title: Gramene: development and integration of trait and gene ontologies for rice.
abstract: 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 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.
authors.affiliation: Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Jaiswal
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Junjian
authors.initials: J
authors.lastname: Ni
authors.forename: Kuan
authors.initials: K
authors.lastname: Chang
authors.forename: Wei
authors.initials: W
authors.lastname: Zhao
authors.forename: Steven
authors.initials: S
authors.lastname: Schmidt
authors.forename: Xiaokang
authors.initials: X
authors.lastname: Pan
authors.forename: Kenneth
authors.initials: K
authors.lastname: Clark
authors.forename: Leonid
authors.initials: L
authors.lastname: Teytelman
authors.forename: Samuel
authors.initials: S
authors.lastname: Cartinhour
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.forename: Susan
authors.initials: S
authors.lastname: McCouch