Dose response models data formats¶
Dose response models¶
Dose response models are specified using three tables: the dose response models table holds the dose response model definitions (id, name, description) and other information about the dose response models. The dose response model benchmark doses table records the benchmark doses and (optionally) the model parameters for specific substances and covariates. The dose response model benchmark doses uncertainty table records results from bootstrap runs for the benchmark doses per substance/covariate combination.
Dose response models¶
Each dose response model has a unique id, a name (optional), and description (optional). Also, each dose response model is associated with a specific dose response experiment (idExperiment) from which the data used to create the model is obtained, a response (idResponse), one or more substances, and, optionally, specific covariates considered by the dose response model. The combination of the benchmark response type and the associated value define the benchmark response of the model. The dose unit specifies the unit used for the doses, and if applicable, the model equation can be specified.
Table aliases: DoseResponseModels, DoseResponseModel.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idDoseResponseModel |
AlphaNumeric(50) |
The unique identification code of the fitted dose response model. |
idDoseResponseModel, idModel |
Yes |
idExperiment |
AlphaNumeric(50) |
The identification code of the experiment from the dose response model. |
experimentCode, experimentId |
Yes |
Name |
AlphaNumeric(100) |
The name of the dose response model. |
Name |
No |
Description |
AlphaNumeric(200) |
Description of the dose response model. |
Description |
No |
Substances |
AlphaNumeric |
Code or comma separated list of the codes of the substances in the Dose Response Model. E.g., ‘Cyproconazole, Thiram’. |
Substances |
Yes |
idResponse |
AlphaNumeric |
The response of the dose response model. |
idResponse, Response |
Yes |
Covariates |
AlphaNumeric |
The covariates considered by the dose response model. |
Covariates, Covariate |
No |
BenchmarkResponse |
Numeric |
The value of the benchmark response or critical effect size. |
BenchmarkResponse, CriticalEffectSize, CES |
Yes |
BenchmarkResponseType |
BenchmarkResponseTypes | Specifies how the benchmark response is expressed. E.g., using a percent change in mean response or, for quantal response types, in terms of extra risk, additional risk, or ED50. |
BenchmarkResponseType, HazardEffectSizeType, CriticalEffectSizeType |
No |
LogLikelihood |
Numeric |
Loglikelihood of the model fit. |
LogLikelihood |
No |
DoseUnit |
AlphaNumeric(50) |
The dose unit (if not specified, then mg/kg is assumed). |
DoseUnit, UnitDose |
No |
ModelEquation |
AlphaNumeric(500) |
If available, the model equation of the dose response model (R model equation) or the identifier of the dose response model type. |
ModelEquation, DoseResponseModelEquation, Equation |
No |
Dose response model benchmark doses¶
The benchmark responses and benchmark doses belonging to the dose response models are recorded per substance/covariate in the dose response model benchmark doses table. Optionally, if the model equation of the dose response model has been specified in the dose response models table, the model parameter values for this specific substance/covariate can be specified here.
Table aliases: DoseResponseModelBenchmarkDoses.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idDoseResponseModel |
AlphaNumeric(50) |
The identification code of the dose response model to which this record belongs. |
idDoseResponseModel |
Yes |
idSubstance |
AlphaNumeric(50) |
The code of the substance. |
idSubstance, SubstanceId, SubstanceCode, Substance |
Yes |
Covariates |
AlphaNumeric(500) |
Comma separated list of the covariate values for which this benchmark dose applies. |
Covariates, Covariate |
No |
BenchmarkDose |
Numeric |
The (nominal) benchmark dose (BMD). |
BenchmarkDose, BMD, CED |
Yes |
BenchmarkDoseLower |
Numeric |
Benchmark dose lower uncertainty bound (BMDL). |
BenchmarkDoseLower, BMDL, CEDL |
No |
BenchmarkDoseUpper |
Numeric |
Benchmark dose upper uncertainty bound (BMDU). |
BenchmarkDoseUpper, BMDU, CEDU |
No |
ModelParameterValues |
AlphaNumeric(500) |
Parameter values for dose response models. |
ParameterValues |
No |
Dose response model benchmark dose bootstraps¶
Empirical uncertainty values of the benchmark benchmark doses of dose response models can be recorded in the dose response model benchmark doses bootstraps table. The uncertainty set identifier (idUncertaintySet) can be specified to retain correlations between uncertainty records that originate from the same bootstrap run.
Table aliases: DoseResponseModelBenchmarkDosesBootstraps, DoseResponseModelBenchmarkDosesUncertain.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idDoseResponseModel |
AlphaNumeric(50) |
The identification code of the dose response model to which this record belongs. |
idDoseResponseModel |
Yes |
idUncertaintySet |
AlphaNumeric(50) |
The uncertainty set identifier. |
idUncertaintySet, UncertaintyId |
Yes |
idSubstance |
AlphaNumeric(50) |
The code of the substance. |
idSubstance, SubstanceId, SubstanceCode, Substance |
Yes |
Covariates |
AlphaNumeric(500) |
Comma separated list of the covariate values for which this benchmark dose applies. |
Covariates |
No |
BenchmarkDose |
Numeric |
Benchmark dose (BMD). |
BenchmarkDose, BMD, CED |
Yes |