2 Creating Studies and Study Templates

This section contains the following topics:

"About Studies, Study Templates, and Libraries"
"Creating and Using Studies and Study Templates"
"Using the Validation Lifecycle"

When you log in, select a study and a lifecycle mode to work in:

About Studies, Study Templates, and Libraries

An Oracle Health Sciences Data Management Workbench (Oracle DMW) study consists of sets of tables, programs, and other components that allow you to review, clean, and analyze clinical data. When you start using the system you must create new studies, explicitly defining each component in a partially automated process.

When appropriate, you can mark a study as a template. The template includes all study components, including transformations and validation checks as well as clinical data models. You can then apply the template to new studies. Applying a template creates a copy of each study template component's metadata in the new study. You can modify or delete template components and add components as required. You can build up a set of study templates; for example, for different therapeutic areas or study types.

Libraries contain clinical data models, which are groups of tables. Library models are available across studies and are intended to be used as standards. When you create a study model from a library model, the system maintains a relationship between the two. If you update the library model, you can propagate the changes to any study model created from it.

By contrast, applying a study template is a simple Copy operation. The system does not maintain a relationship between the original template and the copy, and you cannot update study objects automatically if their corresponding template object is updated.

You also create code lists in a library for use as lists of allowed column values. Code lists remain in the library for reference; they are not copied into studies.

Note:

You create other objects used in the data review process, including tags, flags, and categories, in the Administration page. They are not study components and are not part of study templates, but are available for use in any study; see Chapter 8, "Administration."

Study templates and libraries contain only metadata, or object definitions. Studies also contain metadata, but to use the objects (data models, tables, programs and so on) you must install them. Installation creates object instances and the actual database tables and packages required to store data and run programs. For more information on object definitions and instances, see the Oracle Life Sciences Data Hub Application Developer's Guide.

Creating and Using Studies and Study Templates

A DMW study or study template includes:

Clinical data models, each containing a set of tables. Each data model is intended for a particular purpose; for example, reviewing data or transforming data into standard CDISC-formats for analysis; see Chapter 3, "Creating Clinical Data Models" for more information.

Note:
Input clinical data models—models that receive data directly from InForm or a lab—are not included in study templates. They must reflect the exact structure of the source data and are created from the source data for each study. Only one InForm model can be in a study.
Mappings and transformation programs to read data from one clinical data model and write to the next ; see "Transforming Data to Standard Structures".
Validation check programs to validate data in a clinical data model and raise discrepancies; also called edit checks; see "Creating Validation Checks".
Saved custom listings created by data managers, medical reviewers, or other end users to analyze and clean data; see Chapter 11, "Reviewing Data".
Business areas to support data visualization tools; see "Setting Up a Data Visualization Tool".

Tip:

You can apply only one study template to a study. Oracle recommends creating study templates that are as complete as possible for each study type, and then deleting any tables, validation checks, or other components not needed in a particular study after applying the template.

This section contains the following topics:

"Creating a Study"
"Applying a Template to a Study"
"Creating Study Components"
"Making a Study Available as a Template"

Creating a Study

To create a study:

On the Home page, click the Add icon (+) in the Studies pane.
Enter a name and description for the study.
Select the following attributes if appropriate:
- Template: If selected, this study is available as a template for other studies. You can select this setting later, after testing the study; see "Making a Study Available as a Template".
- Active: Select this check box to indicate that the study is being set up or is ongoing. Deselect the box to indicate that the study is closed. The system does not use this field in Release 2.3.1.
Therapeutic Area (or other category): Select the category to which the study belongs. The label for this field and the choices available are customizable by your company. The libraries you develop of clinical data models will be divided into these categories; see "Setting Up Library and Study Categories".
Study Size: Select Small, Medium, or Large to indicate the amount of patient data to be collected in this study relative to other studies. The system uses this setting to help determine which partition to use for this study's data in certain cross-study internal tables; see "Configuring Partitioning" for more information.

You cannot change this value after saving.
Save.

Applying a Template to a Study

If a study template already exists that suits your needs, apply it to your study. You can apply only one template to a study.

To see a template in order to decide if you want to use it, query for it in the Studies pane of the Home page, then navigate to its clinical data models, transformations, and validation checks. You can also look at its Listings pages.

To apply a template to your study:

In the Home page, create or open your study.
Go to Study Configuration, then click the Study Templates node. The system displays a list of study templates with their descriptions.
If necessary, query by example to find the template you want:
1. If empty fields are not already displayed above each column, click the Filter icon.
2. In the empty field above the Study Name column, enter all or part of the template's name.
3. In the empty field above the Description column, enter a key word that should be in the description, such as the therapeutic area or other study type for which the template is intended.
4. Press Enter.
Select the template and click Apply Template to Study.

Creating Study Components

You can add components manually to complete the study:

Create an input clinical data model—set of tables—for each external study data source, including InForm and each lab. The system automatically creates tables with the same structure as in the source system and loads data into them; see "Creating a Study Clinical Data Model" for more information.
Create target clinical data models for reviewing and analyzing data. You can develop standard library clinical data models and reuse them in multiple studies.
Create code lists and associate them with table columns to define lists of allowed values. Code lists are available for use in all studies; see "Creating Code Lists".
Create a transformation for each target data model: Map one or more source data models to each target model and map tables in the source models to tables in the target model. Define table mappings as joins, unions, pivots, unpivots, or directo one-to-one mappings, and the system generates the supporting program code. Map columns in source tables to columns in target tables, using expressions and functions as required. See Chapter 5, "Transforming Data to Standard Structures" for more information.
Write validation (edit) checks to detect discrepant data; see Chapter 6, "Creating Validation Checks" for more information.

In addition, create tags and categories for use in filtering discrepancies and managing your discrepancy workflow. Create flags for use in reviewing data and tracking subject/visit status. These are available for use in all studies; see Chapter 8, "Administration".

Making a Study Available as a Template

If you want to make your study available for use as a template for other studies, mark it as a template:

On the Home page Studies pane, select the study and click the Edit icon.
Edit the description to make it easy for others to decide whether to select this study for use as a template. The maximum length is 2000.

Tip:
Oracle recommends developing company standards for this purpose.
Select the Template check box.
Click OK.

Using the Validation Lifecycle

When you create a study, the system automatically creates three lifecycle areas for the study. Within each lifecycle area, each clinical data model has its own database schema. Each lifecycle area has a different purpose:

Development to create clinical data models, transformation programs, and validation checks either manually or from a study template or library as required for the study. You can load data into the development lifecycle schema and do initial testing and fine-tuning and begin formal testing there.
Quality Control for formal testing of all study components.
Production to load, review, and clean production study data. The system prevents destructive changes to tables and models in a production environment.

You select the lifecycle area you want to work in on the Home page in the bottom left corner. To change from one lifecycle area to another you must return to the Home page, select the lifecycle area and reselect the study if necessary, and then go back to the page you were working in.

As you test study components in the development or quality control lifecycle areas, you promote them to the next lifecycle stage: from development to quality control or from quality control to production. You can associate documents supporting the change in validation status, such as log files or signoff documents, with the study component.

As soon as you promote them they become visible with the new validation status in the next lifecycle area. However, you must install the current version of the object in the higher lifecycle area for the changes to take effect.

Similarly, if you need to make a change to a study component with a validation status of either quality control or production, the system changes its status to development as soon as you check it out. You make your changes, install the study component, test it and promote it when appropriate.

You can set an object's validation status to Retired. If the object is executable, like transformations or validation check batches, it can no longer be executed. This has no effect on objects currently in use, but prevents creating other objects based on the retired object as part of a study template or library.