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Resources

FAIR enabling resources

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

  • SBML: Use of the Systems Biology Markup Language (SBML) as a harmonized publication and exchange format for PBK models, which should bridge the gap between the various different model implementation languages that are currently used by PBK model developers.
  • PBPK ontology: Use of the (currently being developed) PBPK ontology for annotation of all model elements (e.g., compartments, species, parameters).
  • ChEBI: Use of the ChEBI ontology for chemical identifiers to relate PBK model substance applicability domain, chemical species, and chemical-specific parameters to chemicals.
  • NCBI Taxonomy Database: Use of the NCBI Taxonomy Database to link the model applicability domain to controlled terminology for animal species.

FAIR PBK tools

The below list of tools supporting the FAIR PBK standard:

  • FAIR PBK Inspector: An online tool to help and annotating and validating SBML (or Antimony) PBK model implementations for compliance with the FAIR PBK standard.
  • SBML PBK Utils: A small Python package that contains utility functions for FAIR PBK model implementation in SBML. It provides a number of utility functions and classes for annotating, validating and running SBML PBK models.
  • SBML PBK Workflow: GitHub workflow for automated generation of annotated SBML files from Antimony PBK model implementations combined with annotations provided in CSV file annotations.

FAIR PBK models

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

  • EuroMix PBK re-implementation: FAIR PBK re-implementation of the EuroMix PBK model in Antimony.
  • PFAS PBK model: PFAS PBK model implementation in Antimony based on the PFOA and PFOS PBK model by Loccisano et al. (2011) and the subsequently modified version thereof by Westerhout et al. (2024).
  • FAIR PBK Demonstration models: A collection simple PBK model implementations in Antimony demonstrating how different modelling choices that are possible can be translated to PBK model implementations in Antimony.

Generic resources

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

  • SBMLutils: This python package provides convenient utilities for manipulation and annotation of SBML models. It also serves as a major source of inspiration of the SBML PBK Utils package, which is tailored to the sub-domain of PBK models.
  • libSBML: This python package provides the essential functionality for manipulating SBML models in python. For instance, for enriching SBML model implementations with annotations, units and descriptions of the model elements.