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Oracle® Health Sciences Data Management Workbench User's Guide
Release 2.4
E52292-02
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Contents
Title and Copyright Information
Preface
Audience
Documentation Accessibility
Finding Information and Patches on My Oracle Support
Finding Oracle Documentation
Related Documents
Conventions
Part I Setting Up Studies
1
Introduction
Data Aggregation and Standardization
Data Review and Cleaning
Identifying Discrepant Data
Listings Pages
Discrepancies Page
Custom Flags
Customizing the Workflow
Integration with Oracle Health Sciences InForm
Integration with Labs
Integration with SAS
Integration with Oracle Thesaurus Management System
Integration with Informatica
Integration with Data Visualization Tools
Integration with Oracle Life Sciences Data Hub
2
Creating Studies and Study Templates
Creating the First Study
Creating a Study
Associating a Study with a TMS Domain Element
Force Rederivation
Making a Study Available as a Template
Creating the Next StudiesâReusing Studies and Study Components
Study Templates
Library Clinical Data Models
Study Component Copies
Cross-Study Objects
Understanding the Validation Lifecycle and Installation
3
Creating Clinical Data Models
Creating a Study Clinical Data Model
Adding Tables to a Clinical Data Model
Copying Tables
Adding Tables from a File
Adding Subject Visit and Subject Tables
Copying Default Subject Visit or Subject Table
Subject Visit Table
Subject Table
Defining Tables to Support Filtering in the Listings Pages
How Filters Work
Subject Visit Table
Subject and Visit SDTM Variable Columns in
All
Tables
Adding and Modifying Tables Manually
Setting Blinding-Related Attributes
Setting the Data Processing Attribute
Adding Constraints to a Table
Linking a TMS Set to a Table in a Target Clinical Data Model
Adding Columns to a Table
Adding Columns Manually
Using SDTM Identifiers for Columns
Specifying Masking Attributes for a Column
Configuring the Oracle Health Sciences InForm Connector
Selecting Internal InForm Tables and Views
Loading InForm Metadata
Loading Data
Suspending and Resuming Data Loading
Scheduling Data Loads in the Production Lifecycle Area
Comparing Oracle DMW and InForm Metadata
Automatic Metadata Change Detection and Synchronization
Metadata Change Detection During Data Loading
Metadata Change Detection During Metadata Loading
Metadata Change Detection After Changes to the Remote Location Definition
InForm Configuration Privileges
Configuring File Watcher
Configuring File Watcher for a Model
Setting SAS Data Load Parameters
Setting Text Data Load Parameters
Creating File Specifications
Suspending and Resuming File Loading
Migrating a Release 2.3 File Watcher to 2.3.1 or Higher
Viewing Detected Files and Forcing Actions
Installation and Checkout
Data Blinding
Blinding Data in Input Models
Blinding Data in Target Models
Blinding Data in Custom Listings and Validation Check Listings
Unblinding Data
Updating Validation Status
Applying Security
Assigning User Groups to Objects
Modifying Clinical Data Models
Manually Modifying a Non-InForm Model
Modifying an InForm Input Model
Manual Changes Not Allowed in InForm Models
Manual Changes Allowed in InForm Models
Upgrading a Clinical Data Model to the Latest Library Version
Rolling Back Changes to the Last Production Version
Modifying a Table
Removing a Clinical Data Model
Viewing Data
4
Using Libraries
Creating and Modifying Library Clinical Data Models
Creating a Library Clinical Data Model
Modifying a Library Clinical Data Model
Deleting a Clinical Data Model
Creating Code Lists
Code List Examples
Removing a Code List
5
Transforming Data to Standard Structures
Mapping Models, Tables, and Columns
Creating Model Mappings
Creating Table Mappings
Using Side Models
Copying Table-Level Transformations
Using Automap
Mapping Tables Manually
Adding Expressions on Mapped Sources
Creating a Self-Join in a Transformation
Creating Staging Tables
Marking Target Tables and Columns as Not Used
Creating Column Mappings
Undoing Mappings
Undo Multiple Mappings
Undo a Single Table or Column Mapping
Cascading Blinding and Masking
Cascading Blinding
Cascading Masking
Table Transformation Types
Direct
Join
Union
Pivot
Unpivot
Custom
Using the Expression Builder for Transformations and Blinding Criteria
