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

Acknowledgement

Harold Solbrig, Mayo ClinicJulie Evans, CDISCTom Oniki, Ph.D., IHCJoey Coyle, M.D., IHCLacey Hart, Mayo ClinicStan Huff, M.D., IHCRebecca Kush, Ph.D., CDISC Christopher Chute, M.D., Dr. PH, Mayo

Clinic

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.

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.

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

triplesSPARQL

– A standard RDF query language.Semantic Wikis

– Wiki + Semantic Web– Collaboration + Knowledge engineering

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.

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.

CDISC Standards

• CDASH - Clinical Data Acquisition Standards Harmonization• SDTM - Study Data Tabulation Model

System Architecture

Data Standards and CEMs in RDF store

CDISC Data StandardsIn ODM and Spreadsheet

CEMs in CEML XML

SPARQL Endpoint and Standard Semantic Query Services

Standards Representation and Harmonization in Semantic Wikis

Semantic WikiFrontend Module

Semantic RepositoryModule

RDF TransformationModule

RDF Transformation RDF Transformation

Semantic Query Interface Module

Prototype Implementation1) 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.

SPARQL Query Example – Retrieve descriptions for all

codelists in SDTM

SPARQL Query Example – Retrieve all variables from domain DM

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

SPARQL Query Example – Retrieve all qualifiers for StandardLabPanel CEM

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.

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.

References

http://informatics.mayo.edu/sharp/opencem/index.php/Main_Page