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@PHES-ODM

Public Health and Environmental Surveillance Open Data Model (PHES-ODM)

The PHES-ODM is an open science project of data standards & structures -and tools to support their use- for environmental surveillance of public health threats.

The Public Health Environmental Surveillance Open Data Model (PHES-ODM, or ODM)

Lifecycle: development License: CC BY 4.0

Description

PHES-ODM began as an open data model for wastewater-based surveillance of SARS-CoV-2. PHES-ODM Versions 2 & 3 expand the original ODM to include surface and air testing, in addition to water. These later versions allow for tracking of public health threats in any environment, and include robust support for reporting biologics, toxins, and/or other health risks.

The ODM strives to improve environmental and wastewater surveillance through interoperable data. The ODM follows an open science approach, including including FAIR Guiding Principles. People and institutions can contribute to the development of the ODM and the ODM seeks to support a wide range of users. As part of that mission, the ODM team have developed a suite of tools to support use and uptake of the model. Repositories for the tools can be found here, and include a validator, a sharing tool, a mapping tool, and a pipeline to transform PCR outputs directly into ODM.

Documentation and Citations

For the complete documentation for the model, please consult the documentation website. To cite the model, or read more scholarly accounts of its contruction and structure, please consult the paper published for version 2 of the model:

Therrien, J.-D., Thomson, M., Sion, E.-S., Lee, I., Maere, T., Nicolaï, N., Manuel, D. G., & Vanrolleghem, P. A. (2024). A comprehensive, open-source data model for wastewater-based epidemiology. Water Science and Technology, 89(1), 1–19. https://doi.org/10.2166/wst.2023.409

or the pre-print currently available on arXiv for version 3 of the model:

Thomson, M., Therrien, J.-D., Hizon, N., Lin, J., Wellman, M., Sion, E.-S., Bennett, C., Van Rolleghem, P., & Manuel, D. (2026). The Public Health and Environmental Surveillance Open Data Model (PHES-ODM) Version 3: An Open, Relational Data Model and Interoperability Framework for Wastewater Surveillance. 2604.18762. Preprint. arXiv, cs.DB. https://arxiv.org/abs/2604.18762.

Data and metadata dictionary

The ODM is comprised of 19 report tables and 7 look-up tables, linked to each other based on logic relationships. The following figure provides an overview of the different data sources that are currently captured.

Schematic representation of the ODM

Entity Relationship Diagram

The ODM is modular in its structure, and all tables are not mandatory. The structure is scalable as well to be only as complex as users need it to be, with much of the model existing optionally, but supporting all possible use-cases.

Artifacts List - See artifact list in asset list folder.

Acknowledgements

Development and maintenance of the ODM is the result of a collaboration between researchers from multiple institutions:

  • The University of Ottawa
  • CIHR Coronavirus Variants Rapid Response Network (CoVaRR-Net)
  • Project TEXAS, supported by the Canadian Institutes of Health Research (CIHR) under the framework of the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR)
  • Université Laval
  • CHEO Research Institute
  • modelEAU
  • CentrEau - Centre québécois de recherche sur la gestion de l'eau
  • Public Health Agency Canada
  • Ministry of Environment, Conservation, and Parks - MECP Ontario
  • European Comission Joint Research Centre
  • The Ottawa Hospital Research Institute

Popular repositories Loading

  1. PHES-ODM PHES-ODM Public

    The Public Health Environmental Surveillance Open Data Model (PHES-ODM, or ODM). A data model, dictionary and support tools for environmental surveillance.

    Python 57 18

  2. PHES-ODM-Validation PHES-ODM-Validation Public

    A toolkit to assist in validating whether data conforms to the PHES-ODM dictionary.

    Python 5

  3. PHES-ODM-Doc PHES-ODM-Doc Public

    The documentation website for Public Health Environmental Surveillance Open Data Model (PHES-ODM).

    R 2

  4. PHES-ODM-Map PHES-ODM-Map Public

    Transform data from various database formats to ODM.

    1

  5. PHES-ODM-sharing PHES-ODM-sharing Public

    Python

  6. .github .github Public

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