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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. Acknowledgement. Harold Solbrig , Mayo Clinic Julie Evans, CDISC Tom Oniki , Ph.D., IHC Joey Coyle, M.D., IHC

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Guoqian Jiang, MD, PhD Mayo Clinic

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  1. 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

  9. 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

  10. 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.

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

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

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

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

  15. 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.

  16. 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.

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

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