Resources

FAIR enabling resources

The following resources provide the building blocks of the FAIR PBK standard.

Ontologies and standards

The FAIR PBK standard builds upon existing standards and ontologies.

Resource	Description
SBML	The Systems Biology Markup Language (SBML) is the selected harmonized exchange format for PBK models.
PBPKO	Ontology for annotation of PBK model elements (compartments, species, parameters).
ChEBI	Chemical Entities of Biological Interest: ontology for chemical identifiers.
NCBI Taxonomy	Database for controlled terminology of animal species.

FAIR PBK tools

The tools in the table below support development of PBK models compliant with the FAIR PBK standard.

Resource	Description
SBML PBK Utils	Small Python package with utilities for annotating, validating, and running SBML PBK models.
SBML PBK Workflow	GitHub Actions workflow to generate annotated SBML files from Antimony PBK implementations using CSV annotations.

FAIR PBK models

The table below lists open source PBK models that are developed to comply with the FAIR PBK standard.

Model	Description
EuroMix PBK re-implementation	FAIR PBK re‑implementation of the EuroMix PBK model in Antimony.
PFAS PBK model	Antimony implementation of PFAS PBK kinetics based on Loccisano et al. (2011) with subsequent modifications by Westerhout et al. (2024).
FAIR PBK Demonstration models	Collection of small Antimony PBK example models illustrating different modelling choices and translations to PBK implementations.

Generic tools and resources

The resources below are not specific to the FAIR PBK standard, but are more generic tools for the development of FAIR PBK models.

Resource	Description
SBMLutils (Python)	Python utilities for manipulation and annotation of SBML models; a major source of inspiration for the SBML PBK Utils package.
libSBML (Python)	Official Python bindings for libSBML providing core functionality to create, manipulate, annotate, validate, and read/write SBML models.