2011-12-02 Open PHACTS at STM Innovation


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A 5-minute flash session (timed 15 secs/slide) presented by Richard Kidd at the STM Innovation Seminar 2011.

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2011-12-02 Open PHACTS at STM Innovation

  1. 1. In vivo Safety Pipeline PatentsLiterature SAR News
  2. 2. data integration
  3. 3. data integration data integrationdata integration data integration data integration data integration data integration data integration data integration data integration
  4. 4. The Innovative Medicines Initiative EC funded public-private partnership for pharmaceutical researchFocus on key problems Efficacy Safety Education & Training Knowledge Management
  5. 5. Open PHACTS an infrastructure projectDevelop / apply a set of robust standards…Implementing the standards in a semantic integration platform (“Open Pharmacological Space”)…Delivering services to support on-going drug discovery programs in pharma and public domainMix ideal with the pragmatic. Build open that can accommodate non-open components in the real world.
  6. 6. 23 partners 9 pharma 14 academic/SME/society 5 new partners in the process
  7. 7. Pharma bring...Pre-competitive collaborationAgreement on standards, approachesResearch questions drive developmentClear use casesDrive and direction
  8. 8. Example research questionsGive all compounds with IC50 < xxx for target Y in species W and Z plus assay dataWhat substructures are associated with readout X (target, pathway, disease, …)Give all experimental and clinical data for compound XGive all targets for compound X or a compound with a similarity > y%73 questions identified across consortium
  9. 9. What does „Open‟ mean?OPS Open - open access to allOPS Consortia - data sets licensed just to the consortiaOPS Academia - fully open to academia“My OPS”Open SourceOpen Access Infrastructure. GUI and back-end platform, online or download both + data for local setupOpen Services: for example, RSC servicesOpen Data + Private Data: licensing fun for all the familyCommercial providers: abstract service interface to swap in commercial and open source platforms
  10. 10. Agile Development: 6 month ‘lash up’• Produce a working ‘lash up’ system• Constrained to technologies in consortium + a few data sources• Focused on 2 prioritized research questions • All oxidoreductase inhibitors active <100nM in both human and mouse • For a given compound [clozapine], give me the interaction profile with [human or mouse] targets• Minimum requirements: two data sources (one targets, one compounds) and able to produce answers in ‘manual time’.
  11. 11. ‘lash-up’: youtube.com/openphacts
  12. 12. UTOPIA Documents (U Manchester)
  13. 13. Sustainability and community Data in and data out Consortium (pharma) members Public and commercial databases Publishers Services built on OPS
  14. 14. Sustainability $After 3 years?Pharma customersPublic fundersServices built on topPublishing data in
  15. 15. Focus and futureOne area - pharmacology“Production Level” softwareSemantic pragmatics: everyday useby scientists not informaticians Developers (Builders)An infrastructure that can be builtupon, to provide a stable foundationfor further pre-competitive informatics End userscollaboration (Drivers)
  16. 16. NanopublicationsCapturing scientific information in the Triple Store
  17. 17. Onwards and UpwardsConnection between developers and usersArchitectureServices: e.g. entity identification and resolutionand representing similarity, ORCID, DataCiteModels: RDF / Nanopublication model spec andguidelinesPrototypeMarch 2012: Internal Prototype DeliverySeptember 2012: Release 1st Prototype
  18. 18. Why should you care?Will be first real large scale semantic data integration project – a pilot that can be extendedProvides a single delivery format and pipeline to your customers?
  19. 19. Find out more?Email meApr/May 2012 - a workshop and intro for publishersalso for data providers/vendors
  20. 20. Time’s Up!About your speaker: Name: Richard Kidd Company: RSC Tel: +44 1223 432344 Email: kiddr@rsc.org Social Media: @open_phacts slideshare.com/open_phacts Lash-up: youtube.com/openphacts