1. Guoqian Jiang, MD, PhD Mayo Clinic
OpenCEM Wiki: A Semantic-Web-based Repository for Supporting Harmonization of Clinical Study Data Standards and Clinical Element Models
Guoqian Jiang, MD, PhD
Mayo Clinic

2. Acknowledgement Harold Solbrig, Mayo Clinic Julie Evans, CDISC
Tom Oniki, Ph.D., IHC
Joey Coyle, M.D., IHC
Lacey Hart, Mayo Clinic
Stan Huff, M.D., IHC
Rebecca Kush, Ph.D., CDISC
Christopher Chute, M.D., Dr. PH, Mayo Clinic

3. Introduction
Harmonization between clinical study data standards and clinical element models (CEMs) would maximize the reuse of the CEMs across the context of clinical study and secondary use, and enable system interoperability.
An integrative semantic repository can be very useful for lowering the barriers to the access of data standards and enabling effective harmonization between them.

4. Semantic Web Technology
Semantic Web technology provides a scalable framework for semantic data integration of heterogeneous resources and enables semantic sharing.
In a previous study, we developed a CDISC SHARE prototype for supporting collaborative harmonization of clinical study data elements leveraging Semantic Web technology.

5. Semantic Web Technologies
The Resource Description Framework (RDF)
A W3C standard
A directed, labeled graph data model for representing information in the Web
Encodes data in the form of subject-predicate-object triples
SPARQL
A standard RDF query language.
Semantic Wikis
Wiki + Semantic Web
Collaboration + Knowledge engineering

6. Objective
To develop and evaluate a semantic repository for supporting harmonization of clinical study data standards and clinical element models (CEMs) using Semantic Web technology.

7. Materials We collected the following standards:
the CDISC clinical study data standards:
CDASH standards in CDISC Operational Data Model (ODM) XML format;
SDTM standards in Excel spreadsheet;
CDISC Terminologies in ODM XML format.
the Intermountain Healthcare Clinical Element Models (CEMs) in CEML XML format.

8. CDISC Standards
CDASH - Clinical Data Acquisition Standards Harmonization
SDTM - Study Data Tabulation Model

11. System Architecture
Standards Representation and Harmonization in Semantic Wikis
Semantic Wiki
Frontend Module
SPARQL Endpoint and Standard Semantic Query Services
Semantic Query
Interface Module
Data Standards and CEMs in RDF store
Semantic Repository
Module
RDF Transformation
RDF Transformation
CDISC Data Standards
In ODM and Spreadsheet
CEMs in CEML XML
RDF Transformation
Module

12. Prototype Implementation
1) We used an open XML2RDF transformation web service to convert those clinical data standards and CEMs in XML into RDF triples.
2) We used an open source RDF store called 4store to integrate the data standards and CEMs in the RDF model.
3) We established a SPARQL endpoint using built-in services from 4store.
4) In the frontend module, we implemented a Semantic MediaWiki platform with a number of semantic extensions.

14. SPARQL Query Example – Retrieve descriptions for all codelists in SDTM

16. SPARQL Query Example – Retrieve all variables from domain DM

18. SPARQL Query Example – Retrieve all permissible values for the codelist “ETHNIC”

20. SPARQL Query Example – Retrieve all qualifiers for StandardLabPanel CEM

21. Summary
We demonstrated how the data elements and the CEM elements are represented in wiki pages through dynamic semantic queries against the RDF store.
The platform has the potentials for enabling collaborative harmonization between clinical study data standards and CEMs.

22. Future Work
To solicit the requirements and workflow process of data standards harmonization from the community.
To incorporate the advance SPARQL rules for rule-based inference and consistency check.
To incorporate the advanced OWL (Web Ontology Language) representation of CEMs.

23. References