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Open Access Highly Accessed Data Note

CastorDB: a comprehensive knowledge base for Ricinus communis

Shalabh Thakur1, Sanjay Jha2 and Bharat B Chattoo1*

Author Affiliations

1 Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, The M. S. University of Baroda, Vadodara-390002, India

2 Department of Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, Gujarat-396450, India

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BMC Research Notes 2011, 4:356  doi:10.1186/1756-0500-4-356

Published: 13 September 2011

Abstract

Background

Ricinus communis is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, R. communis genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of R. communis is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant.

Findings

CastorDB is a specialized and comprehensive database for the oil seed plant R. communis, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein.

Conclusion

CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners.