The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research


Background: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing segmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the "German Corona Consensus Dataset" (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data. Methods: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. Results: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, anamnesis, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. Conclusion: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.

Citation: medrxiv;2020.07.27.20162636v1,[Preprint]

Date Published: 29th Jul 2020

Registered Mode: by DOI

Authors: Julian Sass, Alexander Bartschke, Moritz Lehne, Andrea Essenwanger, Eugenia Rinaldi, Stefanie Rudolph, Kai Uwe Heitmann, Joerg Janne Vehreschild, Christof von Kalle, Sylvia Thun

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Sass, J., Bartschke, A., Lehne, M., Essenwanger, A., Rinaldi, E., Rudolph, S., … Thun, S. (2020, July 29). The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research. []. Cold Spring Harbor Laboratory.

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Created: 30th Jul 2020 at 18:09

Last updated: 30th Jul 2020 at 18:12

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