Guoqian Jiang, MD, PhD

farmpaintlickInternet and Web Development

Oct 21, 2013 (3 years and 7 months ago)

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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

Data Standards and
CEMs

in RDF store

CDISC Data Standards

In ODM and Spreadsheet

CEMs

in CEML XML

SPARQL Endpoint and Standard Semantic Query Services

Standards Representation and Harmonization in Semantic
Wikis

Semantic Wiki

Frontend Module

Semantic Repository

Module

RDF Transformation

Module

RDF Transformation

RDF Transformation

Semantic Query

Interface Module

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