Cdisc2 rdf overveiw
-
Upload
kerstin-forsberg -
Category
Documents
-
view
2.993 -
download
0
description
Transcript of Cdisc2 rdf overveiw
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