Dose response data data formats¶
The meta-data of dose response experiments (such as name, description, etc.) are specified in the DoseResponseExperiments table.
For presenting the data of these experiments to the system, there are two formats: a single table format (DoseResponseData) and a relational data format (three tables DoseResponseExperimentDoses, ExperimentalUnitProperties, DoseResponseExperimentMeasurements). Usually, the single table format will be the easier one. For internal use in MCRA, this single table data is converted to the relational data format.
Dose response data¶
Dose response data are used to extract assessment group membership or hazard doses . The meta-data of dose response experiments (such as name, description, etc.) are specified in the DoseResponseExperiments table. For presenting the data of these experiments to the system, there are two formats: a single table format (DoseResponseData) and a relational data format (three tables). Usually, the single table format will be the easier one. For internal use in MCRA, this single table data is converted to the relational data format.
Dose response experiments¶
General information about the dose response experiments, such as the (unique) identifier, name, description, the used test-system, and the dose unit is stored in the table DoseResponseExperiments. If the data of an experiment is provided in a single table format, then the fields Time, Covariates, Substances, and Responses are used to map the column header names of the columns of the single data table to these their respective types.
Table aliases: DoseResponseExperiments, DoseResponseExperiment.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idExperiment |
AlphaNumeric(50) |
Unique identification code of the dose effect experiment. |
idExperiment, Id, Code |
Yes |
Name |
AlphaNumeric(100) |
Name of the dose effect experiment. |
Name |
No |
Description |
AlphaNumeric(200) |
Description of the dose effect experiment. |
Description |
No |
Date |
DateTime |
The starting date of the experiment. |
Date |
No |
Reference |
AlphaNumeric(200) |
External reference, for instance, to the experiment protocol and/or supporting material. |
Reference |
No |
ExperimentalUnit |
AlphaNumeric(100) |
The name of the experimental unit of the experiment, e.g., rat, cage, litter, vial, cup, petridish. |
ExperimentalUnit |
No |
DoseRoute |
AlphaNumeric(100) |
For in-vivo test systems, the route in which the dose was administered |
DoseRoute |
No |
Substances |
AlphaNumeric |
Code or comma separated list of the codes of the substances measured in the experiment. E.g., ‘Cyproconazole, Thiram’. Required when presenting the dose-response data in a single table. Make sure that in table DoseResponseData the column headers exactly match these names. |
idSubstance, SubstanceId, SubstanceCode, Substance, idSubstances, SubstanceIds, SubstanceCodes, Substances |
Yes |
DoseUnit |
DoseUnits | Unit of the doses administered in this experiment. |
DoseUnit |
Yes |
Responses |
AlphaNumeric |
Code or comma separated list of codes of the responses measured in the experiment. E.g., ‘AngleM_PQ, Mortality’. Required when presenting the dose-response data in a single table. Make sure that in table DoseResponseData the column headers exactly match these names. |
Responses, Response, idResponses, idResponse |
Yes |
Time |
AlphaNumeric(100) |
Identifier of the time field of the experiment. Required when presenting the dose-response data in a single table and responses are measured at multiple times. Make sure that in the table DoseResponseData the column header of the time-column exactly matches this name. |
Time, Times |
No |
TimeUnit |
TimeUnit |
Unit of the time scale used in the experiments. |
TimeUnit |
No |
Covariates |
AlphaNumeric(200) |
Comma separated list of the names/codes of the covariates of the experiment. E.g. ‘Gender, Inhibitor, GroupingVariable’. Required when presenting the dose-response data in a single table and there are relevant covariates. Make sure that in table DoseResponseData the column headers exactly match these names. |
Covariates, Covariate |
No |
Dose response data¶
Single (two-way) table data format for specifying data of dose response experiments (as alternative for the relational format). The column headers are dynamic and should be defined in the table DoseResponseExperiments through fields Substances and Responses (and, optionally, Covariates and Time). For responses given as aggregated statistics, also SD, CV, N and Uncertainty are specified as [Datatype:Response]. E.g., ‘SD:Y’, ‘CV:Y’, ‘N:Y’. Uncertainty upper 95%limits are specified as ‘UncertaintyUpper:Y’. For each quantal response an additional column ‘N:[responsename]’is required with binomial totals (e.g. Mortality = 3, N:Mortality = 10).
