Users can now register interest in genes Will receive updates on knockout strain production
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• Users can now register interest in genes • Will receive updates on knockout strain production mousephenotype.org The IMPC home page that provides access to IMPC online resources THE IMPC WEB PORTAL IMPReSS- Standardized protocols • The web portal for standardized phenotyping protocols • Protocols based on conferences, calls, and an online forum • IMPReSS will provide mappings between measurements and phenotypes 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 1) Mallon AM, et al Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. Mamm Genome. 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. 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) Mouse production centers LIMS IMPC database s Disseminat e IMPC Pipeline Export Analysis Standardizing Procedures & Tracking Troubleshooting & Quality Control Statistical Pipeline & Data Integration iMitS 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 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. 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. Ontology Use- Data is annotated to widely used ontologies including the MP, MA, EMAPA to aid in data integration efforts. 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 Acknowledgements We would like to acknowledge members of the MPI2 consortium including: Julian Atienza-Herrero 1 , Chao-Kung Chen 2 , Armida Di Fenza 1 , Richard Easty 3 , Simon Greenaway 1 , Alan Horne 3 , Vivek Iyer 3 , Natasha Karp 3 , Gautier Koscielny 2 , Jeremy C. Mason 2 , David Melvin 3 , Hugh Morgan 1 , Asfand Qazi 3 , Mathew Redden 1 , Ahmad Retha 1 , Luis Santos 1 , Duncan Sneddon 1 , Jonathan W.G. Warren 2 , Henrik Westerberg 1 , Robert Wilson 3 , Gagarine Yaikhom 1 Contact us www.mousephenotype.org/contact-us • The tracking interface used by IMPC partners • Production centers register intent to create a knockout strain • Metrics available to centers and funding agencies • 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 Registration of Interest • Data is indexed using ontologies • Allow users to drill down to the data they want Beta Site • New features are tested on a beta site • Includes • gene page • phenotype page • Data visuallization
description
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: - PowerPoint PPT Presentation
Transcript of Users can now register interest in genes Will receive updates on knockout strain production
• Users can now register interest in genes• Will receive updates on knockout strain production
mousephenotype.orgThe IMPC home page that provides access to IMPC online resources
THE IMPC WEB PORTAL
IMPReSS- Standardized protocols• The web portal for
standardized phenotyping protocols
• Protocols based on conferences, calls, and an online forum
• IMPReSS will provide mappings between measurements and phenotypes
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
1) Mallon AM, et al Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. Mamm Genome. 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.
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)
Mouse production
centers
LIMS IMPCdatabases Disseminate
IMPCPipeline Export Analysis
StandardizingProcedures& Tracking
Troubleshooting&
Quality Control
Statistical Pipeline&
Data Integration
iMitS
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
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.
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.
Ontology Use- Data is annotated to widely used ontologies including the MP, MA, EMAPA to aid in data integration efforts.
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
AcknowledgementsWe 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, Gagarine Yaikhom1
Contact uswww.mousephenotype.org/contact-us
• The tracking interface used by IMPC partners
• Production centers register intent to create a knockout strain
• Metrics available to centers and funding agencies
• 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
Registration of Interest
• Data is indexed using ontologies• Allow users to drill down to the data they want
Beta Site
• New features are tested on a beta site• Includes
• gene page• phenotype page• Data visuallization
