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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.

Key principles

Harmonized exchange format

The standard 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. For the complete set rules and guidelines, see the specification.

Built on established 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

A standard for model implementations

The standard applies to PBK model implementations, being the structural representations of models. It does not cover specific parameter values (e.g. of physiological parameters, partition coefficients) and dosing scenarios. This design ensures models remain flexible and reusable across different contexts.

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 the workflow presented below, enabling a connection between model developers and users:

  • Model developers create models using their preferred software, then convert to annotated FAIR PBK standard for publication.

  • 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).

FAIR PBK Workflow

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
  • About: Background and contributors