SAS Clinical Data Integration 2.5 User’s Guide

SAS Clinical Data Integration 2.5 User’s Guide
SAS
Clinical Data Integration
2.5
®
User’s Guide
SAS® Documentation
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SAS® Clinical Data Integration 2.5: User's Guide
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Contents
What’s New in SAS Clinical Data Integration 2.5 . . . . . . . . . . . . . . . . . . . . . . . ix
PART 1
Introduction
1
Chapter 1 / Overview: SAS Clinical Data Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
What Is SAS Clinical Data Integration? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Typical Workflow in SAS Clinical Data Integration . . . . . . . . . . . . . . . . . . . . . . 4
Recommended Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
PART 2
Information for Clinical Administrators
7
Chapter 2 / Data Standards Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Overview: Data Standards Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Importing Data Standards Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Refreshing Data Standard Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Customizing Data Standard Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Customizing Data Standard Domain Templates . . . . . . . . . . . . . . . . . . . . . . . 23
Managing Controlled Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Managing Data Standard Compliance Checks . . . . . . . . . . . . . . . . . . . . . . . . . 31
Analyzing Domain Use and Promoting a Domain to Be a Template 42
Chapter 3 / Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Overview: Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Run and Save a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
vi Contents
PART 3
Information for Trial Managers
51
Chapter 4 / Studies and Submissions Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Overview: Studies and Submissions Management . . . . . . . . . . . . . . . . . . . . 54
Working with Folder Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Working with Library Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Creating a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Managing Studies and Submissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Monitoring the Statuses of Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Comparing the Metadata of a Standard Domain to Its Template . . . . 80
Information for Clinical Programmers or Data
Managers 83
PART 4
Chapter 5 / SDTM Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Types of Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Creating a Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Domain Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Converting a Domain from One Data Standard to
Another Data Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Importing Domain Tables from a Define.xml File . . . . . . . . . . . . . . . . . . . . . 103
Loading Data into Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Assessing CDISC SDTM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Chapter 6 / ADaM Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Types of ADaM Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Special Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Creating an ADaM Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Promoting an ADaM Data Set to Be a User-Defined Template . . . . . 128
Create an ADaM Data Set from a User-Defined Analysis Data Set 130
Assessing ADaM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Contents
vii
Chapter 7 / Creating a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Transforming SDTM Domains or ADaM Data Sets
into a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Adding Information to the Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Creating the Define.xml file from Customized Data . . . . . . . . . . . . . . . . . . 150
Validating a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Chapter 8 / SAS Transport Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Overview of SAS Transport Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Import a SAS Version 5 Transport File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Export a SAS Version 5 Transport File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
PART 5
SAS Integration Adapter for Medidata Rave
161
Chapter 9 / General Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Define a Medidata Rave Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Enable a SAS Clinical Data Integration User to Log
In to Medidata Rave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Verify That the Medidata Rave Server Has Been
Registered Properly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Chapter 10 / Study Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Manage the Connection between a SAS Clinical
Data Integration Study and a Medidata Rave Study . . . . . . . . . . . . . . . 168
Create a SAS Clinical Data Integration Data Table
Definition from Medidata Rave Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Manage the Medidata Rave Properties of a SAS
Clinical Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Managing the Codelist Table in a SAS Clinical Data
Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Review the Medidata Rave Properties of a SAS
Clinical Data Integration Data Table Definition . . . . . . . . . . . . . . . . . . . . . . 184
viii Contents
Retrieving Medidata Rave Study Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Schedule a Job to Update Study Data from Medidata Rave . . . . . . . . 190
PART 6
Appendixes
191
Appendix 1 / Addition of Users to the Clinical Administrator Group . . . . . . . . . . . . . 193
Appendix 2 / Repair of Clinical Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Appendix 3 / SAS Clinical Data Integration Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
ix
Whatʼs New
What’s New in SAS Clinical Data
Integration 2.5
Overview
SAS Clinical Data Integration 2.5 contains these enhancements:
n
SDTM 3.2 support
n
Define-XML 2.0 support
n
SAS Version 5 transport file handling
n
Creation of metadata from a define.xml file
n
Incremental update of data standard metadata from the SAS Clinical Standards
Toolkit
n
Comment metadata support
n
Controlled terminology handling
n
Data standard management
x What’s New in SAS Clinical Data Integration 2.5
SDTM 3.2 Support
There is full support for the CDISC SDTM 3.2 data standard.
Define-XML 2.0 Support
You can create and validate CDISC Define-XML 2.0 files using SAS Clinical Data
Integration transformations.
SAS Version 5 Transport File Handling
You can use SAS Clinical Data Integration transformations to read and write SAS
Version 5 transport files.
Creation of Metadata from a Define.xml
File
You can import study and table definitions from a define.xml file, including definitions for
SDTM and ADaM.
Data Standard Management
xi
Incremental Update of Data Standard
Metadata from the SAS Clinical
Standards Toolkit
You can update SAS Clinical Data Integration data standard metadata incrementally at
any time with the current definitions from the SAS Clinical Standards Toolkit. You can
select any subset of domain templates and column groups to update. You can update
validation checks with those currently registered to the SAS Clinical Standards Toolkit.
Comment Metadata Support
SAS Clinical Data Integration reads and stores the SAS Clinical Standard Toolkit’s
default comment definitions for tables and columns defined in a data standard. These
comments are written to the output file during define.xml file creation.
Controlled Terminology Handling
SAS Clinical Data Integration supports additional controlled terminology information in
imported terminology tables. SAS Clinical Data Integration transformation support for
controlled terminologies defined outside of the SAS Clinical Standards Toolkit has been
enhanced.
Data Standard Management
Data standard administrators have additional flexibility in managing custom data
standard definitions for their organizations. SDTM domains, SEND domains, and ADaM
xii What’s New in SAS Clinical Data Integration 2.5
data sets in a study can be reassociated with different SAS Clinical Data Integration
data standard definitions. Custom domains and data sets can be promoted from a study
to replace existing definitions within a data standard.
1
Part 1
Introduction
Chapter 1
Overview: SAS Clinical Data Integration . . . . . . . . . . . . . . . . . . . . . . . . . 3
2
3
1
Overview: SAS Clinical Data
Integration
What Is SAS Clinical Data Integration? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Typical Workflow in SAS Clinical Data Integration . . . . . . . . . . . . . . . . . . 4
Overview: Typical Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Workflow Owners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Recommended Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
What Is SAS Clinical Data Integration?
SAS Clinical Data Integration supports the pharmaceutical-industry needs for
transforming, managing, and verifying the creation of industry-mandated data standards
such as those created by Clinical Data Interchange Standards Consortium (CDISC).
SAS Clinical Data Integration relies on SAS Data Integration Studio to provide
centralized metadata management using the SAS Metadata Server and the tools that it
provides to visually transform data. SAS Clinical Data Integration enhances its usability
by adding new metadata types, plug-ins, and wizards. These enhancements help you
perform clinically oriented tasks such as importing data standards, creating studies and
submissions, and adding specialized transformations for mapping clinical data into a
standard data model. SAS Clinical Data Integration leverages the SAS Clinical
Standards Toolkit to provide validation and conformance checking.
4 Chapter 1 / Overview: SAS Clinical Data Integration
SAS Clinical Data Integration enables you to accomplish these goals:
n
improve the consistency of submissions and studies
n
improve the long-term management and growth of data
n
use data standards effectively
n
use a centralized SAS Metadata Server
n
use the powerful and user-friendly features of SAS Data Integration Studio to
manage metadata, generate and execute SAS Clinical Standards Toolkit code, and
visualize the results
Typical Workflow in SAS Clinical Data
Integration
Overview: Typical Workflow
The features and functionality provided by SAS Clinical Data Integration enables the
following workflow:
1 Import a data standard and controlled terminology. (For more information, see
“Importing Data Standards Metadata” on page 11 and “Importing Terminology
Data Sets” on page 24.
2 Create studies and submissions. (For more information, see “Creating a Study or
Submission” on page 64.)
3 Create domains. (For more information, see “Creating a Domain” on page 88.)
4 Standardize and validate data. (For more information, see “Assess CDISC SDTM
Compliance” on page 108 and “Assess ADaM Compliance” on page 132.)
5 Analyze data standard use across studies and submissions. (For more information,
see “Analyzing Domain Use and Promoting a Domain to Be a Template” on page
42.)
Typical Workflow in SAS Clinical Data Integration
5
Workflow Owners
Typically, different people own different tasks in the workflow. However, ownership can
vary depending on the company, and a person might perform tasks in more than one
role. The following user definitions explain the typical owners and their tasks in the
workflow.
Clinical administrator
defines and manages data standards. Analyzes how data standards are
implemented by programmers. Data standards administrators can view trends about
how a domain is used by programmers. These trends might identify a new column to
add to a domain, or point to a custom domain that you should promote into the
standards.
For tasks that are typically performed by clinical administrators, see Chapter 2, “Data
Standards Administration,” on page 9.
Trial manager
defines studies and submissions, defines authorization, and sets the defaults that
programmers use when defining content. Setting defaults ensures that programmers
use the correct version of the data standards.
For tasks that are typically performed by trial managers, see Chapter 4, “Studies and
Submissions Management,” on page 53.
Clinical programmer and data manager
creates standard and custom domains, writes jobs to extract and transform data into
domains, and writes jobs to validate compliance of domains to a data standard.
For tasks that are typically performed by clinical programmers or data managers,
see Chapter 5, “SDTM Domains,” on page 85.
6 Chapter 1 / Overview: SAS Clinical Data Integration
Recommended Reading
For the following documentation, see the SAS Customer Support website at http://
support.sas.com.
n
SAS Data Integration Studio: User's Guide at http://support.sas.com/
documentation/onlinedoc/etls/
n
SAS Clinical Standards Toolkit: User's Guide at http://support.sas.com/
documentation/onlinedoc/clinical/
n
SAS and the Clinical Data Interchange Standards Consortium (CDISC) at http://
www.sas.com/industry/life-sciences/cdisc/
n
SAS Intelligence Platform: System Administration Guide at http://support.sas.com/
documentation/onlinedoc/intellplatform/
7
Part 2
Information for Clinical Administrators
Chapter 2
Data Standards Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 3
Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
8
9
2
Data Standards Administration
Overview: Data Standards Administration . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Importing Data Standards Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Overview: Importing Data Standards Metadata . . . . . . . . . . . . . . . . . . . .
Import Data Standards Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Make a Data Standard Available for General Use . . . . . . . . . . . . . . . . .
11
11
12
14
Refreshing Data Standard Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Overview: Refreshing Data Standard Metadata . . . . . . . . . . . . . . . . . . . . 16
Refresh Data Standard Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Customizing Data Standard Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Overview: Customizing Data Standard Properties . . . . . . . . . . . . . . . . . 18
View and Edit the Property Model of Studies and
Submissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Edit Multiple Column Properties in a Data Standard . . . . . . . . . . . . . . . 20
Edit Multiple Table Properties in a Data Standard . . . . . . . . . . . . . . . . . 21
Customizing Data Standard Domain Templates . . . . . . . . . . . . . . . . . . . . 23
Overview: Customizing Data Standard Domain Templates . . . . . . 23
Managing Controlled Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Overview: Managing Controlled Terminology . . . . . . . . . . . . . . . . . . . . . . 23
Importing Terminology Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Import a Terminology Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Create a Terminology Package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Edit a Terminology Package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
10 Chapter 2 / Data Standards Administration
Managing Data Standard Compliance Checks . . . . . . . . . . . . . . . . . . . . . 31
Overview: Managing Data Standard Compliance Checks . . . . . . . . 31
Creating a Compliance Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
View Compliance Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Create or Edit a Compliance Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Change the Compliance Check Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Delete a Compliance Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Analyzing Domain Use and Promoting a Domain
to Be a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Overview: Analyzing Domain Use and Promoting
a Domain to Be a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Analyze Domain Use and Promote a Domain . . . . . . . . . . . . . . . . . . . . . . 42
Overview: Data Standards
Administration
SAS Clinical Data Integration enables you to centrally define and manage data
standards. You can also analyze how data standards are implemented by
programmers. For example, you can view trends about how a domain is used by
programmers. These trends might identify a new column to add to a standard domain
because programmers are often adding the column during conversion. These trends
might point to frequently created custom domains that should be promoted into the
standards.
Typical user tasks include:
n
“Importing Data Standards Metadata” on page 11
n
“Customizing Data Standard Properties” on page 18
n
“Managing Controlled Terminology” on page 23
n
“Managing Data Standard Compliance Checks” on page 31
n
“Analyzing Domain Use and Promoting a Domain to Be a Template” on page 42
Importing Data Standards Metadata
11
Importing Data Standards Metadata
Overview: Importing Data Standards
Metadata
You define a study relative to a particular data standard, such as CDISC-SDTM or a
data standard from your company, by importing the data standard from the SAS Clinical
Standards Toolkit.
If you want to use a CDISC standard, import data standard metadata from the SAS
Clinical Standards Toolkit. Importing the metadata enables you to update your
environment with new releases of data standards from CDISC. CDISC data standards
are provided with the SAS Clinical Standards Toolkit. For more information, see the
SAS Clinical Standards Toolkit: User's Guide.
After importing a data standard that supports domain templates, column groups, and
validation data sets, these items are displayed in the Data Standards folder in the
Clinical Administration tree. For example, if you select the CDISC-SDTM data
standard type and version 3.1.2, the domain templates (SDTM domains), column
groups (SDTM classes), and validation data sets (compliance checks) are displayed in
a folder that you specify in the Import wizard.
By default, an imported data standard has a status of Inactive. This status enables you
or a data standards administrator to review the template and make changes before
releasing it for general use. When you or the data standards administrator is satisfied
with the template, you can change its status to Active, which makes the template
available for general use. For more information, see “Make a Data Standard Available
for General Use” on page 14.
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
12 Chapter 2 / Data Standards Administration
Import Data Standards Metadata
To import data standards metadata, perform the following steps:
1 In the Clinical Administration tree, select Data Standards, right-click, and then
select Import.
The Import Wizard appears.
2 If the Default Application Server page appears, select one of the application servers
that are listed.
The Default Application Server page appears only when a SAS Foundation
application server is accessed for the first time in a SAS Clinical Data Integration
session. If you are unsure about which application server to select, contact the SAS
installation representative.
Importing Data Standards Metadata
13
3 On the Select Data Standard Type page, select the data standard type, and then
click Next.
The Select Data Standard Version page appears.
4 Select the data standard version to use, and then click Next.
5 On the Define General Properties page, edit the default values.
a Enter a name and an optional description.
Note: It is a best practice not to include spaces in the data standard name.
b (Optional) In the Formal Name field, enter a more descriptive name for the data
standard.
c In the Identifier field, enter a text value to uniquely identify the data standard in
metadata.
A default value is provided, but it might not be unique. The value that you enter is
verified as unique before you continue.
d (Optional) Enter the version and vendor.
6 Click Next.
Several Verify Properties pages appear.
Note: The names of the pages depend on the data standard that you selected.
7 (Optional) Edit the property values.
Note: Properties are an advanced feature in SAS Clinical Data Integration. If you
are uncertain about what property values to select, accept all of the default values.
8 Click Next.
9 (Optional) If the data standard supports validation, on the Validation Library page,
perform the following steps:
a Select a library or create a library.
14 Chapter 2 / Data Standards Administration
For more information about SAS libraries, see the SAS Data Integration Studio:
User's Guide or the SAS Data Integration Studio online Help.
Note:
n
You must have appropriate permissions for the selected library. For more
information about permissions, see SAS Management Console: Guide to
Users and Permissions.
n
The path for the selected library must exist.
n
The library metadata object is created immediately. Even if you close the
Import Model wizard, the library remains.
b Click Next.
Several verification pages appear. The names of the pages depend on the data
standard that you selected.
