Gramene, a tool for grass Genomics

Ware, D. H., Jaiswal, P. J., Ni, J. J., Yap, I., Pan, X. K., Clark, K. Y., Teytelman, L., Schmidt, S. C., Zhao, W., Chang, K., Cartinhour, S., Stein, L. D., McCouch, S. R. (December 2002) Gramene, a tool for grass Genomics. Plant Physiology, 130 (4). pp. 1606-1613. ISSN 0032-0889

DOI: 10.1104/pp.015248


Gramene ( 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.

Item Type: Paper
Uncontrolled Keywords: Avena sativa/genetics Computational Biology/methods Databases, Genetic Expressed Sequence Tags Genome, Plant Genomics/ methods Hordeum/genetics Internet Oryza sativa/genetics Phenotype Physical Chromosome Mapping/methods Plant Proteins/genetics Poaceae/classification/ genetics Triticum/genetics
Subjects: bioinformatics
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
organism description > plant
CSHL Authors:
Communities: CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: Matt Covey
Date: December 2002
Date Deposited: 28 Oct 2013 16:46
Last Modified: 28 Oct 2013 16:46
PMCID: PMC1540266
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