Plant, Animal & Microbe Genomes X Conference

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

Workshop: Controlled Vocabulary/Ontology
            

Gramene: EFFORTS ON DEVELOPMENT AND INTEGRATION OF CONTROLLED VOCABULARY

¹ Department of Plant Breeding, Cornell university, Ithaca, NY-14853, USA

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

³ Cold Spring Harbor Laboratory, 1-Bungtown Road, Cold Spring Harbor, NY-11724, USA

Gramene (http://www.gramene.org) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated sequence data and associated biological information including mutants, phenotypes, polymorphisms and Quantitative Trait Loci. In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. First, a Trait Ontology (TO) will be implemented across the cereal crops and plants to curate and evaluate phenotype comparisons. An initial vocabulary for TO and definitions for TO terms is available at (http://www.gramene.org/plant_ontology/). Second, a Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression and localization of gene and gene products. The TO and PO are both in the early stages of development in collaboration with International Rice Research Institute, TAIR, MaizeDB, International Crop Information System and CIMMYT. Finally, as part of the Gene Ontology consortium, we will classify 4000 confirmed or predicted rice genes. The development of plant specific vocabularies is open for community discussion and will be encouraged by web based submission forms for suggestions, additions or modifications of various ontology terms. The form is available at http://www.gramene.org/plant_ontology/submission/).