PKS

Creating a PKS study

Studies are the fundamental unit of PKS organization. A PKS study stores raw data to be modeled and analyzed in one or more scenarios.

A study can be created from a project loaded in Phoenix (PKS > Save Project as PKS Scenario) or from scratch (PKS > Create Study). In either case, the Create Study dialog is used to define the study components.

If a connection to an instance of PKS is not established, the fields and menus are unavailable in the Create Study dialog.

To establish a PKS connection, select a PKS instance in the instance menu in the Create Study dialog. The selected PKS instance is used to create a new study.
If no instance is available, configure the PKS connection settings as described in “Setting up a PKS connection”.
Click Connect and enter your user name and password in the Connect to PKS dialog and click OK.

If the Prompt option for credentials is selected in the PKS Configuration dialog, the Connect to PKS dialog will display prompting for the PKS user name and password and a user name and password for the proxy connection.

The metadata fields in the Create Study dialog are made available.

PKS metadata fields
Attribute	Description	Data entry	Format
Study Name ^a	Used to identify and locate study in PKS; must be unique within the PKS database	Typed	50 character max
Description	Text describing the study; press Ctrl+Enter for line breaks	Typed	2000 character max
Blinding Type^a	blinding level for the study	Typed or selected from list of prior values	30 character max
Design^a	Experimental structure, e.g., parallel or crossover	Typed or selected from list of prior values	30 character max
Type^a	type of study	Typed or selected from list of prior values	30 character max
Portfolio	Development portfolio to which the study belongs	Typed or selected from list of prior values	50 character max
Project	Development project to which the study belongs	Typed or selected from list of prior values	100 character max
Indication	Primary indication(s) for the study	Typed or selected from list of prior values	50 character max
Compound	Main drug compound(s) under development	Typed or selected from list of prior values	50 character max
State	Whether the study will be locked against changes or not	Selected	Normal or locked
Study Start Date	The date on which the study began	Typed or selected from the calendar popup	YYYY.MM.DD
Study End Date	The date on which the study concluded	Typed or selected from the calendar popup	YYYY.MM.DD

^aRequired field.

In the Properties tab, enter the study name and a description of the study.
Use the menus in the Create Study dialog to select blinding type, design type, study type, portfolio, etc.
To save the study properties, click Save Properties.
Type a name in the File name field and click Save.

The study properties are saved as a .map file.

Load study properties from a file

Click Load Properties. The Open dialog is displayed.
In the Open dialog, select the directory that contains the study properties file.
In the Files of type menu, select one of three study property file types:

•Map (*.map)

•XML (*.xml)

•WNL5 Map (*.pks)

Select the file and click Open to load saved study properties.

Note:To learn more about creating and loading properties, see "PKS study properties".

Select the Study Data tab.
Click Browse Files to select a data source from a file.

Column names in the data source cannot include an apostrophe as it can lead to errors when the data is added to the mapped columns.
Click Browse Projects to select a data source from an open Phoenix project.
Use the Select Source dialog to navigate to a data source in Phoenix.

Note:For more on Study Data, see “Selecting a data source”.

•If the selected data source contains multiple worksheets, the File Import Wizard is displayed.

•In the File Import Wizard, select the worksheet to use as the source for creating the study.

•Additional worksheets can be appended to the study using the Append/Update feature.

Click Map Study Data and then:

•Create a new study mapping as detailed in “Creating and saving a .map file”.

•Load a map from file as detailed in “Loading a study map from a file”.

•Load map from PKS as detailed in “Loading a study map from PKS”.

Click OK, which saves the map settings to the study.

Select the Custom Attributes tab and check the boxes of the custom study attributes to include in the study.
Check OK in the Create Study dialog to display the PKS Save dialog.

Enter an Audit Reason in the Audit Reason field.
Enter your password in the Password field.
Click OK, which displays the PKS Process Manager.

Click Close, which saves the study to the PKS.

The study can also be submitted as a job after which the Phoenix session can be terminated and the processing will continue on the server processed later.

•Select the Submit as Job checkbox to process.

•When the PKS has received the job information the PKS Process Manager can be closed.

•Use the PKS Job Viewer to monitor the processing status.

PKS study properties

Properties can be entered once or saved for future use. Once a properties file has been saved, the file can be loaded during any study creation. Saving the properties file is helpful if multiple projects have the same properties or if you create a study in PKS from this project multiple times. The saved properties can be modified once they have been loaded.

