Transcript Poster: OpenCEMWiki Slides

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 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
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
triples
 SPARQL
– 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
Semantic Wiki
Frontend Module
Standards Representation and Harmonization in Semantic
Wikis
Semantic Query
Interface Module
SPARQL Endpoint and Standard Semantic Query Services
Semantic Repository
Module
RDF Transformation
Module
Data Standards and CEMs in RDF store
RDF Transformation
CDISC Data Standards
In ODM and Spreadsheet
RDF Transformation
CEMs in CEML XML
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.
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/opence
m/index.php/Main_Page