The critical care data exchange format: a proposed flexible data standard for combining clinical and high-frequency physiologic data in critical care. (29th June 2021)

• Record Type: Journal Article
• Authors: Laird, Philip; Wertz, Anthony; Welter, Gus; Maslove, David; Hamilton, Alexander; Heung Yoon, Joo; Lake, Douglas E; Zimmet, Amanda E; Bobko, Ryan; Randall Moorman, J; Pinsky, Michael R; Dubrawski, Artur; Clermont, Gilles
• Is Part Of: Physiological measurement. Volume 42:Number 6(2021)
• Publication Date: 2021-06-29
• Subjects: critical care -- ICU -- data science -- computation medicine -- physiological monitoring -- data sharing -- precision medicine; Physiology -- Measurement -- Periodicals; Patient monitoring -- Periodicals; 612
• DOI: 10.1088/1361-6579/abfc9b
• Languages: English
• ISSNs: 0967-3334

Abstract

Abstract: Objective. To develop a standardized format for exchanging clinical and physiologic data generated in the intensive care unit. Our goal was to develop a format that would accommodate the data collection pipelines of various sites but would not require dataset-specific schemas or ad-hoc tools for decoding and analysis. Approach. A number of centers had independently developed solutions for storing clinical and physiologic data using Hierarchical Data Format—Version 5 (HDF5), a well-supported standard already in use in multiple other fields. These individual solutions involved design choices that made the data difficult to share despite the underlying common framework. A collaborative process was used to form the basis of a proposed standard that would allow for interoperability and data sharing with common analysis tools. Main Results. We developed the HDF5-based critical care data exchange format which stores multiparametric data in an efficient, self-describing, hierarchical structure and supports real-time streaming and compression. In addition to cardiorespiratory and laboratory data, the format can, in future, accommodate other large datasets such as imaging and genomics. We demonstated the feasibility of a standardized format by converting data from three sites as well as the MIMIC III dataset. Significance. Individual approaches to the storage of multiparametric clinical data are proliferating, representing both a duplication of effort and a missed opportunity for collaboration. Adoption of a standardized format for clinical data exchange will enable the development of a digital biobank, facilitate the external validation of machine learning models and be a powerful tool for sharing multiparametric, high frequency patient level data in multisite clinical trials. Our proposed solution focuses on supporting standardized ontologies such as LOINC allowing easy reading of data regardless of the source and in so doing provides a useful method to integrate large amounts of existing data.