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Contents
Title and Copyright Information
Preface
Audience
Change Record
Documentation Accessibility
Finding Information and Patches on My Oracle Support
Finding Oracle Documentation
Related Documents
Conventions
1
Getting Started
About Oracle Thesaurus Management System (TMS)
Usage Models
Full Integration
Partial Integration
No Integration
Dictionary Definition and Customization
Flexible Definition
Customization
The API
Basics of Using TMS
Launching the Application
Getting Started with Your Oracle Health Sciences SSO Account
Changing Your Database Password
Using TMS Windows
Understanding Color Indicators
Changing the Display
Using the Tree Structure
Changing the Sort Order
Options Menu
Showing the Environment
Selecting Multiple Records
Changing the Database Connection
Printing the Contents of a TMS Window
Querying in Windows
Using the Favorites Menu
Getting Help
Online Help
Oracle Help Center
Documentation Accessibility
2
Reports and Batch Jobs
Setting Parameters
General Parameters
Job-Specific Parameters
Scheduling Parameters
Using Parameter Sets to Populate Job Parameters
Saving a Parameter Set
Retrieving a Parameter Set
Running a Job
Checking Job Status
Checking the Status of the Last Job Submitted
Checking Job Status in the Job Status Window
Stopping Job Execution
Part I Setting Up and Administering TMS
3
Administration
Security
Predefined Roles
Enrolling an Administrator
Defining Users
Defining a New User
Assigning and Revoking Roles
Assigning Roles to a User
Revoking Roles from a User
Changing a User's Password
Assigning Data Access Groups to a User
Migrating Account Information from Oracle Clinical
Using Data Access Groups (DAGs) for Security
Defining Security Columns
Creating a DAG
Setting DAG Rules
About DAG Rules
Defining DAG Rules
Rules for External System Data
Rules for Task Allocation
Assigning Users to DAGs
DAG and Settings Inconsistencies Report
About the DAG Settings and Inconsistencies Report
Running the DAG and Setting Inconsistencies Report
Creating and Dropping External System Value Indexes
Customizing Defaults in TMS Windows Using TMS Settings
Profiles
User Profiles
Full List of TMS Settings
OPA Settings
TMS Forms Settings
TMS HTML Settings
Defining the Settings for a Particular Profile
Defining a Setting When No Parent-Child Setting Relationship Exists
Defining a Setting in Parent-Child Relationships
Defining and Maintaining Profiles
Assigning Profiles to Users
Adding a Profile to a User's Set of Profiles
Configuring a User's Profile Search Order
Setting TMS Preferences with Reference Codelist Values
Reference Codelists in Integrated and Nonintegrated Environments
Editing Reference Codelists
TMS_CONFIGURATION
CREATEGLOBALVTA
GLOVTAAPPRREQD
DOMVTAAPPRREQD
NONAPPRVTAUSED
ALLOWGLOVTAS
MAINTAINEXT
SUPPRESNAMDRELS
WRKFLWINFALLVSN
VTAAPPRFLAG
DTAPPRFLAG
CLCLEARCOMMENT
CLCLEARACTION
AUTOGLOVTAS
SYNCREFRESHMV
ADVDICTFEATURES
EMBEDDEDTMS
OCDISCINTCOMM
MTRECCLASSHOUR
DOMACTAPPRREQD
DEALLOCONLY
NONAPPRDICTCODE
Changing TMS_CONFIGURATION Settings After Data Has Been Processed
Other Installation-wide Codelists
TMS_LANGUAGES
TMS_QUERY_TYPE
TMS_SOURCE_MAT_VIEWS
TMS_TAL_POOL_CONFIGURATION
TMS_X_SEARCH
Local Codelists
REPORTS_CONFIG
TMS_DSI
Autoclassification
Using Search Objects
Domain Match
Custom Search Objects
Creating Global VTAs during Autoclassification
Running Autoclassification
Synchronization
Scheduling Frequency
Data Processed During Synchronization
Synchronization Processing Order
Running Synchronization
Writing a Procedure to Change the Dictionary Display
Writing a Dictionary Term Display Procedure
Controlling the Use of Materialized Views
Choosing Materialized or Regular Views for Each External System Value
Creating Source Term Views
Including the Materialized Views Refresh in the Synchronization Process
Refreshing Source Term Materialized Views
Enabling Context Searches for Non-English Dictionaries
Refreshing the Context Server Index
Analyzing Tables
