Plant, Animal & Microbe Genomes X Conference

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

Bioinformatics: Databases
             

DATABASE DESIGN AND IMPLEMENTATION FOR GRAMENE

¹ Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724

² USDA-ARS Center for Agricultural Bioinformatics, 626 Rhodes Hall, Cornell Theory Center, Ithaca, NY 14853

³ Department of Plant Breeding, Cornell University, Ithaca NY 14853-1901

Gramene is a relational database for comparative grass genomics. The technological core of Gramene is the Oracle database management system. Gramene's database is in the early development stage and currently consists of three schemas that define tables containing information on sequences, maps and ontologies. The sequence schema was converted from the EnsEMBL core schema for human genome project. Rice genomic sequences and their annotations from GenBank have been retrieved and loaded into the database. The map schema has been developed for comparative mapping. Genetic maps of grasses, the rice physical map and markers have been inserted into the database based on that schema. The ontology schema, modified from the GO database schema of Berkeley Drosophila Genome Project, has been implemented for controlled vocabularies. Data, including QTL, traits, strains, and references, are currently maintained in the legacy AceDB database, RiceGenes. The above three schemas from the Oracle database have their own table spaces and data files and are managed by different users, respectively. However, the user of one schema not only can insert, select and update data stored within his/her own schema but also can retrieve data from other two schemas.