Linked data in pharma it univ 2 april 2012

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Linked data in pharma it univ 2 april 2012

  1. 1. Linked Data in Pharmaceutical R&DPhD Informatics Seminar, IT UniversityKerstin ForsbergAstraZeneca, R&D, SwedenClinical Information Strategykerstin.l.forsberg@astrazeneca.comkerfors on Twitter, Google+, LinkedIn, Slideshare, Blogspot, citulike
  2. 2. What is this? DBpedia WikiData Schema.org
  3. 3. Some recent headlines! How DBpedia treats Wikipedia as a Database Wikipedia’s Next Big Thing: Wikidata, A Machine- Readable, User-Editable Database Funded By Google, Paul Allen And Others Yandex (Russia’s leading search engine) joins Google, Yahoo! and Bing to collaborate on Schema.org
  4. 4. What is this? http://dbpedia.org/resource/IT_University http://dbpedia.org/resource/Stockholm http://education.data.gov.uk/id/school/123065 http://schema.org/CollegeOrUniversity http://research.data.astrazeneca.com/id/clinicalstudy/D5890C00003 http://linkedct.org/resource/trial/nct00244608/
  5. 5. Pharmaceutical Research and Development
  6. 6. Complexity Pathophysiology? Phenotypes? Targets? Costs? Biomarkers? QoL? Outcomes? Association and interpretation Health care, pharma, academia, of all data needed authorities and payers. has become a too complex task Shared datasetsfor individuals, or even teams to handle. Different decisions and different types of applications.
  7. 7. Why is it so hard … See slide 1-5 in the slide pack from Open PHACTS presented at BioIT World Expo Europe – Oct 2011 by Prof. Carole Goble on SlideShare http://www.slideshare.net/open_phacts/open-phacts-bioit-world-europe-cag-111013
  8. 8. Web of Documents Web 3.0Web of (Linked) Data An Intro To The Semantic Web: Why You Need To Know About It Sooner Than Later , by Samantha Wong Image Source: Frederic Martin
  9. 9. Opportunities Organized for associations Prepared for not yet defined use Ready for automation where computers can function alongside us to  Mitigate the complexity in discovering, accessing, connecting and interpreting information  Improve the productivity in managing information
  10. 10. Semantic Web Standard Stack
  11. 11. RDF Triples  Resource Description Framework (RDF): a general model of how any piece of data and representations of knowledge can be expressed as so called triples. subject predicate object (or value) Stockholm type place Stockholm capital Sweden Stockholm subject Port cities in Sweden Stockholm areaCode “+46-8” “http://en.wikipedia.org/wiki/Stockholm” Stockholm primaryTopic
  12. 12. RDF Triples  Triples can be aggregated into graphs with subject and objects as nodes, and predicates as arcs. type place capital Sweden Stockholm subject Port cities in Sweden areaCode “+46-8” “http://en.wikipedia.org/wiki/Stockholm” primaryTopic
  13. 13. RDF Triples  Graphs of triples can be extended across different sources and for different purpose. type place type CountryCDISC capital Sweden Stockholm subject Port cities in Sweden subject CDISC Interchange EU 2012 areaCode “+46-8” Gothenburg “http://en.wikipedia.org/wiki/Stockholm” primaryTopic
  14. 14. RDF Triples  RDF Schema and the RDF based Web Ontology Language (OWL) add a typing mechanism to classify subjects and objects into hierarchies of types Thing subClass Place subClass subClassOrganization Event subClass Adm.Area subClass type subClass Business type place Event type CountryCDISC capital Sweden type Stockholm subject Port cities in Sweden subject CDISC Interchange EU 2012 areaCode “+46-8” Gothenburg “http://en.wikipedia.org/wiki/Stockholm” primaryTopic
  15. 15. RDF Triples  Simple Knowledge Organization System (SKOS) is a thin RDF based vocabulary that can be used to build terminologies of broader/narrower concepts. Populated places in EuropeOrganization broader narrower type Cities in Business type place Sweden EventCDISC broader capital Sweden narrower type Stockholm subject Port cities in Sweden subject CDISC Interchange EU 2012 areaCode “+46-8” Gothenburg “http://en.wikipedia.org/wiki/Stockholm” primaryTopic
  16. 16. 4 Principles for Linked Data …… and 5 stars for Linked Open Data • Use URIs (Uniform Resource Identifiers) as names for things. • Use HTTP URIs so that people can look up (dereference) those names. • When someone looks up a URI, provide useful information. • Include links to other URIs so that they can discover more things. Source: Linked Open Data star scheme by example More resources introducing and describing the Linked Data idea
  17. 17. Linked Open Data cloudRichard Cyganiak and Anja Jentzschhttp://lod-cloud.net/Growing Linked Open Data Cloudhttp://youtu.be/TXFYSWuEOOw
  18. 18. Linked Enterprise Data Source: What does Open Data mean for Enterprises? More resources introducing and describing the Linked Data idea
  19. 19. I’m encouraged by …• … what actually can be done by applying Linked Data principles, together with a stepwise implementation and pragmatic application of crucial building blocks, to … Health Care and Life Sciences (HCLS) Interest Group• … improve the research and commercial Linking Open Drug Data utility of information • Organized for associations • Prepared for not yet defined use EU project The Large Knowledge Collider Linked Life Data • Ready for automation where computers can function alongside us to A 2-page summary of our learnings from participating in these external projects:  Mitigate the complexity in discovering, Linked Data in Pharma, 2011, Bo Andersson and Kerstin Forsberg accessing, connecting and interpreting information  Improve the productivity in managing1 information9

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