Note: This information is provided only as a reference. It enables you to review
the metadata before storing it. You cannot make changes to this information. If
you see problems in the metadata, contact whomever is responsible for
registering the data standard in the SAS Clinical Standards Toolkit.
10 Click Next.
11 Review the summary, and then click Finish.
12 (Optional) Make the data standard available for general use.
For more information, see “Make a Data Standard Available for General Use” on
page 14.
Make a Data Standard Available for General
Use
To make a data standard available for general use, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards.
Importing Data Standards Metadata
2 Select the data standard, right-click, and then select Properties.
The Data Standard Properties dialog box appears.
3 Click the Properties tab.
4 In the Active row, change false to true.
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16 Chapter 2 / Data Standards Administration
5 Click OK.
Refreshing Data Standard Metadata
Overview: Refreshing Data Standard
Metadata
You can refresh the metadata in a data standard. Refreshing the metadata
accomplishes the following:
n
rereads the data standard metadata of the data standard that is currently registered
in the SAS Clinical Standards Toolkit
n
enables you to update a subset of the data standard in SAS Clinical Data Integration
without the need to reimport the full data standard from the SAS Clinical Standards
Toolkit
n
minimizes the impact of revisions on users
Here is the metadata that can be refreshed in a data standard:
n
domain templates
Refresh one or more domain templates of a SAS Clinical Data Integration data
standard with domain template definitions from the same data standard that is
currently registered in the SAS Clinical Standards Toolkit.
n
column groups
Refresh the column groups in SAS Clinical Data Integration from the data standard
that is currently registered in the SAS Clinical Standards Toolkit.
n
validation checks
Refresh the validation checks to restore them to the version of the data standard that
is currently registered in the SAS Clinical Standards Toolkit.
Refreshing Data Standard Metadata
Refresh Data Standard Metadata
To refresh data standard metadata, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards.
2 Select the data standard, right-click, and then select Refresh Metadata for
Standard.
The Refresh Metadata for Standard wizard appears.
3 (Optional) Select one or more domain templates, and then click Next.
The Column Groups page appears.
4 (Optional) Select one or more column groups, and then click Next.
The Refresh Validation Data page appears.
5 (Optional) Select the Refresh Validation Data check box, and then click Next.
6 Click Finish.
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18 Chapter 2 / Data Standards Administration
The selected metadata is refreshed.
Customizing Data Standard Properties
Overview: Customizing Data Standard
Properties
SAS Clinical Data Integration provides a common property model. This model defines
the properties for which metadata can be collected. These properties are derived from
CDISC data standards, but they are implemented so that you can customize how they
are used.
For example, if a data standard does not use a property, then you can disable that
property. You can adjust or expand the allowable values for a property. You can add
constraints around the content, such as the minimum and maximum values, the length,
and the default value.
For CDISC data standards, SAS Clinical Data Integration loads all of the CDISC
information for you based on the SAS interpretation of the data standard. However,
interpretations can vary, and you have the flexibility to apply your own interpretation.
Property values are inherited by newly created instances of the data standard template.
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
View and Edit the Property Model of Studies
and Submissions
To view and edit the property model of studies and submissions, perform the following
steps:
1 In the Clinical Administration tree, select Study or Submission, right-click, and
then select Edit Property Model.
Customizing Data Standard Properties
The Edit Property Model Defaults dialog box appears.
2 Select a property from the Properties list.
The associated values are displayed to the right of the list. If Use Lookups is
selected, values are displayed in the Lookup Value list.
3 Specify the label and the minimum and maximum length.
4 (Optional) Enter or select the default value.
5 To specify the values for a property that uses lookup values, select the Use
Lookups check box. Then, perform any of the following steps:
n
To enable users to enter a value that is not in the list, select the Lookups are
Customizable check box.
19
20 Chapter 2 / Data Standards Administration
You can then specify the minimum and maximum length.
n
To add a value, click Add, enter the value in the Add lookup value dialog box,
and then click OK.
n
To delete a value, select a value in the Lookup Value list, and then click Delete.
6 Click OK.
Edit Multiple Column Properties in a Data
Standard
To edit multiple column properties in a data standard, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards, and then expand a
data standard.
2 Select either Column Groups or Domain Templates.
3 Right-click, and select Clinical Column Properties.
The Clinical Column Properties wizard appears.
Customizing Data Standard Properties
4 (Optional) Select one or more tables, and then click Next.
Note: All tables are selected by default.
The Property Value Updates page appears.
5 Select a property.
6 Select one or more columns.
7 Click Update.
The Property Value Update dialog box appears.
8 Enter or select a value, and then click OK.
9 Click Finish.
Edit Multiple Table Properties in a Data
Standard
To edit multiple table properties in a data standard, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards, and then expand a
data standard.
2 Select Domain Templates.
3 Right-click, and select Clinical Table Properties.
The Clinical Table Properties wizard appears.
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22 Chapter 2 / Data Standards Administration
4 (Optional) Select one or more tables, and then click Next.
Note: All tables are selected by default.
The Property Value Updates page appears.
5 Select a property.
6 Select one or more tables.
7 Click Update.
The Property Value Update dialog box appears.
8 Enter or select a value, and then click OK.
9 Click Finish.
Managing Controlled Terminology
23
Customizing Data Standard Domain
Templates
Overview: Customizing Data Standard
Domain Templates
You can make changes to the domain templates for the data standard by customizing
domain clinical properties and domain column clinical properties.
To customize domain template metadata, see “Edit Domain Properties” on page 97.
To customize domain template column metadata, see “Edit Domain Column Properties”
on page 98.
Managing Controlled Terminology
Overview: Managing Controlled Terminology
SAS Clinical Data Integration enables you to manage controlled terminology. Controlled
terminology is a set of possible values for something. For example, controlled
terminology for the valid values of yes and no could be expressed as (1-Yes, 2-No).
A terminology table is a SAS data set that contains controlled terminology data. SAS
Clinical Standards Toolkit provides CDISC terminology tables.
A terminology package is a group of terminology tables. The data standards
administrator creates terminology packages. The data standards administrator manages
the granularity of the terminology and the groups to which the terminologies are
available. For example, the following is the granularity of the terminology and the group
to which it is available:
n
a study or submission
n
the transformations that use the controlled terminology
24 Chapter 2 / Data Standards Administration
When a new study or submission is created, the trial manager selects the terminology
package to use for the study or submission. This information is used by the CDISCSDTM Compliance transformation and the CDISC-Define Creation transformation.
If multiple terminology data sets are specified for a study or submission, changing the
order of the terminology data sets affects the order in which the terminology tables are
applied during a transformation. If a controlled term is defined several times, the first
value found is the value used.
Importing Terminology Data Sets
To manage controlled terminology, you import CDISC terminology data sets from SAS
Clinical Standards Toolkit. A wizard imports the controlled terminology and creates the
associated terminology data set.
After a terminology data set is imported, you can verify that the import was successful.
You can open, delete, or rename the terminology data sets using SAS Data Integration
Studio. For more information, see SAS Data Integration Studio: User's Guide or the
SAS Data Integration Studio online Help.
You can create, rename, or change the order in which the terminology tables in the data
set are applied during a transformation.
See Also
n
“Import a Terminology Data Set” on page 24
n
“Create a Terminology Package” on page 26
n
“Edit a Terminology Package” on page 28
Import a Terminology Data Set
Note: You must have the appropriate permissions to import a terminology data set.
To import a terminology data set, perform the following steps:
1 In the Clinical Administration tree, select New  Terminology Data Set.
The New Terminology Dataset wizard appears.
Managing Controlled Terminology
25
2 Select the terminology standard data set to import, and then click Next.
The Terminology Version page appears.
3 Select the terminology version to use, and then click Next.
The Terminology Data Set Name page appears.
4 (Optional) Enter a name and description, and then click Next.
The Terminology Data Sets Folder page appears.
5 Select the folder in which to create the terminology data set, and then click Next.
The Terminology Library page appears.
6 From the SAS Library drop-down list, select the library that contains the imported
terminology table or create a library.
For information about using the New Library Wizard to create a library, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online
Help.
26 Chapter 2 / Data Standards Administration
Note: The selected library must have Create permission for the user who is
currently logged on.
7 Click Next
The Summary page appears.
8 Click Finish.
See Also
“Importing Terminology Data Sets” on page 24
Create a Terminology Package
Note: You must have the appropriate permissions to create a terminology data set. For
more information, see Appendix 1, “Addition of Users to the Clinical Administrator
Group,” on page 193.
To create a terminology package, perform the following steps:
1 In the Clinical Administration tree, select Terminology Packages, right-click, and
then select New Terminology Package.
The New Terminology Package wizard appears.
Managing Controlled Terminology
2 Enter a name, an optional version number, and an optional description.
3 Click Next.
The Terminology Sets page appears.
4 To add a terminology set, perform the following steps:
a Click Add.
The Add Terminology Sets wizard appears.
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28 Chapter 2 / Data Standards Administration
b Select a SAS library or create a library, and then click Next.
For information about creating a new library or editing a library, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online
Help.
The Source Terminology Tables page appears.
c Select one or more tables in the library, and then click Finish.
5 To order the data sets, select a data set on the Terminology Sets page, and then
click Move Up or Move Down.
6 Click Finish.
Edit a Terminology Package
To edit a terminology package, perform the following steps:
1 In the Clinical Administration tree, expand Terminology Packages.
Managing Controlled Terminology
2 Select a terminology package, right-click, and then select Properties.
The Controlled Terminology Properties dialog box appears.
3 Edit the properties.
4 To add a terminology set, perform the following steps:
a Click the Properties tab, and then click Add.
The Add Terminology Sets wizard appears.
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30 Chapter 2 / Data Standards Administration
b Select a SAS library or create a library, and then click Next.
For information about creating a new library or editing a library, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online
Help.
The Source Terminology Tables page appears.
c Select one or more tables in the library, and then click Finish.
5 To order the terminology data sets, select a data set on the Properties tab, and then
click Move Up or Move Down.
6 Click OK.
Managing Data Standard Compliance Checks
31
Managing Data Standard Compliance
Checks
Overview: Managing Data Standard
Compliance Checks
A set of compliance checks can be associated with each data standard. The data
standards administrator can add new compliance checks and customize existing
compliance checks for a data standard. Using these checks, you validate a clinical
domain to determine whether it complies with the data standard. You perform validation
by running a job that contains the CDISC-SDTM Compliance transformation or the
CDISC-ADaM Compliance transformation.
The data standards administrator can customize validation for a data standard in the
Manage Compliance Checks wizard. A compliance check can have an Active or Draft
status. In the CDISC-SDTM Compliance transformation, where compliance checks are
applied to clinical domains, non-administrator users can select and use only compliance
checks that have an Active status. Only administrators can use compliance checks that
have a Draft status. The Draft status enables administrators to set up and run
compliance transformations to verify custom compliance checks. When an administrator
is satisfied with the compliance check, the administrator changes the status to Active,
and then the check is available to all clinical programmers.
Note: You must have the appropriate permissions to manage data standard
compliance checks. For more information, see Appendix 1, “Addition of Users to the
Clinical Administrator Group,” on page 193.
See Also
n
“View Compliance Checks” on page 34
n
“Create or Edit a Compliance Check” on page 35
n
“Change the Compliance Check Status” on page 41
n
“Delete a Compliance Check” on page 41
32 Chapter 2 / Data Standards Administration
Creating a Compliance Check
Overview: Creating a Compliance Check
Note: To create a compliance check, you must be an advanced user who understands
how validation works using the SAS Clinical Standards Toolkit. SAS Clinical Standards
Toolkit is invoked by the SAS code that is generated from a compliance transformation
that uses validation. For more information about the SAS Clinical Standards Toolkit, see
SAS Clinical Standards Toolkit: User's Guide.
The SAS Clinical Standards Toolkit provides a set of compliance checks for the data
standards that support validation. SAS Clinical Data Integration imports these
compliance checks when you import your data standards. You can create additional
compliance checks and add them to the set.
The syntax for the following settings is determined by SAS Clinical Standards Toolkit:
n
Domain and domain column specifications
n
Code source
n
Terminology lookup and reporting
For task information, see “Create or Edit a Compliance Check” on page 35.
Domain Specification String and Column Specification String
Values Requirements
A value for the domain specification string and column specification string must meet
the following requirements:
n
Brackets must be matched.
n
Valid characters are letters (A-Z and a-z), digits (0 to 9), or the underscore (_).
n
The _ALL_ syntax specifier cannot be used.
n
The maximum length is 200 characters.
Check ID Value Requirements
A value for a check ID must meet the following requirements:
Managing Data Standard Compliance Checks
33
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length is eight characters.
n
The value must be unique among all check IDs for any compliance check belonging
to that data standard.
Check Type Value Requirements
A value for the check type must meet the following requirements:
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length is 20 characters.
Severity Value Requirements
A value for the severity must meet the following requirements:
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length is 40 characters.
Error Message Value Requirements
A value for the error message must meet the following requirements:
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length is 500 characters.
Description Value Requirements
A value for the description must meet the following requirements:
n
The value must contain at least one non-whitespace character.
34 Chapter 2 / Data Standards Administration
n
All characters are valid. However, single and double quotation marks cannot be
used together in the description. Use only single quotation marks or only double
quotation marks.
n
The maximum length is 500 characters.
Code Source Value Requirements
A value for the code source must meet the following requirements:
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length is 32 characters.
Code Value Requirements
A value for the code must meet the following requirements:
n
All characters are valid. However, single and double quotation marks cannot be
used together in the description. Use only single quotation marks or only double
quotation marks.
n
The maximum length is 2000 characters.
Lookup Type and Lookup Source Value Requirements
A value for the lookup type and lookup source must meet the following requirements:
n
The value must contain at least one non-whitespace character.
n
All characters, except single and double quotation marks, are valid.
n
The maximum length for a lookup type is 20 characters.
n
The maximum length for a lookup source is 32 characters.
View Compliance Checks
To view compliance checks, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards.
Managing Data Standard Compliance Checks
35
2 Select a data standard, right-click, and then select Manage Compliance Checks.
The Manage Compliance Checks wizard appears.
Note: If the data standard does not support compliance checking, or it does not
have a compliance check installed, then a message appears.
3 To view only the Check ID and Description columns, clear the Show details check
box.
By default, the Available checks table displays details for each compliance check.
Note: You can sort the table by clicking on any column heading.
4 Click Close.
Create or Edit a Compliance Check
Start the Wizard
For conceptual information, see “Creating a Compliance Check” on page 32.
36 Chapter 2 / Data Standards Administration
Note: If the Next and Finish buttons are dimmed on a page in the wizard, one or more
of the values on the page are not valid, or a required value is missing. Review the
requirements for each value, and make corrections as needed.
To start to create or edit a compliance check, perform the following steps:
1 View the compliance checks.
For more information, see “View Compliance Checks” on page 34.
2 To create a compliance check, right-click a compliance check, and then select
Customize.
The Customize Compliance Check wizard appears.
3 To edit a compliance check, perform the following steps:
a Right-click a compliance check, and then select Make Draft.
Managing Data Standard Compliance Checks
37
To edit a compliance check, it must have a status of Draft.
b Right-click the compliance check, and then select Edit.
The Edit Compliance Check wizard appears.
Specify the Check Properties Values
To specify the check properties values, perform the following steps:
1 On the Check Properties page, edit the values by performing the following steps:
a If you are creating a compliance check, enter a check ID.
The value must meet the requirements; see “Check ID Value Requirements” on
page 32.
b Select or enter a check type.
38 Chapter 2 / Data Standards Administration
The value must meet the requirements; see “Check Type Value Requirements”
on page 33.
c Select or enter a severity.
The value must meet the requirements; see “Severity Value Requirements” on
page 33.
d Enter a description.
