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Semantic Models for CDISC BasedStandards and Metadata ManagementPresented at CDISC Interchange Europe, Stockholm, 19 April...
Key Message• Things converge to create new and unique  opportunities.       The coverage and maturity of existing CDISC s...
Two real world use of semantic webstandards and linked data principles© CDISC 2012                           3
Today’s Situation• “Not if and when, but how” to best adopt CDISC  based data standards is becoming the leading  question....
An Emerging Insight• The CDISC standards is all about the meaning of  what is studied in the biological and clinical reali...
RDF Triples• Resource Description Framework (RDF)  A general model of how any piece of data, and  representations of knowl...
RDF Triples• Triples can be aggregated into graphs with subject  and objects as nodes, and predicates as arcs.            ...
RDF Triples             • Graphs of triples can be extended across different               sources and for different purpo...
RDF Triples               • RDF Schema and the RDF based Web Ontology                 Language (OWL) add a typing mechanis...
RDF Triples                • Google, Bing (Microsoft) and Yahoo use OWL                  publish a joint vocabulary.      ...
RDF Triples              • NCI use OWL to publish NCI Thesaurus (the                source for CDISC’s CT:s) in an RDF/XML...
Linked Open Data Cloudhttp://lod-cloud.net/Richard Cyganiak and Anja Jentzsch              © CDISC 2012           12
Real world use• Two examples of how sponsors have started to  use semantic web standards and apply linked data  principles...
Roche Biomedical MDRSchema Architecture          Production                           Partial / Future                    ...
Roche Biomedical MDRContent• External content       SDTM 1.2, SDTMIG 3.1.2       NCI Thesaurus, CDISC Controlled Termino...
Roche Biomedical MDR                                                      Production                                      ...
Roche Biomedical MDRSystem Architecture                       Content                       Management                    ...
Roche Biomedical MDRValue Proposition• Current       Integrated knowledge, metadata, and data standards        management...
Key Message• We now see all of these things converge to create  new and unique opportunities.       The coverage and matu...
TopBraid Semantic               Modeling Workbench© CDISC 2012                        20
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Roche Global Data               Standards Browser© CDISC 2012                       29
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Publishing and Item               Level Versioning© CDISC 2012                         38
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Using Web Services to               Export to…© CDISC 2012                           42
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Oh well, if you really               want that Excel sheet© CDISC 2012                            44
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Semantic models for cdisc based standards and metadata management

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Semantic models for cdisc based standards and metadata management