Running Scripts to Gather Schema Statistics for the 12c Optimizer
Adding and Configuring WebLogic Server Data Sources
Add Data Sources
Configure Maximum Connections
Configure Inactive Connection Timeout
TMS Lite Browser Administration
Granting User Privileges for Using the TMS Lite Browser
Creating a Launch Page, Button, or Link for the TMS Lite Browser
Creating or Customizing a Launch Page to Use Provided Scripts
Sample Java Script for Launching in a New Window without Tool or Menu Bar
Sample JavaScript for Checking if Compatibility View Is On
Customizing the TMS Lite Browser URL to Support Additional Databases or Automatic Login
Enabling and Disabling Automatic Login
Enabling Automatic Login
Disabling Automatic Login
Enabling TMS Lite Browser Logs
Using the About Window
Troubleshooting
Report Error
Restart Application Server After Redeploying TMS Lite Browser
Cannot Log In to Application
4
Integrating TMS with Oracle Clinical
Managing the TMS/Oracle Clinical Workflow
First Review in TMS
Manual Classification
Applying an Action
Sending a Discrepancy Message
First Review in Oracle Clinical
Setting First Review
Batch Validation in an Integrated OC/TMS Environment
OC and TMS Data Exchanged During Batch Validation
Running Only the TMS Portion of Batch Validation
Batch Validation Execution Order
Effect of TMS Errors on Batch Validation
Setting Up Data Collection in Oracle Clinical
Defining and Using Question Sets
Defining a Question Set
Defining Question Set Variables
Defining Questions
Defining a Parent Question
Defining a Child Question
Using a Derived Question as a Parent Question
Associating Child Questions with Question Set Variables
Associating Questions with Question Groups and DCMs
Planning Question Groups and DCMs for RDC Special Listings
Adding Derived Questions to an Ongoing Study
Linking an Oracle Clinical Study to TMS
Linking a Project with a TMS Dictionary and Domain
Linking a Study to a TMS Dictionary and Domain
Using a New Version of a Dictionary for an Ongoing Study
Upgrading to a New Dictionary Version with the Same Structure
Upgrading to a New Dictionary Version with a New Structure
Accessing Oracle Clinical Data in TMS
Setting Integration Reference Codelist Values
OCL_OPTIONS_TYPE_CODE
TMS_OPTIONS
DISCREPANCY REV STATUS CODE
OCL_STATE
5
Integrating TMS with Other Systems
Using TMS with Other Oracle Health Sciences Applications
Using TMS with Oracle Clinical
Using TMS with the Remote Data Capture Option
Using TMS with AERS
Integrating TMS with Non-Oracle Systems
Full Integration
Partial Integration
Using TMS with Disconnected Systems
Setting Up Disconnected System Integration
Setting Up the Sponsor Instance
Setting Up the Source Instance
Creating Directories on the Database Server
Defining the External Source Data System
Running the DSI Initialization Job
Register Remote Databases
Defining Disconnected System Integrations
Defining X Areas
Defining XML Tag Mappings
Setting DSI Preferences with Reference Codelist Settings
Synchronizing Dictionary Contents Between Sites
Granting User Privileges
Using DSI from the Source Site
Processing Source Data
Exporting Data
Sending the XML File to the Sponsor Site
Importing Data
Updating External System Data
Using DSI from the Sponsor Site
Importing Data
Processing Source Site Data
Exporting Data
Sending the XML File to the Source Site
Removing X Area Data from the Sponsor Site
Viewing XML File and Record Statuses
Viewing File and Record Status
Deleting Files
Setting the Filter
Viewing Error Files
DSI Batch Jobs
Export DSI Data
Import DSI Data
Export Active X Areas
Export X Areas by External System/Instance
Import X Areas by External System/Instance
Delete DSI X Areas
Delete Remote DSI Databases
Force Rederivation
Defining External System Information in TMS
Where External System Information Appears
Defining the External System in TMS
Setting Up External System Columns and Details
Define External System Columns
Define Column Details
Defining Views and Functions in the External System