The value must meet the requirements; see “Description Value Requirements” on
page 33.
e In the Initial Status list, the default is always Draft.
Note: After you test this check using the compliance transformation, you can set
the status to Active.
2 Click Next.
The Domains page appears.
Specify the Domains
(Optional) To specify the domains, perform the following steps:
1 To enable the Domain Specification field for editing, and disable the Domains
Referenced table, select the Direct Edit (Advanced) check box.
2 (Optional) In the Domains Referenced table, edit a row to adjust the values for the
domain.
Note:
n
When creating a compliance check, the Domains Referenced table might
not be displayed. The table’s appearance depends on the type of compliance
check that you have selected.
n
When editing a compliance check, the Domains Referenced table appears
only when the domain specification for the compliance check includes one or
more domain IDs or domain specifiers.
Managing Data Standard Compliance Checks
39
3 In the Domain Specification field, enter the full domain specification string that is
passed to SAS Clinical Standards Toolkit.
The value must meet the requirements; see “Domain Specification String and
Column Specification String Values Requirements” on page 32.
4 Click Next.
The Domain Columns page appears.
Specify the Domain Columns
(Optional) To specify the domain columns, perform the following steps:
1 To enable the Column Specification field for editing, and to disable the Columns
Referenced table, select the Direct Edit (Advanced) check box.
2 (Optional) In the Columns Referenced table, edit a row to adjust the values for the
column.
Note: The Columns Referenced table appears only when the column specification
includes one or more column IDs or column specifiers.
3 In the Column Specification field, enter the full column specification string that is
passed to the SAS Clinical Standards Toolkit.
The value must meet the requirements; see “Domain Specification String and
Column Specification String Values Requirements” on page 32.
4 Click Next.
The Check Code page appears.
Specify the Check Code Values
(Optional) To specify the check code values, perform the following steps:
1 To enable the Code Source drop-down list and the Code field for editing, select the
Direct Edit (Advanced) check box.
2 (Required) In the Code Source list, select or enter a macro provided by the SAS
Clinical Standards Toolkit.
40 Chapter 2 / Data Standards Administration
Note:
n
The Code Source list appears only when the column specification includes
one or more column IDs or column specifiers.
n
For more information about the macros, see the SAS Clinical Standards
Toolkit: User's Guide.
3 In the Code field, enter the code to pass to the SAS Clinical Standards Toolkit.
SAS Clinical Data Integration does not validate the syntax in the code. However, it
does validate that the value requirements are met. For more information, see “Code
Value Requirements” on page 34.
Note: All code must be consistent with the selected code source. And, the code
must be valid SAS code.
4 Click Next.
If a terminology lookup is included in the compliance check, the Controlled
Terminology Lookup page appears. Otherwise, the Reporting Options page appears.
Specify the Controlled Terminology Lookup Values
(Optional) If a terminology lookup is included in the compliance check, specify the
values by performing the following steps:
1 To enable the Lookup Type and Lookup Source drop-down lists for editing, select
the Direct Edit (Advanced) check box.
2 (Required) In the Lookup Type list, select or enter the type of terminology lookup.
Note: SAS Clinical Data Integration does not validate whether the type exists.
3 (Required) In the Lookup Source list, you can select or enter the source of the
terminology lookup.
Note: SAS Clinical Data Integration does not validate whether the source exists.
4 Click Next.
The Reporting Options page appears.
Managing Data Standard Compliance Checks
41
Specify the Reporting Options Values
(Optional) To specify the reporting options, perform the following steps:
1 To enable the Error Message field, select the Direct Edit (Advanced) check box.
2 To specify that all violations for the compliance check are reported every time the
validation is run, select the Report All Violations check box.
If you clear this check box, only the first violation is reported.
3 In the Error Message field, enter the text to write to the data set when a violation is
detected.
You can use substitution variables in this field.
4 Click Finish.
Change the Compliance Check Status
To change the status of a compliance check, select one or more compliance checks,
right-click, and then select either Make Draft or Make Active.
Delete a Compliance Check
To delete a compliance check, select one or more compliance checks, right-click the
compliance check, and then select Delete.
The compliance check is deleted from the table and from persistent storage for the data
standard.
42 Chapter 2 / Data Standards Administration
Analyzing Domain Use and Promoting a
Domain to Be a Template
Overview: Analyzing Domain Use and
Promoting a Domain to Be a Template
You can analyze how standard domains and custom domains are used in studies and
submissions. With this usage information, you can perform these tasks:
n
identify custom domains that are used enough to become domain templates
Typically, a custom domain is used within a single study or submission. The custom
domain is available only to the study or submission in which it is defined. However,
when a custom domain is promoted to be a domain template, the custom domain
can be included in any study or submission.
n
replace a current domain template with a revised version
Replacing a current domain template enables you to incrementally evolve a data
standard rather than creating a new one.
Here are the requirements to promote a domain:
n
The domain template name and identifier are required.
n
The domain template name and identifier must be unique within a data standard.
n
The domain template identifier must be a valid SAS data set name.
See Also
“Promoting an ADaM Data Set to Be a User-Defined Template” on page 128
Analyze Domain Use and Promote a Domain
To analyze domain use and promote a domain, perform the following steps:
1 In the Clinical Administration tree, expand Data Standards.
Analyzing Domain Use and Promoting a Domain to Be a Template
43
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
2 Right-click a data standard, and then select Analyze Model Usage.
The Analyze Model Usage dialog box appears.
The Studies/Submissions list displays all of the studies and submissions that
currently use the selected data standard.
3 From the Studies/Submissions list, select one or more items.
4 To limit the domains to display, select a type from the Show domains of type drop-
down list.
5 Click Show Domain Details.
44 Chapter 2 / Data Standards Administration
In the Domain details list, a summary of the domains and domain columns appears.
Each domain that is included in the selected study or submission appears as a
column in the list.
6 To see the details of a domain, double-click the folder to expand the rows.
Blue boxes specify the columns that are in each domain.
7 To view which study, folder within a study, or submission a domain is associated
with, select a domain from the Domain drop-down list.
The full metadata path appears adjacent to Domain path.
8 To promote a domain, perform the following steps:
a Select a domain from the Domain drop-down list, and then click Promote.
The Domain Template Name and Identifier dialog box appears.
b Enter a name and identifier for the domain template.
c Click OK.
9 Click Close in the Analyze Model Usage dialog box.
10 To verify that a domain template was created from the custom domain, perform the
following steps:
a In the Clinical Administration tree, expand the selected data standard.
b Expand Domain Templates.
Analyzing Domain Use and Promoting a Domain to Be a Template
The new domain template appears in this folder.
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46 Chapter 2 / Data Standards Administration
47
3
Reports
Overview: Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Run and Save a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Overview: Reports
You use the reports feature in SAS Data Integration Studio to generate SAS Clinical
Data Integration reports. Clinical administrators can generate reports to show the
following information:
n
basic study information that is defined in the metadata
n
basic submission information that is defined in the metadata
n
standards that are defined in the metadata
n
controlled terminology packages
Note: For detailed information about running reports and selecting options, see the
SAS Data Integration Studio: User's Guide or the SAS Data Integration Studio online
Help.
48 Chapter 3 / Reports
Run and Save a Report
To run and save a SAS Clinical Data Integration report, perform the following steps:
1 Select Tools  Reports.
The Reports dialog box appears.
2 In the Show field, select Clinical.
3 Select a SAS Clinical Data Integration report.
4 (Optional) Specify the path to the location in which to save the report by entering a
location or by clicking Browse to navigate to a location.
Note: It is a good idea to browse to examine the file folder hierarchy and to check
the path. The folder must be on the server and must not be a local folder.
5 Enter the name.
6 Click the Run and view a report icon ( ).
The report is run and saved.
Run and Save a Report
The Report View dialog box appears.
7 Choose whether to view the report.
For more information about viewing a report, see the SAS Data Integration Studio:
User's Guide or the SAS Data Integration Studio online Help.
Note: A report opens only if the Default Location field contains a valid path.
49
50 Chapter 3 / Reports
51
Part 3
Information for Trial Managers
Chapter 4
Studies and Submissions Management . . . . . . . . . . . . . . . . . . . . . . . . . 53
52
53
4
Studies and Submissions Management
Overview: Studies and Submissions Management . . . . . . . . . . . . . . . . 54
Working with Folder Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Overview: Working with Folder Templates . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Access Permissions for Folder Templates . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Folder Name Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Folder Descriptions Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Create a Folder Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Create a Folder within a Folder Template . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Duplicate a Folder Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
View and Modify the Properties of a Folder
Template or a Folder within a Folder Template . . . . . . . . . . . . . . . . . . 59
Working with Library Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Overview: Working with Library Templates . . . . . . . . . . . . . . . . . . . . . . . . . 60
Access Permissions for Library Templates . . . . . . . . . . . . . . . . . . . . . . . . . 60
Library Templates Descriptions Requirements . . . . . . . . . . . . . . . . . . . . . 61
Library Templates Name Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
libref Name Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Create a Library Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
View and Modify Library Template Properties . . . . . . . . . . . . . . . . . . . . . . 63
Delete a Library Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Creating a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Overview: Creating a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . . . 64
Folder Organization of Studies and Submissions . . . . . . . . . . . . . . . . . . 65
Name Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
54 Chapter 4 / Studies and Submissions Management
Description Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Create a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Create a Study from a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Managing Studies and Submissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Edit the Properties of a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . 72
Edit Multiple Column Properties in a Study or Submission . . . . . . . 73
Edit Multiple Table Properties in a Study or Submission . . . . . . . . . . 75
Delete a Study or Submission . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Import a Codelist Table into a Study or
Submission from a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Monitoring the Statuses of Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Overview: Monitoring the Statuses of Domains . . . . . . . . . . . . . . . . . . . . 78
Monitor the Progress of a Study or Submission . . . . . . . . . . . . . . . . . . . . 78
Comparing the Metadata of a Standard Domain
to Its Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Overview: Comparing the Metadata of a
Standard Domain to Its Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Refresh the Metadata of a Standard Domain . . . . . . . . . . . . . . . . . . . . . . . 81
Overview: Studies and Submissions
Management
SAS Clinical Data Integration studies and submissions are the top-level containers for
all of the content and metadata created during the course of an entire study. A study
contains study-level metadata and content. A submission contains aggregated
metadata and content, or a collection of studies.
In SAS Clinical Data Integration, a trial manager can centrally define and manage study
definitions, set up default content, and monitor the progress of the domain mapping
process.
Before you create a study or submission, you can define the defaults for the study or
submission. You can use folder templates to maintain consistent metadata organization
Working with Folder Templates
55
in a study and submission when it is created. You can use library templates to maintain
consistent use of SAS librefs. This consistency is necessary when you have standard
programs and macros that are dependent on consistent SAS librefs.
For each study and submission, you can define one or more default data standards.
When defining a data standard, remember that you are affecting the available data
standard selections in all SAS Clinical Data Integration wizards within that study or
submission. Only the data standards that you define as the defaults are displayed.
These default settings ensure that you are always using the correct version of a data
standard for a study or submission. After you create a study or submission, default
content is created automatically.
Because all activities and relationships are stored in metadata, SAS Clinical Data
Integration can produce a summary of the statuses of all activities for a selected study
or submission. If you have multiple programmers working on the same study or
submission, you can easily see what domains have been created, what domains are
used in a mapping process, and whether a validation transformation is using a certain
domain. If you are using change management, you can view who is working on the
study or submission. For more information about change management, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Working with Folder Templates
Overview: Working with Folder Templates
You can enforce a uniform folder structure across submissions and studies by creating
a folder template. You can select a folder template when you create a study or
submission.
You can create any number of folder templates. You can create any number of folders
within a folder template, and you can create any depth of hierarchy.
A folder template appears in the Clinical Administration tree when you expand
Defaults  Folder Templates.
56 Chapter 4 / Studies and Submissions Management
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
See Also
n
“Create a Study or Submission” on page 66
n
“Create a Folder Template” on page 57
n
“View and Modify the Properties of a Folder Template or a Folder within a Folder
Template” on page 59
n
“Duplicate a Folder Template” on page 58
n
“Create a Folder within a Folder Template” on page 58
Access Permissions for Folder Templates
To more easily manage study structure at the department level, you can control which
users can access a folder template. This eliminates the need to create a global list of
templates, which might result in the selection of an inappropriate template during the
creation of a study.
Note: The access permissions that you specify for a folder template are not propagated
to the objects that are created from the folder template.
For more information about access permissions on the Authorization tab, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Folder Name Requirements
A folder name must meet the following requirements:
n
The maximum length is 60 characters.
n
The name must not be the same as any existing folder name in the same parent
folder. The comparison check is not case sensitive.
n
The name cannot include whitespace characters.
Working with Folder Templates
Folder Descriptions Requirements
The maximum length of a description for a folder is 200 characters.
Create a Folder Template
To create a folder template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults.
2 Right-click Folder Templates and select New Folder Template.
The New Folder Template dialog box appears.
3 Enter a name and an optional description.
The name and the description must meet the requirements; see “Folder Name
Requirements” on page 56 and “Folder Descriptions Requirements” on page 57.
4 Click OK.
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58 Chapter 4 / Studies and Submissions Management
5 (Optional) Create folders within the folder template hierarchy.
For more information, see “Create a Folder within a Folder Template” on page 58.
See Also
“Working with Folder Templates” on page 55
Create a Folder within a Folder Template
To create a folder within a folder template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults  Folder Templates.
2 Select a folder template or a folder within a folder template, right-click, and then
select New Folder.
A new node appears under the selected item. The name is selected, ready to edit.
3 Enter the name, and press Enter.
The name must meet certain requirements. (See “Folder Name Requirements” on
page 56.)
See Also
n
“Working with Folder Templates” on page 55
n
“View and Modify the Properties of a Folder Template or a Folder within a Folder
Template” on page 59
Duplicate a Folder Template
To duplicate a folder template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults  Folder Templates.
2 Right-click a folder template, and select Duplicate.
The Duplicate Folder Template dialog box appears.
Working with Folder Templates
3 Enter a name and an optional description.
4 Click OK.
View and Modify the Properties of a Folder
Template or a Folder within a Folder
Template
To view and modify the properties of a folder template or a folder within a folder
template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults  Folder Templates.
2 Right-click a folder template or a folder within a folder template and select
Properties.
The Folder Template Properties dialog box appears.
3 Enter a name and an optional description.
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60 Chapter 4 / Studies and Submissions Management
The name and the description must meet the requirements; see “Folder Name
Requirements” on page 56 and “Folder Descriptions Requirements” on page 57.
4 Click OK.
See Also
“Working with Folder Templates” on page 55
Working with Library Templates
Overview: Working with Library Templates
You can share a default library reference across studies and submissions by creating a
library template. You can select a library template when you create a study or
submission.
The library templates that are available appear in the Clinical Administration tree
when you expand Defaults  Library Templates.
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
See Also
n
“Create a Library Template” on page 62
n
“Create a Study or Submission” on page 66
n
“View and Modify Library Template Properties” on page 63
Access Permissions for Library Templates
To more easily manage study structure at the department level, you can control which
users can access a library template.
Working with Library Templates
61
Note: The access permissions that you specify for a library template are not
propagated to the objects that are created from the library template.
For more information about access permissions on the Authorization tab, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Library Templates Descriptions
Requirements
The maximum length of a description for a library template is 200 characters.
Library Templates Name Requirements
A library template name must meet the following requirements:
n
The maximum length is 60 characters.
n
The name must not be the same as any existing library template name in the study
or submission. The comparison check is not case sensitive.
libref Name Requirements
A libref name must meet the following criteria:
n
The first character must be an alphabetic character or an underscore.
n
Each subsequent character must be an alphabetic character, integer, or an
underscore.
n
The maximum length is eight characters.
n
The name must not be the same as any existing library template name in the study
or submission. The comparison check is not case sensitive.
