EpiJSON: A unified data-format for epidemiology

Thomas J.R. Finnie*, Andy South, Ana Bento, Ellie Sherrard-Smith, Thibaut Jombart

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)

Abstract

Epidemiology relies on data but the divergent ways data are recorded and transferred, both within and between outbreaks, and the expanding range of data-types are creating an increasingly complex problem for the discipline. There is a need for a consistent, interpretable and precise way to transfer data while maintaining its fidelity. We introduce 'EpiJSON', a new, flexible, and standards-compliant format for the interchange of epidemiological data using JavaScript Object Notation. This format is designed to enable the widest range of epidemiological data to be unambiguously held and transferred between people, software and institutions. In this paper, we provide a full description of the format and a discussion of the design decisions made. We introduce a schema enabling automatic checks of the validity of data stored as EpiJSON, which can serve as a basis for the development of additional tools. In addition, we also present the R package 'repijson' which provides conversion tools between this format, line-list data and pre-existing analysis tools. An example is given to illustrate how EpiJSON can be used to store line list data. EpiJSON, designed around modern standards for interchange of information on the internet, is simple to implement, read and check. As such, it provides an ideal new standard for epidemiological, and other, data transfer to the fast-growing open-source platform for the analysis of disease outbreaks.

Original languageEnglish
Pages (from-to)20-26
Number of pages7
JournalEpidemics
Volume15
DOIs
Publication statusPublished - 1 Jun 2016

Bibliographical note

Funding Information:
EpiJSON was created during “ Hackout 2: Graphical Resources for Infectious Disease Epidemiology in R ” ( https://sites.google.com/site/hackout2/ ), an event funded by the Medical Research Council (MRC) Centre for Outbreak Analysis and Modelling and the National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) for Modelling Methodology ( NIHR-HPRU-2012-100-80 ). We thank Neil Ferguson, Zak Kadrou and Susannah Fisher for their invaluable help hosting and organising this event. TJ is funded by MRC and NIHR . AS is partly funded by the Liverpool School of Tropical Medicine .

Funding Information:
EpiJSON was created during “Hackout 2: Graphical Resources for Infectious Disease Epidemiology in R” (https://sites.google.com/site/hackout2/), an event funded by the Medical Research Council (MRC) Centre for Outbreak Analysis and Modelling and the National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) for Modelling Methodology (NIHR-HPRU-2012-100-80). We thank Neil Ferguson, Zak Kadrou and Susannah Fisher for their invaluable help hosting and organising this event. TJ is funded by MRC and NIHR. AS is partly funded by the Liverpool School of Tropical Medicine. This work has been partially funded by the EC Research Executive Agency in the 7th Framework Programme, (SEC-2013.4.1-4: Development of decision support tools for improving preparedness and response of Health Services involved in emergency situations) under grant number FP7-SEC-2013–608078—IMproving Preparedness and Response of HEalth Services in major criseS (IMPRESS).TF would like to thank Tomasz Zatorski and Matthew Bull for their technical advice and sensible suggestions and Ian Hall and Steve Leach for their support of this work.We would also like to thank the two anonymous reviewers whose constructive comments helped to strengthen this manuscript.

Funding Information:
This work has been partially funded by the EC Research Executive Agency in the 7th Framework Programme, (SEC-2013.4.1-4: Development of decision support tools for improving preparedness and response of Health Services involved in emergency situations) under grant number FP7-SEC-2013–608078—IMproving Preparedness and Response of HEalth Services in major criseS (IMPRESS).

Publisher Copyright:
© 2016 .

Keywords

  • Communications standards
  • Databases
  • Epidemics
  • Outbreaks
  • Software

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