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Linked Data Approach for Integration of Human Health & Environmental Data

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Best practices and platforms for access and reuse of scientific data and models. We explore a Linked Data approach for data integration, modeling and interoperability. …

Best practices and platforms for access and reuse of scientific data and models. We explore a Linked Data approach for data integration, modeling and interoperability.
Delivered by Bernadette Hyland at EPA & Society of Toxicology Scientific Workshop titled: "Building for Better Decisions: Multi-scale Integration of Human Health and Environmental Data..
Delivered 8-May-2012 at EPA Research Triangle Park, NC USA.

Published in: Technology, Education

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  • 1. Linked Data Approach for Integration of Human Health and Environmental Data Building for Better Decisions: Multi-scale Integration of Human Health and Environmental Data 8-11 May 2012 By: Bernadette Hyland, Chair, W3C Government Linked Data WG CEO, 3 Round Stones, Inc Email. bhyland@3roundstones.com Twitter: @BernHyland This presentation: http://slideshare.net/3roundstonesTuesday, May 8, 12 1
  • 2. • Linked Data is about publishing and consuming data using international data standards • Based on 20 year old idea • A system of linked information systemsTuesday, May 8, 12 2
  • 3. Tuesday, May 8, 12 3
  • 4. Photo credit: http://www.flickr.com/photos/sjungling/5974860/Tuesday, May 8, 12 4
  • 5. A HISTORY OF SILOS $ cat foo.txt | grep blah | sort 1970s 1980s 1990s A neat little package Client-Server The Early WebTuesday, May 8, 12 5
  • 6. There is a better way to connect data ... • No one vendor owns it • It scales ... to Web-scale • Doesn’t require a super model • Based on International Data Exchange Standards (RDF, SPARQL)Tuesday, May 8, 12 6
  • 7. What is next for Data in the Web? • What is next for Open Data on the Web • Structured data on the Web is quickly becoming mainstream • Authorities beginning to appreciate a new way to publish and consume contentTuesday, May 8, 12 7
  • 8. Tuesday, May 8, 12 8
  • 9. Tuesday, May 8, 12 9
  • 10. “Linked Data means Cooperation without coordination” -- David Wood, PhDTuesday, May 8, 12 10
  • 11. Governments Goals: Governmental transparency and/or improved internal efficiencies (data warehouses)Tuesday, May 8, 12 11
  • 12. Hardware/Software Vendors Goal: Improve interoperability between products and product linesTuesday, May 8, 12 12
  • 13. Retailers Goal: Improve click-throughs on search resultsTuesday, May 8, 12 13
  • 14. Book Publishers Goals: Improve internal manuscript pipelines, expose additional ways of finding and using contentTuesday, May 8, 12 14
  • 15. New MediaTuesday, May 8, 12 15
  • 16. Linked Data in Context Universal Client Ubiquitous, reusable applications URL Curation Universal Connection Logic and interlinking Web of Data Universal DatabaseTuesday, May 8, 12 16
  • 17. Tuesday, May 8, 12 17
  • 18. Tuesday, May 8, 12 18
  • 19. Tuesday, May 8, 12 19
  • 20. Why is RDF important? • It is an international standard for publishing data on the Web (public and private) • Data exchange model • Serializations include RDF/XML, N-triples, N3, Turtle ... • It is the future of using the WebTuesday, May 8, 12 20
  • 21. What you can do ... • Good = Use Data Standards (RDF) to publish metadata about data and models, at a minimum • Better = Use RDF to publish all your data • Best = Link your data + models • Web architecture, Web-scaleTuesday, May 8, 12 21
  • 22. Tuesday, May 8, 12 22
  • 23. Tuesday, May 8, 12 23
  • 24. WE VE SEEN THIS BEFORETuesday, May 8, 12 24
  • 25. Tuesday, May 8, 12 25
  • 26. Tuesday, May 8, 12 26
