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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



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


CDASH (Geoff/
Mitra
)


SDTM (Daniel/Scott)


SEND (Scott/
Frederik
)


ADaM

(Josephine/Phil)

2

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”

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/


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

Core Schemas: Meta Model

Meta model schema (
mms
)

(Data definition, the core part of ISO 11179)

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

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

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