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. CDISC2RDF Human readable documentation of different CDISC’s data standards CDISC2RDF Schemas (based on the core of ISO11179) Directly machine computable and queryable Linked Clinical Data Standards 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”

6. CDISC2RDF Human readable documentation of different CDISC’s data standards CDISC2RDF Schemas (based on the core of ISO11179) Directly machine computable and queryable Linked Clinical Data Standards 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” Project team: Frederik Malfait (IMOS consulting, working for Roche), Kerstin Forsberg (AstraZeneca), Charlie Mead and Eric Prud’hommeaux (W3C HCLS), Phil Ashworth (Top Quadrant), Sam Hume (Clinical Standard Governance Organisation, AstraZeneca, and CDISC ODM team), Laura Hollink (Vrije Universiteit, Amsterdam, and EUREKA projekt) Sponsors: Jonathan Chainey (Data Standard Office, Roche), Tom Plaster (Integrative Informatics Semantic Framework, AstraZeneca), Frank van Harmelen (Vrije Universiteit, Amsterdam) and Irene Polikoff (TopQuadrant). Blog: http://cdisc2rdf.com/http://cdisc2rdf.com/ Google Code: https://code.google.com/p/cdisc2rdf/ (under Source)https://code.google.com/p/cdisc2rdf/

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

8. CDISC2RDF Overview of Ontologies: Schemas Meta model schema (mms) (Data definition, the core part of ISO 11179) Controlled Terminology schema (cts) (a few additional properties from the NCI Thesaurus export) SDTM 1.2 schema (sdtms) (Classifiers: Data Element roles and types) 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) Controlled Terminology schema (cts) (a few additional properties from the NCI Thesaurus export) SDTM 1.2 schema (sdtms) (classificiers: Data Element roles and types) SDTM 3.1.2 IG schema (sdtmigs) (a few additional properties) SDTM IG 3.1.2 domains SDTM 1.2 model CDASH CT value sets ADaM CT value sets SDTM CT value 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 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 1.2 model Example: --ACN Screenshots from the ontology tool: TopBraid Composer TopBraid Composer

12. CDISC2RDF SDTM Model 1.2 Schema and Model + IG 3.1.2 Schema and Domains 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 3.1.2 IG schema (sdtmigs) (a few additional properties) SDTM IG 3.1.2 domains SDTM 1.2 model Example: --ACN Example: AEACN Screenshots from the ontology tool: TopBraid Composer 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 properties from the NCI Thesaurus export) SDTM CT value sets Example: ”DRUG INTERRUPTED” in Codelist ”ACN” (Action Taken with Study Treatment) Screenshots from the ontology tool: TopBraid Composer TopBraid Composer

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

15. CDISC2RDF Import / Transform SDTM CT in Annotated Excel to a SDTM CT ontology SDTM CT value sets TopBraid Composer Import Import file: SDTM Codelist, annotated to map the CDISC2RDF schema for Controlled Terminologies Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies Screenshots from the ontology tool: TopBraid Composer 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 IG 3.1.2 domains SDTM CT value sets SDTM 1.2 schema (sdtms) (classifications: Data Element roles and types) SDTM 3.1.2 IG schema (sdtmigs) (a few additional properties) SDTM 1.2 model Import file: SDTM IG 3.1.2 annotated using CDISC2RDF SDTM IG Schema Annotations Import/Transform using TopBraid Composer This one is yet not published