62 Chapter 4 / Studies and Submissions Management
Create a Library Template
To create a library template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults.
2 Right-click Library Templates and select New Library Template.
The New Library Template dialog box appears.
3 Enter a name for the library and a name for the libref.
The names must meet the requirements; see “Library Templates Name
Requirements” on page 61 and “libref Name Requirements” on page 61.
4 (Optional) Enter a description.
The description must meet certain requirements. (See “Library Templates
Descriptions Requirements” on page 61.)
5 Click Finish.
Working with Library Templates
View and Modify Library Template Properties
To view and modify library template properties, perform the following steps:
1 In the Clinical Administration tree, expand Defaults  Library Templates.
2 Select a library template, right-click, and then select Properties.
The Library Template Properties dialog box appears.
3 Enter a name for the library and a name for the libref.
The names must meet the requirements; see “Library Templates Name
Requirements” on page 61 and “libref Name Requirements” on page 61.
4 (Optional) Enter a description.
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64 Chapter 4 / Studies and Submissions Management
The description must meet certain requirements. (See “Library Templates
Descriptions Requirements” on page 61.)
5 Click OK.
Delete a Library Template
To delete a library template, perform the following steps:
1 In the Clinical Administration tree, expand Defaults  Library Templates.
2 Select one or more library templates, right-click, and then select Delete.
Creating a Study or Submission
Overview: Creating a Study or Submission
You create a study or submission by providing basic object metadata such as name,
description, and content location in the metadata tree. Then, SAS Clinical Data
Integration collects metadata about the item. For example, a study collects metadata
such as protocol title, indication, and phase. After metadata is collected, the versions of
the data standards that can be used for the study or submission are defined.
Note: Only an administrator can set the default content for a study or submission. For
more information, see Appendix 1, “Addition of Users to the Clinical Administrator
Group,” on page 193.
You can create a study from a study definition in a define.xml file. If the define.xml file
contains multiple study definitions, only the first study definition is imported.
See Also
n
“Create a Study or Submission” on page 66
n
“Create a Study from a Define.xml File” on page 69
Creating a Study or Submission
n
65
“Creating a Domain” on page 88
Folder Organization of Studies and
Submissions
A study or submission can be located at the root of the hierarchy in the Folders tree
(Study 1 and Submission 1 in the following figure) or within a general folder (Study 2
and Submission 2).
Figure 4.1
Illustration of Basic Folder Hierarchy
You can create more complex hierarchies based on the containment rules shown in the
following table:
Table 4.1
Folder Containment Rules
Content
Container
Study
Submission
Study
not allowed
not allowed
Submission
allowed
not allowed
Using the containment rules, here is an example of a more complex folder hierarchy:
66 Chapter 4 / Studies and Submissions Management
Figure 4.2
Illustration of Complex Folder Hierarchy
Name Requirements
A study or submission name has a maximum length of 60 characters.
Description Requirements
A study or submission description has a maximum length of 200 characters.
Create a Study or Submission
To create a study or submission, perform the following steps:
1 In the Folders tree, right-click a folder, and then select New  Study or
Submission.
The New Study or New Submission wizard appears.
Creating a Study or Submission
67
2 Enter a name and an optional description.
The name must meet certain requirements. (See “Name Requirements” on page
66. )The description must meet certain requirements. (See “Description
Requirements” on page 66.)
3 Select a folder template.
For more information, see “Working with Folder Templates” on page 55.
4 To change the location of the study or submission, click Browse, and then select a
new location.
For information about the location of a study or submission, see “Folder
Organization of Studies and Submissions” on page 65.
5 Click Next.
The Data Standards Selection page appears.
6 (Optional) Select one or more data standards.
68 Chapter 4 / Studies and Submissions Management
All active data standards to which you have access are displayed.
Note: You cannot select multiple items for the same data standard.
7 Click Next.
The Properties page appears.
8 (Optional) Specify the property values.
The properties that appear on this page and their default values are predetermined
by the administrator's configuration of the data standard’s property model.
Note: Do not use single quotation marks, double quotations marks, or hyphens in
the property value fields.
9 Click Next.
The Library Selection page appears.
10 (Optional) Select one or more libraries to associate with the study or submission.
The libraries that are available on this page are predetermined by the default content
for a study or submission. For more information, see “Working with Library
Templates” on page 60.
11 Click Next.
The Controlled Terminology page appears.
12 (Optional) To select a controlled terminology package to associate with the study or
submission, perform the following steps:
a Click Add.
The Available Terminology Packages dialog box appears. The controlled
terminology packages that are available, as predetermined by the administrator,
are listed.
b Select a package, and then click OK.
13 To remove a selected controlled terminology package, click Remove.
Creating a Study or Submission
69
14 If you are creating a study, click Finish.
15 If you are creating a submission, click Next.
The Contributing Studies page appears.
16 (Optional) Select one or more studies to associate with the submission, and then
click Finish.
All studies to which you have access are displayed.
See Also
n
“Creating a Study or Submission” on page 64
n
“Edit the Properties of a Study or Submission” on page 72
n
“Creating a Domain” on page 88
Create a Study from a Define.xml File
To create a study from a study definition in a define.xml file, perform the following steps:
1 In the Folders tree, right-click a folder, and then select New  Study From Define.
The New Study From Define wizard appears.
70 Chapter 4 / Studies and Submissions Management
2 Click Browse, select a define.xml file on your local computer, and click Open.
3 Click Next.
The General Information page appears.
4 (Optional) Enter a name and a description.
Note: The name and description are automatically derived from the define.xml file.
However, you can change the values.
The name must meet certain requirements. (See “Name Requirements” on page
66. )The description is not required. If you provide a description, it must meet certain
requirements. (See “Description Requirements” on page 66.)
5 Select a folder template.
For more information, see “Working with Folder Templates” on page 55.
6 To change the location of the study, click Browse, and then select a new location.
Creating a Study or Submission
71
For information about the location of a study, see “Folder Organization of Studies
and Submissions” on page 65.
7 Click Next.
The Data Standards Selection page appears.
8 (Optional) Select one or more data standards to associate with the study.
All active data standards to which you have access are displayed.
9 Click Next.
The Properties page appears.
10 (Optional) Specify the property values.
The properties that appear on this page and their default values are predetermined
by the administrator’s configuration of the data standard’s property model.
The attribute values that are specified in the define.xml file and that map to SAS
Clinical Data Integration properties are imported.
Note: Do not use single quotation marks, double quotations marks, or hyphens in
the property value fields.
11 Click Next.
The Library Selection page appears.
12 (Optional) Select one or more libraries to associate with the study.
The libraries that appear on this page are predetermined by the default content of a
study. For more information, see “Working with Library Templates” on page 60.
13 Click Next.
The Controlled Terminology page appears.
14 (Optional) To select a controlled terminology package to associate with the study,
perform the following steps:
a Click Add.
72 Chapter 4 / Studies and Submissions Management
The Available Terminology Packages dialog box appears. The controlled
terminology packages that appear are predetermined by the administrator.
b Select a controlled terminology package, and then click OK.
15 To remove a selected controlled terminology package, click Remove.
16 Click Finish.
See Also
n
“Creating a Study or Submission” on page 64
n
“Edit the Properties of a Study or Submission” on page 72
Managing Studies and Submissions
Edit the Properties of a Study or Submission
To edit the properties of a study or submission, perform the following steps:
1 In the Clinical Administration tree, expand Studies or Submissions.
2 Select the study or submission, right-click, and then select Properties.
The Study Properties or the Submission Properties dialog box appears.
Managing Studies and Submissions
73
3 Select the tab that contains the information that you want to edit, edit the
information, and then click OK.
For more information about any tab except the Study tab, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help. The
Study tab displays Read-Only information.
See Also
“Create a Study or Submission” on page 66
Edit Multiple Column Properties in a Study or
Submission
To edit multiple column properties in a study or submission, perform the following steps:
1 In the Folders tree, select a folder that contains one or more domains, right-click,
and then select Clinical Column Properties.
The Clinical Column Properties wizard appears.
74 Chapter 4 / Studies and Submissions Management
2 (Optional) Select one or more tables, and then click Next.
Note: All tables are selected by default.
The Property Value Updates page appears.
3 Select a property.
4 Select one or more columns.
5 Click Update.
The Property Value Update dialog box appears.
6 Enter or select a value, and then click OK.
7 Click Finish.
Managing Studies and Submissions
Edit Multiple Table Properties in a Study or
Submission
To edit multiple table properties in a study or submission, perform the following steps:
1 In the Folders tree, select a folder that contains one or more domains, right-click,
and then select Clinical Table Properties.
The Clinical Table Properties wizard appears.
2 (Optional) Select one or more tables, and then click Next.
Note: All tables are selected by default.
The Property Value Updates page appears.
3 Select a property.
4 Select one or more tables.
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76 Chapter 4 / Studies and Submissions Management
5 Click Update.
The Property Value Update dialog box appears.
6 Enter or select a value, and then click OK.
7 Click Finish.
Delete a Study or Submission
To delete a study or submission, perform the following steps:
1 In the Clinical Administration tree, expand Studies or Submissions.
2 Right-click the study or submission, and then select Delete.
3 Click OK to confirm the deletion.
The study or submission is deleted, but the associated folder and its contents are
not.
4 To delete the contents of the associated folder, in the Folders tree, right-click the
folder, and then select Delete.
Note: If you do not have the correct permissions, you cannot delete a folder. You
cannot delete the root folder of a study or submission in the Folders tree unless you
have first deleted the item from the Clinical Administration tree.
See Also
“Create a Study or Submission” on page 66
Managing Studies and Submissions
77
Import a Codelist Table into a Study or
Submission from a Define.xml File
To import a codelist table into a study or submission from a define.xml file, perform the
following steps:
1 In the Folders tree, right-click a study or submission, and then select New 
Codelist Table From Define.
The New Codelist Table From Define wizard appears.
2 Click Browse adjacent to the Source field, and then select a define.xml file.
3 Click Next.
78 Chapter 4 / Studies and Submissions Management
The Codelist Selection page appears.
4 Select one or more codelist tables, and click Next.
The Table and Library Specification page appears.
5 Enter a name and optional description.
6 Select a library, and click Next.
The Summary page appears.
7 Review the information, and then click Finish.
Monitoring the Statuses of Domains
Overview: Monitoring the Statuses of
Domains
You can monitor the statuses of domains to determine the progress of mapping the
source data. In addition, you can determine whether a domain has been validated for
compliance with a data standard.
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
Monitor the Progress of a Study or
Submission
To monitor the progress of a study or submission, perform the following steps:
1 In the Clinical Administration tree, expand Studies or Submissions.
2 Select a study or submission, right-click, and then select Monitor Domain Status.
Monitoring the Statuses of Domains
79
The Domain Status dialog box appears.
The Domains table reports the following information:
n
the name of the domain
n
the ID of the domain
n
the description of the domain
n
whether the domain contains defined mapping jobs (that is, the domain contains
a job where the domain is a target)
n
whether the domain contains defined compliance jobs (that is, the domain is
selected to be validated)
n
whether the domain is locked and by whom
80 Chapter 4 / Studies and Submissions Management
Comparing the Metadata of a Standard
Domain to Its Template
Overview: Comparing the Metadata of a
Standard Domain to Its Template
You can compare the metadata of a standard domain to its template and you can
refresh the metadata. When you compare the metadata, the standard domain is
compared with the standard domain template from which it was created. Then, you can
choose to refresh the metadata of the standard domain with the standard domain
template metadata.
Refreshing the metadata of a standard domain replaces the metadata of the standard
domain (in whole or in part) with the metadata of the standard domain template.
Refreshing the metadata of a standard domain is useful when the properties of the
domain have been changed in a way that is no longer applicable.
Note: You can refresh the metadata of a standard domain only if the domain was
based on a standard domain template.
Consider the following points when selecting an item to refresh:
n
If you refresh a column, all of its properties are refreshed.
n
To refresh some properties of a column, expand the Columns node, and then select
the check boxes for each property that you want to refresh.
n
To update the standard domain metadata to match the standard domain template
metadata, select the root node check box.
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
Comparing the Metadata of a Standard Domain to Its Template
81
Refresh the Metadata of a Standard Domain
To refresh the metadata of a selected standard domain, perform the following steps:
1 In the Folders tree, expand a folder, expand a study or submission, and then
expand any subfolders to locate a standard domain.
2 Select a standard domain, right-click, and then select Refresh Domain.
3 If a message appears that indicates that the standard domain template from which
the domain was created and the standard domain are identical, choose whether to
continue or not.
4 In the Refresh Domain dialog box, expand the nodes in either tree to view the
differences.
5 (Optional) Click View Differences.
Only the properties that are different from the domain template appear.
6 (Optional) In the Standard Domain Template tree, select the check box adjacent to
one or more items to refresh.
82 Chapter 4 / Studies and Submissions Management
7 Click Apply Checked.
If there are no remaining differences to apply, or if you chose to update the standard
domain metadata to match the standard domain template metadata, then the
Refresh Domain dialog box changes to view-only mode.
8 Click Close.
83
Part 4
Information for Clinical Programmers or Data
Managers
Chapter 5
SDTM Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Chapter 6
ADaM Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Chapter 7
Creating a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Chapter 8
SAS Transport Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
84
85
5
SDTM Domains
Types of Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Standard Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Custom Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Creating a Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Overview: Creating a Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Create a Standard Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Create a Custom Domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Create a Custom Domain from an Existing Domain . . . . . . . . . . . . . . . 93
Add Domain Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Domain Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Edit Domain Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Edit Domain Column Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Converting a Domain from One Data Standard to
Another Data Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Overview: Converting a Domain from One Data
Standard to Another Data Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Convert a Domain from One Data Standard to
Another Data Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Importing Domain Tables from a Define.xml File . . . . . . . . . . . . . . . . . 103
Overview: Importing Domain Tables a Define.xml File . . . . . . . . . . 103
Create a Domain from a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Loading Data into Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Overview: Loading Data into Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
86 Chapter 5 / SDTM Domains
Generating Unique Sequence Numbers as an
Identifier Variable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Assessing CDISC SDTM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Overview: Assessing CDISC SDTM Compliance . . . . . . . . . . . . . . . . . 108
Assess CDISC SDTM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Types of Domains
Standard Domain
A standard domain is created from a data standard that defines the domain template.
When you create a standard domain, the new domain is a copy of the domain template.
You can use as many domain templates as you need. The domain templates that you
use to create domains are copied into a folder. Associations in the domain template
metadata associate the domain template copy in this folder to the data standard from
which it originated. These associations enable you to customize the domain template
copy without affecting the data standard. In addition, these associations enable you to
validate the copy to determine whether any customizations in the copy do not conform
to the data standard.
All standard domains within a folder must be associated with the same data standard. If
you want to create a copy of the standard domain using a different version of the data
standard, you must create the copy in a different folder. SAS Clinical Data Integration
provides domain templates that conform to existing data standards.
After selecting the standard domain templates that you want to use, you can assign a
library. The library is where the physical data is created when the job is run.
Custom Domain
During a study, there might not be an appropriate domain template for the domain that
you want to create. In this case, you can create a custom domain. The custom domain
uses the data model defined by the data standard to create the appropriate columns
and metadata.
Types of Domains 87
For example, SDTM defines a data model that is based on creating domains from
groups of columns, specifically identifiers, interventions, events, findings, and timings.
SAS Clinical Data Integration generalizes the concept of grouping columns with the
term column group. A column group makes up a portion of a complete table.
Note: To create a custom domain, the data standard must have column groups.
The key criterion for creating a custom domain is whether it is meant to hold data for
interventions, events, or findings. In SAS Clinical Data Integration, interventions, events,
or findings are considered conditional column groups. You can select only one
conditional column group per custom domain.
