ArticleGigaScience2022
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
What it found
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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
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 42 citations in OpenAlex.
- Pooled it
- Enriching Public Pathogen Genomic Records With Patient Metadata: Quantitative Study and Exploratory Case Analysis.JMIR bioinformatics and biotechnology · 2026Article
- Expanding the PHES-ODM: A Comprehensive, Open-Source Data Model for the Future of Wastewater-Based Epidemiology.Microorganisms · 2026Article
- High acceptability of a national platform for public health genomic data sharing and surveillance in Australia: a mixed methods study.BMC global and public health · 2026Article
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Methods for safely sharing dual-use genetic data.Frontiers in microbiology · 2026Article
- The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance.Microbial genomics · 2026Article
- A Metadata-Driven Framework for Strengthening Pathogen Genomics Lessons from SARS-CoV-2.medRxiv : the preprint server for health sciences · 2025Article
- Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.Cell genomics · 2025Review
- 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
- Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis.JMIR research protocols · 2025Article
- The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.Microbial genomics · 2024Article
- Precision public health in the era of genomics and big data.Nature medicine · 2024Review
- SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network.mSystems · 2024Article
- PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.Microbial genomics · 2024Article
- Article
- Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.Microbial genomics · 2023Article
- Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration.BMJ global health · 2023Article
- On the collection and integration of SARS-CoV-2 genome data.Biosafety and health · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
33 authors at 20 institutions in 16 countries.
Funding
Abstract
backgroundThe Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard.
resultsAs such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories.
conclusionsWell-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI's BioSample database.
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What OpenQuestion 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 OpenQuestion graph.