Alitora Innovation Networks


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Alitora Systems presents Innovation Networks for Life Sciences at Semantic Technology Conference 2009.

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Alitora Innovation Networks

  1. 1. <ul><li>Presenter: </li></ul><ul><li>Marc Hadfield </li></ul><ul><li>(917) 991-9685 </li></ul><ul><li> </li></ul>Building Innovation Networks in the Life Sciences
  2. 2. <ul><li>Marc Hadfield, President and CTO </li></ul><ul><ul><li>Creator of Alitora Technology </li></ul></ul><ul><ul><ul><li>Semantic Database </li></ul></ul></ul><ul><ul><ul><li>Natural Language Processing applied to Life Sciences </li></ul></ul></ul><ul><li>Alitora Systems </li></ul><ul><ul><li>Semantic Software co. </li></ul></ul><ul><ul><li>Software-as-a-Service/Platform-as-a-Service </li></ul></ul>
  3. 3. How can we: Surface & Distribute Insights from Unstructured Data? Or: How do we deliver to you the interesting bits of knowledge out of a lot of text?
  4. 4. Problem: Insights from Data Silos Case Study: Eli Lilly / Life Science
  5. 5. Solution: Natural Language Processing? Transform a pile of Documents into A pile of Facts . We still have a pile.
  6. 6. Solution: Natural Language Processing + Linked Relationships via Ontologies? What in the network is important ?
  7. 7. Solution: Natural Language Processing + Linked Relationships + Relevancy? Relevant to whom?
  8. 8. Solution: Natural Language Processing + Linked Relationships + Relevancy + Collaboration. Ah Ha! Relevant information can find me via my context. My colleagues can help.
  9. 9. Then we can Surface & Distribute Insights Deploy solution as a service so Insights can be embedded anywhere.
  10. 10. People Databases, Ontologies News, PR, Documents, Reports Innovation Network
  11. 11. Innovation Network - DEMO Web Application Application Plug-In
  12. 12. Alitora Systems Architecture <ul><li>Interface </li></ul><ul><ul><li>Web, Cytoscape </li></ul></ul><ul><li>ASAPI Webservice </li></ul><ul><ul><li>Search, Collaborate </li></ul></ul><ul><ul><li>Annotate </li></ul></ul><ul><ul><li>Process Documents </li></ul></ul><ul><li>kHarmony Semantic DB </li></ul><ul><ul><li>Semantic / Graph DB </li></ul></ul><ul><li>Alitora Foundry </li></ul><ul><ul><li>NLP Components </li></ul></ul>
  13. 13. Collaboration, Entitlement <ul><li>Scope: User, Colleague, Team, Organization, Database Segment </li></ul><ul><li>Entitlements are Semantic Statements </li></ul><ul><li>Cross-Department </li></ul><ul><ul><li>Single Organization </li></ul></ul><ul><ul><li>Independent Segments for Departments and Databases </li></ul></ul><ul><li>Cross Organization (“in the Cloud”) </li></ul><ul><ul><li>Multiple Organization Deployment </li></ul></ul><ul><ul><li>Secure Shared Segments </li></ul></ul><ul><ul><li>Example: Pharmaceutical and CRO </li></ul></ul><ul><li>Web Service </li></ul><ul><ul><li>accessed by Enterprise Applications </li></ul></ul><ul><ul><ul><li>i.e. Documentum, Sharepoint, LDAP </li></ul></ul></ul>
  14. 14. Innovation Network kHarmony™ Data Representation: Each Object has Properties “ chunks” of RDF Unique URI “ Core” RDFs Model
  15. 15. Innovation Network kHarmony™ HyperEdges: Statements about Statements Track Provenance Difficult in RDF alone (everything “reified”)
  16. 16. kHarmony™ Relevancy <ul><li>Function[] </li></ul><ul><ul><li>Graph Topology Metrics </li></ul></ul><ul><ul><li>Paths to User </li></ul></ul><ul><ul><li>Time </li></ul></ul><ul><ul><li>Properties </li></ul></ul><ul><ul><ul><li>including “certainty” </li></ul></ul></ul><ul><ul><li>Neighbor Properties </li></ul></ul>Confidential
  17. 17. Semantic Collaborative Statements
  18. 18. Semantic Knowledge Statements Domain Ontology + Instance Statements
  19. 19. Semantic Knowledge Statements Direct or Inferred
  20. 20. Text Mine Unstructured Data: Semantic Parse Graph Representation <ul><li>“ Suppression of endogenous Bim greatly inhibits Gadd45a induction of apoptosis.” </li></ul><ul><li>[action, inhibit, </li></ul><ul><li>[action, suppress, </li></ul><ul><li>[unknown], </li></ul><ul><li>[gp, endogenous Bim] </li></ul><ul><li>], </li></ul><ul><li>[action, induce, </li></ul><ul><li>[gp, Gadd45a], </li></ul><ul><li>[process, apoptosis] </li></ul><ul><li>], </li></ul><ul><li>] </li></ul>
  21. 21. Entity and Relationship Normalization <ul><li>Heuristics </li></ul><ul><li>Bayesian </li></ul><ul><li>String Similarity </li></ul><ul><li>Abbreviation Expansion </li></ul><ul><li>Species Context </li></ul><ul><li>Output a “score” </li></ul>Confidential Copyright Alitora Systems, Inc. 2009
  22. 22. Innovation Network <ul><li>Current Platform Applications for Customers & Partners: </li></ul><ul><li>Life Science BI and R&D </li></ul><ul><li>Social Network, Contextual Content </li></ul><ul><li>Media, Real Time Web </li></ul><ul><li>Brand Tracking, Real Time Web </li></ul>“ Semantics-as-a-Service” “ Platform-as-a-Service”
  23. 23. Innovation Network - DEMO <ul><li>Demo Semantic Mash-Up: </li></ul><ul><li>Alitora Systems API </li></ul><ul><li>Alitora Foundry Biomedical Parser </li></ul><ul><li>Yahoo News Feeds </li></ul><ul><li>OpenCalais API </li></ul><ul><li>10 Biomedical Data sources, Freebase data </li></ul><ul><li>GWT-based Web Interface </li></ul><ul><li>Cytoscape-based Graph Visualization </li></ul>
  24. 24. Innovation Network - DEMO Web Application Application Plug-In … including OpenCalais
  25. 25. Contact Information <ul><li>Alitora Systems </li></ul><ul><li>155 Water Street </li></ul><ul><li>New York, NY 11201 </li></ul><ul><li>(917) 463-4776 </li></ul><ul><li>[email_address] </li></ul>
  26. 26. Innovation Network Interface
  27. 42. Innovation Network
  28. 43. Alitora Foundry Toolkit <ul><li>Test and Train Annotators </li></ul>
  29. 44. Alitora Foundry Toolkit <ul><li>Other Annotators: </li></ul><ul><ul><li>OpenCalais (Business Relationships) </li></ul></ul><ul><ul><li>Oscar3 (Chemical Names) </li></ul></ul><ul><ul><ul><li> </li></ul></ul></ul><ul><ul><ul><li>Nico Adams, et al. </li></ul></ul></ul><ul><ul><ul><li>University of Cambridge </li></ul></ul></ul>