The Pistoia Alliance Biology Domain Strategy April 2011

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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.

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The Pistoia Alliance Biology Domain Strategy April 2011

  1. 1. Michael Braxenthaler, PhD<br />External Liaison Officer, The Pistoia Alliance<br />Strategic Alliances, Pharma Research & Early Development Informatics, Roche<br />Pistoia Alliance Conference<br />Boston, MA – April 12th 2011<br />The Pistoia AllianceBiology Domain Strategy<br />
  2. 2. Agenda<br />Recap: Pistoia Mission and Domains<br />Hands-On Example: Sequence Services<br />Expanding the Concept<br />Many Partners – How Do They Fit?<br />Roadmap: Where next?<br />
  3. 3. Recap: Pistoia Mission & Vision<br />Lowering the barriers to innovation<br />by improving inter-operability of R&D business processes <br />through pre competitive collaboration<br />
  4. 4. Pistoia Activity Domains<br />Biology/<br />Translational Research<br />“Understanding Disease”<br />Chemistry Live<br />“Linking Structure with Outcome”<br />Scientific Collaboration<br />
  5. 5. Pistoia Activity Domains<br />Biology/<br />Translational Research<br />“Understanding Disease”<br />Chemistry Live<br />“Linking Structure with Outcome”<br />Scientific Collaboration<br />
  6. 6. Agenda<br />Recap: Pistoia Mission and Domains<br />Hands-On Example: Sequence Services<br />Expanding the Concept<br />Many Partners – How Do They Fit?<br />Roadmap: Where next?<br />
  7. 7. Sequence Services Phase 1 (2010)<br />Sequence Services in the Cloud<br />7<br />
  8. 8. Sequence Services Phase 2 (2011)<br />Management and Analysis of Next Generation Sequencing Data<br />“Bring analysis to the data”<br />e.g. 1,000 Genomes<br />
  9. 9. Sequence Services – Key Features<br />Establishes cloud-based secure services<br />Provides public data and tools<br />Allows private data and tools<br />Allows commercial third party data and tools<br />Provides scientifically aware collaboration space<br />9<br />
  10. 10. Agenda<br />Recap: Pistoia Mission and Domains<br />Hands-On Example: Sequence Services<br />Expanding the Concept<br />Many Partners – How Do They Fit?<br />Roadmap: Where next?<br />
  11. 11. Sequence<br />Services<br />Complexity of Service-Enablement<br />Expanding the Concept<br />Hosting &<br />integration of private data<br />Multi-tenant Security<br />Large Scale<br />Analytics<br />11<br />
  12. 12. Sequence<br />Services<br />Secure integrated multi-domain information services<br />Hosting &<br />integration of private data<br />Multi-tenant Security<br />Complexity of Service-Enablement<br />Large Scale<br />Analytics<br />Breadth of Information Integrated (content)<br />Sequences<br />Expression<br />Scientific<br />Literature<br />Expanding the Concept<br />Biological<br />Networks<br />12<br />
  13. 13. Sequence<br />Services<br />Secure integrated multi-domain information services<br />Hosting &<br />integration of private data<br />Multi-tenant Security<br />ELIXIR<br />Complexity of Service-Enablement<br />EATRIS<br />SAGE<br />Large Scale<br />Analytics<br />caBIG<br />…<br />Breadth of Information Integrated (content)<br />Sequences<br />Expression<br />Scientific<br />Literature<br />Expanding the Concept<br />Biological<br />Networks<br />13<br />
  14. 14. Pistoia Ambition<br />Foster the evolution of a global collaborative information ecosystem of <br />secure <br />integrated<br />interoperable<br />internal/external information services <br />
  15. 15. Agenda<br />Recap: Pistoia Mission and Domains<br />Hands-On Example: Sequence Services<br />Expanding the Concept<br />Many Partners – How Do They Fit?<br />Roadmap: Where next?<br />
  16. 16. Many Partners – How Do They Fit<br />
  17. 17. Life Sciences Information Ecosystem<br />The scenario:<br />All industry data services are delivered in an interoperable form so that I can <br /><ul><li>buy target data from commercial providers mined from literature,
  18. 18. connect to public services from EBI and NCBI,
  19. 19. and use open source, commercial, and proprietary analysis tools
  20. 20. in a trusted hosted environment.</li></li></ul><li>Life Sciences Information Ecosystem<br />The scenario:<br />All industry data services are delivered in an interoperable form so that I can <br /><ul><li>buy target data from commercial providers mined from literature,
  21. 21. connect to public services from EBI and NCBI,
  22. 22. and use open source, commercial, and proprietary analysis tools
  23. 23. in a trusted hosted environment.</li></ul>The cast:<br />Life Science<br />Scientist<br />Service Provider<br />Commercial<br />Content Provider<br />Software<br />Vendor<br />Public<br />Content Provider<br />Life Science IT<br />
  24. 24. Life Sciences Information Ecosystem<br />Increases utilization of a public good and provides commercial advocacy for government investment<br />Hosted solutions are fit for purpose and easy to use. I can find everything I need.<br />Decreases costs and increases the value of the software by reducing number of interfaces that need to be supported.<br />Pistoia compliant services lower cost and decrease time to deliver customer solutions.<br />Increases value of products as data is more easily consumed. Eliminates middleman who reformats, sells data repacked as more consumable.<br />Pistoia compliant services lower cost and decrease time to deliver customer solutions.<br />Life Science<br />Scientist<br />Service Provider<br />Commercial<br />Content Provider<br />Software<br />Vendor<br />Public<br />Content Provider<br />Life Science IT<br />
