TY - JOUR
KW - Avena sativa
KW - Computational Biology
KW - Databases, Genetic
KW - Expressed Sequence Tags
KW - Genome, Plant
KW - Genomics
KW - Hordeum
KW - Internet
KW - Oryza sativa
KW - Phenotype
KW - Physical Chromosome Mapping
KW - Plant Proteins
KW - Poaceae
KW - Triticum
AU - Doreen Ware
AU - Pankaj Jaiswal
AU - Junjian Ni
AU - Immanuel Yap V
AU - Xioakang Pan
AU - Ken Clark
AU - Leonid Teytelman
AU - Steven Schmidt
AU - Wei Zhao
AU - Kuan Chang
AU - Sam Cartinhour
AU - Lincoln Stein
AU - Susan McCouch
AB - 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.
BT - Plant physiology
C1 - http://www.ncbi.nlm.nih.gov/pubmed/12481044?dopt=Abstract
DA - 2002 Dec
IS - 4
J2 - Plant Physiol.
LA - eng
N2 - 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.
PY - 2002
SP - 1606
EP - 13
T2 - Plant physiology
TI - Gramene, a tool for grass genomics.
VL - 130
SN - 0032-0889
ER -