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Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
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BabelFSH-a toolkit for an effective HL7 FHIR-based terminology provision.

Joshua Wiedekopf1, Tessa Ohlsen2, Ann-Kristin Kock-Schoppenhauer2

  • 1Institute of Medical Biometry and Statistics, Section for Clinical Research IT, University of Luebeck and University Hospital Schleswig-Holstein, 160 Ratzeburger Allee, 23562, Luebeck, Germany. j.wiedekopf@uni-luebeck.de.

Journal of Biomedical Semantics
|November 29, 2025
PubMed
Summary

BabelFSH is an open-source toolkit that converts diverse terminologies into HL7 FHIR resources, enhancing healthcare interoperability. This tool supports large-scale projects by efficiently managing complex code systems and value sets for terminological services.

Keywords:
HL7 FHIRKnowledge basesTerminology as topicTerminology servers

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Area of Science:

  • Health Informatics
  • Computational Linguistics
  • Software Engineering

Background:

  • HL7 FHIR (Fast Healthcare Interoperability Resources) terminological services (TS) are crucial for healthcare interoperability.
  • Existing terminologies require conversion into FHIR resources for TS utilization.
  • Large-scale healthcare projects necessitate efficient management of extensive value sets and code systems.

Purpose of the Study:

  • To develop a comprehensive, extensible, and accessible toolkit for FHIR terminology conversion.
  • To enable terminology authors and FHIR profilers to provide standardized TS for large-scale terminological artifacts.

Main Methods:

  • Developed BabelFSH, a converter toolkit based on the HL7 FHIR Shorthand (FSH) specification.
  • Utilized an adaptable plugin architecture to decouple content definition from metadata.
  • Guided development by formalized design goals.

Main Results:

  • BabelFSH successfully addressed all eight design goals.
  • Demonstrated performance and completeness using Alpha-ID-SE for rare disease diagnosis coding.
  • The tool is actively used in a national FHIR TS content delivery pipeline, proving its usability for FHIR developers.

Conclusions:

  • BabelFSH effectively meets the requirements for central research FHIR TS within Germany's federated FHIR infrastructure.
  • Identified areas for improvement in validation message precision.
  • The toolkit's design supports future use cases, including direct conversion from legacy systems.