  • 27. Tuesday, May 8, 12 27
  • 28. Tuesday, May 8, 12 28
  • 29. Tuesday, May 8, 12 29
  • 30. Tuesday, May 8, 12 30
  • 31. Tuesday, May 8, 12 31
  • 32. Tuesday, May 8, 12 32
  • 33. Tuesday, May 8, 12 33
  • 34. CDC Open  Government   Linked  Data EPA Data Cloud DBpedia US  Census Pub  Med Clinical Ontology NLM Business Ontology Social  Media Internal Portal  Data Facebook Physicians TwiCer Services EMR Loca*ons Data Clinical  Condi*on  SpecificTuesday, May 8, 12 34
  • 35. Value Proposition • Decrease costly emergency department visits • Reduce hospital re-admissions after treatment • Improved self-care and medication compliance • Education of triggers and disease managementTuesday, May 8, 12 35
  • 36. Func*onal  Model 1.  Define  target  popula*on  and  clinical  data  from  electronic   medical  record 2.  Iden*fy  sources  of  open  government  data  related  to   environmental,  weather,  and  other  variables  related  to   chronic  pulmonary  disease  exacerba*ons 3.  Combine  open  content  from  NLM,  PubMed,  Medline  to   support  educa*on 4.  Leverage  a  Linked  Data  approach,  using  Open  Source  and   interna*onal  data  exchange  standards  (RDF) 5.    Alert  pa*ent  of  possible  hazardous  condi*ons  and   recommend  appropriate  ac*onsTuesday, May 8, 12 36
  • 37. Leverage  Linked  Data,  Open  Source  &  Standards Web  of  Data SMS CDC DBpedia EPA Pub  Med US  Census NLM Email CA-­‐email-­‐message.jpg Web EMRTuesday, May 8, 12 37
  • 38. Tuesday, May 8, 12 38
  • 39. Shows: 1) Air Quality data from US EPA 2) Anonymized EMR data 3) Doctor’s details from CSV file Uses Callimachus, a Linked Data Management PlatformTuesday, May 8, 12 39
  • 40. Tools & best practices? • Large and small vendors are involved in Linked Data • From Oracle, IBM to 3 Round Stones • Listing of active projects, companies and research See http://dir.w3.org/ • Best practices, see http://www.w3.org/2011/gld/charterTuesday, May 8, 12 40
  • 41. • Callimachus is a framework for data-driven applications based on Linked Data principles • Callimachus allows Web developers to easily create data driven applications for the Web • It is Open Source (FLOSS) • http://callimachusproject.orgTuesday, May 8, 12 41
  • 42. http://www.w3.org/2011/gld/charterTuesday, May 8, 12 42
  • 43. DELIVERABLES Community Directory Best Practices for Publishing Linked Data Procurement, vocabulary selection, URI construction, versioning, stability, legacy data issues Cookbook for Linked Open Data Standard Vocabularies Metadata, Statistical “Cube” Data, People, Organizational structuresTuesday, May 8, 12 43
  • 44. Tuesday, May 8, 12 44
  • 45. Recommendations • Be prepared for the scientific community & public to demand that your data be published in re-usable format (RDF) • Demand your vendors use Open Source whenever possible • Incentivize industry & STM publishers to do the right thing • Open vs. proprietary technologies & data formats ... be OPEN • Beware of semantic “pixie dust” - be “an educated consumer” (and scientist!) • Solutions must embrace International Standards and published Best Practices (W3C, OMG, IETF) • Define a URI Policy and Strategy, document it and ensure scientists use it! • Leverage the work of others and work cooperatively... • Our future is all connected through your work...Tuesday, May 8, 12 45
  • 46. This work is Copyright © 2011-2012 3 Round Stones Inc. It is licensed under the Creative Commons Attribution 3.0 Unported License Full details at: http://creativecommons.org/licenses/by/3.0/ You are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work Under the following conditions: Attribution. You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Share Alike. If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one.Tuesday, May 8, 12 46