This section covers the following topics:

•“Creating and Saving Properties to a file”

•"Loading properties files"

Creating and Saving Properties to a file

Load a Phoenix project file (*.phxproj) or create a new project.
Select PKS > Create Study.
If Phoenix is not already connected to PKS, click Connect and enter your login credentials in the Connect to PKS dialog.
In the Study Name field, type a study name.
Enter a description in the Description field.
Use the menus in the Create Study dialog to specify Blinding Type, Design, Type, Portfolio, etc.
A red asterisk (*) denotes a required study property.
Click Save Properties to save the study properties.
In the Save As dialog, enter a file name and select a location in which to save the .map file.
Click Save to save the .map file.

Loading properties files

Load a Phoenix project file (*.phxproj) or create a new project.
Select PKS > Create Study.
If Phoenix is not already connected to PKS, click Connect and enter your login credentials in the Connect to PKS dialog.
Click Load Properties to load a file with saved study properties.
In the Open dialog, select a .map file or a .pks file.

Phoenix WinNonlin study properties are saved as a .map file.
WinNonlin 5.3 study properties are saved as a .pks file.
Click Open, which loads the study properties.

•If necessary, users can further modify study properties after the properties are loaded.

•Enter a new name or description in the Study Name and Description fields, or use the menus to modify study properties such as Blinding Type, Design, Type, etc.

PKS study data

If study files are saved to the study library, no mapping is necessary. However, if a study is going to be saved to the PKS from Phoenix, the data source and its columns must to be mapped before creating the study in the PKS. Only one data source needs to be selected. The data source can be imported from a disk or selected from an open project.

Once a data source is selected the observation data, demographic data, and other data must be mapped to the appropriate columns. A .map file can be created and saved or properties can be loaded from a previously created .map file.

“Selecting a data source”
“Mapping study data”

•“Creating and saving a .map file”

•“Loading a study map from a file”

•“Loading a study map from PKS”

Note:If a sample, dose, or demographic source field contains multiple values, use one of the following options to prevent leading zeros or commas from being stripped:

•include a space between the values (e.g., “01, 2, 3”)

•include quotes in the value, so in a CSV file, it would be “”01,2,3””

•include any non-numeric characters in the value

Selecting a data source

Load a Phoenix project file (*.phxproj) or create a new project.
Select PKS > Create Study.
If Phoenix is not already connected to PKS, click Connect and enter your login credentials in the Connect to PKS dialog.
In the Properties tab, make sure the study property fields contain the appropriate selections.
Select the Study Data tab.

There are two ways to add a data source: selecting a file from a disk or selecting a worksheet in a Phoenix project.

To select a file from a disk:

•Click Browse Files.

•In the Open dialog, select a worksheet or workbook then click Open.

•In the Options area of the File Import Wizard, specify any additional import options.

•Click Finish to add the worksheet or workbook.

To select a file from a Phoenix project:

•Click Browse Projects.

•In the Select Source dialog, click the (+) signs beside workbooks and operational object results to locate a data source.

•Use the pointer to select the data source.

•Click Select.

The Select Object dialog closes and the selected data source is listed in the Data Source field.

Mapping study data

Study data can be mapped to PKS structures and saved as a .map file, loaded from an existing map file on a disk, or loaded from an existing .map file in the PKS.

•"Creating and saving a .map file"

•"Loading a study map from a file"

•"Loading a study map from PKS"

Creating and saving a .map file

Load a Phoenix project file (*.phxproj) or create a new project.
Select PKS > Create Study.
In the Create Study dialog, select the Study Data tab.
In the Study Data tab, select a data source and click Map Study Data.

In the Study Mapping dialog, all the source columns in the worksheet are listed on the left. All of the different contexts for mapping are shown as tabs on the right.
To map a column to a Subject Identifier, Demographic, Samples, or Doses context, click and drag the source column from the list on the left to the list in the context tab. For example, drag the column that uniquely identifies subjects from the Source Column list to the list in the Subject Identifiers tab.

•Use the Remove button to unmap a selected column.

•Enter an alternative name for the selected column by typing it in the Target Name field.

•Select the mapped column in the list to display attributes that can be modified.

Specify column attributes and defaults for data collection points or treatments.

•If the attribute values are in a separate column, click and drag that column to the attribute field.
(For example, if units are recorded as a separate column in the data source, click and drag that column name from the Source Column list to the Units attribute text field.)

•If the attribute value is always the same (i.e., static), enter that value and select the Static checkbox.

The Demographics tab maps subject data such as demographics and covariates.The selected demographic columns must contain values that exist once per subject. That is, the values are not time or visit dependent.

The Samples tab is for mapping time-dependent sample results. Samples and Doses tabs contain more attribute selections than Subject Identifiers or Demographics. These attributes are listed in the following tables.