Define Views in the External System
Define Functions in the External System
Setting Up External System Drill-down Queries
Defining the Name and External System for a Query
Defining Query Columns
6
Defining and Loading Dictionaries
Dictionary Types
Strong Dictionaries
Weak Dictionaries
Virtual Dictionaries
Filter Dictionaries
About Filter Dictionaries
Using MedDRA SMQs in TMS
Filter Dictionary Rules
Defining Informative Notes for SMQ Algorithms
Maintaining Filter Dictionaries
Searching Filter Dictionaries Using the TMS Lite Browser
Nonunique Coding Level Dictionaries
Classifying High-Level Terms Based on Indication
Planning Strong Dictionary Structure
Uniqueness of Terms
Defining Relationships Between Dictionary Levels
Mandatory Relations
Cardinality
Primary Links and Primary Path Links
Grouping Levels
Classifying Verbatim Terms to a Group Level
Requiring a Primary Link to a Group Level
Group Level Constraints
Tree Structure Display of Group Levels
Deriving Terms
Derivation Path
Setting Up Derivation Within a Dictionary
Enforcing the Structure
Strong Dictionary Structure in Other Forms
Defining a Dictionary
Defining the Basic Dictionary Settings
Defining the Dictionary Levels
Defining Relations Between Levels (Strong Dictionaries Only)
Level Selection in the Define Dictionaries Window
Defining Relations Between Levels
Defining Level Details
Understanding Level Details
Defining a Dictionary's Level Details
Setting the Dictionary's Status to Active
Defining Dictionary-wide Informative Notes Before Activation
Loading a Dictionary
Required Setup
About Load Scripts
Load Script Requirements
API Packages
Load Scripts and Activation Groups
Downloading Sample Scripts
Activating Loaded Terms
Creating or Assigning an Activation Group
Running the Activate Preliminary Data Batch Job from the GUI
Running Activation from SQL*Plus
Add Validation Code (Optional)
Refreshing the Context Server Index
Gathering Statistics to Improve Performance
About Activation
Rules Enforced
Database Tables
Activation Failure Messages
DML Transactions
More Information on Activation
Evaluating Dictionary Contents
Maintain Data Repository Window
Preliminary Repository Report
Defining Links Between Dictionaries
Defining a Cross-Dictionary Link
Defining a Translation Derivation Link
Defining Filter Dictionary Links
Creating Domains and Assigning Dictionaries to Domains
Creating a Domain
Assigning a Dictionary to a Domain
Unassigning a Dictionary from a Domain
7
Defining Other TMS Elements
Defining HTML Layouts
Defining HTML Layout Functions
Sample Package Specification
Defining an HTML Layout Function
Defining the Layout Name and Function
Defining the Layout Columns
Deleting a Layout
Customizing Report Templates
Downloading a Report Template
Modifying a Report Template
Uploading a Custom Report Template
Updating or Deleting a Custom Report Template
Defining and Using Actions
Action Types
Answerable Actions
Unaswerable Actions
Internal Actions
Using Actions
Defining an Action
Defining Search Objects
Defining a Search Object
Setting the Search Objects for a Dictionary
Specifying the Use of a Search Object with a Particular Dictionary
Removing a Search Object's Association with a Dictionary
Deleting a Search Object
Creating Custom Search Algorithms
Writing a Search Algorithm for Autoclassification
Writing a Search Algorithm for Candidate Term Generation
Writing a Search Algorithm for Extended Searches
Defining Named Relations
About Named Relations
Types of Named Relations
Defining Named Relations
Defining Dictionary NRLs
Writing Named Relation Activation Rules
Defining Informative Note Attributes
Overview of Informative Notes and Attributes
Defining an Informative Note Attribute
Defining Informative Note Attribute Properties
Defining the Details for the Informative Note Attribute
Making Informative Note Attributes Available for Dictionaries and Record Types
Defining Dictionary-wide Informative Notes
Entering Variables in Dictionary-wide URL Informative Notes
