Michael Braxenthaler (Roche and external liaison officer for Pistoia) describes the Pistoia Alliance biology domain strategy at the first Pistoia Alliance Conference in April 2011.

1. Michael Braxenthaler, PhD External Liaison Officer, The Pistoia Alliance Strategic Alliances, Pharma Research & Early Development Informatics, Roche Pistoia Alliance Conference Boston, MA – April 12th 2011 The Pistoia AllianceBiology Domain Strategy

2. Agenda Recap: Pistoia Mission and Domains Hands-On Example: Sequence Services Expanding the Concept Many Partners – How Do They Fit? Roadmap: Where next?

3. Recap: Pistoia Mission & Vision Lowering the barriers to innovation by improving inter-operability of R&D business processes through pre competitive collaboration

4. Pistoia Activity Domains Biology/ Translational Research “Understanding Disease” Chemistry Live “Linking Structure with Outcome” Scientific Collaboration

5. Pistoia Activity Domains Biology/ Translational Research “Understanding Disease” Chemistry Live “Linking Structure with Outcome” Scientific Collaboration

6. Agenda Recap: Pistoia Mission and Domains Hands-On Example: Sequence Services Expanding the Concept Many Partners – How Do They Fit? Roadmap: Where next?

7. Sequence Services Phase 1 (2010) Sequence Services in the Cloud 7

8. Sequence Services Phase 2 (2011) Management and Analysis of Next Generation Sequencing Data “Bring analysis to the data” e.g. 1,000 Genomes

9. Sequence Services – Key Features Establishes cloud-based secure services Provides public data and tools Allows private data and tools Allows commercial third party data and tools Provides scientifically aware collaboration space 9

10. Agenda Recap: Pistoia Mission and Domains Hands-On Example: Sequence Services Expanding the Concept Many Partners – How Do They Fit? Roadmap: Where next?

11. Sequence Services Complexity of Service-Enablement Expanding the Concept Hosting & integration of private data Multi-tenant Security Large Scale Analytics 11

12. Sequence Services Secure integrated multi-domain information services Hosting & integration of private data Multi-tenant Security Complexity of Service-Enablement Large Scale Analytics Breadth of Information Integrated (content) Sequences Expression Scientific Literature Expanding the Concept Biological Networks 12

13. Sequence Services Secure integrated multi-domain information services Hosting & integration of private data Multi-tenant Security ELIXIR Complexity of Service-Enablement EATRIS SAGE Large Scale Analytics caBIG … Breadth of Information Integrated (content) Sequences Expression Scientific Literature Expanding the Concept Biological Networks 13

14. Pistoia Ambition Foster the evolution of a global collaborative information ecosystem of secure integrated interoperable internal/external information services

15. Agenda Recap: Pistoia Mission and Domains Hands-On Example: Sequence Services Expanding the Concept Many Partners – How Do They Fit? Roadmap: Where next?

16. Many Partners – How Do They Fit

18. connect to public services from EBI and NCBI,

19. and use open source, commercial, and proprietary analysis tools

21. connect to public services from EBI and NCBI,

22. and use open source, commercial, and proprietary analysis tools

23. in a trusted hosted environment.The cast: Life Science Scientist Service Provider Commercial Content Provider Software Vendor Public Content Provider Life Science IT

24. Life Sciences Information Ecosystem Increases utilization of a public good and provides commercial advocacy for government investment Hosted solutions are fit for purpose and easy to use. I can find everything I need. Decreases costs and increases the value of the software by reducing number of interfaces that need to be supported. Pistoia compliant services lower cost and decrease time to deliver customer solutions. Increases value of products as data is more easily consumed. Eliminates middleman who reformats, sells data repacked as more consumable. Pistoia compliant services lower cost and decrease time to deliver customer solutions. Life Science Scientist Service Provider Commercial Content Provider Software Vendor Public Content Provider Life Science IT

25. Life Sciences Information Services Business Services Data marketplace Solution marketplace Hosting environment Collaboration Services/Solutions Scientific Services/Solutions Biology Services/Solutions Chemistry Services/Solutions

26. Agenda Recap: Pistoia Mission and Domains Hands-On Example: Sequence Services Expanding the Concept Many Partners – How Do They Fit? Roadmap: Where next?

