Poster: "Omics": technologies and resources

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Abs # 996: The Gramene Database: A Comparative Genomics Resource for Grasses

Presenter:	Jaiswal, Pankaj , Contact Author
Authors	Jaiswal, Pankaj  (A)   Ware, Doreen  (B) (D)  Ni, Junjian  (A)   Yap,  Immanuel  (A)   Ren, Liya  (B)   Youens-Clark, Ken  (B)   Spooner, William  (B)   Ratnapu, Kiran  (B)   Fogleman, Molly A (A)   Casstevens, Terry M (C)   Buckler, Edward S (C) (D)  Stein, Lincoln  (B)   McCouch, Susan R (A)
Affiliations:	(A): Department of Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA (B): Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA (C): Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853 (D): USDA-ARS, Cornell University, Ithaca NY 14853 USA
Web Site:	http://www.gramene.org

Gramene (www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. The database combines a semi-automatically generated analyses 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 an anchor model for moving across species within the grass family Poaceae. 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 (ontologies) to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Genes and 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 structures (anatomy) and growth stages, and Trait Ontology terms which are specific to rice. Through this effort, the database is fostering candidate gene discovery using the comparisons of genetic and genomic maps from all the major cereal crops and their associations to the phenotype features such as mutant FSTs and QTL mapped on them.