Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
             

CURATION OF RICE PHENOTYPIC AND GENOTYPIC DATA IN THE GRAMENE DATABASE

¹ Department of Plant Breeding, Cornell University, Ithaca, New York, 14853, USA

² USDA-ARS Center for Agricultural Bioinformatics, Ithaca, New York, 14853, USA

³ Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA

Gramene (http://www.gramene.org) is a comparative mapping resource for the grasses and a repository for rice functional mutations and quantitative trait loci (QTLs) curated from the literature. A major challenge for curators will be the development of a uniform method to curate and integrate phenotypic descriptions within the database. To address this challenge, in a collaborative effort with IRRI, ICIS, MaizeDB and CIMMIT, Gramene researchers are developing a Trait Ontology to represent and describe phenotypic information for rice and other grasses, focusing primarily on functional mutants and quantitative trait loci (QTLs). A wide range of other information that is useful in establishing associations between phenotype and genotype will also be included, such as map position of genes and/or QTLs, descriptions of germplasm (accessions, mapping populations, mutant backgrounds and other genetic stocks), environmental conditions, statistical methodology used to identify QTLs, mutagenesis techniques, etc. Citations from PubMed, AGRICOLA, BIOSIS, CAB abstracts, and other public sources will be fully annotated. A web-accessible submission form will allow outside scientists to submit information about mutants, QTLs or other phenotypic studies directly to the Gramene database and will facilitate interaction between database developers and end users. An overview of the phenotypic data in Gramene will be presented with an emphasis on descriptions of phenotypes using controlled vocabulary.