The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Autor: Gill IS; University of British Columbia, Vancouver, BC, Canada., Griffiths EJ; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Dooley D; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Cameron R; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Savić Kallesøe S; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., John NS; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Sehar A; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Gosal G; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Alexander D; Cadham Provincial Laboratory, Winnipeg, MB, Canada., Chapel M; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Croxen MA; Alberta Precision Labs, Edmonton, AB, Canada.; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada., Delisle B; Laboratoire de santé publique du Québec, Montréal, QC, Canada., Di Tullio R; Public Health Ontario Laboratory, Toronto, ON, Canada., Gaston D; Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada., Duggan A; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Guthrie JL; Public Health Ontario Laboratory, Toronto, ON, Canada., Horsman M; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Public Health Ontario Laboratory, Toronto, ON, Canada., Joshi E; Public Health Ontario Laboratory, Toronto, ON, Canada., Kearny L; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Knox N; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Lau L; The Hospital for Sick Children, Toronto, ON, Canada., LeBlanc JJ; Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada., Li V; Alberta Precision Labs, Edmonton, AB, Canada., Lyons P; Public Health Agency of Canada, Moncton, NB, Canada., MacKenzie K; Roy Romanow Provincial Laboratory, Regina, SK, Canada., McArthur AG; Michael G. DeGroote Institute for Infectious Disease Research & Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada., Panousis EM; Michael G. DeGroote Institute for Infectious Disease Research & Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada., Palmer J; Public Health Ontario Laboratory, Toronto, ON, Canada., Prystajecky N; University of British Columbia, Vancouver, BC, Canada.; BCCDC Public Health Laboratory, Vancouver, BC, Canada., Smith KN; Eastern Health, St. John's, NL, Canada., Tanner J; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Townend C; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Tyler A; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Van Domselaar G; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Hsiao WWL; University of British Columbia, Vancouver, BC, Canada.; Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Jazyk: angličtina
Zdroj: Microbial genomics [Microb Genom] 2023 Jan; Vol. 9 (1).
DOI: 10.1099/mgen.0.000908
Abstrakt: Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.
Databáze: MEDLINE