27. Sequence Services Secure integrated multi-domain information services Hosting & integration of private data Multi-tenant Security ELIXIR Complexity of Service-Enablement EATRIS SAGE Large Scale Analytics caBIG … Breadth of Information Integrated (content) Sequences Expression Scientific Literature Biology Domain Roadmap Biological Networks 22

28. Generic NGS related use case Biological samples Sample metadata Anonymized samples clinical information NGS DNA seq, RNA-seq Candidate list Scientific literature text mining Public canonical pathways Internal bionetwork information Biological insight: “understanding disease”

29. Pistoia Activities Biological samples Sample metadata Anonymized samples clinical information NGS DNA seq, RNA-seq Candidate list Sequence Services Scientific literature text mining Public canonical pathways Internal bionetwork information Biological insight: “understanding disease”

30. Pistoia Activities Biological samples Sample metadata Anonymized samples clinical information NGS DNA seq, RNA-seq Candidate list Sequence Services Scientific literature text mining SESL Public canonical pathways Internal bionetwork information Biological insight: “understanding disease”

31. Disease Dossier SESL (Semantic Enrichment of Scientific Literature) Multiple Consumers Knowledge Applications ‘Consumer’ Firewall Service Layer Std Public Vocabularies Common Service Broker Open Stds Assertion & Meta Data Mgmt Transform / Translate Business Rules Integrator Supplier Firewall Content Providers Db 2 Db 4 Corpus 1 Corpus 5 Db 3 26

32. SESL (Semantic Enrichment of Scientific Literature) Phase 1 completed Demonstrated that knowledge brokering is technically feasible A unique consortium from three cultures: industry, publishers and academia sharingcosts and risks Raised awareness of biomedical community need and business opportunity Currently waiting for alignment with IMI OPS project

33. Pistoia Activities Biological samples Sample metadata Anonymized samples clinical information NGS DNA seq, RNA-seq Candidate list Sequence Services Scientific literature text mining SESL Public canonical pathways Internal bionetwork information Biological Networks Biological insight: “understanding disease”

34. Biological Networks The external landscape covering pathways/biological networks is fairly complex Fits directly with Pistoia’s ambition to signpost existing work Proposal Establish a working group to map this landscape and develop a proposal how Pistoia should proceed in this area (3 months).

35. Pistoia Activities Biological samples Sample metadata Anonymized samples clinical information NGS DNA seq, RNA-seq Candidate list Sequence Services Scientific literature text mining SESL Public canonical pathways Vocabulary Services Internal bionetwork information Biological Networks Biological insight: “understanding disease”

36. Vocabulary Paper Dictionaries & Dollars. Why core biomedical vocabularies matter to life-science industry Lee Harland, Chris Larminie, Susanna-AssuntaSansone, Mark Burfoot, JasminSaric, Michael Braxenthaler, Enoch Huang, Michael Cantor, Wendy Filsell, John Wise and Ian Dix Abstract The life science industries are in the midst of developing new business models based around “networked research and development” such as open innovation, pre-competitive alliances, public-private consortia and academic partnerships. While these offer much in transforming the way applied science is done, they bring with it major information management challenges in environments. Here we look at the role of basic biological and chemical vocabularies in this process, and propose that increased efforts in this space are essential to commercial success. We identify the gaps in current industry infrastructure and describe the business, technology and logistical hurdles that must be addressed to support a diverse set of use cases including biomarker discovery, translational medicine and contract research organisation interactions. Our review concludes with a series of suggested next steps that prepare the way for a more proactive engagement in this area.

37. Vocabulary Services Many commercial and non-commercial providers and consumers of vocabularies, taxonomies, ontologies No service environment to provide and maintain a consistent and consistently used set of core terminologies Proposal Engage consulting firm to clarify the existence of a solid business case

38. Biology Domain Roadmap

39. Thank You!