ArticleJournal of the American Medical Informatics Association : JAMIA2023
Scalable and interpretable alternative to chart review for phenotype evaluation using standardized structured data from electronic health records.
Article in Journal of the American Medical Informatics Association : JAMIA, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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The trial behind it
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
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review of Algorithms for Identifying Pediatric Neurodevelopmental Outcomes.Pharmacoepidemiology and drug safety · 2025Pooled it
- A comparison of Fast Healthcare Interoperability Resources and Observational Medical Mutcomes Partnership electronic health record data within the All of Us Research Program.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- Ten-Year Risk of Primary Malignant Brain Tumors After Buprenorphine vs Naltrexone Exposure: A Retrospective Cohort Study Using the Epic Cosmos Database.medRxiv : the preprint server for health sciences · 2026Article
- RadAnnotate: Large Language Models for Efficient and Reliable Radiology Report Annotation.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2026Article
- Signal Fidelity Index-aware calibration for addressing distributional shift in predictive modeling across heterogeneous real-world data.Scientific reports · 2025Article
- Confidence-linked and uncertainty-based staged framework for phenotype validation using large language models.Journal of the American Medical Informatics Association : JAMIA · 2025Article
- Parkinsonism in Alzheimer's disease without Lewy bodies in association with nigral neuron loss: A data-driven clinicopathologic study.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Inductive reasoning with large language models: A simulated randomized controlled trial for epilepsy.Epilepsy research · 2025Article
- Standardized patient profile review using large language models for case adjudication in observational research.NPJ digital medicine · 2025Article
- A Standardized Guideline for Assessing Extracted Electronic Health Records Cohorts: A Scoping Review.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2025Article
- Inductive reasoning with large language models: a simulated randomized controlled trial for epilepsy.medRxiv : the preprint server for health sciences · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
objectivesChart review as the current gold standard for phenotype evaluation cannot support observational research on electronic health records and claims data sources at scale. We aimed to evaluate the ability of structured data to support efficient and interpretable phenotype evaluation as an alternative to chart review. MATERIALS AND
methodsWe developed Knowledge-Enhanced Electronic Profile Review (KEEPER) as a phenotype evaluation tool that extracts patient's structured data elements relevant to a phenotype and presents them in a standardized fashion following clinical reasoning principles. We evaluated its performance (interrater agreement, intermethod agreement, accuracy, and review time) compared to manual chart review for 4 conditions using randomized 2-period, 2-sequence crossover design.
resultsCase ascertainment with KEEPER was twice as fast compared to manual chart review. 88.1% of the patients were classified concordantly using charts and KEEPER, but agreement varied depending on the condition. Missing data and differences in interpretation accounted for most of the discrepancies. Pairs of clinicians agreed in case ascertainment in 91.2% of the cases when using KEEPER compared to 76.3% when using charts. Patient classification aligned with the gold standard in 88.1% and 86.9% of the cases respectively.
conclusionStructured data can be used for efficient and interpretable phenotype evaluation if they are limited to relevant subset and organized according to the clinical reasoning principles. A system that implements these principles can achieve noninferior performance compared to chart review at a fraction of time.
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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.