Standardized, machine-readable metadata for genomic surveillance of enteric microbial organisms
The Genomics for Food Safety (GenFS) Metadata Workgroup is a cross-agency collaboration involving the U.S. Department of Agriculture (USDA), Centers for Disease Control and Prevention (CDC), National Center for Biotechnology Information (NCBI), and Food and Drug Administration (FDA).
The workgroup’s goal is to expand and standardize contextual metadata for enteric pathogen surveillance and research in the United States—transitioning from predominantly free-text data to structured, machine-readable formats that support interoperability and advanced analysis.
The One Health Enteric Metadata Package was developed by integrating and extending:
This package is designed to comprehensively represent the full One Health sampling space for enteric microbes.
The package consists of:
A set of attributes applicable across all sample types, capturing general sample and isolate information.
(Sub-packages are domain-specific groupings of attributes tailored to particular sample types.)
Four domain-specific sub-packages covering major sampling contexts:
- Human and animal hosts
- Food samples
- Food production and processing environments
- Environmental sources (e.g., water, air, natural environments)
- Controlled vocabularies and ontology-backed terms
- Curated picklists for consistent data entry
- Defined attribute requirements and guidance
- Example use cases contributed by participating agencies
This package enables high-quality, structured metadata collection to support:
- Pathogen surveillance relevant to Food Safety
- Integration of genomic and contextual data
- Machine learning and advanced analytics
- Investigations of:
- Virulence and pathogenicity
- Environmental adaptation and stress tolerance
- Antimicrobial resistance
- Risk assessment
- Source attribution
- Download the latest full package or sub-packages from the Releases section of this repository.
- Select the sub-package(s) appropriate for your sample type.
- Use alongside submission workflows such as NCBI BioSample.
A generic submission template is also available via the NCBI BioSample Submission Portal:
https://submit.ncbi.nlm.nih.gov/biosample/template/
The metadata package is organized into:
- A core attribute set shared across all samples
- Four domain-specific sub-packages aligned to One Health sample types
Each sub-package includes:
- Attribute definitions
- Guidance and examples
- Requirement levels (e.g., required, recommended, optional)
Questions, suggestions, or proposed improvements can be submitted via the Issues page of this repository.
This work is a collaborative effort across USDA, CDC, NCBI, and FDA, with contributions from multiple domain experts supporting One Health data standardization.
This work is licensed under a Creative Commons Attribution 4.0 International License.
