The SMART Text2FHIR Pipeline

Abstract

Objective: To implement an open source, free, and easily deployable high throughput natural language processing module to extract concepts from clinician notes and map them to Fast Healthcare Interoperability Resources (FHIR). Materials and Methods: Using a popular open-source NLP tool (Apache cTAKES), we create FHIR resources that use modifier extensions to represent negation and NLP sourcing, and another extension to represent provenance of extracted concepts. Results: The SMART Text2FHIR Pipeline is an open-source tool, released through standard package managers, and publicly available container images that implement the mappings, enabling ready conversion of clinical text to FHIR. Discussion: With the increased data liquidity because of new interoperability regulations, NLP processes that can output FHIR can enable a common language for transporting structured and unstructured data. This framework can be valuable for critical public health or clinical research use cases. Conclusion: Future work should include mapping more categories of NLP-extracted information into FHIR resources and mappings from additional open-source NLP tools.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

Research reported in this publication was supported by three contracts 90AX0022, 90AX0019, 90AX0031, and 90C30007 from the Office of the National Coordinator of Health Information Technology; the Centers for Disease Control and Prevention of the U.S. Department of Health and Human Services (HHS) as part of a financial assistance award (The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement, by CDC/HHS, or the U.S. Government). A cooperative agreement from the National Center for Advancing Translational Sciences U01TR002623; Grants from the National Library of Medicine (R01LM012973, R01LM012918); and the Boston Children's Hospital PrecisionLink Initiative. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding sources.

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Data Availability

This manuscript does not describe created data but software resources, which are available at open source repositories linked in the manuscript.

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