Informatics for the International Mouse Phenotyping Consortium
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
THE IMPC WEB PORTAL
Overview
The International Mouse Phenotyping Consortium (IMPC) is:
• Generating a knockout mouse strain for almost every proteincoding 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
Key IMPC Resources
IMPReSS- Standardized protocols
iMitS
•
•
•
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 tracking interface
used by IMPC partners
Production
centers
register intent to create
a knockout strain
Metrics available to
centers and funding
agencies
•
•
•
•
The Many Roles of the IMPC Informatics Team
Mouse
production
centers
Standardizing
Procedures
& Tracking
LIMS
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
Analysis
IMPC
databases
Troubleshooting
&
Quality Control
Disseminate
Statistical Pipeline
&
Data Integration
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.
mousephenotype.org
Registration of Interest
Contact us
www.mousephenotype.org/contact-us
Automated Statistical Analysis- A statistical package in
the widely used R environment is being developed to
automate genotype-to-phenotype associations.
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.
Conclusion
•
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
automated statistical pipeline
•
The IMPC web portal is under a rapid development cycle with
features being added after user testing. For the latest see:
The IMPC home page that provides access to IMPC online resources
•
Beta Site
Comprehensive Search Features
be
made
by
an
Data from the first knockout mouse lines phenotyped as part of
the IMPC project will be available for analysis soon
References
• Users can now
interest in genes
register
• Will receive updates on
knockout strain production
• New features are tested on a
beta site
• Includes
• gene page
• phenotype page
• Data visuallization
will
beta.mousephenotype.org
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, Gagarine Yaikhom1
Online forum- A forum focused on production and
phenotyping protocols for the IMPC community with
over a hundred users.
QC Tools
•
Export
The web portal for
standardized
phenotyping protocols
Protocols based on
conferences,
calls,
and an online forum
IMPReSS will provide
mappings
between
measurements
and
phenotypes
Ontology Use- Data is annotated to widely used
ontologies including the MP, MA, EMAPA to aid in data
integration efforts.
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
IMPC
Pipeline
Data Wranglers- Dedicated personnel that work with
mouse centers to ensure data is uploaded correctly and of
high quality.
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(910):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):63240.. PubMed PMID: 22940749.
Funding
• Data
is
ontologies
indexed
using
• Allow users to drill down to
the data they want
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)