ArticleJAMIA open2022
OpenSep: a generalizable open source pipeline for SOFA score calculation and Sepsis-3 classification.
Article in JAMIA open, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Associations of Heart Rate Trajectories with Mortality and AKI Occurrence in Septic Patients: A Retrospective Study from MIMIC-IV and eICU Databases.Journal of clinical medicine · 2026Article
- Dexmedetomidine on supraventricular tachycardia in critical illness: a time-dependent propensity score matching study.Critical care (London, England) · 2026Article
- Impact of atherosclerotic cardiovascular disease on mortality in ICU sepsis patients: a retrospective MIMIC-IV cohort study.BMJ open · 2025Article
- Sepsis and septic shock case identification from electronic health records: an open-source workflow and comparison of cohorts by criteria.Critical care (London, England) · 2025Article
- Article
- External validation of the Epic sepsis predictive model in 2 county emergency departments.JAMIA open · 2024Article
- An optimal antibiotic selection framework for Sepsis patients using Artificial Intelligence.NPJ digital medicine · 2024Article
- Use of Inhaled Epoprostenol in Patients With COVID-19 Receiving Humidified, High-Flow Nasal Oxygen Is Associated With Progressive Respiratory Failure.CHEST critical care · 2023Article
- OpenSep: a generalizable open source pipeline for SOFA score calculation and Sepsis-3 classification.JAMIA open · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
EHR-based sepsis research often uses heterogeneous definitions of sepsis leading to poor generalizability and difficulty in comparing studies to each other. We have developed OpenSep, an open-source pipeline for sepsis phenotyping according to the Sepsis-3 definition, as well as determination of time of sepsis onset and SOFA scores. The Minimal Sepsis Data Model was developed alongside the pipeline to enable the execution of the pipeline to diverse sources of electronic health record data. The pipeline's accuracy was validated by applying it to the MIMIC-IV version 1.0 data and comparing sepsis onset and SOFA scores to those produced by the pipeline developed by the curators of MIMIC. We demonstrated high reliability between both the sepsis onsets and SOFA scores, however the use of the Minimal Sepsis Data model developed for this work allows our pipeline to be applied to more broadly to data sources beyond MIMIC.
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Registered trials
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