Open Access Software

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

Morris A Swertz123*, K Joeri van der Velde12, Bruno M Tesson2, Richard A Scheltema2, Danny Arends12, Gonzalo Vera2, Rudi Alberts4, Martijn Dijkstra5, Paul Schofield6, Klaus Schughart4, John M Hancock7, Damian Smedley3, Katy Wolstencroft8, Carole Goble8, Engbert O de Brock9, Andrew R Jones10, Helen E Parkinson3, members of the Coordination of Mouse Informatics Resources (CASIMIR)6, Genotype-To-Phenotype (GEN2PHEN) Consortiums1 and Ritsert C Jansen12

Author Affiliations

1 Genomics Coordination Center, Department of Genetics, University Medical Center Groningen and University of Groningen, 9700 RB Groningen, The Netherlands

2 Groningen Bioinformatics Center, University of Groningen, 9750 AA Haren, The Netherlands

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

4 Experimental Mouse Genetics, Helmholtz Center for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany

5 Center for Medical Biomics, University of Groningen, Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands

6 Physiological Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK

7 Bioinformatics Group, MRC Harwell, Harwell, Oxfordshire OX11 0RD, UK

8 Information Management Group, School of Computer Science, University of Manchester, Kilburn Building, Oxford Road, Manchester M13 9PL, UK

9 Department of Business and ICT, Faculty of Economics and Business, University of Groningen, 9700 AV Groningen, The Netherlands

10 Department of Pre-Clinical Veterinary Science and Veterinary Pathology, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 7ZJ, UK

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Genome Biology 2010, 11:R27  doi:10.1186/gb-2010-11-3-r27

Published: 9 March 2010

Abstract

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org webcite) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.