Users can now register interest in genes Will receive updates on knockout strain production

1. Users can now register interest in genes Will receive updates on knockout strain production iMitS Beta Site New features are tested on a beta site Includes • gene page • phenotype page • Data visuallization THE IMPC WEB PORTAL The International Mouse Phenotyping Consortium (IMPC) is: Generating a knockout mouse strain for almost every protein-coding gene in the next decade Characterizing each strain using a standardized, broad-based phenotyping pipeline. Supported by the MPI2 consortium consisting of experts from EMBL-EBI, MRC Harwell, and the Wellcome Trust Sanger Institute The MPI2 consortium is: Centralizing, analyzing, and integrating all phenotype data generated by IMPC partners Standardizing phenotype protocols to allow comparison of data across centers Using dedicated ‘data wranglers’ to work with IMPC partners to ensure proper transfer and quality control of data occurs. Developing a statistical analysis pipeline that will automate genotype-to-phenotype associations. Annotating all data with biomedical ontologies to enhance data integration.  The community is invited to sign up to receive strain production updates and to evaluate the presentation of data as we develop the IMPC web portal: www.mousephenotype.org Overview The MPI2 consortium is involved in all aspects of the IMPC pipeline from tracking mouse production to data integration and dissemination efforts Genotype-to-phenotype associations will be made by an automated statistical pipeline The IMPC web portal is under a rapid development cycle with features being added after user testing. For the latest see: beta.mousephenotype.org Data from the first knockout mouse lines phenotyped as part of the IMPC project will be available for analysis soon Conclusion Funding mousephenotype.org The IMPC home page that provides access to IMPC online resources User driven design- We test all of our online components with biomedical researchers to improve the utilit and ease of use of the IMPC web portal. References This resource is developed and maintained by the MPI2 consortium Funding supported by the NIH Common Fund Mechanism: U54 HG006370– Mouse Phenotyping Informatics Infrastructure – MPI2 The imits resource was initially developed developed by the I-DCC, supported by the European Union (Project number: 223592) The web portal for standardized phenotyping protocols Protocols based on conferences, calls, and an online forum IMPReSS will provide mappings between measurements and phenotypes IMPReSS- Standardized protocols Data is indexed using ontologies Allow users to drill down to the data they want Registration of Interest 1) Mallon AM, et al Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. MammGenome. 2012 Oct;23(9-10):641-. PMID: 22991088. 2) Brown SD, Moore MW. The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping. Mamm Genome. 2012 Oct;23(9-10):632-40.. PubMed PMID: 22940749. The tracking interface used by IMPC partners Production centers register intent to create a knockout strain Metrics available to centers and funding agencies Andrew Blake (1), Terrence Meehan (2) , Steve Brown (1), Paul Flicek (2), Ann-Marie Mallon (1), Helen Parkinson (2), William Skarnes (3) and members of the IMPC consortium (1) MRC Harwell, Harwell, UK, (2) EMBL-EBI, Hinxton, UK, (3) Wellcome Trust Sanger Institute, Hinxton, UK Informatics for the International Mouse Phenotyping Consortium QC tools are available to data providers Unusual data patterns are highlighted as part of quality control Data wranglers will sign off on data after passing QC The Many Roles of the IMPC Informatics Team Key IMPC Resources Data Wranglers- Dedicated personnel that work with mouse centers to ensure data is uploaded correctly and of high quality. Online forum- A forum focused on production and phenotyping protocols for the IMPC community with over a hundred users. The MPI2 consortium coordinates production of mice, harmonize protocols and data export across centers, associate genes to phenotypes using an automated statistical pipeline, and performs data integration to gain new insights into human disease. Automated Statistical Analysis- A statistical package in the widely used R environment is being developed to automate genotype-to-phenotype associations. QC Tools Comprehensive Search Features Ontology Use- Data is annotated to widely used ontologies including the MP, MA, EMAPA to aid in data integration efforts. Acknowledgements We would like to acknowledge members of the MPI2 consortium including: Julian Atienza-Herrero1, Chao-Kung Chen2, Armida Di Fenza1, Richard Easty3, Simon Greenaway1, Alan Horne3, Vivek Iyer3, Natasha Karp3, Gautier Koscielny2, Jeremy C. Mason2, David Melvin3, Hugh Morgan1, Asfand Qazi3, Mathew Redden1, Ahmad Retha1, Luis Santos1, Duncan Sneddon1, Jonathan W.G. Warren2, Henrik Westerberg1, Robert Wilson3, GagarineYaikhom1 Contact us IMPC Pipeline Export Analysis Mouse production centers IMPC databases LIMS Disseminate Standardizing Procedures & Tracking Troubleshooting & Quality Control Statistical Pipeline & Data Integration www.mousephenotype.org/contact-us