2 Creating Studies and Study Templates

You build up a collection of studies and study components that you can reuse. As you develop study components you validate them and promote them to a higher lifecycle status, optionally with supporting documents.

Creating the First Study

For the first study, you must explicitly create everything you need. Oracle DMW automates some of the tasks.

Table 2-1 Basic Steps Required to Create the First Study

What You Do	Where to Find Information	What Oracle DMW Does For You
Name the study and set attribute values	"Creating a Study"
Create input data models to hold data in the same format as in the source	"Creating a Study Clinical Data Model"	Imports metadata from InForm, creates tables from files for lab data sources.
Create target data models for reviewing and analyzing data. You may prefer to do this in a library.	"Creating a Study Clinical Data Model" or "Creating a Library Clinical Data Model"	Creates tables from files; provides SDTM subject and subject visit tables.
Create data transformations from input models to target models	Chapter 5, "Transforming Data to Standard Structures"	Does automapping, provides a query builder, generates joins, unions, pivots, and unpivots, validates.
Create validation (edit) checks	Chapter 6, "Creating Validation Checks"	Provides a query builder.

Creating a Study

1. On the Home page, click the Add icon in the Studies pane.

2. Enter a name and description for the study.

3. Template: If selected, this study is available as a template for other studies. You can select this setting later, after testing the study.

4. 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; see "Setting Up Library and Study Categories".

5. 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 Database Partitioning" for more information.

   You cannot change this value after saving.

6. Save.

Associating a Study with a TMS Domain Element

To use Oracle Thesaurus Management System (TMS) to code terms in a study, specify the dictionaries and TMS domains to use.

• TMS Base Terminology: The system lists the terminologies (dictionaries) defined in the local TMS instance. Using a terminology is enabled only by selecting a TMS domain.

• TMS Domain: Select the base terminology you need, then select the TMS domain through which to use it.

  Domain Terminology: When you select a TMS domain, the system displays the name defined for the rendition of the dictionary used in the domain. The domain terminology may be a virtual dictionary, meaning a version of the base dictionary that is frozen at a particular point in time.

See "Setting Up Coding in TMS" for more information.

Force Rederivation

Click Force Rederivation to run the Force Rederivation job once, immediately. A confirmation message appears because running the job may take a long time.

Normally, transformations send only new or changed data to TMS for processing. Use the Force Rederivation job to process all data when you have made structural changes related to TMS in an ongoing study such as:

• Adding columns to target tables to hold derived data.

• Updating a dictionary to a new version with a different structure from the old one.

• Changing domain-related settings in the TMS reference codelist TMS_CONFIGURATION.

  Note:

  The Force Rederivation job has no relation to defining TMS for a study.

Making a Study Available as a Template

To make your study available for use as a template for other studies, mark it as a template:

1. On the Home page Studies pane, select the study and click the Edit icon.

2. 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.

3. Select the Template check box.

4. Click OK.

Creating the Next Studies—Reusing Studies and Study Components

As you build up studies and components, you can reuse them in several ways.

Study Templates

Mark a study as a template to reuse it in its entirety. You can delete or mark as Not Used any components you do not need after you apply the template to a new study. The template includes clinical data models, transformations, validation checks, and custom listings. You can build up a set of study templates—for example, for different therapeutic areas or study types.

Study templates include all target clinical data models, all transformations, validation checks, custom listings, and business areas for data visualizations.

Note:

You can apply only one study 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:

1. In the Home page, create or open your study.

2. Go to Study Configuration, then click the Study Templates node. The system displays a list of study templates with their descriptions.

3. 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.

4. Select the template and click the Apply Template to Study icon.

Library Clinical Data Models

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 allowed column values. Code lists remain in the library for reference; they are not copied into studies.

See Chapter 4, "Using Libraries" for more information.

Study Component Copies

You can copy components from other studies or study templates:

• Clinical data models

• Tables

• Transformations

• Validation checks

• Custom Listings

For more information see the chapter on each component.

Cross-Study Objects

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."

Understanding the Validation Lifecycle and Installation

You select a lifecycle area context —Development, Quality Control, or Production—on the Home page in the bottom left corner. You may have access to only one or two lifecycles.

Lifecycle Areas For each study, the system creates three lifecycle areas. Each lifecycle area has a different purpose:

• Use Development to create clinical data models, transformation programs, and validation checks either manually or from a library, study, or study template. Load data into the development lifecycle schema and do initial testing there.

  To modify a model, transformation or validation check in Quality Control or Production, you must check it out, creating a new object version, which is always in Development. The existing installed version of the object in the QC and Production areas continues to function as before until you promote the new version to QC or Production and install it there.

• Use Quality Control for formal testing of all study components (optional). This is equivalent to the UAT InForm environment.

• Use Production to load, review, and clean production study data. The system prevents destructive changes to tables and models in a production environment.

Supporting Documents When you promote an object to the next lifecycle stage, you can associate documents supporting the change in validation status, such as log files or signoff documents, with the object version.

InForm Metadata Comparison When you promote an InForm clinical data model, the system calls the Compare Metadata job to compare the Oracle DMW metadata to the InForm metadata in the lifecycle stage to which the model is being promoted. If there are differences, promotion does not take place. Instead the metadata comparsion report appears.

Installation When you promote an object, it is immediately visible in the new lifecycle area. However, you must install it for the changes to take effect.

Within each lifecycle area, each clinical data model has its own database schema. When you upgrade an object to a new lifecycle area, the system clones it from its current schema to the higher lifecycle area schema. Installation creates or updates the actual database tables and the packages for all the model's programs: the transformation programs that write to tables in the model and the validation checks and saved custom listings that run on data in the model.

The system prevents destructive changes such as dropping or shortening columns in Production. However, if there are destructive changes in Development or Quality Control, the system drops and replaces the table and all its data is deleted. In an InForm model, the system compares the model metadata with the InForm metadata in the higher lifecycle area. If there are differences, the installation does not take place and the comparison report appears.

See "Object Ownership" and the Oracle Life Sciences Data Hub Application Developer's Guide for more information.