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Mining phenotype databases to identify mouse models of clinical relevance

Michelle Simon and Ann-Marie Mallon . Mining phenotype databases to identify mouse models of clinical relevance. Introduction. Introduction – EUMODIC EuroPhenome ( www.europhenome.org ) EMPRESS ( European Mouse Phenotyping Resource of Standardised Screens) ) Data capture procedure.

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Mining phenotype databases to identify mouse models of clinical relevance

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  1. Michelle Simon and Ann-Marie Mallon Mining phenotype databases to identify mouse models of clinical relevance

  2. Introduction • Introduction – EUMODIC • EuroPhenome (www.europhenome.org) • EMPRESS (European Mouse Phenotyping Resource of Standardised Screens) ) • Data capture procedure. • Data display / Website. • Other phenotyping portals – Sanger mouse portal, K312 Portal • IMPC • Overview of IMPC • MPI2 Consortium • Informatics Plans • Worked Example. • Tasks.

  3. INTRODUCTION - EUMODIC • EUMODIC • Pilot project to phenotype 500 mouse mutants using standardised pipelines called EMPReSSlim (battery of simple tests to detect defects in as many body systems as possible) • e.g. SHIRPA, Clinical Chemistry etc • Actual phenotype measurements are captured

  4. INTRODUCTION – EUMODIC (II) • Partners • MRC Harwell UK • Institut Clinique de la Souris France • Helmholtz ZentrumMünchenGermany • The Wellcome Trust Sanger Institute UK • CMHD, Canada • Each clinic has its own version of the phenotyping pipelines • EuroPhenome (www.europhenome.org) • Raw and automatically annotated phenotype data from high throughput projects such as EUMODIC

  5. EuroPhenome Data Capture

  6. EMPRESS (EUROPEAN MOUSE PHENOTYPING RESOURCE OF STANDARDISED SCREENS)

  7. EMPRESS • Experimental Procedures designed by Scientists • Standard operating procedures (SOPs). • SOPs stored in EMPReSS RDBMS • Standardised Mouse Phenotyping (across centres and consortiums) • Defined measured parameters with bounds • Defined derived parameters • Environmental and other Metadata recorded • Ontology Annotation (Mammalian Phenotype and Entity Quality PATO approaches)

  8. EMPRESS Search procedures http://empress.har.mrc.ac.uk/ • Comprehensive database of standardised phenotyping protocols.

  9. EMPRESS Four different phenotyping pipelines Procedures

  10. EMPReSS Unique Empress Identifier Different Parameters Ontology Annotation - Mammalian Phenotype Measurement types and increments

  11. EMPReSS SLIM, Primary Phenotyping Screen 21 different procedures

  12. Phenotype Data Capture Automatic data annotation of significant phenodeviants with MP ontology terms

  13. EuroPhenome Data Annotation Model

  14. EUROPHENOME STATISTICS Number of Lines

  15. Data in Europhenome • 502Lines • 2,505 • 30,276 Mice

  16. Number of Lines with significant annotations by Procedure

  17. EUROPHENOME (Gene Search)

  18. www.europhenome.org

  19. PHENOTYPE SEARCH

  20. PHENOMAP

  21. XRAYS

  22. SANGER MOUSE PORTAL

  23. http://www.sanger.ac.uk/mouseportal

  24. International Mouse Phenotyping Consortium (IMPC)

  25. IMPC 22 Academic, Government Institutes • MRC Harwell (Steve Brown, current Chair Steering Comm.; Tom Weaver) • Sanger Institute (Allan Bradley, Dave Adams, Karen Kennedy) • NIH KOMP2 • BASH, Baylor (Monica Justice) • DTCC (UC Davis (Kent Lloyd), TCP, Charles River, Children’s Hospital Oakland RI) • Jackson Lab (Karen Svenson) • Toronto Centre for Phenogenomics(Colin McKerlie) • Helmholtz Zentrum Munich (Martin Hrabe de Angelis) • Institut Clinique de la Souris (YannHerault) • Australian Phenomics Network (Adrienne McKenzie) • RIKEN BioResourceCenter(Yuichi Obata) • MARC (Xiang Gao) • CNR (GlaucoToccinniValentini) • EBI (Paul Flicek) • Secretariat (Mark Moore, Executive Director; JoergRossbacher) • FUNDERS • MRC (Nathan Richardson, Clare Newland) • NIH (Jane Peterson, Eric Green, Jim Battey, Colin Fletcher, Martin Guyer) • Wellcome Trust (Michael Dunn, Clare McVicker) • Infrafrontier(Martin Hrabe de Angelis) • Genome Canada (Cindy Bell) • European Commission (Observer status) • Canadian Institutes of Health Research, CIHR (Jane Aubin)

  26. What is IMPReSS? • IMPReSS: International Mouse PhenotypingResource of Standardised Screens • Launched Tue 13th March 2012 • The successor of EMPReSS - Inherits historical Pipelines, adds IMPC Pipeline • New architecture, new site, plus some more features

  27. IMPReSS – IMPC Pipeline • Adult pipeline agree and embryonic pipeline in development

  28. Key Concepts: 3Ps Pipeline 3Ps have unique identifiers, Keys, e.g: IMPC_001_001_005_001 Procedure contains *:* MeasuredParameter MetadataParameter contains *:*

  29. Ontology Associations • Ontology Associations • Structured, controlled vocabulary used worldwide by scientists to describe phenotypes and beyond • Various Collections but MP is popular • Predefined option choices for high throughput ontology annotation • Procedure: Open Field • Measured Parameter: Distance Travelled • MP:0001399 - Hyperactivity • MP:0001402 - Hypoactivity • MP:0003313 - Abnormal locomotor activation • Can compare baselines against mutants by ontologies associated with the mice to identify phenotypes and variations and can also QC submitted data

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