This repository includes:
- A relational dictionary that captures wastewater based surveillance data and metadata. It consists of 150+ variables categorized in 10 tables. Both English and French versions are supported;
- Documentation describing how to use the data model;
- Template files that can be used to record data in the ODM format;
- Scripts to set up a relational database according to the ODM schema.
Wastewater-based surveillance (WBS) of SARS-CoV-2 is developing and expanding rapidly during the current COVID-19 pandemic. WBS has demonstrated itself as valuable public health tool with an increasing number of municipalities that have identified new SARS-CoV-2 transmission using wastewater testing prior to clinical testing. Wastewater testing has also identified new surges and waves that has informed early public health response. Internationally, there are over 2000 testing sites in over 50 countries.
WBS has a history informing public health action through its use to monitor health threats such as polio, antimicrobial resistance, as well as illicit drugs, among others. However, as a surveillance tool for pandemic purposes, the program is relatively new and there are implementation gaps. Currently, there is little to no controlled vocabulary on how WBS results should ideally be reported. Hence, the idea of a WBS data model that captures all relevant fields that should ideally be reported on when sharing WBS data.
The ODM strives to improve wastewater surveillance through the development of an open data structure, including metadata and vocabulary. OMD operates under the guidance of an international steering committee. Working groups can be ongoing or created to address specific tasks and projects. Note that we adhere to the FAIR Guiding Principles with recognition of benefit from a common data structure, including metadata and vocabulary.
See metadata for variable names and definitions. Cliquez ici pour la version française.
Issues, suggestions and pull requests are welcomed. contributing for more information.
- GH issues or email [email protected].
- Code of conduct.
- Follow the
devbranch for upcoming changes. Also follow version changes in issues, discussions, and projects.
Institues across Canada and worldwide have adopted the ODM to structure SARS-CoV-2 WBS data. Programs that use the ODM include Canada's National Microbiology Laboratory (NML), Ontario's Wastewater Initiative by the Ministry of Environment, Conservation, and Parks (MECP), uOttawa, le Centre québécois de recherche sur la gestion de l'eau, Université Laval, and CETO Epidemiologic platform.
A dashboard using the Ottawa data can be found at: 613covid.ca. The CentrEau webpage host the dashboard for the province of Québec.
- data validation;
- data cleaning and data transformation;
- data visualization;
- data modelling;
See roadmap for more details.
Working group members maintain other repositories with tools that use the OMD, including:
- data visualization.
- methods to convert Excel tables that are not in ODM format into ODM data frame.
Website content is published under a Creative Commons CC BY 4.0 license, which requires users to attribute the source and license type (CC BY 4.0) when sharing our data or website content.
See license for more information.
Development and maintenance of the ODM is the result of a collaboration between researchers from multiple institutions:
- uOttawa
- Université Laval
- The Ottawa Hospital
- Ottawa Public Health
- 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
- Coronavirus Variants Rapid Response Network (CoVaRR-Net)
Nicolaï N., Therrien J.-D., Maere. T, Pileggi V., Swerdfeger H., Vanrolleghem P.A., Manuel D. (2021) Open Data Model for collecting, quality-ensuring and sharing of SARS-CoV-2 data and metadata, EU4S Sewage Sentinel System for SARS CoV-2 - 5th Town Hall Meeting, e-poster, https://api.ltb.io/show/ABCWX