title: Gramene, a tool for grass genomics.
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.
authors.affiliation: Cold Spring Harbor Laboratory, New York 11724, USA.
authors.forename: Doreen H
authors.initials: DH
authors.lastname: Ware
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.forename: Junjian
authors.initials: J
authors.lastname: Ni
authors.forename: Immanuel V
authors.initials: IV
authors.lastname: Yap
authors.forename: Xioakang
authors.initials: X
authors.lastname: Pan
authors.forename: Ken Y
authors.initials: KY
authors.lastname: Clark
authors.forename: Leonid
authors.initials: L
authors.lastname: Teytelman
authors.forename: Steven C
authors.initials: SC
authors.lastname: Schmidt
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
authors.forename: Kuan
authors.initials: K
authors.lastname: Chang
authors.forename: Sam
authors.initials: S
authors.lastname: Cartinhour
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
authors.forename: Susan R
authors.initials: SR
authors.lastname: McCouch
mesh_terms: D018554:Avena / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D001467:Hordeum / Q000235:genetics; D020407:Internet; D012275:Oryza / Q000235:genetics; D010641:Phenotype; D020161:Physical Chromosome Mapping / Q000379:methods; D010940:Plant Proteins / Q000235:genetics; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D014908:Triticum / Q000235:genetics
chemical_list: D010940:Plant Proteins