Overview of the CDISC2RDF ontologies and a first overview of the import/transformation for standards-as-is into machine processable OWL/RDF. See also http://cdisc2rdf.com/
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