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

This is the publisher’s final pdf. The published article is copyrighted by Hindawi Publishing Corporation and can be found at: http://www.hindawi.com/journals/ijg/. The journal title, Comparative and Functional Genomics, has been changed to the International Journal of Genomics.Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops\ud and a community resource for rice. We are populating and curating Gramene with\ud annotated rice (Oryza sativa) genomic sequence data and associated biological information\ud including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait\ud Loci (QTL). In order to support queries across various data sets as well as across external\ud databases, Gramene will employ three related controlled vocabularies. The specific goal of\ud Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal\ud crops to facilitate phenotypic comparisons both within and between the genera. Second, a\ud vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation\ud of morphological and anatomical feature information with respect to expression,\ud localization of genes and gene products and the affected plant parts in a phenotype. The\ud TO and PO are both in the early stages of development in collaboration with the\ud International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology\ud Consortium. Finally, as part of another consortium comprising macromolecular databases\ud from other model organisms, the Gene Ontology Consortium, we are annotating the\ud confirmed and predicted protein entries from rice using both electronic and manual\ud curation