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Comparative and Functional Genomics
Volume 3 (2002), Issue 2, Pages 132-136
Conference Review

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

1Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA
2USDA-ARS Center for Agricultural Bioinformatics, 626 Rhodes Hall, Cornell Theory Center, Ithaca, NY 14853, USA
3Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
4Department of Plant Breeding, 418-Bradfield Hall, Cornell University, Ithaca, NY 14853-1901, USA

Received 13 February 2002; Accepted 14 February 2002

Copyright © 2002 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Gramene ( is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.