  1. 1. Semantic Models for CDISC BasedStandards and Metadata ManagementPresented at CDISC Interchange Europe, Stockholm, 19 April2012, byKerstin Forsberg, R&D, AstraZenecaFrederik Malfait, IMOS Consulting and Hoffmann-La Roche© CDISC 2012 1
  2. 2. Key Message• Things converge to create new and unique opportunities.  The coverage and maturity of existing CDISC standards.  The establishment of these standards within the industry.  The use of these standards as a foundation for metadata driven systems.  The upcoming role of semantic web standards and linked data principles.• See also presentation and blog post from last year’s conference: Linking Clinical Data Standards© CDISC 2012 2
  3. 3. Two real world use of semantic webstandards and linked data principles© CDISC 2012 3
  4. 4. Today’s Situation• “Not if and when, but how” to best adopt CDISC based data standards is becoming the leading question.• We see a variety of CDISC standards at different levels of maturity, not linked together and published in different formats.• Sponsors are faced with challenges on all levels: architecture, process, and application.© CDISC 2012 4
  5. 5. An Emerging Insight• The CDISC standards is all about the meaning of what is studied in the biological and clinical reality (often referred to as concepts).• How these concepts are represented as data elements from protocol to submission, and beyond.• We are dealing with semantics and metadata for biomedical and clinical research knowledge and data.• “Put semantic into the semantic” Use semantic web standards and linked data principles.© CDISC 2012 5
  6. 6. 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© CDISC 2012 6
  7. 7. RDF Triples• Triples can be aggregated into graphs with subject and objects as nodes, and predicates as arcs. type City capital Sweden Stockholm subject Port cities in Sweden areaCode “+46-8” “http://en.wikipedia.org/wiki/Stockholm” primaryTopic© CDISC 2012 7
  8. 8. RDF Triples • Graphs of triples can be extended across different sources and for different purpose. type City 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 © CDISC 2012 8
  9. 9. RDF Triples • RDF Schema and the RDF based Web Ontology Language (OWL) add a typing mechanism to classify subjects and objects into hierarchies. Thing subClass Place subClass subClassOrganization Event Adm.Area subClass subClass type subClass Business type City 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 © CDISC 2012 9
  10. 10. RDF Triples • Google, Bing (Microsoft) and Yahoo use OWL publish a joint vocabulary. Thing subClass Place subClass subClass Organization Event Adm.Area subClass subClass subClass Business City Event CountryExempelhttp://schema.org/City © CDISC 2012 10
  11. 11. RDF Triples • NCI use OWL to publish NCI Thesaurus (the source for CDISC’s CT:s) in an RDF/XML format. Hematology Laboratory Test CDISC Laboratory CDISC Laboratory Procedure Test Name Test Terminology Terminology subClass Has NCIHD Concept in Concept in Parent Subset Subset Hemoglobin Measurement definition “A quantitative measurement of the amount of hemoglobin present in a sample.”NCI Thesaurushttp://ncicb.nci.nih.gov/download/evsportal.jsp © CDISC 2012 11
  12. 12. Linked Open Data Cloudhttp://lod-cloud.net/Richard Cyganiak and Anja Jentzsch © CDISC 2012 12
  13. 13. Real world use• Two examples of how sponsors have started to use semantic web standards and apply linked data principles.  AstraZeneca: • Integrative Informatics (i2) program establishing the components to let a Linked Data cloud grow across AstraZeneca R&D  Roche • Implementing an internally built MDR.© CDISC 2012 13
  14. 14. Roche Biomedical MDRSchema Architecture Production Partial / Future CDISC Standards Metadata Management Knowledge Management© CDISC 2012 14
  15. 15. Roche Biomedical MDRContent• External content  SDTM 1.2, SDTMIG 3.1.2  NCI Thesaurus, CDISC Controlled Terminology• Integrated Data Standards, Roche and Genentech  Safety and every Roche TA, ~ 2000 data elements  Data Collection and Data Tabulation• Value level metadata  Lab measurements, Unit conversions, Questionnaires• Looking at metadata for  SDTM Conformance Checking, Biomarker (HGNC), …© CDISC 2012 15
  16. 16. Roche Biomedical MDR Production Partial Information Architecture FutureTransformation ModelsStudy & ProjectLevel Metadata Roche GlobalData Standards CDISC PRM CDASH SDTM ADaM DefineData Standards Biomedical +++ BRIDG +++ SHARE +++ NCI Thesaurus +++ Data Element Concepts +++Domain Model Study Data Data Data Regulatory Design Collection Tabulation Analysis Submission © CDISC 2012 16
  17. 17. Roche Biomedical MDRSystem Architecture Content Management Content Publishing Metadata Repository Single Point of Access© CDISC 2012 17
  18. 18. Roche Biomedical MDRValue Proposition• Current  Integrated knowledge, metadata, and data standards management  System independent information asset  Single point of access• Future  Leverage the SOA interface to create a framework for integrated metadata driven workflow  Integrate MDR and Component Based Authoring capabilities (study design, protocol, CSR)© CDISC 2012 18
  19. 19. Key Message• We now see all of these things converge to create new and unique opportunities.  The coverage and maturity of existing CDISC standards.  The establishment of these standards within the industry at large.  The use of these standards as a foundation for metadata driven systems.  The upcoming role of semantic web standards and linked data principles.© CDISC 2012 19
  20. 20. TopBraid Semantic Modeling Workbench© CDISC 2012 20
  21. 21. © CDISC 2012 21
  22. 22. © CDISC 2012 22
  23. 23. © CDISC 2012 23
  24. 24. © CDISC 2012 24
  25. 25. © CDISC 2012 25
  26. 26. © CDISC 2012 26
  27. 27. © CDISC 2012 27
  28. 28. © CDISC 2012 28
  29. 29. Roche Global Data Standards Browser© CDISC 2012 29
  30. 30. © CDISC 2012 30
  31. 31. © CDISC 2012 31
  32. 32. © CDISC 2012 32
  33. 33. © CDISC 2012 33
  34. 34. © CDISC 2012 34
  35. 35. © CDISC 2012 35
  36. 36. © CDISC 2012 36
  37. 37. © CDISC 2012 37
  38. 38. Publishing and Item Level Versioning© CDISC 2012 38
  39. 39. © CDISC 2012 39
  40. 40. © CDISC 2012 40
  41. 41. © CDISC 2012 41
  42. 42. Using Web Services to Export to…© CDISC 2012 42
  43. 43. © CDISC 2012 43
  44. 44. Oh well, if you really want that Excel sheet© CDISC 2012 44
  45. 45. © CDISC 2012 45
  46. 46. © CDISC 2012 46
  47. 47. © CDISC 2012 47
  48. 48. © CDISC 2012 48
  49. 49. © CDISC 2012 49
  50. 50. © CDISC 2012 50
  51. 51. © CDISC 2012 51
  52. 52. © CDISC 2012 52
  53. 53. © CDISC 2012 53

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