In addition to selecting a conditional column group, you must specify identifiers and
timing. You must also select the individual columns that you want to include in the
custom domain. Some column names must be prefixed with the identifier. If you select a
column that has this requirement, SAS Clinical Data Integration automatically creates
the correct column name with the prefix. You can define keys and set the column order
before the domain is created.
You can also create a custom domain based on an existing domain. Select an existing
domain that most closely satisfies your needs, duplicate it, and then modify it as
needed.
See Also
n
“Create a Standard Domain” on page 88
n
“Create a Custom Domain” on page 90
n
“Create a Custom Domain from an Existing Domain” on page 93
n
“Edit Domain Column Properties” on page 98
n
“Add Domain Columns” on page 96
88 Chapter 5 / SDTM Domains
Creating a Domain
Overview: Creating a Domain
After you create a study or submission, you create domains within that study or
submission. You can create a domain only in a folder that is the root folder of a study or
submission, or in a subfolder within the root folder of a study or submission. The domain
can be a standard domain or a custom domain.
Note: In a study folder, a domain that you create is marked with the SAS Clinical Data
Integration icon . This icon helps you distinguish domains from other non-clinical
tables.
Note: If you are working in a SAS Data Integration Studio project repository, domains
that you create are created in that project repository. The project repository can be
versioned. However, complex clinical objects such as data standards, studies, and
submissions, cannot be versioned.
See Also
“Create a Study or Submission” on page 66
Create a Standard Domain
To create a domain using a standard domain template, perform the following steps:
1 In the Folders tree, select a study or submission folder, right-click, and then select
New  Standard Domain(s).
The New Standard Domain(s) wizard appears.
Creating a Domain
89
2 To change the default location of the domain, click Browse, and then select a new
location.
By default, the location is set to the folder that you selected in step 1.
3 Click Next.
The Data Standard Selection page appears.
4 Select a data standard.
The data standards in the list are associated with the study or submission in which
the domain is to be created.
5 Click Next.
The Domain Template Selection page appears.
6 Select one or more domain templates to use to create the domain.
90 Chapter 5 / SDTM Domains
If a domain already exists in the target folder with the same ID or with the same
name as a selected domain template, then a warning message appears. You must
specify a valid name or ID before you can proceed.
7 Click Next.
The Library Selection page appears.
8 (Optional) Select a library to assign to the domain.
The library can be any library in the study or submission. If no libraries exist within
the study or submission root folder or within a subfolder of the study or submission
root folder, a message appears.
Note: You can create a domain without assigning a library. Later, you can create a
library and assign it to the domain. However, if you use the domain in a job without
first assigning a library, the job fails. The job generates errors that indicate you must
assign a library. If you attempt to open the domain to view the contents and records,
the open fails, and an error message appears.
9 Click Finish.
Create a Custom Domain
To create a custom domain, perform the following steps:
1 In the Folders tree, select a study or submission folder, right-click, and then select
New  Custom Domain.
The New Custom Domain wizard appears.
Creating a Domain
91
2 To change the default location of the domain, click Browse, and then select a new
location.
By default, the location is set to the folder that you selected in step 1.
3 Click Next.
The Data Standard Selection page appears.
4 Select a data standard.
The data standards in this list are associated with the study or submission in which
the domain is to be created.
5 Click Next.
The General Information page appears.
6 Enter a name and an identifier, and then click Next.
Note: The name and identifier cannot be the same as the name or identifier of a
domain template in the data model.
92 Chapter 5 / SDTM Domains
The Domain Information page appears.
7 (Optional) Specify the property values for the new domain.
8 Click Next.
The Library Selection page appears.
9 (Optional) Select a library to assign to the domain.
The library can be any library in the study or submission. If no libraries exist within
the study or submission root folder or within a subfolder of the study or submission
root folder, a message appears.
Note: You can create a domain without assigning a library. Later, you can create a
library and assign it to the domain. However, if you use the domain in a job without
first assigning a library, the job fails. The job generates errors that indicate you must
assign a library. If you attempt to open the domain to view the contents and records,
the open fails, and an error message appears.
10 Click Next.
The Column Group Selection page appears.
11 Select one or more conditional column groups to use in the new domain.
Column groups are groups of columns that are available to all new domains in a
data standard. This page displays the core column groups that are available to all
new domains in the data standard.
Note: Column groups can differ depending on the selected data model.
12 Click Next.
The Column Selection page appears.
13 Using Add and Remove, move columns between the list Available Columns and
the Selected Columns list.
You can add columns individually or as a group.
14 (Optional) To customize column properties, perform the following steps:
Creating a Domain
93
a Click Next.
The Column Elaboration page appears.
b Edit the properties for selected columns.
The Selected Columns table displays all of the selected columns and their
properties. Not all properties can be edited. The properties vary by data model.
c (Optional) To change the column order, select a column, and then click Move Up
or Move Down.
d (Optional) If two or more columns are keys, change the key order by clicking
Order Keys.
The Order Domain Keys dialog box appears. Select a key, and then click Move
Up or Move Down to adjust its order. Click OK to save the key order.
15 Click Finish.
Create a Custom Domain from an Existing
Domain
CAUTION! Use this process to create a custom domain instead of using the
standard SAS Data Integration Studio copy-and-paste method. The copy-and-paste
method does not copy important domain metadata.
To create a custom domain using an existing domain, perform the following steps:
1 In the Folders tree, select a study or submission folder, right-click, and then select
New  Custom Domain From Existing.
The New Custom Domain From Existing Domain wizard appears.
94 Chapter 5 / SDTM Domains
2 To change the default location of the domain, click Browse, and then select a new
location.
By default, the location is set to the folder that you selected in step 1.
3 Click Next.
The Data Standard Selection page appears.
4 Select a data standard.
The data standards in this list are associated with the study or submission in which
the domain is to be created.
5 Click Next.
The Domain Selection page appears.
6 Select a domain.
The Available Domains by Study/Submission list displays the studies and
submissions and their domains for the selected data standard. Expanding a study or
Creating a Domain
95
submission node displays all of the domains in the study or submission. Both
standard and custom domains can be selected.
7 Click Next.
The General Information page appears.
8 Enter the name and identifier for the new domain, and then click Next.
The Domain Information page appears.
Note: The name and identifier cannot be the same as the name or identifier of a
domain template in the data model.
9 Specify the property values for the new domain, and then click Next.
The Library Selection page appears.
10 (Optional) Select a library to assign to the domain.
The library can be any library in the study or submission. If no libraries exist within
the study or submission root folder or within a subfolder of the study or submission
root folder, a message appears.
Note: You can create a domain without assigning a library. Later, you can create a
library and assign it to the domain. However, if you use the domain in a job without
first assigning a library, the job fails. The job generates errors that indicate you must
assign a library. If you attempt to open the domain to view the contents and records,
the open fails, and an error message appears.
11 Click Next.
The Column Elaboration page appears.
12 Specify the properties for selected columns.
The Selected Columns table displays all of the selected columns and their
properties. Not all properties can be edited. The properties vary by data model.
13 (Optional) To change the column order, select a column, and then click Move Up or
Move Down.
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14 (Optional) If two or more columns are keys, change the key order by clicking Order
Keys.
The Order Domain Keys dialog box appears. Select a key, and then click Move Up
or Move Down to adjust its order. Click OK to save the key order.
15 Click Finish.
Add Domain Columns
To add domain columns, perform the following steps:
1 In the Folders tree, select a domain, right-click, and then select Properties.
The Properties dialog box appears.
2 Click the Columns tab.
The domain columns are listed.
3 Click the New Column button
.
A new entry appears as the last row of the table.
Domain Properties
4 Enter a name and description for the column.
5 Edit the default column characteristics, if necessary.
6 Click OK, or edit the column’s properties.
7 Repair the domain column.
For more information, see “Repair a Domain or Domain Column” on page 199.
Domain Properties
Edit Domain Properties
To edit domain properties, perform the following steps:
1 In the Folders tree, select a domain, right-click, and then select Properties.
The Properties dialog box appears.
2 Select the tab that contains the information that you want to edit, and then edit the
information.
97
98 Chapter 5 / SDTM Domains
Note: Property values cannot contain double quotation marks.
For more information about any tab except the Clinical tab, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
3 (Optional) To change properties for the domain, click the Clinical tab.
The Properties table enables you to enter values and select values from lists,
depending on the property definition.
Note:
n
You might not be able to edit some property values.
n
Some properties of a domain, such as Archive Title, appear in CRT-DDS files
that are generated by SAS Clinical Data Integration. The CRT-DDS files can
contain metadata about the domain. If you plan to generate CRT-DDS files
that include metadata about a domain, ensure that the metadata is complete
by supplying values for the corresponding properties of the domain. For more
information about updating properties, see “Edit Domain Properties” on page
97.
4 Click OK.
Edit Domain Column Properties
To edit domain column properties, perform the following steps:
1 In the Folders tree, select a domain, right-click, and then select Properties.
The Properties dialog box appears.
Domain Properties
2 Click the Columns tab.
The domain columns are listed.
3 Right-click a column, and then select Properties.
The Column Properties dialog box appears.
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100 Chapter 5 / SDTM Domains
4 Select the tab that contains the information that you want to edit, and then edit the
information.
Note: Property values cannot contain double quotation marks.
For more information about any tab except the Clinical tab, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
5 To change properties for the domain column, click the Clinical tab.
The Properties tables enables you to enter text and select values from lists
depending on the property definition.
Note: You might not be able to edit some property values.
6 (Optional) To specify that the column is automatically designated a key when a
custom domain is created, select the value true for the Contributes to Key
property.
Converting a Domain from One Data Standard to Another Data Standard
101
7 Click OK twice.
Converting a Domain from One Data
Standard to Another Data Standard
Overview: Converting a Domain from One
Data Standard to Another Data Standard
You can convert a domain in a study or submission to be associated with a data
standard other than the current data standard. Converting a domain might be needed in
these situations:
n
You want to upgrade to a newer version of the same data standard.
n
You want to change to a different data standard that is compatible with the current
data standard.
n
You want to merge a SEND domain with a custom SDTM+ data standard.
By converting a domain, you can reorganize domains relative to your data standards
without modifying jobs that reference the domain.
CAUTION! The property model for the new data standard might differ from the
current data standard. Validate the properties of the converted domain against the
expected properties of the new data standard. For more information, see “Refresh the
Metadata of a Standard Domain” on page 81.
Note: Before you convert a domain to another data standard, ensure that the study (or
the folder in the study) contains domains from only one data standard. Although SAS
Clinical Data Integration prevents mixing domains from different data standards, there
are ways in SAS Data Integration Studio to mix domains from different data standards.
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Convert a Domain from One Data Standard to
Another Data Standard
To convert a domain from one data standard to another data standard, perform the
following steps:
1 In the Folders tree, select a study or a folder in a study, right-click, and then select
Properties.
The Properties dialog box appears.
2 Click the Domains tab.
Note: If the Domains tab does not appear, the study or folder does not contain a
domain. Create a domain in the study or folder, and then return to this step. For
more information, see “Overview: Creating a Domain” on page 88.
3 Click Change adjacent to the Data Standard field.
The Change Standard Association of Domains dialog box appears.
4 Select a compatible data standard, and then click OK.
Importing Domain Tables from a Define.xml File
103
5 In the Properties dialog box, click OK.
6 Validate the properties of the converted domain against the expected properties of
the new data standard. For more information, see “Refresh the Metadata of a
Standard Domain” on page 81.
Importing Domain Tables from a
Define.xml File
Overview: Importing Domain Tables a
Define.xml File
You can create a domain by importing the domain definition from a define.xml file. This
enables you to rapidly define the metadata necessary to add the domain to the
repository.
The domain is created as a custom domain.
Create a Domain from a Define.xml File
To create a domain from a define.xml file, perform the following steps:
1 In the Folders tree, right-click a study, submission, or a folder within a study or
submission.
2 Select New  Domain(s) From Define.
The New Domain(s) From Define wizard appears.
104 Chapter 5 / SDTM Domains
3 Click Browse adjacent to the Source field, and then select a define.xml file.
4 (Optional) Click Browse adjacent to the Location field, and then select a location in
which to create the domain.
5 Click Next.
The Data Standard Selection page appears.
6 Select a data standard to associate with the domain, and then click Next.
The Domain Selection page appears.
7 Select one or more domains to import, and then click Next.
The Library Selection page appears.
8 (Optional) Select a library to associate with the imported domain, and then click
Next.
The Summary page appears.
Loading Data into Domains
105
9 Review the summary information, and then click Finish.
Loading Data into Domains
Overview: Loading Data into Domains
You load study data into a domain (convert the study data into CDISC SDTM target
files) by creating a SAS Data Integration Studio job. The job that you create to load the
data uses standard SAS Data Integration Studio functionality. The job does not require
any functionality from SAS Clinical Data Integration.
For more information about creating a job, see the SAS Data Integration Studio: User's
Guide or the SAS Data Integration Studio online Help.
Generating Unique Sequence Numbers as an
Identifier Variable
Overview: Generating Unique Sequence Numbers as an Identifier
Variable
Some of the domains in the CDISC SDTM data standard model require a sequence
number as an identifier variable (–SEQ). This sequence number ensures the
uniqueness of records for each subject within a data set.
For example, a study might contain a series of vital signs collected during each visit. On
some days, several readings were taken for heart rate and blood pressure. Before you
can load study data into the SDTM VS domain, you need to uniquely identify each of
these vital signs for each subject. This means that when you convert the study data, you
need to populate each domain and populate the VSSEQ variable.
Use the Subject Sequence Generator transformation to generate a unique sequence
number across subjects in a domain. After running the Subject Sequence Generator
transformation, another variable is generated. This variable enables you to uniquely
identify each vital sign.
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Note: For detailed information about creating a job with a transformation, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Generate Unique Sequence Numbers
To generate unique sequence numbers with the Subject Sequence Generator
transformation, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 From the Folders tree, drag and drop and drop the source table for the domain onto
the diagram.
3 In the Transformations tree, expand Clinical, and then drag and drop Subject
Sequence Generator onto the diagram.
4 Drag the cursor from the source table to the input port of the transformation.
This action connects the source to the Subject Sequence Generator transformation.
5 In the Transformations tree, expand the Access folder, and then drag and drop
Table Loader onto the diagram.
6 Drag the cursor from the output table to the input port of the Table Loader.
This action connects the Subject Sequence Generator_OUTPUT table to the Table
Loader.
7 From the Folders tree, drag and drop the SDTM VS domain that you want to
populate onto the diagram.
8 Drag the cursor from the output port of the Table Loader to the input port of the
SDTM VS domain.
This action connects the Table Loader to the SDTM VS domain (the data target).
9 In the diagram, double-click Subject Sequence Generator.
The Subject Sequence Generator Properties dialog box appears.
Loading Data into Domains
107
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
10 Click the Options tab.
11 (Optional) From the Update Source drop-down list, select a value.
n
NO indicates that the source table is not modified (that is, PROC SORT output is
sent to a work table).
n
YES indicates that the source table is modified directly by PROC SORT in the
code generation.
12 From the Sequence Key Variable drop-down list, select the name of the sequence
variable in the target domain (–SEQ).
13 In the Business Keys list, adjust the order of the available keys.
This list identifies the keys in the source table. Use these keys to sort the data.
14 From the Subject Variable drop-down list, select a variable.
The subject variable represents the unique subject identifier (USUBJID).
15 Click OK.
16 Save and run the job.
SAS Data Integration Studio generates the SAS code for transforming, and then
submits the code to SAS. The –SEQ variable is populated with a sequence number
that is unique for each record for each subject.