Table aliases: TwoWayDoseResponseData, DoseResponseDataTwoWay, DoseResponseData.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idExperiment |
AlphaNumeric(50) |
Unique identification code of the dose effect experiment. |
idExperiment, Experiment, Code |
No |
Experimental unit |
AlphaNumeric(50) |
Experimental unit numbers or identifiers. The column name of the experimental unit should be as specified in the dose response experiment record. |
ExperimentalUnit, ExperimentalUnits, Experimental unit |
No |
Substance(s) |
AlphaNumeric(100) |
One or more columns with doses for each substance, in the unit as specified in the dose response experiment table. The column name(s) should match the substance codes listed in the comma-separated list of the substances field of the dose response experiment record. |
Yes |
|
Response(s) |
AlphaNumeric(100) |
One or more columns with results for each response, in the unit(s) as specified in the dose response experiment table. The column name(s) should match the response codes listed in the comma-separated list of the responses field of the dose response experiment record. |
Yes |
|
Time |
Numeric |
The column containing the observed response times. The column name (header) should match that of the Time column in the dose response experiment record. |
No |
|
Covariate(s) |
AlphaNumeric(100) |
The column(s) containing additional properties of the experimental unit. The column name (header) should match the codes of the comma-separated covariates list in the dose response experiment record. |
No |
Relational dose response data¶
In the relational data format, dose response experiment data are specified using the triplet of tables: DoseResponseExperimentDoses, DoseResponseExperimentMeasurements, and ExperimentalUnitProperties. These tables describe, respectively, the experiment designs (including the administered substance doses), the response measurements, and additional properties of the experimental units of the experiment.
Dose response experiment doses¶
The table DoseResponseExperimentDoses describes the experiment design, being a complete specification of which doses of which substances were applied to which experimental unit and if relevant at what time.
Table aliases: DoseResponseExperimentDoses, DoseResponseExperimentDose.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idExperiment |
AlphaNumeric(50) |
Identification code of the experiment to which this design record belongs. |
idExperiment, Experiment |
Yes |
idExperimentalUnit |
AlphaNumeric(50) |
Identification code of the experimental unit to which the dose is applied. |
idExperimentalUnit, ExperimentalUnit |
Yes |
Time |
Numeric |
The time of administration of the dose. |
Time |
No |
idSubstance |
AlphaNumeric(50) |
Code of the substance that was administered. |
idSubstance, SubstanceId, SubstanceCode, Substance |
Yes |
Dose |
Numeric |
The dose that was administered. |
Dose |
Yes |
Experimental unit properties¶
The table ExperimentalUnitProperties are used to specify additional properties of the experimental units of the experiment. For instance, the gender of the rat, in case rats are the experimental units.
Table aliases: ExperimentalUnitProperties, ExperimentalUnitProperty.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idExperiment |
AlphaNumeric(50) |
Identification code of the experiment. |
idExperiment, Experiment |
Yes |
idExperimentalUnit |
AlphaNumeric(50) |
Identification code of the experimental unit. |
idExperimentalUnit, ExperimentalUnit |
Yes |
PropertyName |
AlphaNumeric(50) |
Name of the experimental unit property. |
Property, Name |
Yes |
Value |
AlphaNumeric(100) |
Value of the experimental unit property. |
PropertyValue |
No |
OtherProperty |
Other properties of experimental units are automatically parsed, using the column name (header) as property name. |
No |
Dose response experiment measurements¶
The table DoseResponseMeasurements describes the measurements that were done in the experiments. That is, for each response and experimental unit, at each observation time, one measurement should be recorded. If the response is an aggregated statistic, then this record may also include a standard deviation and number of units over which was aggregated.
Table aliases: DoseResponseExperimentMeasurements, DoseResponseExperimentMeasurement, DoseResponseMeasurements, DoseResponseMeasurement.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idExperiment |
AlphaNumeric(50) |
Identification code of the experiment to which this measurement belongs. |
idExperiment, Experiment |
Yes |
idExperimentalUnit |
AlphaNumeric(50) |
Identification code of the experimental unit from which the measurement is taken. |
idExperimentalUnit, ExperimentalUnit |
Yes |
idResponse |
AlphaNumeric(50) |
Identifier of the response that is measured. |
idResponse, Response |
Yes |
Time |
Numeric |
Time of observation. |
Time |
No |
ResponseValue |
Numeric |
The measured response. |
ResponseValue, Value |
Yes |
SD:Response |
Numeric |
For aggregated responses, the standard deviation of the measurement. |
SD:Response, ResponseSD |
No |
CV:Response |
Numeric |
For aggregated responses, the coefficient of variation (cv) of the measurement. |
CV:Response, ResponseCV |
No |
N:Response |
Numeric |
For aggregated responses, the number of units over which was aggregated. |
N:Response, ResponseN |
No |
UncertaintyUpper:Response |
Numeric |
Optionally, measurement uncertainty quantification in terms of the upper value (i.e., an estimate of 95th percentile). |
UncertaintyUpper:Response, ResponseUncertaintyUpper, UncertaintyUpper, Upper |
No |