Transcript EmergingTechnologies..

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
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
queryable Linked Clinical Data
Standards
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
queryable Linked 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 (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
of different CDISC’s data
standards
Directly machine computable and
queryable Linked Clinical Data
Example: ”DRUG INTERRUPTED” in
Standards
Codelist ”ACN” (Action Taken with
Study Treatment)
Example: --ACN
Screenshots from the ontology tool:
TopBraid Composer
Example: AEACN
CDISC2RDF
Overview of Ontologies: Schemas
Meta model schema (mms)
(Data definition, the core part of ISO 11179)
SDTM 1.2 schema (sdtms)
Controlled Terminology schema (cts)
(Classifiers: Data Element roles
and types)
(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
ADaM CT
value sets
SDTM CT
value sets
SDTM 1.2 schema (sdtms)
Controlled Terminology schema (cts)
(classificiers: Data Element roles
and types)
(a few additional properties
from the NCI Thesaurus export)
SDTM 3.1.2 IG schema
(sdtmigs)
(a few additional properties)
SDTM 1.2
model
SDTM IG 3.1.2
domains
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
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)
Screenshots from the ontology tool:
TopBraid Composer
SDTM 1.2
model
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 3.1.2 IG schema
(sdtmigs)
SDTM 1.2
model
SDTM IG 3.1.2
domains
(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)
(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
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)
(classifications: Data Element
roles and types)
SDTM 1.2
model
SDTM 3.1.2 IG schema
(sdtmigs)
(a few additional properties)
Annotations
This one is yet not published
Import file: SDTM IG 3.1.2 annotated
using CDISC2RDF SDTM IG Schema
Import/Transform
using TopBraid
Composer
SDTM CT
value sets
SDTM IG 3.1.2
domains