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We want to push back to CDISC and NCI, and other
CDISC2RDF                                           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                                     Directly machine computable
 of different CDISC’s data                                        and queryable Linked Clinical
 standards                                                        Data Standards


               Project team:
               Frederik Malfait (IMOS consulting, working for Roche), 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/
               Google Code: https://code.google.com/p/cdisc2rdf/ (under Source)
CDISC2RDF



                               CDISC2RDF Schemas
                          (based on the core of ISO11179)

 Human readable documentation                                             Directly machine computable
 of different CDISC’s data                                                and queryable Linked Clinical
 standards                                                                Data Standards     Example: ”DRUG INTERRUPTED” in
                                                                                               Codelist ”ACN” (Action Taken with
                                                                                               Study Treatment)




                                                         Example: --ACN

                          Screenshots from the ontology tool:
                                                                              Example: AEACN
                                TopBraid Composer
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 properties
               from the NCI Thesaurus export)
                                                                   SDTM 3.1.2 IG schema
                                                                       (sdtmigs)
                                                                   (a few additional properties)
CDISC2RDF
Overview of Ontologies: Schemas and Standards


                                                   Meta model schema (mms)
                                          (Data definition, the core part of ISO 11179)



CDASH CT
value sets
                                                                   SDTM 1.2 schema (sdtms)               SDTM 1.2
                                                                  (classificiers: Data Element roles
                                                                               and types)
                                                                                                          model
ADaM CT      Controlled Terminology schema (cts)
                    (a few additional properties
value sets
                 from the NCI Thesaurus export)
                                                                                                       SDTM IG 3.1.2
                                                                     SDTM 3.1.2 IG schema
                                                                                                         domains
SDTM CT                                                                  (sdtmigs)
                                                                     (a few additional properties)
value sets
CDISC2RDF
SDTM Model 1.2

                                                                                       Example: --ACN


                                            Meta model schema (mms)
                                       (Data definition, the core part of ISO 11179)




                                             SDTM 1.2 schema (sdtms)
                                                                                         SDTM 1.2
                                               (Classifiers: Data Element
                                             Compliance, Roles and Types)                 model




 Screenshots from the ontology tool:
       TopBraid Composer
CDISC2RDF
SDTM Model 1.2 + IG 3.1.2

                                                                                       Example: --ACN


                                            Meta model schema (mms)
                                       (Data definition, the core part of ISO 11179)




                                             SDTM 1.2 schema (sdtms)
                                                                                         SDTM 1.2
                                               (Classifiers: Data Element
                                             Compliance, Roles and Types)                 model


                                                                                       SDTM IG 3.1.2
                                               SDTM 3.1.2 IG schema
                                                                                         domains
                                                   (sdtmigs)
                                               (a few additional properties)


                                                                                       Example: AEACN




 Screenshots from the ontology tool:
       TopBraid Composer
CDISC2RDF
CT Schema and CT:s


                                            Meta model schema (mms)
                                       (Data definition, the core part of ISO 11179)




                                       Controlled Terminology schema (cts)                    SDTM CT
                                                (a few additional properties
                                             from the NCI Thesaurus export)
                                                                                              value sets

                                                                                       Example: ”DRUG INTERRUPTED” in
                                                                                       Codelist ”ACN” (Action Taken with
                                                                                       Study Treatment)




 Screenshots from the ontology tool:
       TopBraid Composer
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 sets
          drawn from NCI Thesaurus)




                                                   Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies
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 CT
                                                                                                                   value sets




 Screenshots from the ontology tool:
       TopBraid Composer
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)                      SDTM 1.2
                                                   (classifications: Data Element
                                                          roles and types)
                                                                                                model



                                                    SDTM 3.1.2 IG schema
                                                        (sdtmigs)
                                                    (a few additional properties)




                                                                        This one is yet not published
                              Annotations        Import file: SDTM IG 3.1.2 annotated
                                                 using CDISC2RDF SDTM IG Schema

                                                                            Import/Transform
                                                                             using TopBraid
                                                                               Composer


                                                          SDTM IG 3.1.2
                               SDTM CT                      domains
                               value sets

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Cdisc2 rdf overveiw

  • 1. We want to push back to CDISC and NCI, and other CDISC2RDF 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 Directly machine computable of different CDISC’s data and queryable Linked Clinical standards Data Standards Project team: Frederik Malfait (IMOS consulting, working for Roche), 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/ Google Code: https://code.google.com/p/cdisc2rdf/ (under Source)
  • 2. CDISC2RDF CDISC2RDF Schemas (based on the core of ISO11179) Human readable documentation Directly machine computable of different CDISC’s data and queryable Linked Clinical standards Data Standards Example: ”DRUG INTERRUPTED” in Codelist ”ACN” (Action Taken with Study Treatment) Example: --ACN Screenshots from the ontology tool: Example: AEACN TopBraid Composer
  • 3. 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 properties from the NCI Thesaurus export) SDTM 3.1.2 IG schema (sdtmigs) (a few additional properties)
  • 4. CDISC2RDF Overview of Ontologies: Schemas and Standards Meta model schema (mms) (Data definition, the core part of ISO 11179) CDASH CT value sets SDTM 1.2 schema (sdtms) SDTM 1.2 (classificiers: Data Element roles and types) model ADaM CT Controlled Terminology schema (cts) (a few additional properties value sets from the NCI Thesaurus export) SDTM IG 3.1.2 SDTM 3.1.2 IG schema domains SDTM CT (sdtmigs) (a few additional properties) value sets
  • 5. CDISC2RDF SDTM Model 1.2 Example: --ACN Meta model schema (mms) (Data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms) SDTM 1.2 (Classifiers: Data Element Compliance, Roles and Types) model Screenshots from the ontology tool: TopBraid Composer
  • 6. CDISC2RDF SDTM Model 1.2 + IG 3.1.2 Example: --ACN Meta model schema (mms) (Data definition, the core part of ISO 11179) SDTM 1.2 schema (sdtms) SDTM 1.2 (Classifiers: Data Element Compliance, Roles and Types) model SDTM IG 3.1.2 SDTM 3.1.2 IG schema domains (sdtmigs) (a few additional properties) Example: AEACN Screenshots from the ontology tool: TopBraid Composer
  • 7. CDISC2RDF CT Schema and CT:s Meta model schema (mms) (Data definition, the core part of ISO 11179) Controlled Terminology schema (cts) SDTM CT (a few additional properties from the NCI Thesaurus export) value sets Example: ”DRUG INTERRUPTED” in Codelist ”ACN” (Action Taken with Study Treatment) Screenshots from the ontology tool: TopBraid Composer
  • 8. 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 sets drawn from NCI Thesaurus) Import file: SDTM Codelist Elements annotated to map CDISC2RDF schema for Controlled Terminologies
  • 9. 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 CT value sets Screenshots from the ontology tool: TopBraid Composer
  • 10. 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) SDTM 1.2 (classifications: Data Element roles and types) model SDTM 3.1.2 IG schema (sdtmigs) (a few additional properties) This one is yet not published Annotations Import file: SDTM IG 3.1.2 annotated using CDISC2RDF SDTM IG Schema Import/Transform using TopBraid Composer SDTM IG 3.1.2 SDTM CT domains value sets