Passing Data as Input Parameter Values
Passing Metadata as Input Parameter Values
Passing Constant Values
Developing a Library of SQL Functions
Validating Mappings
Validation Error Messages
Installing a Transformation
Running a Transformation
Modifying a Transformation
Upgrading a Mapping to Reflect Model Metadata Changes
Creating a Custom Program
Enabling Data Lineage Tracing in a Custom Program
Add Auxiliary Columns to the Target Table
Populate the Auxiliary Columns
Creating a Custom Program in Oracle Life Sciences Data Hub
Completing the Transformation
Sample Programs that Populate Auxiliary Columns with the Source Surrogate Key
Example SAS Program
Example PL/SQL Program
Sample Program that Calls the API to Set a Flag
How the System Tracks Data Lineage
Context Example
6
Creating Validation Checks
Creating a Validation Check Batch
Copying Validation Checks
Creating a Validation Check
Building the Validation Check Query
Selecting Columns to Display in VC Listings
Selecting Packages
Adding Table Aliases for a Self-Join
Specifying Criteria
Defining Validation Check Details
Installing Validation Checks
Using the Expression Builder in Validation Checks and Custom Listings
Running a Validation Check Batch
Modifying a Validation Check
Reordering Validation Checks
Disabling and Enabling a Validation Check
Upgrading a Validation Check Batch
Creating a Custom Validation Check
7
Configuring Your Discrepancy Workflow
Discrepancy States and Allowed Transitions
Actions
Out-of-the-Box Workflow
Predefined Actions
Out-of-the-Box Workflows
Lab Workflow Example
InForm Workflow Example
Creating a Custom Workflow by Creating and Editing Actions
8
Administration
Setting Up and Monitoring File Watchers
Registering Folder Locations
Changing the Root Folder Location
Selecting the Distributed Processing Server
Archiving Data Files
Creating and Modifying Study File Watchers
Monitoring File Watchers
Study Folder Name/File Name Mismatch Report
Viewing and Setting Up Lab Data Sources
Adding a Lab Data Source
Modifying a Lab Data Source
Deleting a Lab Data Source
Setting Up Oracle Health Sciences InForm Integration
Viewing and Setting Up InForm Data Sources
Adding or Modifying a Remote Location
Adding or Modifying a Web Service Location
Removing a Remote Location or Web Service Location
Modifying a Remote Location or Web Service Location
Selecting InForm Tables and Views
Available InForm Tables and Views
Viewing and Creating Categories
Viewing and Creating Discrepancy Tags
Creating or Modifying a Tag
Modifying Existing Tags
Creating and Using Flags
Creating a Flag
Flag Rules
Comparing Flags, Tags, and Categories
Setting Up Coding in TMS
Defining TMS Sets
Defining TMS Set Columns
About TMS Processing
New and Updated Data Processed in TMS
TMS Autoclassification and Synchronization
System Interaction and Data Statuses
Force Rederivation
Viewing Scheduled Jobs
Setting Up Security
About Security
Simple Security Setup
Custom Security Setup
Setting Up Library and Study Categories
Setting Up Custom Program and Function Categories
Configuring Database Partitioning
Partitioned Tables
Developing Guidelines for Setting Study Size
Specifying the Number of Similarly Sized Studies per Partition
Assignment Algorithm
Applying Snapshot Labels
Loading Reference Tables
Setting Up a Data Visualization Tool
Setting Profiles
How to Log In to Oracle Applications Profile Forms
Use Character Semantics
Increase the Maximum Number of Nested Domains
Append Username to Discrepancy Text
Change Study Category User Interface Label
Registering Root Folders for File Watcher Watched Folders
Registering Root Folders for File Watcher Archive Folders
Setting Blinding Behavior for InForm Hidden Items
Make Discrepancy Categories Mandatory
Make Discrepancy Actions Mandatory
Hosted Environments
Set Login-Related Profile Values
Setting Lookup Values
Reasons for Change
Number of Studies per Partition
9
Data Processing
Data Processing Types and Modes
Reload Processing
Full
Incremental
Unit of Work Processing
Full UOW
Incremental UOW
UOW Load
Data Processing in Transformation Programs
Populating Surrogate Keys for Data Lineage Tracing
Automatically Triggering Transformations and Validation Checks by Upstream Processes
Example
Data Processing in Validation Check Programs
Loading Data
Processing Data Loads from Files
Processing InForm Data Loads
