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Related Experiment Video

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Querying clinical data in HL7 RIM based relational model with morph-RDB.

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  • 1Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain. fpriyatna@fi.upm.es.

Journal of Biomedical Semantics
|October 7, 2017
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Summary

This study introduces a virtual SPARQL endpoint for accessing relational clinical trial data, enhancing data freshness. Optimized query translation ensures acceptable performance for semantic interoperability in multi-institutional research.

Keywords:
Clinical dataR2RMLSPARQL

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Area of Science:

  • Bioinformatics
  • Clinical Informatics
  • Data Management

Background:

  • Semantic interoperability is crucial for multi-institutional post-genomic clinical trials.
  • Accessing heterogeneous data sources requires integrated views.
  • Previous RDB2RDF approaches using materialized datasets led to data staleness.

Purpose of the Study:

  • To present a solution for real-time access to relational data for clinical trials.
  • To overcome data freshness limitations of materialized RDF datasets.
  • To enable semantic interoperability through virtual RDF data sources.

Main Methods:

  • Developed an ontology based on the HL7 v3 Reference Information Model.
  • Created R2RML mappings to link the ontology with a relational database.
  • Utilized morph-RDB to create a virtual, non-materialized SPARQL endpoint.

Main Results:

  • A virtual SPARQL endpoint was successfully exposed over relational data.
  • The system provides a unified view of heterogeneous data sources.
  • Data freshness is maintained by avoiding materialization.

Conclusions:

  • Optimized SPARQL-to-SQL query translation enables efficient querying.
  • SPARQL queries can be issued to underlying relational data with acceptable performance.
  • The solution facilitates semantic interoperability in collaborative clinical research.