RDC Action Informative Notes
Defining a Dictionary Version Informative Note
8
Upgrading to a New Dictionary Version
Upgrading TMS Dictionaries
Running the Autoprocess VTAs/VTIs Job
Running Dictionary Upgrade Reports
Dictionary Impacts Report
Predict VTA/VTI Report
Site Impacts Report
Omission Impacts Report
Cross Dictionary Impacts Report
Maintaining Predictionary Terms and Relationships
About the Maintain Predictionary VTAs/VTIs Tabs
Common Procedure for Using All Tabs
Setting the Filter and Querying
Declassifying Terms
Reclassifying Terms
Classifying Terms
Deleting Terms and Relations
Common Fields in the Maintain Predictionary VTAs/VTIs Window
Common Fields in the Upper Tabs
Common Fields in the Repository Tab
9
Allocating Tasks to TMS Users
About Task Allocation
Setting Up Task Allocation
Setting Task Allocation Reference Codelist Values
Adding Workers to the Task Allocation System
Setting Each Worker's Capacity
Setting Each Worker's Availability
Maintaining User Tasks Allocation Pools
Allocating Tasks to Workers
Using Direct Allocation
Using Automatic Pool Allocation
Using Manual Allocation by Term
Tracking Users' Workloads
Tracking Workloads in the Task Allocation by Quantity Window
Tracking Workloads as Activities
Task Allocation Algorithms
Direct Allocation Algorithm
Automatic Pooled Allocation Algorithm
Pooled
Pooled by Workload
Unfulfillable Assignments Report
Part II Managing Classifications
10
Omission Management
Classification Concepts
Classifying Terms Manually
Query for Unclassified Verbatim Terms
Look for a Good Match
Classify a Term
Apply an Action to a Term
Applying an Action
Applying a Discrepancy Message
Creating an Informative Note for the Classification
DT Filter for Auxiliary Information
Using the Extended Search Button
The Above Button
The Below Button
The Indication Button
Classifying Indication Omissions
Approving and Unapproving VTAs
Understanding the Approve VTAs Window
Changing the Subtype and Adding Comments
Approving a Nonapproved VTA
Declassifying a VTA
Browsing the Audit Trail
Approving Action Assignments
Understanding the Approve Action Assignments Window
Distinct and All Action Assignments
Distinct and All Action Assignment Audit Trail
Buttons
Approving a Nonapproved Internal Action Assignment
Modifying the Action Assignment
Term Statuses
Using the Status/Notes Pop-up Window
Status History
Note History
Adding a Note to a Term
Using the VT History Window
Creating and Using Activity Lists
Using Activity Lists
Setting Filters and Creating Activity Lists
Setting Filters
Saving Filter Settings as an Activity
Maintaining Activity Lists
Omission Management Reports
VTA/VTI Creation Report
Classification Statistics Report
VT Domain Differences Report
VT Auxiliary Classifications Report
Unclassifiable Indication Omissions Report
Indications Assignments Report
11
VTA and VTI Maintenance
Promoting and Demoting VTAs
About the Window
Global and Domain VTAs
When You Promote a Domain VTA to Global Status
Demoting Global VTAs to Domain Status
Approval Status for Global and Domain VTAs
Informative Notes
Promoting a VTA
Demoting a VTA
Maintaining Action Assignments
About the Maintain Action Assignments Window
Assigning an Action to a Term
Rejecting an Action Assignment
Modifying an Existing Action Assignment
Reclassifying and Declassifying Verbatim Terms
About the Reclassify Verbatim Terms Window
Common Fields in the Distinct and All VTAs/VTIs Tabs
Distinct Verbatim Term Assignments
All VTAs/VTIs
Repository Terms
Reclassifying a Verbatim Term
Declassifying a Verbatim Term
Reclassifying Indication Assignments
Performing High-Level Reclassification
Rules and Constraints
The High-Level Reclassification Window
Lists
Upper Block: Classifications
Lower Block: Higher-level Terms
Performing High-Level Reclassification
Modify Classification
Undo Classification
Copying Domains
Planning a Domain Copying Operation
Copying Domain Information Using the TMS User Interface
Copying Domain Information with the TMS API
