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: Zipped CSV Excel

Kinetic model instances

Kinetic model instances.

Accepted table names: KineticModelInstances, KineticModelInstance.

Table 224 Table definition for Kinetic model instances.
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.

Table 225 Table definition for Kinetic model instance parameters .
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: Zipped CSV Excel

Kinetic model absorption factors

Kinetic absorption factors

Accepted table names: KineticAbsorptionFactors, KineticAbsorptionFactor, AbsorptionFactors, AbsorptionFactor.

Table 226 Table definition for Kinetic model absorption factors .
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: Zipped CSV Excel

Kinetic conversion factors

Kinetic conversion factors

Accepted table names: KineticConversionFactors, KineticConversionFactor.

Table 227 Table definition for Kinetic conversion factors.
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