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