Overview: Towards a European open source knowledge management infrastructure. Scott Wagers, MD BioSci Consulting

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1 Overview: Towards a European open source knowledge management infrastructure Scott Wagers, MD BioSci Consulting

2 Innovative Medicines Initiative: Joining Forces in the Healthcare Sector U-BIOPRED Annual Meeting January 2013

3 Key Concepts Non-competitive collaborative research for EFPIA companies Competitive calls to select partners of EFPIA companies (IMI beneficiaries) Open collaboration in public-private consortia (data sharing, dissemination of results) U-BIOPRED Annual Meeting January 2013

4 IMI Calls covering the drug life cycle Idea generation Basic Research and Non-human testing Human testing Regulatory Appoval HTA and Pharmacovigilance Key deliverables of the projects Diseases, e.g. cancer, diabetes, schizophrenia, depression Tools, e.g. stem cells, patients reporting outcome Biomarkers identification Safety Pharmacovigilance and Health Technology Assessment Education and Training Knowlegde Management U-BIOPRED Annual Meeting January 2013

5 Translational Research Information and Knowledge Management Service

6 U-BIOPRED (Unbiased BIOmarkers in PREDiction of respiratory disease outcomes) a 5-year European project to understand more about severe asthma

7 Hypothesis The use of biomarker profiles comprised of various types of high-dimensional data, integrated with an innovative systems biology approach into distinct phenotype handprints, will enable significantly better prediction of therapeutic efficacy than single or even clustered biomarkers of one data type, and will identify novel targets.

8 What UBIOPRED is producing: Large cohort & biobank of deeply phenotyped adult and paediatric patients Handprints : stratification of severe asthma Preclinical models more reflective of clinical disease A GMP viral challenge exacerbation model

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10 members subjects variables samples data points

11 Big Data needs Big Ideas - Eric Perakslis

12 transmart Translational Data Warehouse Solution for U-BIOPRED

13 Requirements of the call Start with a proven platform, transmart Deliverables reflecting demands of actual Efficacy and Safety projects Small consortium Limit funding in the first phase. Explicit consortium capabilities & skills

14 Translational Research Information and Knowledge Management Service 20M Euro Oct-2012 Sept-2017 Sustainable Open Platform 2B Euro Public Private Partnership The IMI Research Agenda Requires an 2B Open Euro Knowledge Public Private Management Partnership Infrastructure

15 Consortium of 16 Partners Academic/Pharma/Coordination/Standards EFPIA Lead Analytics Academic Lead Development Imperial College London AstraZeneca Universite Du Luxembourg Sanofi Roche Pfizer Merck Serono Lundbeck Professional Development TR Projects Janssen idbs Glaxo SmithKline Lilly Hosting CNRS CDISC Biosci Consulting Bayer Standards Coordination

16 Objectives Service: Deploy and host a platform based on transmart technology. Provide training, support, and consultation for IMI projects

17 Objectives Platform: Develop a TR KM platform that is: sustainable interoperable collaborative re-usable open source scalable Conduct research & development

18 Objectives Content: Establish a unique European TR data resource that supports cross-organisation studies. Populate etriks with active data and integrate standardised legacy TR study data.

19 Objectives Community: Form an international TR analytics & informatics community. Influence international TR standardisation activities.

20 Biosci Consulting (Collaboration Management) Work Packages WP Number WP Name WP Leads WP1 Platform Deployment CNRS/JPNV WP2 Platform Development Imperial/Sanofi/Pfizer WP3 Data Standards Roche/IDBS/Merck/CDISC WP4 WP5 WP6 Curation and Analysis Management and Sustainability Community and Outreach Luxembourg/Sanofi AstraZeneca/BioSci Consulting Janssen/BioSci Consulting WP7 Ethics GSK/CNRS/Bayer/Sanofi

21 1. Ensure the legacy of project data/results 2. Facilitate dataset integration 3. Increase operational efficiency 4. Establish a common set of standards Linked In Discussion Group: etriks

22 Engagement and Governance etriks Client Project Project Lead Platform Deployment IMI Client Project Delivery Package 1 Delivery Package 2 Delivery Package 3 etriks Account Manager Demand For etriks Planning Meeting Decision Project Lead etriks Delivery Package etriks Resources Data Standards Curation and Analysis Ethics Platform Development Community and Outreach Feedback Go Sanctioning etriks Executive Committee Delivery Packages Execution Progress Updates Project Input Deliveries Quad Reports

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24 etriks support of UBIOPRED Hosting Infrastructure Develop security model Data migration from Oracle to Postgres version of transmart Data standards development / adoption Support of clinical content curation Develop training module Pre-clinical and animal model data analysis Business analysis of data needs and fit with transmart

25 Service Challenges What will transmart be? Something to point to.

26 etriks PLATFORM Founded on transmart GPL v3 Open Source Translational Data Warehouse Building upon Janssen s Award Winning Translational Informatics System Demonstrated Success with the U-BIOPRED IMI Project

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30 TM Hackathon/Tech Strategy ~50 Developers, 3 days in London, Feb June transmart 1.1 Stable Postgres version Data services Security Export Plugin framework September transmart 1.2 Faceted Search SOLR Indexing (unified search) TBD - Research branch Mongo Db NGS

31 Service Challenges What will transmart be? Something to point to.

32 Public server demo

33 Service Challenges What will transmart be? Something to point to.

34 Potential Projects Project Name Project Contact Therapeutic Area Data Type Summary IMI Round IMI U-BIOPRED P Sterk Severe Asthma Clinical, Omics, Animal Models 1st IMI OncoTrack D Henderson Colon Cancer Clinical, Next Generation Sequencing, Protein Arrays Cellbased Assays, Animal Models, Cancer Stem Cells 2nd IMI ABI RISK D Sikkema Julie Davidson Biopharmaceutical Risk Assessment Clinical observations, Legacy cohorts, Cell-based assays, Gene Expression, Long-term studies 3rd IMI PREDECT J Hickman Prostate, Breast and Lung Cancer Tissue Micro-Arrays, In Vitro Culture Models, GEMM Animal Models 2nd IMI ND4BB MRC-ABPI RA-MAP IMI NEWMEDS IMI Predict-TB K Brown Phil Gribbon J Issacs S Brockbank K Stoller S Kapoor P Bordes G Davis Combating Antimicrobial Resistance Pharmacology, In vivo, Clinical, omics Rheumatoid Arthritis Clinical, Omics Not IMI Depression & Schizophrenia Clinical, Pre-Clinical 6th Tuberculosis Clinical, Pre-Clinical PK/PD 3rd 1st

35 1. Ensure the legacy of project data/results 2. Facilitate dataset integration 3. Increase operational efficiency 4. Establish a common set of standards Linked In Discussion Group: etriks