹ Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA

² Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

³ USDA-ARS Center for Agricultural Bioinformatics, 626 Rhodes Hall, Cornell Theory Center, Ithaca, NY 14853, USA

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. It combines a semi-automatically generated database of cereal genomic and EST 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 within the grass family. Comparative maps of rice, maize, sorghum, barley, wheat and oat are anchored to each other by a set of curated correspondences as well as by sequence similarity of ESTs and genomic markers. 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 which have been adopted by numerous model species databases. Genetic variants, including phenotypes, are annotated using Plant Ontology terms, for plant anatomy and growth stages common to all plants, and Trait Ontology terms which are specific to rice. We will demonstrate how Gramene tools may be used to perform searches and queries of interest to biologists.