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Assessing CDISC SDTM Compliance
Overview: Assessing CDISC SDTM
Compliance
You assess the structural and content compliance of a domain with a data standard
(such as CDISC SDTM) by using the CDISC-SDTM Compliance transformation. You
can assess an individual domain or a set of domains. The process assesses whether
the selected domains comply with the data standard.
Note: For detailed information about creating a job with a transformation, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Assess CDISC SDTM Compliance
To assess CDISC SDTM compliance, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
SDTM Compliance onto the diagram.
The Diagram tab displays the CDISC-SDTM Compliance transformation and the
Results and Metrics work tables.
Assessing CDISC SDTM Compliance
109
3 (Optional) To store the Results and Metrics work tables in a permanent location,
perform the following steps:
Note: By default, the work tables are written to a temporary work location.
a Right-click each Work Table icon ( ), and then select Properties.
The Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
b Click the Physical Storage tab, select a SAS library for the Location field, and
then click OK.
4 In the diagram, double-click CDISC-SDTM Compliance.
The CDISC-SDTM Compliance Properties dialog box appears.
5 Click the Data Standard tab.
All active SDTM data standards are displayed.
6 Select a data standard, and then click the Tables tab.
110 Chapter 5 / SDTM Domains
The studies and submissions are displayed.
7 Expand a study or submission to view its domains.
8 Select the domains to validate, or select the study or submission to select all of its
domains.
Note: You can select domains from multiple studies and submissions.
9 Click the Checks tab.
10 If no compliance checks are displayed, perform the following steps:
a Click Add.
The Add Compliance Check(s) dialog box appears with a list of all available
compliance checks.
b Click Show details.
Detailed information about each compliance check appears.
Assessing CDISC SDTM Compliance
111
Note: If you imported the CDISC SDTM 3.1.2 data standard, then compliance
checks for this data standard also appear in the Standard column in the Checks
tab. A check that has the value CDISC-SDTM applies to both the CDISC SDTM
3.1.1 and CDISC SDTM 3.1.2 standards. A check that has the value CDISC-SDTM
3.1.2 applies to the CDISC SDTM 3.1.2 standard only.
c Select one or more checks, click Add Selected, and then click Close.
Note: Some check IDs are listed more than once. When you select Show
details, you can view information that makes the individual compliance check
unique. For example, consider the check ID SDTM0001:
n
In the first record, Source is Janus and Severity is Note. If the domain
fails this compliance check, then the Results work table reports a note.
n
In the second record, Source is WebSDM and Severity is Warning. If the
domain fails this compliance check, then the Results work table reports a
warning.
To be efficient, choose only a subset of the compliance checks. It is inefficient to
run the same compliance checks multiple times if the only differences between
the checks are severity and source.
11 (Optional) Click the Reports tab, and perform the following steps:
a Perform one of the following steps:
n
Select Report by Domain and the Generate Domain Report check box
n
Select Report by Check and the Generate Check Report check box
b Perform one of the following steps:
n
Click Browse adjacent to Browse to Folder, and then navigate to a server
folder.
n
In the Server Folder field, enter the name of a server folder.
The folder must be on the server and must not be a local folder.
112 Chapter 5 / SDTM Domains
c Enter a name for the report in the Report File Name field, and then specify the
report output format.
d To limit the number of records to include in the report, enter a number in the
Limit # of records to field.
If you leave this field blank, all records are included in the report.
e Select the panels to include in the report and whether informational messages
are included.
12 Click OK to close the CDISC-SDTM Compliance Properties dialog box.
A green check mark adjacent to the CDISC-SDTM Compliance transformation
indicates that the transformation is complete.
Note: If you see in the lower right corner of the transformation, click and
review the error information that appears. A typical error is that selected domains do
not contain an assigned library. Correct any errors before running the job.
13 Click Run.
SAS Data Integration Studio generates the SAS code for validating the selected data
standard model, and then submits the code to SAS. The Results and Metrics work
tables are generated.
14 Review the Results work table to see the results of the compliance checks.
You might want to connect the Results and Metrics work tables as input to the code
that is used to generate formatted reports of the results.
Note: You might encounter errors or warnings in the SAS log during job execution.
These errors or warnings do not mean that validation was unsuccessful. Most errors
that halt a validation are reported in the Results work table. As a general rule, the
Results work table reports failures and provides information about the cause of the
failures. For more information about validation, see the SAS Clinical Standards
Toolkit: User Guide.
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6
ADaM Data Sets
Types of ADaM Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Overview: Types of ADaM Data Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
ADAE Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
ADSL Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
BDS Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Special Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Variables with xx, y, and zz Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Wildcard Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Creating an ADaM Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Overview: Creating an ADaM Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Data Set Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Data Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Variables to Include in the Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Compliance Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Data Set Keys and Nullable Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Complete Set of Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Create an ADaM Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Create an ADaM Data Set from a Define.xml File . . . . . . . . . . . . . . . . 126
Promoting an ADaM Data Set to Be a User-Defined Template . 128
Overview: Promoting an ADaM Data Set to Be a
User-Defined Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Promote an ADaM Data Set to Be a User-Defined Template . . . 128
114 Chapter 6 / ADaM Data Sets
Create an ADaM Data Set from a User-Defined
Analysis Data Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Assessing ADaM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Overview: Assessing ADaM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Assess ADaM Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Types of ADaM Data Sets
Overview: Types of ADaM Data Sets
The ADaM data set can be one of these types:
n
ADAE (Analysis Dataset for Adverse Events)
n
ADSL (Analysis Dataset for Subject Level)
n
BDS (Basic Data Structure analysis data set)
ADAE Data Set
An ADAE data set relies on one or more of the treatment variables (for example, TRTP,
TRTA, TRTxxP, and TRTxxA) in an ADSL data set. Therefore, you must create an
ADSL data set before an ADAE data set. When you create an ADAE data set, you must
include the ADSL data set as a source data set.
ADSL Data Set
Only one ADSL data set can be associated with a study or submission.
BDS Data Set
The BDS data set contains two variables that are required and are key fields: USUBJID
and PARAMCD. They are automatically selected to be included in the data set.
Special Variables
115
The variable AVISIT is also a key field, but it is conditional. You must explicitly select it if
your BDS data set includes visit-specific data.
Special Variables
Variables with xx, y, and zz Parameters
Overview: Variables with xx, y, and zz Parameters
Some ADaM variables contain embedded parameters that require values. These
parameters can be a single digit (denoted by y in the name of the variable) or two digits
(denoted by xx or zz in the name of the variable). Example names of such variables are
CRITy, TRTxxP, and ANLzzFL. Some variables contain multiple parameters, such as
TRxxPGy.
If you include a variable with a parameter in an ADaM data set, you must select the
value (or values) to use for the parameter. The values of the parameters become part of
the variable’s name.
For example, if the variable TRxxPGy is used, and you select values 01 and 02 for xx,
and 3 and 4 for y, these variables are created: TR01PG3, TR01PG4, TR02PG3, and
TR02PG4.
Note: An ADaM data set might contain only a subset of the values that are associated
with the xx, y, and zz parameters.
xx Parameter
The xx parameter represents a two-digit period. Single digits are padded with a leading
zero. Valid values are 01–99.
When planning to create an ADaM data set, consider the periods to include in the
analysis. Then, assign a unique two-digit number to each period.
y Parameter
The y parameter represents a single-digit grouping or category, an analysis criterion, or
an analysis range. Valid values are 1–9.
116 Chapter 6 / ADaM Data Sets
When planning to create an ADaM data set, consider the groups or categories, analysis
criteria, and ranges to include in the analysis. Then, assign a unique single-digit number
to each.
These tables indicate how the y parameter is used in various variables.
Table 6.1
ADSL Grouping Variables
Variable
Description of y
SITEGRy, SITEGRyN
The index of a site-grouping algorithm
RACEGRy, RACEGRyN
Denotes the index for a particular pooling or grouping of
race
TRxxPGy, TRxxPGyN
The index for a particular planned pooled treatment
TRxxAGy, TRxxAGyN
The index for a particular actual pooled treatment
Table 6.2
BDS Grouping Variables
Variable
Description of y
TRTPGy, TRTPGyN
The planned pooled treatment scheme
TRTAGy, TRTAGyN
The actual pooled treatment scheme
PARCATy, PARCATyN
A parameter category
AVALCATy
An analysis category
BASECATy, CHGCATy,
PCHGCATy
A baseline category
R2AyLO, R2AyHI, AyLO, AyHI
An analysis range
SHIFTY, SHIFTyN
A group
CRITy, CRITyFL, CRITyFN
An analysis criterion
Special Variables
117
zz Parameter
The zz parameter represents a two-digit index for the zzth record selection algorithm.
Single digits are padded with a leading zero. Valid values are 01–99.
When planning to create an ADaM data set, consider the record-selection algorithms to
use. Then, assign a two-digit number to each algorithm.
Wildcard Variables
Some ADaM variables contain a wildcard character that requires a value. A wildcard is
denoted by an underscore (_) in the name of the variable. Example names of such
variables are _DTF, _STM, and _SDTM.
If you include a variable with a wildcard in an ADaM data set, you must select the value
to substitute for the wildcard and a value to substitute for the ellipsis (…) in the variable
description.
Note: The variable name is limited to no more than eight characters.
Note: Part of the variable description is automatically generated. You cannot change
this text.
For example, here is the wildcard variable _STM:
In this example, the value for Name prefix replaces the underscore in the name _STM.
And, the value for Description suffix replaces the ellipsis. The generated variable
name becomes prefSTM. The generated description becomes Start Time of
descSuffix.
118 Chapter 6 / ADaM Data Sets
Creating an ADaM Data Set
Overview: Creating an ADaM Data Set
You create an ADaM data set in a study or submission. At least one ADaM data
standard must be associated with the study or submission. If more than one ADaM data
standard is associated with the study or submission, you must choose the data standard
to use.
The name of an ADaM data set must start with AD, and must be between three and
eight characters in length.
Note: SAS Clinical Data Integration automatically provides AD in the name.
See Also
“Create an ADaM Data Set” on page 120
Data Set Properties
You can view and assign values to the properties that are associated with a data set
and its variables.
Data Sources
The data source for an ADaM data set can be an SDTM domain, another ADaM data
set, or any SAS data sets that are associated with the study or submission.
Variables to Include in the Data Set
You can select which variables to include in an ADaM data set. The variables are listed
by category. The variables that are available to you are based on the type of ADaM data
set that you choose to create.
Creating an ADaM Data Set
119
Note: Certain variables are required and cannot be removed. The names of these
variables are contained in [ ].
After you have selected the variables, you can specify this information about the
variables:
n
the order of the variables
n
whether a variable is nullable (can have a null value)
n
the variables that are part of the key
n
the order of the key variables
Compliance Checks
There are dependencies between some variables and rules that govern the inclusion or
exclusion of some variables. You can check that these dependencies and rules are
satisfied before you create an ADaM data set.
Here are some examples of dependencies and rules:
n
If the TRTxxAN variable is included in a data set, the TRTxxA variable must be
included.
n
An ADSL data set must contain at least one TRTxxP variable.
n
An ADAE data set must contain one or more of the ADSL variables TRTP, TRTA,
TRTxxP, and TRTxxA.
Data Set Keys and Nullable Variables
You can choose to make a variable in an ADaM data set a key and to enable the
variable to have a null value (nullable).
Here are the rules for data set keys:
n
There must be at least one key variable.
n
At least one key variable cannot be nullable.
120 Chapter 6 / ADaM Data Sets
Complete Set of Variables
Before you create an ADaM data set, you review the complete set of variables that you
have chosen to include in the data set. For traceability, the source folder, source data
set, source variable, and source derivation are shown for each variable.
If a variable is associated with a variable in a source data set, the values are supplied
automatically. Otherwise, provide the values.
For each variable, a source derivation field is provided so that you can enter a
description or SAS code that describes how the data is mapped from the source data
into the variable.
TIP Best practices for traceability require that you provide information about the
origin of the data in a data set.
Create an ADaM Data Set
Specify Data Set Location and Type
To create an ADaM data set, perform the following steps:
1 In the Folder tree, select an ADaM-specific study or submission, and then select
New  Analysis Dataset.
The New Analysis Dataset wizard appears.
Creating an ADaM Data Set
121
2 (Optional) Click Browse, and navigate to the location of an ADaM-specific study or
submission.
3 Click Next.
If the study or submission contains multiple ADaM standards, the Analysis Standard
Selection page appears. Otherwise, the Analysis Dataset Type page appears.
4 If the Analysis Standard Selection page appears, select a standard, and click Next.
The Analysis Dataset Type page appears.
5 Select an analysis data set type, and click Next.
For more information, see “Overview: Types of ADaM Data Sets” on page 114.
The General Information page appears.
Specify General Information and Data Set Properties
1 Enter a name and an identifier.
122 Chapter 6 / ADaM Data Sets
Note: There can be only one ADSL analysis data set in a study or submission. It
must be named ADSL.
2 Click Next.
The Analysis Dataset Properties page appears.
3 (Optional) Specify the properties.
For more information, see “Data Set Properties” on page 118.
4 Click Next.
The Library Selection page appears.
Specify Library
1 (Optional) Select a library.
2 Click Next.
The Source Datasets page appears.
Specify Data Sources
1 (Optional) Select one or more source data sets.
For more information, see “Data Sources” on page 118.
2 Click Next.
If you selected one or more source data sets, the Select Variables from Source
Datasets page appears. Otherwise, the Select analysis variables page appears.
Specify Variables and Check Compliance
1 On the Select Variables from Source Datasets page, perform the following steps:
a Select a source data set and one or more source variables.
b Click Add.
The variable appears in the Added Variables table.
Creating an ADaM Data Set
123
c (Optional) To review variables that do not conform, select one or more variables
from the Source Variables table or the Added Variable table, and click NonCompliance.
The Compliance Check Failures dialog box appears. Each non-compliant
variable is listed with the reason why it does not comply.
d To remove an added variable, select a variable in the Added Variable table, and
click Remove.
2 On the Select analysis variables page, use the arrows to move variables between
the Available Variables list and the Selected Variables list.
Note: Certain variables are required and cannot be removed. The names of these
variables are contained in [ ].
TIP You can select a category to move all of the variables in the category at one
time.
For more information, see “Variables to Include in the Data Set” on page 118.
3 (Optional) To determine whether the selected variables comply with the rules
concerning the dependencies between variables, perform the following steps:
a Click Check Compliance.
The Compliance Failures dialog box appears.
For more information, see “Compliance Checks” on page 119.
b Review the error messages, and click Cancel.
4 Click Next.
If you selected a variable with a parameter, one or more pages appear so that you
can specify values for the parameters.
For more information, see “Variables with xx, y, and zz Parameters” on page 115
and “Wildcard Variables” on page 117.
124 Chapter 6 / ADaM Data Sets
Specify Variable Parameters
Note: You must provide at least one value for each variable parameter. Without a value
for each variable parameter, the variables cannot be generated.
1 If the Specify the Grouping Variables page appears, perform the following steps:
a From the Grouping(y) Variables table, select one or more variables.
b From the Values list, select one or more values, and click Assign.
c Click Next.
2 If the Specify the Period Variables page appears, perform the following steps:
a From the Period(xx) Variables table, select one or more variables.
b From the Values list, select one or more values, and click Assign.
TIP To limit the number of values, enter a value in the Maximum value field,
and press Enter.
c Click Next.
3 If the Specify the Record Selection Algorithm Variables page appears, perform the
following steps:
a From the Record Selection(zz) Variables table, select one or more variables.
b From the Values list, select one or more values, and click Assign.
TIP To limit the number of values, enter a value in the Maximum value field,
and press Enter.
c Click Next.
4 If the Wildcard Variables page appears, perform the following steps:
a From the Wildcard Variable Templates table, select one or more variables.
Creating an ADaM Data Set
125
b Enter a value in the Name prefix field and the Description suffix field.
c Click Add.
