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Semantic models for cdisc based standards and metadata management
 

Semantic models for cdisc based standards and metadata management

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  • Red marks the use of examples from http://schema.org/, i.e. Google’s, Yahoo’s and Bing’s (i.e. Microsoft’s) joint effort, webmasters can use to markup their pages in ways recognized by these search engines. See http://schema.rdfs.org/ for a RDF Schema representation of it
  • Red marks the use of examples from http://schema.org/, i.e. Google’s, Yahoo’s and Bing’s (i.e. Microsoft’s) joint effort, webmasters can use to markup their pages in ways recognized by these search engines. See http://schema.rdfs.org/ for a RDF Schema representation of it

Semantic models for cdisc based standards and metadata management Semantic models for cdisc based standards and metadata management Presentation Transcript

  • 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
  • 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
  • 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.• 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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.  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
  • Roche Biomedical MDRSchema Architecture Production Partial / Future CDISC Standards Metadata Management Knowledge Management© CDISC 2012 14
  • 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
  • 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
  • Roche Biomedical MDRSystem Architecture Content Management Content Publishing Metadata Repository Single Point of Access© CDISC 2012 17
  • 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
  • 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
  • TopBraid Semantic Modeling Workbench© CDISC 2012 20
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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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