Specification
The FAIR PBK standard sets out rules for publishing PBK model code as digital objects to promote interoperability and reusability. These rules are described below.
File format
| ID | Rule | Description | Motivation |
|---|---|---|---|
| F01 | Use SBML L3 v2+ XML | PBK model implementations should be published in xml file format using the Systems Biology Markup Language (SBML) level 3 version 2 or higher. | Widely supported, machine-readable |
| F02 | Annotate model and elements with SBML annotation scheme | The model and model elements described by the SBML file should be annotated using the therefore available annotation scheme (see SBML specification). | Enables semantic clarity and interoperability |
| F03 | Specify units via SBML unit definitions | The units of the model and model elements described by the SBML file should specified using the therefore available system for unit definitions (see SBML specification). | Ensures consistency accross tools and prevents scaling/interpretation errors |
Model rules
| ID | Rule | Description | Motivation |
|---|---|---|---|
| G01 | No hardcoded dosing parameters | The PBK model implementation should NOT contain parameters specifying the dosing. These should be added via events in model simulations. | Enables modular interoperability, avoids hardcoded study-specific assumptions |
| M01 | Define time resolution with timeUnits | The time resolution of the model should be specified via the model-level timeUnits. | Enables syntactic clarity, ensures correct temporal interpretation |
| M02 | Define amounts via substanceUnits | The amounts unit of the model should be specified via the model-level substanceUnits. | Enables semantic consistency, prevents unit ambiguity |
| M03 | Define volumes via volumeUnits | The volume unit of the model should be specified via the model-level volumeUnits. | Enables semantic consistency, prevents unit ambiguity |
| M04 | Define extents via extentUnits | The extent unit of the model should be specified via the model-level extentUnits. | Enables semantic consistency, prevents unit ambiguity |
| M05 | Add MIRIAM BQM_HAS_TAXON annotation (species, NCBI Taxonomy) | The model should have at least one model-level BQM_HAS_TAXON MIRIAM annotation, specifying the animal species of the model using a NCBI Taxonomy identifier. | Enables semantic interoperability and cross-species integration |
| M06 | Add MIRIAM BQB_HAS_PROPERTY annotation (chemicals, ChEBI) | The chemical applicability domain of the model should be specified using the BQB_HAS_PROPERTY MIRIAM annotation, specifying the model chemical(s) a ChEBI identifier. | Ensures consistency, explicitly ties model to (classes of) chemical entities |
Compartments annotation
| ID | Rule | Description | Motivation |
|---|---|---|---|
| C01 | Assign volume units to compartments | All compartments should be assigned a unit representing a volume. | Enables syntactic clarity and quantitative scaling |
| C02 | Annotate with PBPK ontology (BQM_IS) | All compartments should have a BQM_IS MIRIAM element annotation linking them to a compartment of the PBPK ontology. | Enables semantic interoperability by mapping model compartments to shared ontology |
| C03 | Unique PBPKO class for each compartment | Each compartment should be associated with a different PBPKO compartment class. | Enables ontological clarity, prevents duplicate/misaligned semantics |
Species annotation
| ID | Rule | Description | Motivation |
|---|---|---|---|
| S01 | Assign amount units to species | All species should be assigned a unit representing an amount. | Enables numerical clarity, avoids ambiguous concentration vs. amount |
| S02 | Annotate with PBPK ontology (BQM_IS) | All species should have a BQM_IS MIRIAM element annotation linking them to a output parameter of the PBPK ontology. | Enables semantic clarity by linking to ontology-defined output parameter |
| S03 | Annotate with ChEBI chemical (BQB_IS) | All species should have a BQB_IS MIRIAM element annotation linking them to one of the ChEBI chemical identifiers defined for the model (see M06). | Enables semantic interoperability, ensures consistent chemical reference |
| S04 | Link species to a compartment | All species should be linked to a compartment. | Ensures structural clarity |
Parameter annotation
| ID | Rule | Description | Motivation |
|---|---|---|---|
| P01 | Assign units to parameters | All parameters should be assigned a unit. | Enables numerical consistency and prevents scaling errors |
| P02 | Annotate with PBPK ontology (BQM_IS) | All parameters should have a BQM_IS MIRIAM element annotation linking them to a parameter of the PBPK ontology. | Enables semantic clarity by linking to ontology-defined parameter type |
| P03 | Unique PBPKO class for each parameter | Each parameter should be associated with a different PBPKO parameter class. | Enables ontological clarity, avoids semantic overlap |
| P04 | Params in biochem/physicochem class must also have ChEBI (BQB_IS) | All parameter associated with a biochemical parameter or physicochemical parameter class of the PBPK ontology (see P02) should have a BQB_IS MIRIAM element annotation linking them to one of the ChEBI chemical identifiers defined for the model (see M06). | Enables semantic interoperability by connecting parameter to chemical identity |