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Updated: Oct 19, 2025

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
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Interoperable genetic lab test reports: mapping key data elements to HL7 FHIR specifications and professional

Aly Khalifa1, Clinton C Mason2, Jennifer Hornung Garvin1,3,4

  • 1Department of Biomedical Informatics, School of Medicine, University of Utah, Salt Lake City, Utah, USA.

Journal of the American Medical Informatics Association : JAMIA
|September 27, 2021
PubMed
Summary

The Health Level Seven International (HL7) Fast Healthcare Interoperability Resources Clinical Genomics Implementation Guide (FHIR CG IG) covers most genetic test report data. Suggestions were made for extensions to improve interoperability of genetic testing information.

Keywords:
FHIRbiomedical informaticsgenetic resultsgenetic test reportinginteroperability

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Area of Science:

  • Genomics
  • Bioinformatics
  • Health Informatics

Background:

  • Genetic testing reports are often in inaccessible formats like PDFs or images.
  • This limits integration with advanced informatics solutions, including clinical decision support systems.
  • The Health Level Seven International (HL7) Fast Healthcare Interoperability Resources Clinical Genomics Implementation Guide (FHIR CG IG) aims to standardize genetic data.

Purpose of the Study:

  • To identify key data elements (KDEs) in genetic lab test reports.
  • To map these KDEs to the FHIR CG IG specification.
  • To assess the coverage of the FHIR CG IG and provide recommendations for its development and implementation.

Main Methods:

  • Analysis of sample reports from 4 genetic tests.
  • Review of relevant professional reporting guidelines.
  • Mapping identified key data elements to the FHIR CG IG.

Main Results:

  • Identification of 36 common KDEs across analyzed genetic test reports.
  • Discovery of unique KDEs specific to each genetic test.
  • Mapping revealed that the FHIR CG IG covers the majority of identified KDEs.

Conclusions:

  • The FHIR CG IG is a significant advancement for genetic lab report interoperability.
  • Suggested FHIR extensions could enhance the representation of certain KDEs.
  • Continuous input from the clinical genetics community is crucial for the ongoing development of the FHIR CG IG.