Affiliation:
1. a modelEAU, Université Laval, Québec City, QC G1V 0A6, Canada
2. b Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
3. c European Commission, European Research Council, Joint Research Centre, Ispra, Italy
Abstract
Abstract
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.
Subject
Water Science and Technology,Environmental Engineering
Reference59 articles.
1. Abernathy C., Haddad I., Martin G., Mertic J. & Smith J. 2022 Starting an Open Source Project. Open Source Guide. Available from: https://www.linuxfoundation.org/resources/open-source-guides/starting-an-open-source-project (accessed 16 December 2022).
2. Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater
3. Population Normalization with Ammonium in Wastewater-Based Epidemiology: Application to Illicit Drug Monitoring
4. COVID-19 containment on a college campus via wastewater-based epidemiology, targeted clinical testing and an intervention
5. Big Life Lab 2022a Steering Group Members · Big-Life-Lab/PHES-ODM Wiki [WWW Document]. GitHub. Available from: https://github.com/Big-Life-Lab/PHES-ODM (accessed 23 December 2022).