InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data

doi:10.1111/j.1744-7909.2012.01120.x

J Integr Plant Biol. ›› 2012, Vol. 54 ›› Issue (5): 345-355.DOI: 10.1111/j.1744-7909.2012.01120.x

InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data

Christopher G. Love^1*, Ambrose E. Andongabo², Jun Wang³, Pierre W. C. Carion², Christopher J. Rawlings² and Graham J. King⁴

¹Ludwig Institute for Cancer Research, Centre for Medical Research, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria, 3050, Australia
²Department of Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
³Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
⁴Southern Cross Plant Science, Southern Cross University, P.O. Box 157, Lismore NSW 2480, Australia

Received:2012-01-22 Accepted:2012-03-13 Published:2012-05-01
About author:^*Corresponding author Tel: +015 8276 3133; Fax: +015 8276 0981; E-mail: chris.love@ludwig.edu.au

Abstract

Abstract:

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence-related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: http://www.interstoredb.org

Love CG, Andongabo AE, Wang J, Carion PWC, Rawlings CJ, King GJ (2012) InterStoreDB: A generic integration resource for genetic and genomic data. J. Integr. Plant Biol. 54(5), 345–355.

Key words: QTL, bioinformatics, databases

Christopher G. Love, Ambrose E. Andongabo, Jun Wang, Pierre W. C. Carion, Christopher J. Rawlings, and Graham J. King. InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data[J]. J Integr Plant Biol., 2012, 54(5): 345-355.

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InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data

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