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Emerging Technologies

Emerging Technologies. Semantic Web and Data Integration This meeting will start at 5 min past the hour As a reminder, please place your phone on mute unless you are speaking. 31 May 2013. Emerging Technologies. Semantic Web and Data Integration. 31 May 2013. Meeting Agenda.

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Emerging Technologies

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  1. Emerging Technologies Semantic Web and Data Integration This meeting will start at 5 min past the hour As a reminder, please place your phone on mute unless you are speaking 31 May 2013

  2. Emerging Technologies Semantic Web and Data Integration 31 May 2013

  3. Meeting Agenda Representing CDISC Standards in RDF Sub-Team Updates ISO11179 Assessment sub-project overview Controlled Terminology use case 2

  4. Representing CDISC Standards in RDF Sub-Team Updates CDASH (Geoff/Mitra) SDTM (Daniel/Scott) SEND (Scott/Frederik) ADaM(Josephine/Phil) 2

  5. We want to push back to CDISC and NCI, and other public and internal standard groups, and show in practice how to: “Use (semantic web) standards for standards” CDISC2RDF Schemas(based on the core of ISO11179) Human readable documentation of different CDISC’s data standards Directly machine computable and queryableLinked Clinical Data Standards CDISC2RDF

  6. We want to push back to CDISC and NCI, and other public and internal standard groups, and show in practice how to: “Use (semantic web) standards for standards” CDISC2RDF Schemas(based on the core of ISO11179) Human readable documentation of different CDISC’s data standards Directly machine computable and queryableLinked Clinical Data Standards Project team: Frederik Malfait (IMOS consulting, working for Roche), Kerstin Forsberg (AstraZeneca), Charlie Mead and Eric Prud’hommeaux (W3C HCLS), Phil Ashworth (TopQuadrant), Sam Hume (Clinical Standard Governance Organisation, AstraZeneca, and CDISC ODM team), Laura Hollink (VrijeUniversiteit, Amsterdam, and EUREKA projekt) Sponsors:Jonathan Chainey (Data Standard Office, Roche), Tom Plaster (Integrative Informatics SemanticFramework, AstraZeneca), Frank van Harmelen (VrijeUniversiteit, Amsterdam) and Irene Polikoff (TopQuadrant). CDISC2RDF Blog: http://cdisc2rdf.com/ Google Code: https://code.google.com/p/cdisc2rdf/ (under Source)

  7. CDISC2RDF Schemas(based on the core of ISO11179) Human readable documentation of different CDISC’s data standards Directly machine computable and queryableLinked Clinical Data Standards Example: ”DRUG INTERRUPTED” in Codelist ”ACN” (Action Taken with Study Treatment) CDISC2RDF Example: --ACN Screenshots from the ontology tool: TopBraid Composer Example: AEACN

  8. CDISC2RDF Overview of Ontologies: Schemas Meta model schema (mms)(Data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms)(Classifiers: Data Element roles and types) Controlled Terminology schema (cts)(a few additional propertiesfrom the NCI Thesaurus export) SDTM 3.1.2 IG schema (sdtmigs)(a few additional properties)

  9. CDISC2RDF Overview of Ontologies: Schemas and Standards Meta model schema (mms)(Data definition, the core part of ISO 11179) CDASH CTvalue sets SDTM 1.2 schema (sdtms)(classificiers: Data Element roles and types) SDTM 1.2model Controlled Terminology schema (cts)(a few additional propertiesfrom the NCI Thesaurus export) ADaM CTvalue sets SDTM IG 3.1.2domains SDTM 3.1.2 IG schema (sdtmigs)(a few additional properties) SDTM CTvalue sets

  10. CDISC2RDF Core Schemas: Meta Model Meta model schema (mms)(Data definition, the core part of ISO 11179)

  11. CDISC2RDF SDTM Model 1.2 Schema and Model Example: --ACN Meta model schema (mms)(Data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms)(Classifiers: Data Element Compliance, Roles and Types) SDTM 1.2model Screenshots from the ontology tool: TopBraid Composer

  12. CDISC2RDF SDTM Model 1.2 Schema and Model + IG 3.1.2 Schema and Domains Example: --ACN Meta model schema (mms)(Data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms)(Classifiers: Data Element Compliance, Roles and Types) SDTM 1.2model SDTM IG 3.1.2domains SDTM 3.1.2 IG schema (sdtmigs)(a few additional properties) Example: AEACN Screenshots from the ontology tool: TopBraid Composer

  13. CDISC2RDF CT Schema and CT:s Meta model schema (mms)(Data definition, the core part of ISO 11179) Controlled Terminology schema (cts)(a few additional propertiesfrom the NCI Thesaurus export) SDTM CTvalue sets Example: ”DRUG INTERRUPTED” in Codelist ”ACN” (Action Taken with Study Treatment) Screenshots from the ontology tool: TopBraid Composer

  14. CDISC2RDF Annotation of SDTM CT Excel using CDISC2RDF schemas SDTM CT original format Import file: SDTM Codelist, annotated to map the CDISC2RDF schema for Controlled Terminologies Meta model schema (mms)(data definition, the core part of ISO 11179) Controlled Terminology schema (cts)(structure of CDISC’s value setsdrawn from NCI Thesaurus) Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies

  15. CDISC2RDF Import / Transform SDTM CT in Annotated Excel to a SDTM CT ontology Import file: SDTM Codelist, annotated to map the CDISC2RDF schema for Controlled Terminologies TopBraid Composer Import Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies SDTM CTvalue sets Screenshots from the ontology tool: TopBraid Composer

  16. CDISC2RDF From SDTM Implementation Guideline (IG) in PDF/Excel to OWL/RDF Meta model schema (mms)(data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms)(classifications: Data Element roles and types) SDTM 1.2model SDTM 3.1.2 IG schema (sdtmigs)(a few additional properties) This one is yet not published Import file: SDTM IG 3.1.2 annotated using CDISC2RDF SDTM IG Schema Annotations Import/Transformusing TopBraid Composer SDTM IG 3.1.2domains SDTM CTvalue sets

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