ArticleJournal of biomedical informatics2019
Facilitating phenotype transfer using a common data model.
Article in Journal of biomedical informatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05277116 (The Electronic Medical Records and GEnomics), which is not on this map. Cited by 50 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
The Electronic Medical Records and GEnomics (eMERGE) Network Genomic Risk Assessment
Who cites it
50 citing papers in PubMed.
- Computable phenotypes for research using real-world data: experiences from the NIH pragmatic trials collaboratory.JAMIA open · 2026Article
- Introducing the TOP framework: a novel phenotyping solution for collaborative phenotype algorithm development and application.Journal of biomedical semantics · 2026Article
- Extending the Observational Medical Outcomes Partnership Common Data Model to Support Observational Peripheral Vascular Disease Research.The Journal of surgical research · 2026Observational
- Linking Electronic Health Records for Multiple Sclerosis Research: Comparative Study of Deterministic, Probabilistic, and Machine Learning Linkage Methods.JMIR medical informatics · 2026Article
- A pipeline for enabling path-specific causal fairness in observational health data.Proceedings of the ... Conference on Fairness, Accountability, and Transparency · 2026Article
- CLEAR: A vision to support clinical evidence lifecycle with continuous learning.Journal of biomedical informatics · 2025Article
- Bariatric Surgery Is Associated With Reduced Incidence of Mild Cognitive Impairment and Alzheimer Disease and Related Dementias: A Retrospective Cohort Study.Annals of surgery open : perspectives of surgical history, education, and clinical approaches · 2025Article
- Digital Phenotyping of Rare Endocrine Diseases Across International Data Networks and the Effect of Granularity of Original Vocabulary.Yonsei medical journal · 2025Article
- Harmonizing population health data into OMOP common data model: a demonstration using COVID-19 sero-surveillance data from Nairobi Urban Health and Demographic Surveillance System.Frontiers in digital health · 2025Article
- Cardiovascular care with digital twin technology in the era of generative artificial intelligence.European heart journal · 2024Review
- A framework for sharing of clinical and genetic data for precision medicine applications.Nature medicine · 2024Article
- Towards cross-application model-agnostic federated cohort discovery.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- Using electronic health records for clinical pharmacology research: Challenges and considerations.Clinical and translational science · 2024Review
- Improving reporting standards for phenotyping algorithm in biomedical research: 5 fundamental dimensions.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- Conceptual design of a generic data harmonization process for OMOP common data model.BMC medical informatics and decision making · 2024Review
- A Novel Sentence Transformer-based Natural Language Processing Approach for Schema Mapping of Electronic Health Records to the OMOP Common Data Model.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Variation in Phenotype Definitions in Observational Clinical Research: A Review of Three Conditions.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Review
- Characterizing variability of electronic health record-driven phenotype definitions.Journal of the American Medical Informatics Association : JAMIA · 2023Article
- Translating and evaluating historic phenotyping algorithms using SNOMED CT.Journal of the American Medical Informatics Association : JAMIA · 2023Article
- Using Electronic Health Records for the Learning Health System: Creation of a Diabetes Research Registry.JMIR medical informatics · 2022Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
backgroundImplementing clinical phenotypes across a network is labor intensive and potentially error prone. Use of a common data model may facilitate the process.
methodsElectronic Medical Records and Genomics (eMERGE) sites implemented the Observational Health Data Sciences and Informatics (OHDSI) Observational Medical Outcomes Partnership (OMOP) Common Data Model across their electronic health record (EHR)-linked DNA biobanks. Two previously implemented eMERGE phenotypes were converted to OMOP and implemented across the network.
resultsIt was feasible to implement the common data model across sites, with laboratory data producing the greatest challenge due to local encoding. Sites were then able to execute the OMOP phenotype in less than one day, as opposed to weeks of effort to manually implement an eMERGE phenotype in their bespoke research EHR databases. Of the sites that could compare the current OMOP phenotype implementation with the original eMERGE phenotype implementation, specific agreement ranged from 100% to 43%, with disagreements due to the original phenotype, the OMOP phenotype, changes in data, and issues in the databases. Using the OMOP query as a standard comparison revealed differences in the original implementations despite starting from the same definitions, code lists, flowcharts, and pseudocode.
conclusionUsing a common data model can dramatically speed phenotype implementation at the cost of having to populate that data model, though this will produce a net benefit as the number of phenotype implementations increases. Inconsistencies among the implementations of the original queries point to a potential benefit of using a common data model so that actual phenotype code and logic can be shared, mitigating human error in reinterpretation of a narrative phenotype definition.
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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.