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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:

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slide1
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

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