Format Checks on Loaded Files
Supporting Duplicate Primary Keys in a Load
Part II Reviewing and Cleaning Data
10
Using the Home Page
Selecting a Study
Selecting a Lifecycle Mode
Viewing Data Load Information
Statuses for Uncompleted Jobs
Viewing and Running Transformations
Viewing Transformation Job History
Running a Transformation
Viewing and Running Validation Check Batches
Submit the Validation Check Batch
Viewing Validation Check Batch Job History
Viewing Data Files Not Processed
Changing the User Interface Display
Sorting Rows by Column Values
Sorting on a Single Column
Sorting on Multiple Columns
Showing and Hiding Selected Columns
Changing Column Order
Detaching a Pane
Querying By Example
Using Online Help
Changing Your Password
11
Reviewing Data
Listings Pages
Viewing All Study Data Using Default Listings
Creating and Viewing Custom Listings
Copying Custom Listings
Using the Query Builder to Create Custom Listings
Viewing Validation Check Listings
Actions Available on All Listings Pages
Creating and Using Filters
Creating and Using Filter Groups
Viewing Filters Currently in Effect
Creating and Editing Subject Filters
Creating and Editing Visit Filters
Creating and Editing Subject Visit Flags Filters
Creating and Editing Visit Day Filters
Creating and Editing Visit Date Filters
Creating and Editing Record Flags Filters
Creating and Editing Data Change Date Filters
Creating and Editing Discrepancy Category Filters
Creating and Editing Discrepancy Change Date Filters
Creating and Editing Discrepancy State Dates Filters
Creating and Editing Discrepancy States and Tags Filters
Creating and Editing Discrepancy User Filters
Creating and Editing Discrepancy Origin Filters
Using the Find Feature
Creating Discrepancies Manually
Managing Discrepancies
Showing Discrepancies
Showing Flags
Flagging Data
Viewing Data Lineage
Trace Data Lineage Display
Viewing Blinded Data
Exporting to Excel and CSV
Viewing Data in InForm
12
Cleaning Data
Managing Discrepancies
Acting on Multiple Discrepancies
Modifying a Single Discrepancy
Where Is the Action I Want to Apply?
Discrepancy Display
Managing TMS Discrepancies
Viewing Data and Queries in InForm
Viewing Discrepancy Details
Viewing Discrepancy History
Displaying the Full Record
Creating and Using Discrepancy Filters
Creating and Editing Data Source Filters
Creating and Editing Location (Tables and Models) Filters
Exporting All to Excel
Adding a Comment
Actions
Part III Appendixes
A
Reference Information
Naming Objects
Avoid Special Characters and Reserved Words
Name Length: Keep It Short
Keep Container and Object Names Short for Integrated Development Environments
Automatic Name Truncation
Handling of Duplicate Names: System Appends _1
Naming Studies and Libraries
Customizable Naming Validation Package
Required Syntax for Table Metadata Text Files
Object Ownership
Object Hierarchy
DMW Domain
DMW Utilities Domain
Study Category Domains
Study Domains
Lifecycle Areas
Clinical Data Models
Load Sets
Programs
Transformation Maps
Validation Check Batches and Validation Checks
Custom Listings
Business Areas
Data Marts
Effects of User Group Assignment to Objects
B
Predefined Roles
Predefined Oracle DMW Application Roles
DMW_STUDY_MANAGER
DMW_STUDY_CONFIG
DMW_STUDY_CONSUMER
DMW_LIB_ADMIN
DMW_SYS_ADMIN
Predefined Blinding-Related Roles
LSH Data Blind Break User
LSH Data Unblind User
Predefined Object Security Roles
Oracle DMW_STUDY_DEVELOPER
Clinical Data Models and Query Builder
Blinding
Filters
Data Lineage Tracing
Transformations and Query Builder
Discrepancies and Flags
Validation Checks
InForm
File Watcher
Oracle DMW_STUDY_QC
Clinical Data Models and Query Builder
Blinding
Discrepancies
Filters
Flags
Data Lineage Tracing
Validation Checks
InForm
File Watcher
Transformations and Query Builder
Oracle DMW_STUDY_PROD
Clinical Data Models and Query Builder
Blinding
Discrepancies
Filters
Flags
Data Lineage Tracing
Validation Checks
InForm
File Watcher
Transformations and Query Builder
Oracle DMW_STUDY_ADMIN
Clinical Data Models and Query Builder
Discrepancies
Flags
Filters
Data Lineage Tracing
Validation Checks
InForm
File Watcher
Transformations and Query Builder
Oracle DMW_STUDY_INST_ACCESS
Clinical Data Models and Query Builder
Blinding
Discrepancies
Data Lineage Tracing
Validation Checks
Transformations
Oracle DMW_STUDY_INFORM_CONFIG
InForm
Glossary
Index