Reference "Gramene, a tool for grass genomics"

Reference ID

7071

Title

Gramene, a tool for grass genomics

Source

Plant physiology, 2002, vol. 130, pp. 1606-1613

Authors (13)

Ware-D-H	Jaiswal-P	Ni-J	Yap-I-V
Pan-X	Clark-K-Y	Teytelman-L	Schmidt-S-C
Zhao-W	Chang-K	Cartinhour-S	Stein-L-D
McCouch-S-R

Abstract

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.