The variable is added to the Generated Variables table.
Note: You can add the same variable multiple times as long as the name differs.
d To remove a variable from the Generated Variables table, select the variable,
and click Remove.
e Click Next.
Order Variables
1 (Optional) On the Order the variables page, select one or more variables, and click
Move Up and Move Down below the table to order the variables.
2 (Optional) To order the data set keys, perform the following steps:
a Click Order Keys.
The Order Domain Keys dialog box appears.
b Use Move Up and Move Down to order the keys.
3 Click Next.
The Complete Set of Variables page appears.
Review and Finish
1 Review the set of variables.
TIP Best practices for traceability require that you provide information about the
origin of the data in a data set.
2 To edit a value in the Source Folder, Source Dataset, or Source Variable
columns, double-click a cell and enter a value.
Note: If a variable is associated with a variable in a source data set, the values are
supplied automatically.
126 Chapter 6 / ADaM Data Sets
3 To edit the source derivation of a variable, perform the following steps:
a Select a variable, and click Edit Source Derivation.
The Edit Multiline Property Value for Source Derivation dialog box appears.
b Enter the property value, and click OK.
4 Click Next.
The Summary page appears.
5 Review the summary, and click Finish.
Create an ADaM Data Set from a Define.xml
File
To create an ADaM data set from a define.xml file, perform the following steps:
1 In the Folders tree, select a study or submission specific to ADaM, and then select
New  Analysis Dataset(s) From Define.
The New Analysis Dataset(s) From Define wizard appears.
Creating an ADaM Data Set
127
2 Click Browse adjacent to Source, and navigate to the location of a define.xml file.
3 (Optional) Click Browse adjacent to Location, and then select a location in which to
create the ADaM data set.
4 Click Next.
The Data Standard Selection page appears.
5 Select a data standard to associate with the analysis table, and then click Next.
The Analysis Table Selection page appears.
6 Select one or more analysis tables to import, and then click Next.
The Library Selection page appears.
7 (Optional) Select a library to associate with the analysis table, and then click Next.
The Summary page appears.
8 Review the summary, and then click Finish.
128 Chapter 6 / ADaM Data Sets
Promoting an ADaM Data Set to Be a
User-Defined Template
Overview: Promoting an ADaM Data Set to Be
a User-Defined Template
Typically, an ADaM data set is used within a single study or submission. The ADaM
data set is available only to the study or submission in which it is defined. However,
when an ADaM data set is promoted to be a user-defined template, the data set can be
included in any study or submission.
TIP You can replace a current user-defined template with a revised version.
Replacing a current user-defined template enables you to incrementally evolve a data
standard rather than creating a new one.
Here are the requirements to promote an ADaM data set:
n
The user-defined template name and identifier are required.
n
The user-defined template name and identifier must be unique within a data
standard.
n
The user-defined template identifier must be a valid SAS data set name.
See Also
“Analyzing Domain Use and Promoting a Domain to Be a Template” on page 42
Promote an ADaM Data Set to Be a UserDefined Template
To promote an ADaM data set to be a user-defined template, perform the following
steps:
1 In the Clinical Administration tree, expand Data Standards.
Promoting an ADaM Data Set to Be a User-Defined Template
129
Note: You must have appropriate permissions to view the Clinical Administration
tree. For more information, see Appendix 1, “Addition of Users to the Clinical
Administrator Group,” on page 193.
2 Right-click an ADaM data set, and then select Analyze Model Usage.
The Analyze Model Usage dialog box appears.
The Studies/Submissions list displays all of the studies and submissions that
currently use the selected ADaM data set.
3 From the Studies/Submissions list, select one or more items.
4 To limit the ADaM data sets to display, select a type from the Show domains of
type drop-down list.
5 Click Show Domain Details.
130 Chapter 6 / ADaM Data Sets
In the Domain details list, a summary of the ADaM data sets and data set columns
appears. Each ADaM data set that is included in the selected study or submission
appears as a column in the list.
6 To promote an ADaM data set, perform the following steps:
a Select a data set from the Domain drop-down list, and then click Promote.
The ADaM Template Name and Identifier dialog box appears.
b Enter a name and identifier for the user-defined template.
c Click OK.
7 Click Close in the Analyze Model Usage dialog box.
8 To verify that a template was created from the ADaM data set, perform the following
steps:
a In the Clinical Administration tree, expand the selected data standard.
b Expand Domain Templates.
The new ADaM data set template appears in this folder.
Create an ADaM Data Set from a UserDefined Analysis Data Set
To create an ADaM data set from a user-defined analysis data set, perform the
following steps:
1 In the Folders tree, select an ADaM-specific study, submission, or folder, and then
select New  User-defined Analysis Dataset.
The New Analysis Dataset From User Template wizard appears.
Create an ADaM Data Set from a User-Defined Analysis Data Set
131
2 (Optional) Click Browse, and navigate to the location of an ADaM-specific study or
submission.
3 Click Next.
The Analysis Dataset Type page appears.
4 Select an analysis data set type, and then click Next.
The list contains the data sets that have been promoted to be user-defined
templates.
The General Information page appears.
5 Enter a name and an optional description, and then click Next.
The Analysis Dataset Properties page appears.
6 (Optional) Specify the properties.
For more information, see “Data Set Properties” on page 118.
7 Click Next.
132 Chapter 6 / ADaM Data Sets
The Library Selection page appears.
8 (Optional) Select a library, and then click Next.
The Summary page appears.
9 Review the summary, and then click Finish.
See Also
“Overview: Promoting an ADaM Data Set to Be a User-Defined Template” on page 128
Assessing ADaM Compliance
Overview: Assessing ADaM Compliance
You assess the structural and content compliance of a data set with the ADaM data
standard by using the ADaM Compliance transformation. You can assess an individual
data set or a set of data sets. The process assesses whether the selected data set
complies with the data standard.
Note: For detailed information about creating a job with a transformation, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Assess ADaM Compliance
To assess ADaM compliance, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
ADaM Compliance onto the diagram.
Assessing ADaM Compliance
133
The Diagram tab displays the CDISC-ADaM Compliance transformation and the
Results and Metrics work tables.
3 (Optional) To store the Results and Metrics work tables in a permanent location,
perform the following steps:
Note: By default, the work tables are written to a temporary work location.
a Right-click each Work Table icon ( ), and then select Properties.
The Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
b Click the Physical Storage tab, select a SAS library for the Location field, and
then click OK.
4 In the diagram, double-click CDISC-ADaM Compliance.
The CDISC-ADaM Compliance Properties dialog box appears.
5 Click the Data Standard tab.
134 Chapter 6 / ADaM Data Sets
All active ADaM data standards are displayed.
6 Select a data standard, and then click the Tables tab.
The studies and submissions are displayed.
7 Select an ADaM model and a source model.
8 In the ADaM Tables to Check and the Source Tables to Check lists, expand a
study or submission to view its data sets.
9 Select the data sets to validate, or select the study or submission to select all of its
data sets.
Note: You can select data sets from multiple studies and submissions.
10 Click the Checks tab.
11 If no compliance checks are displayed, perform the following steps:
a Click Add.
The Add Compliance Check(s) dialog box appears with a list of all available
compliance checks.
Assessing ADaM Compliance
135
b Click Show details.
Detailed information about each compliance check appears.
c Select one or more checks, click Add Selected, and then click Close.
12 (Optional) Click the Reports tab, and perform the following steps:
a Perform one of the following steps:
n
Select Report by Domain and the Generate Domain Report check box
n
Select Report by Check and the Generate Check Report check box
b Perform one of the following steps:
n
Click Browse adjacent to Browse to Folder, and then navigate to a server
folder.
n
In the Server Folder field, enter the name of a server folder.
The folder must be on the server and must not be a local folder.
136 Chapter 6 / ADaM Data Sets
c Enter a name for the report in the Report File Name field, and then specify the
report output format.
d To limit the number of records to include in the report, enter a number in the
Limit # of records to field.
If you leave this field blank, all records are included in the report.
e Select the panels to include in the report and whether informational messages
are included.
13 Click OK to close the CDISC-ADaM Compliance Properties dialog box.
A green check mark adjacent to the CDISC-ADaM Compliance transformation
indicates that the transformation is complete.
Note: If you see in the lower right corner of the transformation, click and
review the error information that appears. A typical error is that selected domains do
not contain an assigned library. Correct any errors before running the job.
14 Click Run.
SAS Data Integration Studio generates the SAS code for validating the selected data
standard model, and then submits the code to SAS. The Results and Metrics work
tables are generated.
15 Review the Results work table to see the results of the compliance checks.
You might want to connect the Results and Metrics work tables as input to the code
that will be used to generate formatted reports of the results.
Note: You might encounter errors or warnings in the SAS log during job execution.
These errors or warnings do not mean that validation was unsuccessful. Most errors
that halt a validation are reported in the Results work table. As a general rule, the
Results work table reports failures and provides information about the cause of the
failures. For more information about validation, see the SAS Clinical Standards
Toolkit: User Guide.
137
7
Creating a Define.xml File
Transforming SDTM Domains or ADaM Data
Sets into a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Overview: Transforming SDTM Domains or
ADaM Data Sets into a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Register a New Document File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Transform SDTM Domains or ADaM Data Sets
into a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Adding Information to the Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . 142
Overview: Adding Information to the Define.xml File . . . . . . . . . . . . . 142
Save the Work Tables from a CDISC-Define
Creation Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Adding Annotated CRF and Value-Level
Metadata to the Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Creating the Define.xml file from Customized Data . . . . . . . . . . . . . . 150
Overview: Creating the Define.xml file from Customized Data . 150
Create a Define.xml File Using Customized Data . . . . . . . . . . . . . . . . 151
Validating a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Overview: Validating a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Register a New Document File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Validate a Define.xml File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
138 Chapter 7 / Creating a Define.xml File
Transforming SDTM Domains or ADaM
Data Sets into a Define.xml File
Overview: Transforming SDTM Domains or
ADaM Data Sets into a Define.xml File
The CDISC-Define Creation transformation transforms SDTM domains or ADaM data
sets into a define.xml file. The define.xml file complies with the CRT-DDS standard.
Note: For detailed information about creating a job with a transformation, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Register a New Document File
Before you can create a job that uses a define.xml file, you must register a new
document file. The document file references the target define.xml file.
Note: The target define.xml file is created on the server. If you want to open the target
define.xml file from the job, then the target file must be in a shared location that can be
accessed from the computer on which you are using SAS Data Integration Studio. An
example of a shared location is a network drive.
To register a new document file, perform the following steps:
1 In the Folders tree, right-click a folder, and then select New  Document.
The New Document dialog box appears.
2 Enter a name and an optional description.
3 (Optional) Click Browse adjacent to the Location field, and then navigate to the
location in which to store the document.
4 Click Browse adjacent to the File field, and then navigate to the location of the
define.xml file.
Transforming SDTM Domains or ADaM Data Sets into a Define.xml File
139
5 Click OK.
Transform SDTM Domains or ADaM Data Sets
into a Define.xml File
To transform SDTM domains or ADaM data sets into a define.xml file that complies with
the CRT-DDS standard, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
Define Creation onto the diagram.
3 In the diagram, double-click CDISC-Define Creation.
The CDISC-Define Creation Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
4 Click the Tables tab.
140 Chapter 7 / Creating a Define.xml File
5 From the Data Model Type drop-down list, select the type of table or domain to
include in the define.xml file.
6 From the Study/Submission drop-down list, select a study or submission.
The Available Tables by Study/Submission table displays all data tables that are
associated with the study or submission.
7 Select one or more data tables.
8 If you selected multiple data tables and want to change the order of the data tables
in the define.xml file, perform the following steps:
a Click Order Tables.
The Order Tables dialog box appears.
b Select a data table, and click Move Up and Move Down to change the order.
c Click OK.
9 (Optional) Click the Generation tab, and perform the following steps:
a Enter the header comment text for the define.xml file.
b Select a define version, output encoding, and log level.
c Choose whether to create a define.pdf file and whether to create internal
hyperlinks.
d Select an output style sheet to use.
Note: By default, no output style sheet is used. You can use a default style
sheet provided by SAS Clinical Standards Toolkit, or you can select your own
style sheet.
e Choose whether to save the work tables to a permanent location, and browse to
the location.
Transforming SDTM Domains or ADaM Data Sets into a Define.xml File
141
TIP Saving the work table to a permanent location enables you to further
customize the define.xml file. For more information, see “Adding Information to
the Define.xml File” on page 142.
10 (Optional) Click the Reports tab, and perform the following steps:
a Select the Generate Report check box.
b Perform one of the following steps:
n
Click Browse adjacent to Browse to Folder, and then navigate to a server
folder.
n
In the Server Folder field, enter the name of a server folder.
The folder must be on the server and must not be a local folder.
c Enter a name for the report in the Report File Name field, and then specify the
report output format.
d To limit the number of records to include in the report, enter a number in the
Limit # of records to field.
If you leave this field blank, all records are included in the report.
e Select the panels to include in the report and whether informational messages
are included.
11 Click OK.
12 From the Folders tree, drag and drop the define.xml file onto the diagram.
13 To connect the CDISC-Define Creation transformation to the define.xml file, drag
and drop the cursor from the output port of the transformation to the define.xml file.
14 To store the Results work table in a permanent location, perform the following steps:
Note: By default, the Results work table is written to a temporary work location.
a Right-click the Work Table icon ( ), and then select Properties.
142 Chapter 7 / Creating a Define.xml File
The Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
b Click the Physical Storage tab, select a SAS library for the Location field, and
then click OK.
15 Save and run the job.
SAS Data Integration Studio generates the SAS code for transforming, and then
submits the code to SAS. The define.xml file is created. If a define.xml already exists
in that location, then it is overwritten (if the permissions on the file allow it to be
overwritten). The results are written to the CDISC-Define Creation Results table.
16 Review the Results table, and check for errors or warnings.
You can view the define.xml file by navigating to the location where you created the
document file, and then opening the define.xml file with a Web browser. If the Web
browser fails to open the define.xml file, and displays an error message about an
invalid path, then the define.xml file is located on a drive to which you do not have
access. To resolve the problem, move the define.xml file.
Adding Information to the Define.xml
File
Overview: Adding Information to the
Define.xml File
You can save the data from the CDISC-Define Creation transformation so that you can
edit the tables to add information to the define.xml file that is not represented in the SAS
Clinical Data Integration metadata. The process involves the following tasks:
n
save the data from a CDISC-Define Creation transformation
Adding Information to the Define.xml File
143
For information, see “Save the Work Tables from a CDISC-Define Creation
Transformation” on page 143.
n
include computational algorithm and codelist metadata in the define.xml file
n
add annotated CRF and value-level metadata to the define.xml file
For information, see “Adding Annotated CRF and Value-Level Metadata to the
Define.xml File” on page 145.
Save the Work Tables from a CDISC-Define
Creation Transformation
To save the work tables from a CDISC-Define Creation transformation, perform the
following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
Define Creation onto the diagram.
144 Chapter 7 / Creating a Define.xml File
For information about adding a CDISC-Define Creation transformation, see
“Transforming SDTM Domains or ADaM Data Sets into a Define.xml File” on page
138.
3 In the diagram, double-click CDISC-Define Creation.
The CDISC-Define Creation Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
4 Click the Generation tab.
5 Select the Save work tables to permanent location check box, and then click
Browse adjacent to the Location field.
The Select Path dialog box appears.
Note: The file type is Folder. You can select entries that are folders.
6 Select a folder, and then click OK twice.
Note: The folder must be accessible by the SAS Workspace Server where the code
executes. This means that the folder that appears is not on your local computer, but
is on the SAS Workspace Server. You must have Write access permission to this
folder. If there are tables from a previous CDISC-Define Creation transformation in
this folder, they will be overwritten without any prompting.