Column attributes for samples
Attribute	Description
Unit	Units of measurement.
Status	Indicates data status, for example, below a limit of quantification (BQL), or missing due to dropout or non-adherence. Valid data are finite. The list of statuses is defined by a PKS administrator.
Sample_Number	Sample identifier.
Sample_Matrix	Identifier for the sample matrix.
Sample Description	Further information about the sample.
Analytical Method	Assay or technique used to obtain the sample data.
LLOQ	Lower limit of quantification for the assay. A numerical value.
ULOQ	Upper limit of quantification for the assay. A numerical value.

Column attributes for doses
Attribute	Description
Unit	Units of measurement.
Status	Indicates data status, for example, below a limit of quantification (BQL), or missing due to dropout or non-adherence. Valid data are finite. The list of statuses is defined by a PKS administrator.
Sample_Number	Sample identifier
Sample_Description	Text information about the sample.
State	Text information about the sample.
Route	Variable identifying route, oral, IV, IM, etc., for each dose.

The Data Collection Point tab (and Default Data Collection Point tab) is used to specify columns that contain data used to uniquely identify events where samples were collected or doses were administered. The mappings can be overridden per dose or sample.

Column attributes for collection data
Attribute	Description
Period	Identifier for the period of the study.
Phase	Identifier for phase of the study.
Matrix	Matrix value, if study involves a matrix of analyte and concentration combinations.
Day	Number of days after the study, phase, period started.
Visit	Identifier for the visit during which observation was made/sample was taken.
Analyte	ID of the analyte used.
DCP Description	(Data Collection Point description) use this field for variables that distinguish different measurements stored a single observation column, for example, an indicator variable noting whether a given record contains a measurement of plasma concentration or pain score.
Relative_Nominal_Time	Scheduled time of observation or sampling since last dose.
Nominal_Time_Unit	Units in which time is being reported. Valid units are: sec, min, hr, day, weeks, years.
Relative_Nominal_End_Time	For data that uses infusion dosing, nominal interval end time for infusion.
Relative_Actual_Time	Actual interval time from last dose.
Relative_Actual_End_Time	For data that uses infusion dosing, actual interval end time for infusion.
Actual_Clock_Time	Clock time when the observation was made/sample was taken.

The Treatment tab (and Default Treatment tab) is used to specify columns that uniquely identify administered treatments. Treatment information is combined with data collection point information to uniquely identify events where samples were collected or doses were administered.

Column attributes for treatment data
Attribute	Description
Treatment	Variable identifying the treatment.
Treatment_Description	Additional descriptive field.
Route	Variable identifying route, oral, IV, IM, etc., for each dose.
Regimen	Variable identifying dose regimen.
Fasted_Fed	Variable identifying whether subject ate before dosing.
Formulation	Variable identifying drug formulation for each dose.
State	Additional descriptive field.

The Default Treatment mappings can be overridden per dose or sample.

Click OK. The Save As dialog is displayed.
Select a directory in which to save the .map file and type a name in the File name field. Click Save.
Click the OK in the Study Mapping dialog.

The map file is used to create the study.

Loading a study map from a file

In the Study Data tab of the Create Study dialog, select a data source and click Map Study Data.
Click Load Map from File. which displays the Open dialog.
In the Open dialog, search for and select the .map file.
Click Open to load the .map file.
Click OK to close the Study Mapping dialog.

The loaded mappings are applied and attached to the study.

The mappings are applied to the selected data source as closely as possible. Phoenix displays warning messages if there are any problems with the mappings.

Loading a study map from PKS

In the Study Data tab of the Create Study dialog, select a data source and click Map Study Data.
Click Load Map from PKS.

In the PKS Browser, click the (+) sign beside the study that contains the mappings and select the map file.
Click Select to load the map file.
The loaded mappings are applied and attached to the study.

The mappings are applied to the selected data source as closely as possible. Phoenix displays warning messages if there are any problems with the mappings.
(Optional) Click through the study mapping tabs to make any changes.
Click OK to close the Study Mapping dialog.
In the Save As dialog, save the mapping file.

Detaching PKS objects from source

Objects loaded from PKS can be detached from their PKS source. Detaching an object from its source allows the objects to be edited without a link to a specific PKS source.

To detach a project, select the project in the Object Browser and then select PKS > Detach PKS Settings from Project.

Right-click the project object in the Object Browser and select PKS > Detach Object.

The PKS source information is removed from all items in the project and are editable.

To detach an individual item within a project, right-click the item in the Object Browser and select PKS > Detach Object.

The PKS source information is removed from the selected item in the project and is editable.