  25. 25. Life Sciences Information Services<br />Business Services<br />Data marketplace<br />Solution marketplace<br />Hosting environment<br />Collaboration Services/Solutions<br />Scientific Services/Solutions<br />Biology Services/Solutions<br />Chemistry Services/Solutions<br />
  26. 26. Agenda<br />Recap: Pistoia Mission and Domains<br />Hands-On Example: Sequence Services<br />Expanding the Concept<br />Many Partners – How Do They Fit?<br />Roadmap: Where next?<br />
  27. 27. Sequence<br />Services<br />Secure integrated multi-domain information services<br />Hosting &<br />integration of private data<br />Multi-tenant Security<br />ELIXIR<br />Complexity of Service-Enablement<br />EATRIS<br />SAGE<br />Large Scale<br />Analytics<br />caBIG<br />…<br />Breadth of Information Integrated (content)<br />Sequences<br />Expression<br />Scientific<br />Literature<br />Biology Domain Roadmap<br />Biological<br />Networks<br />22<br />
  28. 28. Generic NGS related<br />use case<br />Biological samples<br />Sample metadata<br />Anonymized samples<br />clinical information<br />NGS<br />DNA seq,<br />RNA-seq<br />Candidate list<br />Scientific literature<br /> text mining<br />Public canonical pathways<br />Internal bionetwork information<br />Biological insight:<br />“understanding disease”<br />
  29. 29. Pistoia Activities<br />Biological samples<br />Sample metadata<br />Anonymized samples<br />clinical information<br />NGS<br />DNA seq,<br />RNA-seq<br />Candidate list<br />Sequence<br />Services<br />Scientific literature<br /> text mining<br />Public canonical pathways<br />Internal bionetwork information<br />Biological insight:<br />“understanding disease”<br />
  30. 30. Pistoia Activities<br />Biological samples<br />Sample metadata<br />Anonymized samples<br />clinical information<br />NGS<br />DNA seq,<br />RNA-seq<br />Candidate list<br />Sequence<br />Services<br />Scientific literature<br /> text mining<br />SESL<br />Public canonical pathways<br />Internal bionetwork information<br />Biological insight:<br />“understanding disease”<br />
  31. 31. Disease Dossier<br />SESL (Semantic Enrichment of Scientific Literature)<br />Multiple<br />Consumers<br />Knowledge<br />Applications<br />‘Consumer’<br />Firewall<br />Service Layer<br />Std Public<br />Vocabularies<br />Common <br />Service Broker<br />Open<br />Stds<br />Assertion & Meta Data Mgmt<br />Transform / Translate<br />Business<br />Rules<br />Integrator<br />Supplier<br />Firewall<br />Content<br />Providers<br />Db 2<br />Db 4<br />Corpus 1<br />Corpus 5<br />Db 3<br />26<br />
  32. 32. SESL (Semantic Enrichment of Scientific Literature)<br />Phase 1 completed<br />Demonstrated that knowledge brokering is technically feasible<br />A unique consortium from three cultures: industry, publishers and academia sharingcosts and risks<br />Raised awareness of biomedical community need and business opportunity<br />Currently waiting for alignment with IMI OPS project<br />
  33. 33. Pistoia Activities<br />Biological samples<br />Sample metadata<br />Anonymized samples<br />clinical information<br />NGS<br />DNA seq,<br />RNA-seq<br />Candidate list<br />Sequence<br />Services<br />Scientific literature<br /> text mining<br />SESL<br />Public canonical pathways<br />Internal bionetwork information<br />Biological<br />Networks<br />Biological insight:<br />“understanding disease”<br />
  34. 34. Biological Networks<br />The external landscape covering pathways/biological networks is fairly complex <br />Fits directly with Pistoia’s ambition to signpost existing work<br />Proposal<br />Establish a working group to map this landscape and develop a proposal how Pistoia should proceed in this area (3 months).<br />
  35. 35. Pistoia Activities<br />Biological samples<br />Sample metadata<br />Anonymized samples<br />clinical information<br />NGS<br />DNA seq,<br />RNA-seq<br />Candidate list<br />Sequence<br />Services<br />Scientific literature<br /> text mining<br />SESL<br />Public canonical pathways<br />Vocabulary<br />Services<br />Internal bionetwork information<br />Biological<br />Networks<br />Biological insight:<br />“understanding disease”<br />
  36. 36. Vocabulary Paper<br />Dictionaries & Dollars. Why core biomedical vocabularies matter to life-science industry<br />Lee Harland, Chris Larminie, Susanna-AssuntaSansone, Mark Burfoot, JasminSaric, Michael Braxenthaler, Enoch Huang, Michael Cantor, Wendy Filsell, John Wise and Ian Dix<br /> <br />Abstract<br />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.<br />
  37. 37. Vocabulary Services<br />Many commercial and non-commercial providers and consumers of vocabularies, taxonomies, ontologies<br />No service environment to provide and maintain a consistent and consistently used set of core terminologies<br />Proposal<br />Engage consulting firm to clarify the existence of a solid business case <br />
  38. 38. Biology Domain Roadmap<br />
  39. 39. Thank You!<br />

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