Submitted to: Comparative and Functional Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 2/14/2002
Publication Date: 3/14/2002
Citation: JAISWAL, P., WARE, D., ZHAO, W., SCHMIDT, S., PAN, X., CLARK, K., TEYTELMAN, L., CARTINHOUR, S.W., STEIN, L., MCCOUCH, S. GRAMENE: DEVELOPMENT AND INTEGRATION OF TRAIT AND GENE ONTOLOGIES FOR RICE. COMPARATIVE AND FUNCTIONAL GENOMICS. 2002. v. 3(2). p. 132-136. Interpretive Summary: Gramene (http://www.gramene.org/) is a database that contains genomic information for rice and other crops in the grass family. It contains a variety of complex data types, including descriptions of agronomically important traits and genetic variations. Unfortunately, the ways in which traits, variations and plant anatomy have been described is not uniform. To address this problem, "controlled vocabularies" have been designed to make it easier to query the database to compare data from one crop to another. The controlled vocabularies are being designed in collaboration with other major plant research groups so that the end result is as standard as possible between species and different databases. This effort will greatly enhance the value of other kinds of data in Gramene, such as DNA sequences and the identities of genes.
Technical 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.