ArticleJAMIA open2019
Developing a scalable FHIR-based clinical data normalization pipeline for standardizing and integrating unstructured and structured electronic health record data.
Article in JAMIA open, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- AI in Medical Questionnaires: Scoping ReviewJournal of medical Internet research · 2025Pooled it
- Establishing core data elements for colorectal cancer and mapping to FHIR resources: Towards interoperable Iranian health information systems.Journal of education and health promotion · 2025Article
- An Interoperable Machine Learning Pipeline for Pediatric Obesity Risk Estimation.Proceedings of machine learning research · 2024Article
- State-of-the-Art Fast Healthcare Interoperability Resources (FHIR)-Based Data Model and Structure Implementations: Systematic Scoping Review.JMIR medical informatics · 2024Article
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- Establishment of a Dataset for the Traditional Korean Medicine Examination in Healthy Adults.Healthcare (Basel, Switzerland) · 2024Article
- Federated Analysis for Privacy-Preserving Data Sharing: A Technical and Legal Primer.Annual review of genomics and human genetics · 2023Review
- Machine Learning-Enabled Clinical Information Systems Using Fast Healthcare Interoperability Resources Data Standards: Scoping Review.JMIR medical informatics · 2023Article
- The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era.NPJ digital medicine · 2023Review
- The SMART Text2FHIR Pipeline.medRxiv : the preprint server for health sciences · 2023Article
- A Standardized Clinical Data Harmonization Pipeline for Scalable AI Application Deployment (FHIR-DHP): Validation and Usability Study.JMIR medical informatics · 2023Article
- Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network.Scientific reports · 2023Article
- The SMART Text2FHIR Pipeline.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2023Article
- FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model.Journal of biomedical informatics · 2022Article
- HL7 FHIR-based tools and initiatives to support clinical research: a scoping review.Journal of the American Medical Informatics Association : JAMIA · 2022Article
- Natural Language Processing and Machine Learning Methods to Characterize Unstructured Patient-Reported Outcomes: Validation Study.Journal of medical Internet research · 2021Article
- The Fast Health Interoperability Resources (FHIR) Standard: Systematic Literature Review of Implementations, Applications, Challenges and Opportunities.JMIR medical informatics · 2021Review
- Sharing Biomedical Data: Strengthening AI Development in Healthcare.Healthcare (Basel, Switzerland) · 2021Article
- Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study.JMIR medical informatics · 2021Article
- Natural Language Processing to Identify Cancer Treatments With Electronic Medical Records.JCO clinical cancer informatics · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
objectiveTo design, develop, and evaluate a scalable clinical data normalization pipeline for standardizing unstructured electronic health record (EHR) data leveraging the HL7 Fast Healthcare Interoperability Resources (FHIR) specification.
methodsWe established an FHIR-based clinical data normalization pipeline known as NLP2FHIR that mainly comprises: (1) a module for a core natural language processing (NLP) engine with an FHIR-based type system; (2) a module for integrating structured data; and (3) a module for content normalization. We evaluated the FHIR modeling capability focusing on core clinical resources such as Condition, Procedure, MedicationStatement (including Medication), and FamilyMemberHistory using Mayo Clinic's unstructured EHR data. We constructed a gold standard reusing annotation corpora from previous NLP projects.
resultsA total of 30 mapping rules, 62 normalization rules, and 11 NLP-specific FHIR extensions were created and implemented in the NLP2FHIR pipeline. The elements that need to integrate structured data from each clinical resource were identified. The performance of unstructured data modeling achieved
conclusionWe demonstrated that the NLP2FHIR pipeline is feasible for modeling unstructured EHR data and integrating structured elements into the model. The outcomes of this work provide standards-based tools of clinical data normalization that is indispensable for enabling portable EHR-driven phenotyping and large-scale data analytics, as well as useful insights for future developments of the FHIR specifications with regard to handling unstructured clinical data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.