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Open Access Research article

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics

Michael Gruenberger1, Rudi Alberts2, Damian Smedley3, Morris Swertz4, Paul Schofield1, The CASIMIR consortium5 and Klaus Schughart2*

Author Affiliations

1 Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK

2 Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr. 7, D-38124 Braunschweig, Germany

3 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

4 Department of Genetics, University Medical Center Groningen & Groningen Bioinformatics Centre, University of Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands

5 http://www.CASIMIR.org.uk/

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BMC Research Notes 2010, 3:16  doi:10.1186/1756-0500-3-16

Published: 22 January 2010

Abstract

Background

The integration of information present in many disparate biological databases represents a major challenge in biomedical research. To define the problems and needs, and to explore strategies for database integration in mouse functional genomics, we consulted the biologist user community and implemented solutions to two user-defined use-cases.

Results

We organised workshops, meetings and used a questionnaire to identify the needs of biologist database users in mouse functional genomics. As a result, two use-cases were developed that can be used to drive future designs or extensions of mouse databases. Here, we present the use-cases and describe some initial computational solutions for them. The application for the gene-centric use-case, "MUSIG-Gen" starts from a list of gene names and collects a wide range of data types from several distributed databases in a "shopping cart"-like manner. The iterative user-driven approach is a response to strongly articulated requests from users, especially those without computational biology backgrounds. The application for the phenotype-centric use-case, "MUSIG-Phen", is based on a similar concept and starting from phenotype descriptions retrieves information for associated genes.

Conclusion

The use-cases created, and their prototype software implementations should help to better define biologists' needs for database integration and may serve as a starting point for future bioinformatics solutions aimed at end-user biologists.