Gramene: development and integration of trait and gene ontologies for rice

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., McCouch, S. (April 2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3 (2). pp. 132-136. ISSN 1531-6912

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URL: http://www.ncbi.nlm.nih.gov/pubmed/18628886
DOI: 10.1002/cfg.156

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 theInternational 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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
bioinformatics > genomics and proteomics > Mapping and Rendering > ontology
organism description > plant
organism description > plant > rice
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: April 2002
Date Deposited: 08 Jan 2014 16:46
Last Modified: 08 Jan 2014 16:46
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28724

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