Resources
The following resources provide the building blocks of the FAIR PBK standard.
Ontologies and standards
The FAIR PBK standard builds upon the following existing standards and ontologies.
| Resource | Description |
|---|---|
| ChEBI | Chemical Entities of Biological Interest - ontology for chemical identifiers. |
| NCBI Taxonomy | Database for controlled terminology of animal species. |
| PBPKO | Ontology for annotation of PBK model elements (compartments, species, parameters). |
| SBML | The Systems Biology Markup Language (SBML) is the selected harmonized exchange format for PBK models. |
FAIR PBK tools
Tools supporting development of PBK models compliant with the FAIR PBK standard.
| Resource | Description |
|---|---|
| FAIR PBK Inspector | Online tool for annotating Antimony and SBML PBK model implementations to make them compliant with the FAIR PBK standard. |
| SBML PBK Utils | Small Python package with utilities for annotating, validating, and running SBML PBK models. |
FAIR PBK models
Open source PBK models that are developed to comply with the FAIR PBK standard.
| Resource | Description |
|---|---|
| EuroMix PBK re-implementation | FAIR PBK re-implementation of the EuroMix PBK model in Antimony. |
| FAIR PBK demonstration models | Collection of small Antimony PBK example models illustrating different modelling choices and translations to PBK implementations. |
| PFAS PBK model | Antimony implementation of PFAS PBK kinetics based on the model presented by Westerhout et al. (2024). |
Generic tools and resources
Generic resources, not specific to the FAIR PBK standard, supporting development of (SBML) FAIR PBK models.
| Resource | Description |
|---|---|
| COPASI | A stand-alone software tool for simulation and analysis of biochemical model that supports models in the SBML standard. |
| libSBML (Python) | Official Python bindings for libSBML providing core functionality to create, manipulate, annotate, validate, and read/write SBML models. |
| SBMLutils (Python) | Python utilities for manipulation and annotation of SBML models; a major source of inspiration for the SBML PBK Utils package. |
| WebIridium | A web-based tool for simulation and analysis of (SBML/Antimony) biological models. |