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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

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 technologies1

Emerging Technologies

Semantic Web and Data Integration

31 May 2013


Meeting agenda

Meeting Agenda

Representing CDISC Standards in RDF Sub-Team Updates

ISO11179 Assessment sub-project overview

Controlled Terminology use case

2


Representing cdisc standards in rdf sub team updates

Representing CDISC Standards in RDF Sub-Team Updates

CDASH (Geoff/Mitra)

SDTM (Daniel/Scott)

SEND (Scott/Frederik)

ADaM(Josephine/Phil)

2


Cdisc2rdf

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


Cdisc2rdf1

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)


Cdisc2rdf2

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


Cdisc2rdf3

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)


Cdisc2rdf4

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


Cdisc2rdf5

CDISC2RDF

Core Schemas: Meta Model

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


Cdisc2rdf6

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


Cdisc2rdf7

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


Cdisc2rdf8

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


Cdisc2rdf9

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


Cdisc2rdf10

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


Cdisc2rdf11

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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