1 Study configuration basics

The following figure illustrates how you can provide data from an electronic clinical data system (such as InForm), labs, or file systems to transform and validate the data in a study using Oracle Health Sciences Data Management Workbench.

Figure 1-1 Example DMW study design

Description of "Figure 1-1 Example DMW study design"

For details on DMW concepts, see this video:

Table 1-1 High-level steps for creating a study

Task	More information
Begin study creation.	Specify a name and other attributes. See Create a study.
(Optional) Apply a study template.	A study template includes clinical data models, transformations, validation checks, and custom listings. You can modify or delete any of these as needed. See Use a study template for details.
Set up importing data from InForm.	Create an input clinical data model of type InForm and set up the InForm Connector for the study. The Connector creates table metadata exactly as it exists in the InForm database. See Create a clinical data model for InForm data.
Set up importing data from labs and other sources using files.	The system administrator must set up File Watcher for the system and for your study. Then create an input clinical data model of type File. See Create a file input clinical data model.
Create or copy target clinical data models.	A target clinical data model is a collection of tables used together for a purpose such as reviewing or analyzing data. You can: Create a model by uploading a metadata file or in the user interface. See Create a target clinical data model for transformed data. Create a model from a library model, which allows you to update the study model whenever the library model is updated. See Create a library clinical data model. Copy a model from another study.
Create or copy transformations.	A transformation reads data from one or more tables in one or more clinical data models and writes data to a table in a different model. See Set up data transformations.
Create or copy validation checks.	Validation checks, or edit checks, check data for a condition and create discrepancies on faulty data. See Create validation checks.
Create public custom listings and filters. Set up static reference data.	See Create custom programs, listings, and filters, and set up reference data.
Integrate with Thesaurus Management System (TMS) for coding (optional).	Specify the terminologies to use for the study. See Assign dictionaries for coding (optional). Map columns to data to be derived from TMS
Load data and run transformations and validation checks on the Home page.	See: Load data from InForm Suspend or resume data file loading Automatic triggering of transformations and validation checks
Upgrade models, transformations, and validation checks to Quality Control (optional) and then Production.	See Validation status and lifecycle stages.

See also:

• Advanced topics

• Create a study
  
• Use a study template
  
• Assign dictionaries for coding (optional)
  

Create a study

For details on creating a study, see this video:

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.

   If the study is available as a template, edit the description to help others decide whether to select this study as a template. The maximum length is 2000.

4. Therapeutic Area (or other category): Select the category the study belongs to. The label for this field and the choices available are customizable by your company.

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 value to help determine which partition to use for this study's data in certain cross-study internal tables.

   Tip:

   You cannot change this value after saving.

6. Click OK.

7. If you are using Oracle Thesaurus Management System as a coding system, click the TMS tab and see Assign dictionaries for coding (optional).

Next: Create clinical data models. Do one or both:

• Use a study template

• Set up clinical data models

Use a study template

A study template is a study that you can copy to another study so that its clinical data models, transformations, and validation check batches become part of the new study. InForm input models are not included in the template.

Note:

You can apply only one study template to a study.

In the new study you can:

• Delete or modify template models, tables, transformations, or validation checks.

• In transformations, mark tables and columns in target models as Not Used.

• Copy or create additional models, tables, transformations, and validation checks. If two components of the same type have the same name, the system appends "_1" to the name of the second component added.

1. Click the Home page icon at the top of any page.

2. In the Home page, select the study you want to copy the template into.

3. Click the Study Configuration icon from the navigation bar. Then, select the Study Template tab. The system displays a list of study templates with their descriptions.

4. Find the template you want to use.

   • You can filter by entering a value in the blank field above any column. If blank fields are not displayed, click the Query By Example icon.

   • To see a template's details, query for it in the Home page, then navigate to its clinical data models, transformations, and validation checks.

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

   Note:

   While the system applies the template you cannot use the Study Configuration pages, including Clinical Data Models, Transformations, or Validation Checks. Click the Refresh icon to see the updated Job Status.

Back to Table 1-1.

Assign dictionaries for coding (optional)

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

Prerequisite: Dictionaries and TMS domains must be defined in TMS.

1. Go to the Home page.

2. Select a study and click the Modify icon in the Studies pane.

3. Click the TMS tab.

4. For each base terminology (dictionary) needed in the study, select a TMS Domain from the drop-down list.

   TMS domains allow you to code terms differently in different studies. Domains also determine TMS system behavior, including whether explicit approval is required for manual classifications.

5. Click OK.

Back to Table 1-1.

• Force rederivation of TMS data
  

Force rederivation of TMS data

Normally, only new or changed data is sent to TMS for processing. Use Force Rederivation to resend all data designated as needing coding in TMS when you have made structural changes such as:

• Adding columns to hold derived data in DMW target tables.

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

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

Running this job triggers the execution of the downstream transformation.

To force rederivation of all data from TMS:

1. Go to the Home page.

2. Select a study.

3. Click the Modify icon in the Studies pane.

4. Click the TMS tab.

5. Click Force Rederivation to run Rederivation once, immediately.

6. A confirmation message appears because the job may take a long time. You can still work while it runs. Click OK.

Note:

Force Rederivation is not part of setting up TMS in a study. You only run it in a live study, after making the changes described above.