Handling Errors that Arise from the Domain Copying Process
Deleting Domain Copying Error Logs
Reassigning Oracle Clinical Elements
Using Domain Copying with Virtual Dictionaries
VTA and VTI Maintenance Reports
Nonapproved VTs Report
Classification to a New Domain Report
Verbatim Term Modifications Report
X Areas with Outstanding Changes Report
12
Repository Maintenance
About Repository Data
Data Currency and Data Source Filters
Controlling the Default Approval Status of New Terms
About the Maintain Repository Data Window
Term and Relation Icons
Current Level and Term
Display of Relationships in Strong Dictionaries
Display of Named Relations
Using an Extended Search
Navigating to Data in the Maintain Repository Data Window
STEP 1: Open the Window and Select Domain and Dictionary
STEP 2: Choose or Create an Activation Group
STEP 3: Choose a Data Currency Option
STEP 4: Choose a Data Source
STEP 5: Choose a Level and Term
Modifying Repository Data in the Maintain Repository Data Window
Maintaining Terms, Relations, and VTAs
Adding and Deleting Relationships Between Terms
Deleting Terms from a Dictionary
Adding a Term to a Dictionary Level
Modifying a Term
Define Strong Relations to Terms in Other Levels
Current Level Block Fields
Upper Block Fields
Resolving High-Level Omissions
Using the Repository Authoring Window
Structure of the Window
Creating New Terms
Creating Named Relations Between Terms
Defining a Primary Path
Deleting Terms
Setting Up Cross-Dictionary Relations
Assign Both Dictionaries to the Same Activation Group and Domain
Creating Cross-Dictionary Relations Between Terms
Grooming Data that Failed Activation
Creating Informative Notes for Terms and Relations
Entering Variables in URL Informative Notes
Using the Maintenance Wizard
Overview of Maintenance Wizard Tasks
Move Relation
Move Term
Move Term and Copy Relations
Move and Merge Term
Merge Term
Exchange Terms
Undoing a Change Before Activation
Viewing and Deleting Dictionary Loading Error Logs
Browsing Dictionary Loading Error Logs
Deleting Dictionary Loading Error Logs
Using the Release Label Authoring Window
Defining a Release Label Named Relation Between Two Terms
Checking Data Before Activation
Transferring Data
Additional Fields
Activating Data
Repository Maintenance Reports
Preliminary Repository Report
Dictionary Version and Release Information Report
Translation Reports to Identify Inconsistent Data
Inconsistent Dictionary Codes Report
Duplicate and Null Dictionary Codes Report
Inconsistent Dictionary Relations Report
Part III Browsing the Data Repository
13
Browsing the Repository in TMS
Browsing Informative Notes
Viewing Data in the Browse Repository Data Window
Viewing Current and Historical Data
Current Level Block
Current Level
Current Term
Changing the Data Displayed
Current Level Block Fields
Level Above Block
Level Below Block
Changing the Sort Order
Viewing Terms Related to the Current Term
Display of Deleted Data in Virtual Dictionaries
Strong Dictionaries in the Drill Down Dictionary Hierarchy Window
Weak Dictionary Folders in the Drill Down Dictionary Hierarchy Window
Understanding the Origin Field
Using a Child Search
Using an Extended Search
Viewing Data in the Browse VT Classification Data Window
Browsing Verbatim Term History
Repository Reports
Date Comparison Report
Dictionary Comparison Report
Dictionary Export Report
14
Using the TMS Lite Browser
Overview
Available Repository Data and Verbatim Terms
User Roles
Accessible Dictionaries
Autoquerying Dictionaries
Searching Across Dictionaries and Domains
Available External System Data
Basic and Complex Searches
TMS Lite Browser Map
Choosing a Type of Search
Exploration Tab Searches
Research Tab Searches
Searching for Terminology Data
Using Special Characters in Searching
Perform a Simple Terminology Search
Perform an Advanced Terminology Search
Step 1: Determine the Terminology Data Set
Step 2: Choose Term Query Criteria
Step 3: Include Related Dictionary Data in the Search
Analyze the Results of a Terminology Search
