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Gramene, a Tool for Grass Genomics

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 cu...

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Published in:Plant physiology (Bethesda) 2002-12, Vol.130 (4), p.1606-1613
Main Authors: Doreen H. Ware, Pankaj Jaiswal, Ni, Junjian, Immanuel V. Yap, Xioakang Pan, Ken Y. Clark, Teytelman, Leonid, Steven C. Schmidt, Zhao, Wei, Kuan Chang, Sam Cartinhour, Stein, Lincoln D., McCouch, Susan R.
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cited_by cdi_FETCH-LOGICAL-c555t-c4a45c4a390ec00adaaa85a10e3ab9909eab4dce0522f46be7147335f744bc933
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container_end_page 1613
container_issue 4
container_start_page 1606
container_title Plant physiology (Bethesda)
container_volume 130
creator Doreen H. Ware
Pankaj Jaiswal
Ni, Junjian
Immanuel V. Yap
Xioakang Pan
Ken Y. Clark
Teytelman, Leonid
Steven C. Schmidt
Zhao, Wei
Kuan Chang
Sam Cartinhour
Stein, Lincoln D.
McCouch, Susan R.
description 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.
doi_str_mv 10.1104/pp.015248
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Ware ; Pankaj Jaiswal ; Ni, Junjian ; Immanuel V. Yap ; Xioakang Pan ; Ken Y. Clark ; Teytelman, Leonid ; Steven C. Schmidt ; Zhao, Wei ; Kuan Chang ; Sam Cartinhour ; Stein, Lincoln D. ; McCouch, Susan R.</creator><creatorcontrib>Doreen H. Ware ; Pankaj Jaiswal ; Ni, Junjian ; Immanuel V. Yap ; Xioakang Pan ; Ken Y. Clark ; Teytelman, Leonid ; Steven C. Schmidt ; Zhao, Wei ; Kuan Chang ; Sam Cartinhour ; Stein, Lincoln D. ; McCouch, Susan R.</creatorcontrib><description>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. 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Ware</creatorcontrib><creatorcontrib>Pankaj Jaiswal</creatorcontrib><creatorcontrib>Ni, Junjian</creatorcontrib><creatorcontrib>Immanuel V. Yap</creatorcontrib><creatorcontrib>Xioakang Pan</creatorcontrib><creatorcontrib>Ken Y. Clark</creatorcontrib><creatorcontrib>Teytelman, Leonid</creatorcontrib><creatorcontrib>Steven C. Schmidt</creatorcontrib><creatorcontrib>Zhao, Wei</creatorcontrib><creatorcontrib>Kuan Chang</creatorcontrib><creatorcontrib>Sam Cartinhour</creatorcontrib><creatorcontrib>Stein, Lincoln D.</creatorcontrib><creatorcontrib>McCouch, Susan R.</creatorcontrib><title>Gramene, a Tool for Grass Genomics</title><title>Plant physiology (Bethesda)</title><addtitle>Plant Physiol</addtitle><description>Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). 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subjects Alleles
Avena - genetics
Computational Biology - methods
Corn
Databases, Genetic
Expressed Sequence Tags
Gene mapping
Genes
Genetic mapping
Genetic variance
Genome, Plant
Genomes
Genomics
Genomics - methods
Grasses
Hordeum - genetics
Hyperlinks
Internet
Oryza - genetics
Phenotype
Physical Chromosome Mapping - methods
Plant Proteins - genetics
Poaceae - classification
Poaceae - genetics
Rice
Sorghum
Triticum - genetics
Update on Gramene
Updates
Wheat
title Gramene, a Tool for Grass Genomics
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