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Oracle® Health Sciences Data Management Workbench User's Guide
Release 2.3.1
Part Number E35217-02
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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 InForm
Integration with Labs
Integration with SAS
Integration with Informatica
Integration with Data Visualization Tools
Integration with Oracle Life Sciences Data Hub
2
Creating Studies and Study Templates
About Studies, Study Templates, and Libraries
Creating and Using Studies and Study Templates
Creating a Study
Applying a Template to a Study
Creating Study Components
Making a Study Available as a Template
Using the Validation Lifecycle
3
Creating Clinical Data Models
About Clinical Data Models
Installation
Data Blinding
Blinding Data in Input Models
Blinding Data in Target Models
Blinding Data in Custom Listings and Validation Check Listings
Unblinding Data
Requirements
Creating a Study Clinical Data Model
Adding Tables to a Clinical Data Model
Adding Tables from a File
Adding and Modifying Tables Manually
Setting Additional Attributes
Defining a Primary Key
Setting Blinding-Related Attributes
Setting Data Processing-Related Attributes
Adding Columns to a Table
Using SDTM Identifiers for Columns
Specifying Masking Attributes for a Column
Adding Constraints to a Table
Adding Subject Visit and Subject Tables
Copying Subject Visit and Subject Tables
Subject Visit Table
Subject Visit Table Requirements
Shipped Subject Visit Table Metadata
Subject Table
Shipped Subject Table Metadata
Defining Tables to Support Filtering in the Listings Pages
How Filters Work
Subject Visit Table
Subject and Visit SDTM Variable Columns in All Tables
Security Privileges for Making Filters Public
Configuring the InForm Connector
Adding or Editing a Remote Location
Adding or Editing a Web Service Location
Loading Data
Suspending and Resuming Data Loading
Scheduling Data Loads in the Production Lifecycle Area
Loading and Synchronizing InForm Metadata
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
Viewing Detected Files and Forcing Actions
Updating Validation Status
Applying Security
Assigning User Groups to Objects
Modifying Clinical Data Models
Modifying a Non-InForm Model Manually
Modifying an InForm Input Model
Manual Changes Not Allowed in InForm Models
Manual Changes Allowed in InForm Models
Removing a Clinical Data Model
Upgrading a Clinical Data Model to the Latest Library Version
Viewing Data
4
Using Libraries
About Library Clinical Data Models
Creating and Modifying Library Clinical Data Models
Creating a Library Clinical Data Model
Modifying Library Clinical Data Models
Removing a Clinical Data Model
Creating Code Lists
Code List Examples
Removing a Code List
5
Transforming Data to Standard Structures
About Transformations
Creating Mappings
Creating Model Mappings
Creating Table Mappings
Marking Target Tables as Not Used
Using Automap
Mapping Tables Manually
Adding Expressions on Mapped Sources
Creating Staging Tables
Creating Column Mappings
Undoing Mappings
Table Transformation Types
Direct
Join
Union
Pivot
Unpivot
Custom
Using the Expression Builder
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 Transformations
Running a Transformation
Modifying a Transformation
Upgrading a Mapping to Reflect Model Metadata Changes
Defining a Custom Program
Enabling Data Lineage Tracing in a Custom Program
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
About Validation Checks
Creating a Validation Check Batch
Creating a Validation Check
Building the Validation Check Query
Selecting Columns to Display in VC Listings
Creating Joins
Specifying Criteria
Defining Validation Check Details
Installing Validation Checks
Running a Validation Check Batch
Modifying a Validation Check
Reordering Validation Checks
Disabling a Validation Check
Upgrading a Validation Check Batch
Creating a Custom Validation Check
7
Configuring Your Discrepancy Workflow
Discrepancy States and Allowed Transitions
Discrepancies on Lab Data
Discrepancies on InForm Data
Communication with InForm
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 Custom Actions
Creating and Editing Actions
8
Administration
Viewing and Setting Up Lab Data Sources
Adding a Lab Data Source
Modifying a Lab Data Source
Removing a Lab Data Source
Viewing and Setting Up InForm Data Sources
Adding a Remote Location
Adding a Web Service Location
Removing a Remote Location or Web Service Location
Modifying a Remote Location or Web Service Location
Setting Up File Watcher for the Instance
Setting Up Root Folders for File Watchers
Setting Up Study Watched Folders
Setting Up the File Watcher Service
Setting Up the Distributed Processing Server for File Watcher
Define Service Locations and Services
Start the DP Server Service
Setting Up Study File Watchers
Creating and Editing Study File Watchers
Selecting the Distributed Processing Server
Monitoring File Watchers
Viewing File Watchers
Stopping and Starting File Watchers
Restarting Watchers that Are Not Working
Suspending and Resuming Automatic Data Loading
Viewing and Creating Categories
Viewing and Creating Discrepancy Tags
Creating a New Tag
Modifying Existing Tags
Creating and Using Flags
Creating a Flag
Flag Rules
Comparing Flags, Tags, and Categories
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 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
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
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 Managing Study 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
Select the Transformation
Submit the Job
Automatically Triggering Transformations and Validation Checks by Upstream Processes
Viewing and Running Validation Check Batches
Submit the Validation Check Batch
Viewing Validation Check Batch Job History
Viewing Data Files Not Processed
Changing 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
Freezing Columns
Detaching a Pane
Querying By Example
Using Online Help
11
Reviewing Data
Viewing All Study Data Using Default Listings
Viewing Validation Check Listings
Creating and Viewing Custom Listings
Using the Query Builder to Create Custom Listings
Selecting Columns to Display in Custom Listings
Creating Joins
Specifying Criteria
Testing and Saving the Query
Modifying Custom Listings
Copying Custom Listings
Creating and Using Filters
Creating and Editing Subject Filters
Creating and Editing Visit Filters
Creating and Editing Visit Day Filters
Creating and Editing Visit Date 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 Date Filters
Using the Find Feature
Creating Discrepancies Manually
Showing Discrepancies
Showing Flags
Flagging Data
Viewing Data Lineage
Viewing Blinded Data
Exporting All to Excel
Exporting All to CSV
12
Cleaning Data
Managing Discrepancies
Acting on Multiple Discrepancies
Editing a Single Discrepancy
Discrepancy Display
Icons
Refresh
Filtering Discrepancies
Filtering by Category
Filtering by Multiple Criteria
Viewing Discrepancy Details
Viewing Discrepancy History
Displaying the Full Record
Exporting to Excel
Adding a Comment
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
Naming Studies and Libraries
Customizable Naming Validation Package
Required Syntax for Table Metadata Text Files
Object Ownership
Effects of User Group Assignment to Objects
Oracle DMW Object Hierarchy
DMW Domain
DMW Utilities
Study Category Domains
Study Domains
Lifecycle Areas
Clinical Data Models
Load Sets
Programs
Transformation Maps
Business Areas
Data Marts
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
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
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
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
DMW_STUDY_ADMIN
Clinical Data Models and Query Builder
Discrepancies
Flags
Filters
Data Lineage Tracing
Validation Checks
InForm
File Watcher
Transformations and Query Builder
DMW_STUDY_INST_ACCESS
Clinical Data Models and Query Builder
Blinding
Discrepancies
Data Lineage Tracing
Validation Checks
Transformations
DMW_STUDY_INFORM_CONFIG
InForm
Glossary
Index