Water Science and Technology (Jan 2024)

A comprehensive, open-source data model for wastewater-based epidemiology

  • Jean-David Therrien,
  • Mathew Thomson,
  • Eugen-Sorin Sion,
  • Ivan Lee,
  • Thomas Maere,
  • Niels Nicolaï,
  • Douglas G. Manuel,
  • Peter A. Vanrolleghem

DOI
https://doi.org/10.2166/wst.2023.409
Journal volume & issue
Vol. 89, no. 1
pp. 1 – 19

Abstract

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The recent SARS-COV-2 pandemic has sparked the adoption of wastewater-based epidemiology (WBE) as a low-cost way to monitor the health of populations. In parallel, the pandemic has encouraged researchers to openly share their data to serve the public better and accelerate science. However, environmental surveillance data are highly dependent on context and are difficult to interpret meaningfully across sites. This paper presents the second iteration of the Public Health Environmental Surveillance Open Data Model (PHES-ODM), an open-source dictionary and set of data tools to enhance the interoperability of environmental surveillance data and enable the storage of contextual (meta)data. The data model describes how to store environmental surveillance program data, metadata about measurements taken on various specimens (water, air, surfaces, sites, populations) and data about measurement protocols. The model provides software tools that support the collection and use of PHES-ODM formatted data, including performing PCR calculations and data validation, recording data into input templates, generating wide tables for analysis, and producing SQL database definitions. Fully open-source and already adopted by institutions in Canada, the European Union, and other countries, the PHES-ODM provides a path forward for creating robust, interoperable, open datasets for environmental public health surveillance for SARS-CoV-2 and beyond. HIGHLIGHTS The PHES-ODM supports the collection, storage, and use of environmental public health data.; The PHES-ODM defines a standardized dictionary to describe environmental surveillance programs.; The PHES-ODM provides metadata attributes to facilitate the interpretation of various data, including sampling, protocols, and geolocation.; The PHES-ODM supports open-science principles, allowing its use as a platform for additional software to facilitate data entry, validation and sharing.;

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