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FAIR PBK Standard

The FAIR PBK standard is an open exchange standard for representing physiologically based kinetic (PBK) models. It promotes interoperability and reusability by providing a harmonized format for sharing models consistently across software platforms, modeling environments, and application domains.

Harmonized exchange format for model implementations

The standard applies to PBK model implementations, being the structural representations of models. It prescribes the use of Systems Biology Markup Language (SBML) as the core exchange format, combined with specific rules for model implementation, unit specification, and semantic annotation. The standard intentionally avoids defining specific parameter values (e.g. of physiological parameters, partition coefficients) and dosing scenarios. This ensures that models remain flexible and reusable across different contexts. For the complete set rules and guidelines, see the specification.

Built on established resources

The FAIR PBK standard builds on the the following resources:

  • SBML: Core markup language for biological models
  • PBPKO Ontology: Domain-specific annotations for PBK model elements
  • ChEBI: Chemical identifiers and ontology
  • NCBI Taxonomy: Species classification

FAIR aligned workflow

The standard recognizes that PBK model developers use diverse tools and languages. Rather than replacing existing practices, it provides a consistent framework for publishing models, making them easier to find, interpret, and reuse.

The standard is designed to support a workflow in which model developers create models using their preferred software, then convert to annotated FAIR PBK standard for publication, and model users discover interoperable models through repositories and integrate them into their own environments.

While focusing on interoperability and reusability, the FAIR PBK standard complements broader FAIR principles. It can be integrated into comprehensive FAIR specifications or implementation profiles (see Use in FIP).

Get Started

  • Full specification: Complete rules and guidelines
  • Use in FIP: Illustration of the use of the standard in a FAIR implementation profile (FIP)
  • Resources: Tools, examples, and references

Contributing

Contributions to both the standard and its documentation are welcome! There are several ways you can support the project:

  • Star the repository - Help increase the project's visibility and reach more people by starring the repository.
  • Open issues and join discussions - Help shape the standard by reporting issues, proposing improvements, or contributing feedback and ideas to existing issues in the project's issue tracker.
  • Develop and publish models compliant with the standard - Use the standard to develop FAIR PBK models and share them in the resources page.
  • Develop tools and software supporting the standard - Build and contribute to tools, software, and integrations that enable the creation, validation, exchange, and use of PBK models compliant with the standard, and share them on the resources page.

Reference

For more extensive information, please refer to the article below:

Kruisselbrink, J., Minnema, J., Deepika, D., Kumar, S., Sharma, S., Gastellu, T., Vogs, C., Westerhout, J., Karakoltzidis, A., Tollefsen, K.E., Zwartsen, A., Palm, M., van Klaveren, J., Ratier, A., Kumar, V., & Engel, J. (2026). An exchange standard for FAIR PBK models in chemical risk assessment - A PARC community effort. Computational Toxicology, 0, 100426. https://doi.org/10.1016/j.comtox.2026.100426