ONTOLOGY DEVELOPMENT AND INTEGRATION IN GRAMENE

¹ Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA

² Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

Gramene (www.gramene.org) is a comparative genome database for grasses (Poaceae) and a community resource for rice. We are populating and curating Gramene with annotated sequence data and associated biological information including mutant phenotypes and quantitative trait loci. In order to support queries across various data sets as well as across external databases, Gramene makes extensive use of three related controlled vocabularies (ontologies) namely, Trait Ontology (TO), Plant Ontology (PO) and Gene Ontology (GO). The TO describes each plant trait as a distinguishable characteristic evaluated in phenotypic comparison. The PO describes the anatomical part in a plant and the developmental stage at which a gene is expressed, a gene product is localized and its associated phenotype is observed. The GO is used to describe the molecular function of a gene product, its role in biological processes and localization in cellular components. The presentation and the training workshop, will emphasize the use of ontology, not only to aid queries of the data set, but also their use in computational data curation and data mining, expediting manual curation, and providing consistency to quality annotation.