FAIR BioHeaders
Reference genomes · Metadata · Provenance
Keep the context.
Carry it with the genome.
FAIR BioHeaders builds an open standard, the FAIR Header Reference genome (FHR), that keeps reference genome metadata and provenance close to sequence data — helping researchers identify the reference used in an analysis and retain the information needed to reproduce it.
About the project
FAIR BioHeaders grew out of a problem described in the FHR standard paper: reference genomes are shared across platforms, repositories, and analyses, but the metadata and provenance that make them interpretable rarely travel with the files. Without that context, cross-platform analysis stalls and data provenance is lost. We build standards and tools that keep that context close to the data so an analysis can be understood and reproduced long after it was run.
What we value
- Provenance travels with the data. Metadata lives alongside the sequence, not in a separate document that can drift away from it.
- Minimal disruption. FHR fits into existing workflows — metadata in FASTA comments and companion representations — so adopting it does not require rebuilding a pipeline.
- FAIR and TRUST. The standard is guided by Findability, Accessibility, Interoperability, and Reuse (FAIR) together with Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST).
- Extensible and expressive. A small set of required fields keeps implementation easy while allowing projects to record more when they need it.
- Low barrier to adoption. Few dependencies and a small codebase make the standard and its tooling straightforward to use and maintain.
How our work fits together with others
Publications we’ve had a part in approach these ideas from different angles:
- Naming — Guidelines for gene and genome assembly nomenclature proposes conventions so assemblies can be identified and linked across datasets and resources.
- Reporting — Toward standardization in arthropod and biodiversity genome projects surveys genome projects and documents the gaps in sample, assembly, quality, and submission reporting that FHR helps close.
- Discovery — AgBioDatabase Finder helps researchers find where data can be deposited and discovered, complementing the metadata carried with the files.
- Community — The future is FAIR places FHR within the wider AgBioData effort to make genomic data easier to discover, integrate, and reuse.
DNA · Structure
Why the hexagon?
Our hexagon comes from the six-membered rings in all four DNA bases: thymine, cytosine, guanine, and adenine. Thymine and cytosine each have one six-membered ring; adenine and guanine have a six-membered ring fused to a five-membered ring.
Patterns in honeycomb, insect eggs, turtle shells, and fruit echo this motif across biodiversity. Explore the structure of DNA.
Use the standard
- Read the FHR specification for metadata fields and schemas.
- Use the FHR file converter to work with supported representations.
- Explore the Nextflow workflows for pipeline integration.
Resources and citation guidance collect the maintained repositories and archive links.
About Us
FAIR BioHeaders is developed and maintained by:
Adam Wright
Software Architect, Ontario Institute for Cancer Research
Adam Wright is a software architect in the Adaptive Oncology Program at the Ontario Institute for Cancer Research, where he has worked since 2012. He builds data infrastructure and curation tooling for genomic resources such as Reactome, WormBase, and the Alliance of Genome Resources, with a focus on making biological data interoperable and reusable. He is a co-author of the FHR standard.
David Molik
Department Head and Associate Professor, Open Publishing Exchange, Kansas State University Libraries
David Molik leads the Open Publishing Exchange and is an associate professor at Kansas State University Libraries. His work spans scholarly communication, research cyberinfrastructure, FAIR and AI-ready data, persistent identifiers, computational reproducibility, and data publishing, and he contributes to agricultural and biodiversity informatics through AgBioData, i5k, and related initiatives. He previously worked as a computational biologist at the USDA Agricultural Research Service and holds a Ph.D. from the University of Notre Dame. He is a co-author of the FHR standard.
Get involved
Visit the FAIR BioHeaders GitHub organization to explore the code and documentation. Report website problems in the website issue tracker; questions about the standard or converters belong in their respective repositories.