ArticleMicrobial genomics2023
The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Antibiotic-Specific Genotype-Phenotype Concordance and Cross-Database Interoperability in PublicInternational journal of molecular sciences · 2026Article
- Unlocking the Power of Data Harmonization in Environmental Health Sciences: A Comprehensive Exploration of Significance, Use Cases, and Recommendations for Standardization Efforts.Environmental health perspectives · 2026Review
- Toward a Common Set of Interface Requirements for Genomic Data Management: Scoping Review.Journal of medical Internet research · 2026Article
- Toward AI foundation models for epidemics: Promise, challenges, and paths forward.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Explainable machine learning of PROGRESS-Plus social factors predicts cognitive trajectories after traumatic brain injury.Scientific reports · 2026Article
- LinkML: an open data modeling framework.GigaScience · 2026Article
- The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance.Microbial genomics · 2026Article
- VIRUS-MVP: a framework for comprehensive surveillance of viral mutations and their functional impacts.NAR genomics and bioinformatics · 2025Article
- Communicating wastewater-based surveillance data to drive action.Journal of water and health · 2025Review
- Opening doors to physical sample tracking and attribution in Earth and environmental sciences.Scientific data · 2025Article
- Estimating the deferred value of pathogen genomic data for secondary use.Scientific data · 2025Article
- SARS-CoV-2 genomic contextual data harmonization: recommendations from a mixed methods analysis of COVID-19 case report forms across Canada.Archives of public health = Archives belges de sante publique · 2025Article
- The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.Microbial genomics · 2024Article
- Article
- A General Primer for Data Harmonization.Scientific data · 2024Article
- A General-Purpose Data Harmonization Framework: Supporting Reproducible and Scalable Data Integration in the RADx Data Hub.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.Journal of public health management and practice : JPHMPArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
35 authors.
Funding
Abstract
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.
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What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.