“fhircrackr”: An R Package Unlocking Fast Healthcare Interoperability Resources for Statistical Analysis

Abstract

Background The growing interest in the secondary use of electronic health record (EHR) data has increased the number of new data integration and data sharing infrastructures. The present work has been developed in the context of the German Medical Informatics Initiative, where 29 university hospitals agreed to the usage of the Health Level Seven Fast Healthcare Interoperability Resources (FHIR) standard for their newly established data integration centers. This standard is optimized to describe and exchange medical data but less suitable for standard statistical analysis which mostly requires tabular data formats. Objectives The objective of this work is to establish a tool that makes FHIR data accessible for standard statistical analysis by providing means to retrieve and transform data from a FHIR server. The tool should be implemented in a programming environment known to most data analysts and offer functions with variable degrees of flexibility and automation catering to users with different levels of FHIR expertise. Methods We propose the fhircrackr framework, which allows downloading and flattening FHIR resources for data analysis. The framework supports different download and authentication protocols and gives the user full control over the data that is extracted from the FHIR resources and transformed into tables. We implemented it using the programming language R [1] and published it under the GPL-3 open source license. Results The framework was successfully applied to both publicly available test data and real-world data from several ongoing studies. While the processing of larger real-world data sets puts a considerable burden on computation time and memory consumption, those challenges can be attenuated with a number of suitable measures like parallelization and temporary storage mechanisms. Conclusion The fhircrackr R package provides an open source solution within an environment that is familiar to most data scientists and helps overcome the practical challenges that still hamper the usage of EHR data for research.

Arbeitsgruppe Interoperabilität: Kerndatensatz und Informationssysteme für Integration und Austausch von Daten in der Medizininformatik-Initiative

“…Für die Selektion wurden je nach Verfügbarkeit verschiedene Verfahren etabliert, u. a. FHIR Search [ 42 ] und HL7 Clinical Quality Language [ 43 ]. Zur Aufbereitung der selektierten und bereitgestellten FHIR-Daten für fachspezifische Analysen durch die Forscher:innen (u. a. mit SPSS [IBM Corporation, Armonk, NY, USA] oder R [The R Foundation, Wien, Österreich]) wurden neue Werkzeuge wie „fhircrackr“ entwickelt [ 44 ].…”

Pitfalls in Analyzing FHIR Data from Different University Hospitals

“…Making imports into statistical software complex. Consequently, a tool named fhircrackr 2 [4] for flattening the tree structure has been implemented.…”