Abstract
The International Mouse Phenotyping Consortium (IMPC) is providing the world’s first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers.
Highlights
The International Mouse Phenotyping Consortium (IMPC) comprises the majority of the world’s largest mouse research centres, working together to generate and characterise a knockout mouse strain for 20,000 protein coding genes (Brown and Moore 2012a, b)
A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC
The IMPC aims to ascribe function to every gene by measuring the physiological and morphological effects that result when a gene is inactivated. It builds upon resources from a number of previous projects including the mutant embryonic stem (ES) cells produced by the International Knockout Mouse Consortium (IKMC) (Ringwald et al 2011; Bradley et al 2012) and by previous, smaller scale high-throughput phenotyping projects such as the Eumorphia and Eumodic projects (Morgan et al 2010)
Summary
The International Mouse Phenotyping Consortium (IMPC) comprises the majority of the world’s largest mouse research centres, working together to generate and characterise a knockout mouse strain for 20,000 protein coding genes (Brown and Moore 2012a, b). The IMPC aims to ascribe function to every gene by measuring the physiological and morphological effects that result when a gene is inactivated. It builds upon resources from a number of previous projects including the mutant embryonic stem (ES) cells produced by the International Knockout Mouse Consortium (IKMC) (Ringwald et al 2011; Bradley et al 2012) and by previous, smaller scale high-throughput phenotyping projects such as the Eumorphia and Eumodic projects (Morgan et al 2010). The Mouse Phenotyping Informatics Infrastructure Consortium (MPI2), a collaborative effort between the European Molecular Biological Laboratories- European Bioinformatics Institute (EMBL-EBI), Medical Research Council Harwell, and the Wellcome Trust Sanger Institute (WTSI), develops the IT infrastructure, databases, analysis software. We present new features of the IMPC informatics platform developed to meet the needs of a growing number of diverse users while addressing increases in data volume and complexity (Table 2)
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