Presentation of Results in the Terminology Search Window
Navigating Through Results
Refining Your Search
Select a Term
Searching for Terms Using Filter Dictionaries
Performing a Simple VTA Filter Search
Performing an Advanced VTA Filter Search
Viewing VTA Filter Search Results
Performing a Simple Source Data Filter Search
Performing an Advanced Source Data Search
Searching for Verbatim Term Assignments (VTAs and VTIs)
Perform a Simple Verbatim Term Search
Perform an Advanced Verbatim Term Search
Terminology
Verbatim Term
Relations
External System
Analyze the Results of a Verbatim Term Search
Presentation of Results in the Verbatim Term Search Window
Refining Your Search
Select a Verbatim Term Record
Viewing Source Data for a Verbatim Term Record
Viewing a Source Data Record with Markup
Viewing Data from an External Drill-down Function or View
Viewing VTA and Omission Status Information
Performing a Simple Verbatim Term Status Search
Performing an Advanced Verbatim Term Status Search
Viewing Verbatim Term Status History Details
Viewing a Term's Action History
Viewing the Action History of an Omission Occurrence
Viewing External System Information for Omissions
Browsing a Dictionary Hierarchy
Introduction to Browsing the Dictionary Hierarchy
Starting a Browsing Session from the Hierarchies Link
Browsing in the Terminology Data Tree Structure
Expanding a Branch One Level Using the Arrow Keys
Expanding a Branch in the Dictionary
Reversing the Orientation of the Tree Window
Launching the Term Details Window
Searching for Source Data
Starting a Simple Search for Source Data
Starting an Advanced Search for Source Data
Application
Verbatim Terms
Term
Entering the Query Criteria
Analyzing Source Data Search Results
Viewing a Source Data Record
Examining a Term's Details and History
Using the Term Details Window
Term (Currency Status)
Paths
Indication Assignments
Related Terms
Related Release Label Terms
Using the Term History Window
Version
Relations
Examining a Relation's Details and History
Using the Relation Details Window
Using the Relation History Window
Examining a Record's Informative Notes
A
Sample Dictionary Definitions
Practice Dictionary CLS
CLS Structure Diagram
CLS Level Definitions
CLS Level Relations Definitions
Sample MedDRA Dictionary
Sample MedDRA Dictionary Structure
Sample MedDRA Dictionary Level Definitions
Sample MedDRA Dictionary Level Relations Definitions
Sample MedDRA Dictionary with a Primary Path
Sample MedDRA Dictionary with a Primary Path Structure
Sample MedDRA Dictionary with a Primary Path Dictionary Level Definitions
Sample MedDRA Dictionary with a Primary Path Level Relations Definitions
Sample MedDRA SMQ Dictionary
Sample MedDRA SMQ Dictionary Structure
Sample MedDRA SMQ Dictionary Level Definitions
Sample MedDRA SMQ Dictionary Level Relation Definitions
Sample WHODrug Format B2 Dictionary
Sample WHODrug Format B2 Dictionary Structure
Sample WHODrug Format B2 Dictionary Level Definitions
Sample WHODrug Format B2 Dictionary Level Relations Definitions
Sample WHODrug Format B3 Dictionary
Sample WHODrug Format B3 Dictionary Structure
Sample WHODrug Format B3 Dictionary Level Definitions
Sample WHODrug Format B3 Dictionary Level Relations Definitions
Sample WHODrug Dictionary with Format C or C3
Sample WHODrug Dictionary with Format C or C3 Structure
Sample WHODrug Dictionary with Format C or C3 Level Definitions
Sample WHODrug Dictionary with Format C or C3 Level Relations Definitions
WHODrug Format C or C3 Data Loaded as TMS Informative Notes
Sample SNOMED Dictionary
Sample SNOMED Dictionary Structure
Sample SNOMED Dictionary Level Definitions
Sample SNOMED Dictionary Level Relations
B
Disconnected System Integration XML Files
XML File Names
XML File Structure
Key to XML File Tags
Validation of Non-TMS XML Files
C
GUI Quick Reference
Quick Reference for TMS Windows
Quick Reference for Batch Job and Reports Windows
Glossary
Index
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