ArticleAMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science2018
Integrating Structured and Unstructured EHR Data Using an FHIR-based Type System: A Case Study with Medication Data.
Article in AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Electronic Health Record and Semantic Issues Using Fast Healthcare Interoperability Resources: Systematic Mapping Review.Journal of medical Internet research · 2024Pooled it
- The detectability paradox: bilingual medical report generation with open-weight models and the limits of human oversight.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- State-of-the-Art Fast Healthcare Interoperability Resources (FHIR)-Based Data Model and Structure Implementations: Systematic Scoping Review.JMIR medical informatics · 2024Article
- The IMPACT framework and implementation for accessible in silico clinical phenotyping in the digital era.NPJ digital medicine · 2023Review
- HL7 FHIR-based tools and initiatives to support clinical research: a scoping review.Journal of the American Medical Informatics Association : JAMIA · 2022Article
- Analyzing Patient Secure Messages Using a Fast Health Care Interoperability Resources (FIHR)-Based Data Model: Development and Topic Modeling Study.Journal of medical Internet research · 2021Article
- A corpus-driven standardization framework for encoding clinical problems with HL7 FHIR.Journal of biomedical informatics · 2020Article
- Ontologies, Knowledge Representation, and Machine Learning for Translational Research: Recent Contributions.Yearbook of medical informatics · 2020Article
- Developing an FHIR-Based Computational Pipeline for Automatic Population of Case Report Forms for Colorectal Cancer Clinical Trials Using Electronic Health Records.JCO clinical cancer informatics · 2020Article
- Article
- The development and electronic delivery of case-based learning using a fast healthcare interoperability resource system.JAMIA open · 2019Article
- Developing a FHIR-based EHR phenotyping framework: A case study for identification of patients with obesity and multiple comorbidities from discharge summaries.Journal of biomedical informatics · 2019Article
- Clinical Workflow and Substance Use Screening, Brief Intervention, and Referral to Treatment Data in the Electronic Health Records: A National Drug Abuse Treatment Clinical Trials Network Study.EGEMS (Washington, DC) · 2019Article
- Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2018Article
- Integration of NLP2FHIR Representation with Deep Learning Models for EHR Phenotyping: A Pilot Study on Obesity Datasets.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational ScienceArticle
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Standards-based modeling of electronic health records (EHR) data holds great significance for data interoperability and large-scale usage. Integration of unstructured data into a standard data model, however, poses unique challenges partially due to heterogeneous type systems used in existing clinical NLP systems. We introduce a scalable and standards-based framework for integrating structured and unstructured EHR data leveraging the HL7 Fast Healthcare Interoperability Resources (FHIR) specification. We implemented a clinical NLP pipeline enhanced with an FHIR-based type system and performed a case study using medication data from Mayo Clinic's EHR. Two UIMA-based NLP tools known as MedXN and MedTime were integrated in the pipeline to extract FHIR MedicationStatement resources and related attributes from unstructured medication lists. We developed a rule-based approach for assigning the NLP output types to the FHIR elements represented in the type system, whereas we investigated the FHIR elements belonging to the source of the structured EMR data. We used the FHIR resource "MedicationStatement" as an example to illustrate our integration framework and methods. For evaluation, we manually annotated FHIR elements in 166 medication statements from 14 clinical notes generated by Mayo Clinic in the course of patient care, and used standard performance measures (precision, recall and f-measure). The F-scores achieved ranged from 0.73 to 0.99 for the various FHIR element representations. The results demonstrated that our framework based on the FHIR type system is feasible for normalizing and integrating both structured and unstructured EHR data.
Identifiers
29888045PMC5961797What OpenQuestion holds
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.