Please wait a minute...

J Integr Plant Biol, 54 (5): 345-355, Research Article
InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data
Christopher G. Love1*, 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
*Corresponding author Tel: +015 8276 3133; Fax: +015 8276 0981; E-mail: chris.love@ludwig.edu.au
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.

---------------------------------------------------
Received: 22 January 2012      Published: 11 April 2012
© 2012 Institute of Botany, Chinese Academy of Sciences
This Article
   Full Text
   Full Text (PDF)
   Supporting information
Services
   E-mail Link to this Article
   Export Citation for this Article
Citing Articles
   Cited By
Google Scholar
   Articles by Christopher G. Love
   Articles by Ambrose E. Andongabo
   Articles by Jun Wang
   Articles by Pierre W. C. Carion
   Articles by Christopher J. Rawlings
   Articles by Graham J. King
PubMed
   Articles by Christopher G. Love
   Articles by Ambrose E. Andongabo
   Articles by Jun Wang
   Articles by Pierre W. C. Carion
   Articles by Christopher J. Rawlings
   Articles by Graham J. King
Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2020 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q
网站备案号:京ICP备16067583号-22