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CastorDB: a comprehensive knowledge base for Ricinus communis
Shalabh Thakur1, Sanjay Jha, Bharat B Chattoo
1Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, The M, S, University of Baroda, Vadodara-390002, India. bharat.chattoo@bcmsu.ac.in.
BMC Research Notes
|September 15, 2011
Summary
CastorDB is a new, user-friendly database integrating diverse data for Ricinus communis research. It provides comprehensive genomic, transcriptomic, and proteomic information to aid understanding of this important oil seed crop.
Area of Science:
- Plant biology
- Bioinformatics
- Genomics
Background:
- Ricinus communis (castor) is a vital non-edible oilseed crop with a partially assembled genome.
- The functions of many castor genes remain unknown, and relevant biological data are scattered.
- A centralized resource is needed to facilitate research on castor.
Purpose of the Study:
- To develop CastorDB, a comprehensive and accessible database for Ricinus communis.
- To integrate scattered information on castor's genome, transcriptome, and proteome.
Main Methods:
- Integrated data from diverse repositories, including gene/protein sequences, expression data, and gene ontology annotations.
- Performed computational analyses for predicting cellular localization, domains, pathways, protein interactions, sumoylation sites, and biochemical properties.
- Developed an intuitive user interface for easy data exploration.
Main Results:
- CastorDB offers integrated primary data (sequences, expression, GO annotations) and derived data (predictions of localization, domains, pathways, interactions, etc.).
- The database provides a user-friendly interface for accessing information on castor genes and proteins.
- It serves as a specialized, comprehensive resource for R. communis.
Conclusions:
- CastorDB is a valuable, user-friendly resource for castor research, focusing on genome, transcriptome, and proteome.
- It consolidates information on protein domains, pathways, localization, sumoylation, expression, and interactions.
- The database aims to accelerate research on the industrially important Ricinus communis.
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