Kinetic models data formats
- Data tables:
Absorption factors
Kinetic model instances
Kinetic model instance parameters
Kinetic models are specified as kinetic model instances that contain parameter specifications of built in kinetic models or as simple absorption factors.
Kinetic model data format
The kinetic model data format specifies PBK model definitions and parameters.
Download empty dataset template:
Kinetic model instances
Kinetic model instances.
Accepted table names: KineticModelInstances, KineticModelInstance.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idModelInstance |
AlphaNumeric (50) |
Unique identification code of the kinetic model instance. |
idModelInstance, Id, Code |
Yes |
idModelDefinition |
KineticModelType |
Identifier of the kinetic model definition for which this is an instance. |
idModelDefinition, ModelDefinition |
Yes |
idTestSystem |
AlphaNumeric (50) |
The species on which the experiment was performed. |
System, TestSystem |
Yes |
Substances |
AlphaNumeric (150) |
Code or comma separated list of the codes of the substances. Unique identification code of substance, Default: valid for all substances. Should be omitted for parameters in the class Physiological |
idSubstance, idSubstances, SubstanceId, SubstanceCode, SubstanceCodes, Substance, Substances |
No |
Reference |
AlphaNumeric (100) |
Reference or author. |
References |
No |
Name |
AlphaNumeric (100) |
Name of the kinetic model instance. |
Name |
No |
Description |
AlphaNumeric (200) |
Additional description of the kinetic model instance. |
Description |
No |
Kinetic model instance parameters
Kinetic model parameters
Accepted table names: KineticModelInstanceParameters, KineticModelInstanceParameter.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idModelInstance |
AlphaNumeric (50) |
Unique identification code of the kinetic model instance to which this parameter belongs |
Id, Code |
Yes |
Parameter |
AlphaNumeric (50) |
Name of the parameter in the kinetic model. |
Yes |
|
Description |
AlphaNumeric (200) |
Description of or reference for the parameter values in the kinetic model. |
No |
|
Value |
Numeric |
Mean. |
MEAN, mean |
Yes |
DistributionType |
ProbabilityDistribution | Distribution. |
DistributionType, Distribution |
No |
CvVariability |
Numeric |
Variability. |
No |
|
CvUncertainty |
Numeric |
Uncertainty. |
No |
Kinetic absorption data format
The kinetic absorption factor data format specifies absorption factors.
Download empty dataset template:
Kinetic model absorption factors
Kinetic absorption factors
Accepted table names: KineticAbsorptionFactors, KineticAbsorptionFactor, AbsorptionFactors, AbsorptionFactor.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idCompound |
AlphaNumeric (50) |
code of substance (must correspond to values in id column of Substances table) |
idSubstance, SubstanceId, SubstanceCode, Substance |
No |
Route |
ExposurePathType | Non-dietary route or pathway, use ‘Oral’, ‘Dermal’, or ‘Inhalation’ to specify the route. |
Route, Pathway |
Yes |
AbsorptionFactor |
Numeric |
absorption factor value |
AbsorptionFactor, Factor |
Yes |
Kinetic conversion data format
The kinetic conversion factor data format specifies conversion factors.
Download empty dataset template:
Kinetic conversion factors
Kinetic conversion factors
Accepted table names: KineticConversionFactors, KineticConversionFactor.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idKineticConversionFactor |
AlphaNumeric (50) |
Id of the kinetic conversion factor |
idKineticConversionFactor, idConversionFactor, idKCFactor |
Yes |
idSubstanceFrom |
AlphaNumeric (50) |
Code of substance (must correspond to values in id column of Substances table) |
idSubstanceFrom, SubstanceIdFrom, SubstanceCodeFrom, SubstanceFrom |
Yes |
ExposureRouteFrom |
ExposureRoute | The exposure route (only applicable if target level is external). If not specified, Dietary is assumed. |
ExposureRoute |
No |
Biological matrix from |
BiologicalMatrix | If applicable, the source matrix of the human body (e.g., blood, urine) to convert from. When specified, the measurements are considered at the level of internal doses. |
MatrixSource, SourceMatrix |
No |
DoseUnitFrom |
DoseUnit | The unit of the substance dose to convert from. |
UnitSource, SourceUnit |
Yes |
ExpressionTypeFrom |
ExpressionType | The expression type or adjustment method of the dose unit (from). This field specifies how the dose unit (source) is adjusted, e.g. for blood lipids for fat soluble biomarkers (‘mg/g lipids’) or the dilution level of the urine (‘mg/g creatinine’). |
ExpressionTypeFrom, AdjustmentMethodFrom |
No |
idSubstanceTo |
AlphaNumeric (50) |
Code of substance (must correspond to values in id column of Substances table) |
idSubstanceTo, SubstanceIdTo, SubstanceCodeTo, SubstanceTo |
Yes |
ExposureRouteTo |
ExposureRoute | The exposure route (only applicable if target level is external) to convert to. If not specified, Dietary is assumed. |
ExposureRoute |
No |
Biological matrix to |
BiologicalMatrix | If applicable, the matrix of the human body (e.g., blood, urine) to convert to. When specified, the measurements are considered at the level of internal doses. |
MatrixTarget, TargetMatrix |
No |
DoseUnitTo |
DoseUnit | The unit of the substance dose to convert to. |
UnitTarget, TargetUnit |
Yes |
ExpressionTypeTo |
ExpressionType | The expression type or adjustment method of the dose unit (to). This field specifies how the dose unit (target) is adjusted, e.g. for blood lipids for fat soluble biomarkers (‘mg/g lipids’) or the dilution level of the urine (‘mg/g creatinine’). |
ExpressionTypeTo, AdjustmentMethodTo |
No |
ConversionFactor |
Numeric |
Conversion factor value |
ConversionFactor, Factor |
Yes |
UncertaintyDistributionType |
BiomarkerConversionDistribution | Distribution type (Uniform or LogNormal). If not specified, the conversion is assumed to be a constant factor. |
UncertaintyDistributionType, UncertaintyDistribution, DistributionType, Distribution |
No |
UncertaintyUpper |
Numeric |
The upper value of the distribution. If the distribution is uniform, then it is the upper bound of the uniform distribution. If the distribution is log-normal, then the upper value is assumed to correspond with the p95 percentile of the distribution. When a distribution is assumed, this value should be greater than the conversion factor. |
UncertaintyUpper, Upper |
No |
Kinetic conversion factor subgroups
Kinetic conversion factor subgroups.
Accepted table names: KineticConversionFactorSGs, KCFactorSubGroups.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idKineticConversionFactor |
AlphaNumeric (50) |
Id of the kinetic conversion factor |
idKineticConversionFactor, idConversionFactor, idKCFactor |
Yes |
ConversionFactor |
Numeric |
Conversion factor value |
ConversionFactor, Factor |
Yes |
AgeLower |
Numeric (50) |
Specifies the lower bound of the age interval (in years) of the kinetic conversion factor subgroup. Individuals belong to a subgroup when the age of the individual is equal or greater than the specified lower bound and smaller than the specified lower age of the next subgroup. |
AgeLower, LowerAge |
No |
Gender |
GenderType | The gender of the kinetic conversion factor subgroup. |
Gender, Sex |
No |
UncertaintyUpper |
Numeric |
The upper value of the distribution. If the distribution is uniform, then it is the upper bound of the uniform distribution. If the distribution is log-normal, then the upper value is assumed to correspond with the p95 percentile of the distribution. When a distribution is assumed, this value should be greater than the conversion factor. |
UncertaintyUpper, Upper |
No |