emerging technologies semantic web and data integration this meeting will start at 5 min past the...
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Emerging TechnologiesSemantic Web and Data Integration
This meeting will start at 5 min past the hourAs 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: AEACNScreenshots 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 3.1.2domains
SDTM 1.2model
CDASH CTvalue sets
ADaM CTvalue sets
SDTM CTvalue 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 1.2model
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 3.1.2domains
SDTM 1.2model
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 CTvalue 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 CTvalue 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 3.1.2domainsSDTM 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 1.2model
Import file: SDTM IG 3.1.2 annotated using CDISC2RDF SDTM IG Schema
Annotations
Import/Transformusing TopBraid
Composer
This one is yet not published