2. Data and Settings Guidelines

Required Data Domains

The Nephrotoxicity Explorer requires:

• subject-level demographics dataset (e.g. ADSL or DM)
• one-row-per-measure laboratary dataset (e.g. ADLB or LB)
• one-row-per-measure vital signs dataset. (e.g. ADVS or VS)

Example datasets are provided in the required format as part of this package under their ADaM CDISC Standard names: ADSL, ADLB, and ADVS.

Column-level and field-level requirements are provided below for each domain along with the respective metadata setting used to tell nepExplorer how to map the data to chart aesthetics.

Data Specifications

Subject-level Dataset (e.g. ADSL or DM)

When a subject is selected within the creatinine scatterplot, the subject-level dataset is used to provide demographic information for the selected subject. Column-level specifications can be found in the table below:

Column-level Specifications

Setting	ADAM Standard	Data Type	Description	Required?
id_col	USUBJID	character	Participant ID	Yes
treatment_col	TRT01P	string	Planned Study Treatment Group
sex_col	SEX	string	Participant Sex
race_col	RACE	string	Participant Race
age_col	AGE	string or number	Participant Age or Age Group

Lab Dataset (e.g. ADLB or LB)

The lab datset is used throughout the application. Creatinine measurements collected in mg/dL units are is required to use the application. Column-level specifications and field-level specifications can be found in the tables below:

Column-level Specifications

Setting	ADAM Standard	Data Type	Description	Required?
id_col	USUBJID	character	a variable that contains IDs for each participant	Yes
visit_col	VISIT	string	visit name	Yes
visitn_col	VISITNUM	number	sort order of visit	Yes
studyday_col	DY	number	study day of visit	Yes
measure_col	TEST	character	a variable that contains the names of each medical sign	Yes
value_col	STRESN	numeric	a variable that contains the results for each medical sign; non-numeric results are removed with a notification thrown to the log	Yes
unit_col	STRESU	character	a variable that contains the units of each medical sign	Yes
baseline_flag	ABLFL	character	Column for assigning baseline visits	Yes

Field-level Specifications

Setting	Measure Name	Column	Description	Required?
measure_values	CREAT	measure_col	Value used for Creatinine in the specified measure column. Must be in mg/dL units.	Yes
measure_values	CYSTC	measure_col	Value used for Cystatin C in the specified measure column.
measure_values	eGFR	measure_col	Value used for Estimated glomerular filtration rate in the specified measure column.
measure_values	eGFRcys	measure_col	Value used for Cystatin C-based Estimated glomerular filtration rate in the specified measure column.
measure_values	ALB/CREAT	measure_col	Value used for Albumin/Creatinine in the specified measure column. Must be in mg/g units for reference lines to display.
measure_values	BUN/CREAT	measure_col	Value used for Blood Urea Nitrogen/Creatinine in the specified measure column.
measure_values	nepFC<XXXX>	measure_col	Value used for indicating lab measure in the specified measure column that should be included in the fold change patient profile chart.

The field-level settings for the lab domain can contain two types of measures which are both specified within the measure_values setting:

• Default Measures: These have predesigned line charts in patient profiles. For example, specifying the eGFR setting causes a raw change eGFR chart to appear within the patient profile. You will find a Default Measures table below that includes all of the potential options you can specify for premade patient profile charts.
• Custom Fold Change Measures: Because the fold change chart in the patient profile has no units, you can specify any lab test. To have a lab test show up within the fold change chart, specify a new setting with the prefix nepFC in the measure_values setting. For example "measure_values" = list("nepFC_CA" = "Calcium"). During your app sessoin, you can interactively change which lab tests you show in the fold change chart with the Select Measures control in the upper right-hand corner of the UI.

Default Measures

Lab Test	Setting Name
Creatinine	CREAT
Cystatin C	CYSTC
Estimated glomerular filtration rate	eGFR
Cystatin C-based Estimated glomerular filtration rate	eGFRcys
Albumin / Creatinine	ALB/CREAT
Blood Urea Nitrogen/Creatinine	BUN/CREAT

Vitals Dataset (e.g. ADVS or VS)

When a subject is selected within the creatinine scatterplot, the vitals dataset is used to provide blood pressure values in the patient profile line charts. Column-level specifications and field-level specifications can be found in the tables below:

Column-level Specifications

Setting	ADAM Standard	Data Type	Description	Required?
id_col	USUBJID	character	a variable that contains IDs for each participant	Yes
visit_col	VISIT	string	visit name
visitn_col	VISITNUM	number	sort order of visit
studyday_col	DY	number	study day of visit
measure_col	TEST	character	a variable that contains the names of each medical sign	Yes
value_col	STRESN	numeric	a variable that contains the results for each medical sign; non-numeric results are removed with a notification thrown to the log
unit_col	STRESU	character	a variable that contains the units of each medical sign
baseline_flag	ABLFL	character	Column for assigning baseline visits

Field-level Specifications

Setting	Measure Name	Column	Description	Required?
measure_values	SYSBP	measure_col	Value used for Systolic Blood Pressure in the specified measure column
measure_values	DIABP	measure_col	Value used for Diastolic Blood Pressure in the specified measure column
baseline_values	Y	baseline_flag	Value used for indicating a Baseline record