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), 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

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

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)

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

CDISC2RDF SDTM Model 1.2

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

CDISC2RDF SDTM Model 1.2 + IG 3.1.2

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

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

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)

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

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