From PDF to RDF – Representing the CDISC Foundational Standards
Geoff LowFrederik Malfait, IMOS Consulting
Scott Bahlavooni, d-WiseMitra Rocca, FDA
CTS Ontology Workshop, 2015
Agenda
• Regulatory Submissions Overview• CDISC Foundational Standards• PhUSE Computational Science Symposium Working
Groups• CDISC Foundational Standards in RDF• Further PhUSE Semantic Technologies Projects
Regulatory Submissions, Current State
Pharma Co. BioTech Inc.
Demog:- SUBJ: 101- GENDER: FEMALE- DOB: 02/22/1975
DM:- USUBJID: 101- SEX: F- BRTHDTC: 1975-02-22
CDISC Foundational Standards
Clinical Data Interchange Standards Consortium (CDISC) Mission:
“…to develop and support global, platform-independent data standards that enable information system interoperability to
improve medical research…”
CDISC Foundational Standards
Machine-Processable CDISC Foundational Standards?
PhUSE CSS Working Groups
PhUSE Computational Science Symposium (CSS) Mission:
“…bring together academia, industry, technology providers and the FDA to collaborate on projects to address unmet computational science needs.”
PhUSE CSS Working Groups
Semantic Technologies Project:• Investigate the application of W3C semantic standards to support the clinical
and non-clinical data life-cycle from protocol development to submission to regulatory agencies
http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology
Representation of CDISC Foundational Standards in RDF
Project Overview:• Representing existing CDISC standards in RDF provides a
foundation for interoperable end-to-end data standards in clinical and non-clinical research
• Separate sub-teams represented individual standards and leveraged CDISC community standards SMEs as needed
• Separate models were consolidated, vetted within the sub-team co-leadership, and a draft posted to GitHub
• Collaborate with CDISC to have the RDF representations adopted as CDISC standards
Representation of CDISC Foundational Standards in RDF
Data Capture Data Tabulations Data Analysis
CDASH v1.1 SEND IG v3.0 SDTM v1.2, v1.3SDTM IG v3.1.2, v3.1.3
ADaM v2.1ADaM IG v1.0
CDISC Controlled Terminology
CDISC Foundational Standards:RDF Walkthrough
• Based on ISO-11179 standard for metadata registries
• Schemas define classes and predicates for ontology to represent CDISC standards
• RDF datasets in Turtle (ttl) for each CDISC data standard and terminology standard
CDISC Foundational Standards:RDF SDTM IG v3.1.2 Walkthrough
CDISC Foundational Standards:RDF SDTM IG v3.1.2 Walkthrough
CDISC Foundational Standards:RDF SDTM IG v3.1.2 Walkthrough
CDISC Foundational Standards:RDF SDTM IG v3.1.2 Walkthrough
Step 1: Publication
• Standards available on Github
https://github.com/phuse-org/rdf.cdisc.org
Step 2: Documentation
Step 3: Acceptance
• The CDISC SHARE Metadata Registry will support export of RDF representations matching those developed within the PhUSE ST Foundational Standards workgroup.
• The NCI controlled terminology representation was updated to match the schema developed.
PhUSE ST Working Groups Activities
• Representation of Analysis Results Metadata to Support Clinical and Non-Clinical Applications
• Representing a Clinical Development Plan in RDF• Representation of Regulations and Guidance in RDF • Representation of the Protocol using RDF• Schedule of Activities model in RDF (using the SDM)• Representation of Eligibility Criteria in RDF • Structured Document Representation using RDF• Document Use Cases for Linked Data in the Clinical Trial Life-Cycle• keyCRF – semantically rich CRFs for EHR integration
Conclusions
• We have been able to bring industry and standards development organizations around to the value of Semantic Technologies.
• There are a number of interesting projects (with active communities) ongoing looking at how we can use Semantic Technologies to improve the way clinical research is done.
• Better trials, better drugs and better Patient Outcomes
Top Related