When creating a define.xml file, select a location into which tables that are created
by the CDISC-Define Creation transformation can be copied.
7 Save and run the job.
SAS Data Integration Studio generates the SAS code for creating the define.xml file,
and then submits the code to SAS. The define.xml file is created. Several tables are
created in the folder that you selected. Depending on the metadata found for the
domain and study, many of these tables will be empty. For more information about
the tables that are created, see the SAS Clinical Standards Toolkit: User's Guide.
Adding Information to the Define.xml File
145
Adding Annotated CRF and Value-Level
Metadata to the Define.xml File
Overview: Adding Annotated CRF and Value-Level Metadata to
the Define.xml File
You can include the annotated Case Report Form (CRF) metadata and value-level
metadata about the domains that you collected during a study. To do this, you edit the
SAS data sets that were generated by the CDISC-Define Creation transformation to
include the metadata. Then, you run the %CRTDDS_WRITE macro to generate the
define.xml file.
Here is example code that includes annotated CRF metadata:
*Lookup OID for the SDTM 3.1.2 standard in MetaDataVersion;
proc sql noprint;
select OID into :mdv from _svWork.MetaDataVersion
where name="CDISC-SDTM 3.1.2";
quit;
*Add records for Annotated CRF;
proc sql;
insert into _svWork.AnnotatedCRFs
set DocumentRef = "BlankCRF",
leafID= "AnnotatedCRF",
FK_MetaDataVersion = "&mdv";
insert into _svWork.MDVLeaf
set ID= "AnnotatedCRF",
href = "./blankcrf.pdf",
FK_MetaDataVersion = "&mdv";
insert into _svWork.MDVLeafTitles
set title= "Blank Annotated CRF",
FK_MDVLeaf = "AnnotatedCRF";
quit;
*reassign srcdata to location of _svWork data sets;
data _null_; path=pathname('_svwork'); rc=libname('srcdata');
rc=libname('srcdata',path);
run;
*create new define.xml file using updated SAS CRT-DDS data sets;
%crtdds_write(_cstCreateDisplayStyleSheet=1);
Here is example code that includes the value-level metadata in the SC domain. The
code includes two values: height without shoes and weight without shoes.
146 Chapter 7 / Creating a Define.xml File
*Lookup OID for the SDTM 3.1.2 standard in MetaDataVersion;
proc sql noprint;
select OID into :mdv from _svWork.MetaDataVersion
where name="CDISC-SDTM 3.1.2";
quit;
*Lookup OID for the SCTEST column in ItemDefs;
proc sql noprint;
select OID into :srccol from _svWork.ItemDefs
where name='SCTEST';
quit;
*add record for a new valuelist SCTESTVALS;
proc sql ;
insert into _svWork.ValueLists
set OID= "SCTESTVALS",
FK_MetaDataVersion = "&mdv";
*add record associating the value list SCTESTVALS to the OID for SCTEST ItemDefs record;
insert into _svWork.ItemValueListRefs
set ValueListOID= "SCTESTVALS",
FK_ItemDefs = "&srccol";
*add records to the ItemDefs data set for each value in the SCTESTVAL value list;
insert into _svWork.ItemDefs
set OID= "VAL001",
Name = "SCTEST",
DataType = "text",
Length = 3,
SASFieldName = "SCTEST",
comment = "Height taken barefoot",
label="Height in inches",
FK_MetaDataVersion = "&mdv"
set OID= "VAL002",
Name = "SCTEST",
DataType = "text",
Length = 4,
SASFieldName = "SCTEST",
comment = "Weight without shoes",
label="Weight in pounds",
FK_MetaDataVersion = "&mdv";
*add records associating the value list SCTESTVALS to rows in the ItemDefs data set;
insert into _svWork.ValueListItemRefs
set ItemOID= "VAL001",
OrderNumber=1,
Mandatory="Yes",
KeySequence=1,
FK_ValueLists = "SCTESTVALS"
set ItemOID= "VAL002",
OrderNumber=2,
Mandatory="Yes",
Adding Information to the Define.xml File
147
KeySequence=2,
FK_ValueLists = "SCTESTVALS";
quit;
*reassign srcdata to location of _svWork data sets;
data _null_; path=pathname('_svwork'); rc=libname('srcdata');
rc=libname('srcdata',path);
run;
*create new define.xml file using updated SAS CRT-DDS data sets;
%crtdds_write(_cstCreateDisplayStyleSheet=1);
For the example code, the define.xml file created contains the value-level metadata for
Height and Weight for the SCTEST column in the SC domain.
Note: If you are viewing an electronic version of this document, you can cut and paste
the example code.
Add Annotated CRF Metadata or Value-Level Metadata to the
Define.xml File
To add annotated CRF metadata or value-level metadata to the define.xml file, perform
the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
Define Creation onto the diagram.
148 Chapter 7 / Creating a Define.xml File
For detailed information about adding a CDISC-Define Creation transformation, see
“Transforming SDTM Domains or ADaM Data Sets into a Define.xml File” on page
138.
3 In the diagram, double-click CDISC-Define Creation.
The CDISC-Define Creation Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
4 Click the Generation tab.
5 Select the Save work tables to permanent location check box, click Browse
adjacent to the Location field, and then select a location.
For more information about saving tables, see “Save the Work Tables from a
CDISC-Define Creation Transformation” on page 143.
6 Click OK twice.
7 Click Run.
The define.xml file is generated, and the SAS data sets used to generate the file are
included.
Adding Information to the Define.xml File
149
8 To add records to the annotatedcrfs, mdvleaf, and mdvleaftitles data sets (for CRF
metadata), or valuelists, itemvaluelistrefs, valuelistitemrefs, and itemdefs data sets
(for value-level metadata), perform the following steps:
a In the Transformations tree, expand Data, and then drag and drop User
Written Code onto the diagram.
b In the diagram, double-click User Written.
The User Written Properties dialog box appears.
For more information about the properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
c (Optional) Click the General tab, and then rename the transformation.
d Click the Code tab.
e From the Code generation mode drop-down list, select All user written.
f
In the code editor, enter the code to include annotated CRF metadata or the
value-level metadata.
For example code, see “Overview: Adding Annotated CRF and Value-Level
Metadata to the Define.xml File” on page 145.
g Click OK.
9 Click Run, and then review the define.xml file to ensure that the annotated CRF
metadata or the value-level metadata is included.
150 Chapter 7 / Creating a Define.xml File
Creating the Define.xml file from
Customized Data
Overview: Creating the Define.xml file from
Customized Data
The CDISC-Define Creation transformation operates on saved data so that SAS
programmers who are familiar with the table model representation for CRT-DDS can
add customizations to a define.xml file. This is a two-step process:
1 Insert custom study metadata into the saved CRT-DDS tables.
2 Generate a customized define.xml file from these updated tables.
Here is example code that creates a define.xml file from saved data. Edit this example
code to point to the location of the customized tables.
%let SASCrtddsTables = %nrquote(\\myCDIServer\mydatatables);
%let DefPath = %nrquote(\\myCDIServer\myDefineLocation);
%let DefFile = %nrquote(define.xml);
%cst_setStandardProperties(_cstStandard=CST-FRAMEWORK,_cstSubType=initialize);
%cst_setStandardProperties(_cstStandard=CDISC-CRTDDS,_cstSubType=initialize);
%let workPath=%sysfunc(pathname(work));
%let _cstSASRefs=work.sasreferences;
%let _cstSASRefsLoc=&workpath;
%let _cstSASRefsName=sasreferences;
%let _cstResultsds=crtdds_results;
%cst_createdsfromtemplate(_cstStandard=CST-FRAMEWORK, _cstType=control,_cstSubType=reference, _cstOutputDS=work.sasreferences);
%LET _CSTSTANDARD=CDISC-CRTDDS;
%LET _CSTSTANDARDVERSION=1.0;
proc sql;
insert into work.sasreferences
values ("CST-FRAMEWORK" "1.2" "messages" "" "messages" "libref" "input" "dataset"
"N" "" "" 1 "" "")
values ("&_cstStandard" "&_cstStandardVersion" "messages" "" "crtmsg" "libref" "input" "dataset"
"N" "" "" 2 "" "")
values ("&_cstStandard" "&_cstStandardVersion" "autocall" "" "auto1" "fileref" "input" "folder" "
N" "" "" 1 "" "")
values ("&_cstStandard" "&_cstStandardVersion" "control" "reference" "control" "libref" "both" "dataset"
"Y" "" "&workpath" . "sasreferences" "")
Creating the Define.xml file from Customized Data
151
values ("&_cstStandard" "&_cstStandardVersion" "sourcedata" "" "srcdata" "libref" "input" "folder"
"N" "" "&SASCrtddsTables" . "" "")
values ("&_cstStandard" "&_cstStandardVersion" "externalxml" "xml" "extxml" "fileref" "output" "file"
"Y" "" "&defpath" . "&deffile" "")
values ("&_cstStandard" "&_cstStandardVersion" "referencexml" "stylesheet" "xslt01" "fileref" "output" "file" "
Y" "" "" . "" "")
;
quit;
%let _cstReallocateSasrefs=1;
%cstutil_allocatesasreferences;
%crtdds_write(_cstCreateDisplayStyleSheet=1,_cstResultsOverrideDS=&_cstResultsDS);
In the example code, edit SASCrtddsTables to specify the location where the saved
data sets exist, and edit DefPath to specify the location to write the resulting define.xml
file.
Note: If you are viewing an electronic version of this document, you can cut and paste
the example code.
Create a Define.xml File Using Customized
Data
To create a define.xml file using customized data, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Data, and then drag and drop User Written
Code onto the diagram.
3 In the diagram, double-click User Written.
The User Written Properties dialog box appears.
4 Click the Code tab.
5 From the Code generation mode drop-down list, select All user written.
6 In the code editor, enter the code to create the define.xml file.
152 Chapter 7 / Creating a Define.xml File
For example code, see “Overview: Creating the Define.xml file from Customized
Data” on page 150.
7 Click OK and then click Run.
8 From the Windows Start menu, select Run, and then enter the location where the
data sets are located (for example, \\myCDIServer\mydata\crtdds_tables).
9 Open the define.xml file to view the customizations that you created.
Validating a Define.xml File
Overview: Validating a Define.xml File
The CDISC-Define Validation transformation assesses the validity of the define.xml file.
Validity is based on the XML standards as defined by CDISC.
Validity is based on the following criteria:
n
The XML is well formed.
n
The XML meets the XML schema specification for the CDISC standard.
Note: For detailed information about creating a job with a transformation, see the SAS
Data Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Register a New Document File
Before you can create a job to validate a define.xml file, you must register a new
document file. The new document file must point to an existing define.xml file in a
location that the SAS Workspace Server can access.
For more information about registering a new document file, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
Validating a Define.xml File
153
Validate a Define.xml File
To validate a define.xml file, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop CDISC-
Define Validation onto the diagram.
3 From the Folders tree, drag and drop the define.xml file onto the diagram.
4 Drag the cursor from the define.xml file to the input port of the transformation.
This action connects the define.xml file to the transformation.
5 To store the Results work table permanently, perform the following steps:
Note: By default, the Results work table is written to a temporary work location.
a Right-click the Work Table icon
, and then select Properties.
The Properties dialog box appears.
154 Chapter 7 / Creating a Define.xml File
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
b Click the Physical Storage tab, select a SAS library for the Location field.
6 (Optional) In the diagram, double-click CDISC-Define Validation.
The CDISC-Define Validation Properties dialog box appears.
a Click the Validation tab, and select a define version to use for the validation.
b Click the Reports tab, and perform the following steps:
a Select the Generate Report check box.
b Perform one of the following steps:
n
Click Browse adjacent to Browse to Folder, and then navigate to a
server folder.
n
In the Server Folder field, enter the name of a server folder.
The folder must be on the server and must not be a local folder.
c Enter a name for the report in the Report File Name field, and then specify
the report output format.
d To limit the number of records to include in the report, enter a number in the
Limit # of records to field.
If you leave this field blank, all records are included in the report.
e Select the panels to include in the report and whether informational messages
are included.
c Click OK to close the CDISC-Define Validation Properties dialog box.
7 Click Run.
SAS Data Integration Studio generates the SAS code for validating, and then
submits the code to SAS. The define.xml file is validated, and then the results are
written to the Validation Results work table.
Validating a Define.xml File
155
If there are errors in the define.xml file, the Validation Results work table provides a
message for each error. An error message includes the line and column number in
the define.xml file that generated the error.
156 Chapter 7 / Creating a Define.xml File
157
8
SAS Transport Files
Overview of SAS Transport Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Import a SAS Version 5 Transport File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Export a SAS Version 5 Transport File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Overview of SAS Transport Files
When this document was published, the Food and Drug Administration expects clinical
and non-clinical data to be delivered in the SAS Version 5 transport format.
SAS Clinical Data Integration provides two transformations to support this goal. One
transformation imports a SAS Version 5 transport file, and one transformation exports a
SAS Version 5 transport file.
Import a SAS Version 5 Transport File
To import a SAS Version 5 transport file, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
158 Chapter 8 / SAS Transport Files
2 In the Transformations tree, expand Clinical, and then drag and drop SAS
Version 5 Transport File Import onto the diagram.
3 In the diagram, double-click SAS Version 5 Transport File Import.
The SAS Version 5 Transport File Import Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
4 Click the Options tab, and then select General from the list on the left.
5 Click Browse adjacent to the SAS Version 5 Transport File field, and then select a
location that is accessible by the remote SAS server.
Note: The Select a File dialog box displays only files with the extension .xpt.
6 Click Browse adjacent to the Imported Data Library field, and then select a
location in which to write the data sets.
7 Click OK to close the SAS Version 5 Transport File Import Properties dialog box.
A green check mark adjacent to the SAS Version 5 Transport File Import
transformation indicates that the transformation is complete.
Note: If you see in the lower right corner of the transformation, click
review the error information that appears.
and
Export a SAS Version 5 Transport File
159
8 Click Run.
9 Verify that there are no errors.
10 Register the tables in the library that was created.
For more information about registering tables, see the SAS Data Integration Studio:
User's Guide or the SAS Data Integration Studio online Help.
Export a SAS Version 5 Transport File
To export a SAS Version 5 transport file, perform the following steps:
1 Create an empty job.
For detailed information about creating an empty job, see the SAS Data Integration
Studio: User's Guide or the SAS Data Integration Studio online Help.
2 In the Transformations tree, expand Clinical, and then drag and drop SAS
Version 5 Transport File Export onto the diagram.
3 In the diagram, double-click SAS Version 5 Transport File Export.
160 Chapter 8 / SAS Transport Files
The SAS Version 5 Transport File Export Properties dialog box appears.
For detailed information about the Properties dialog box, see the SAS Data
Integration Studio: User's Guide or the SAS Data Integration Studio online Help.
4 Click the Export Options tab, click Browse adjacent to the Libref field, and then
select a SAS library.
The list of registered tables in the SAS library appears.
5 Select one or more tables.
6 Click Browse adjacent to the Destination Folder field, and then select a location in
which to write the transport file.
7 To disable overwriting an existing transport file, clear Allow overwrite of existing
transport files.
8 Click OK to close the SAS Version 5 Transport File Export Properties dialog box.
A green check mark adjacent to the SAS Version 5 Transport File Export
transformation indicates that the transformation is complete.
Note: If you see in the lower right corner of the transformation, click
review the error information that appears.
9 Click Run.
10 Verify that there are no errors.
and
161
Part 5
SAS Integration Adapter for Medidata Rave
Chapter 9
General Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Chapter 10
Study Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
162
163
9
General Administration
Define a Medidata Rave Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Enable a SAS Clinical Data Integration User to
Log In to Medidata Rave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Verify That the Medidata Rave Server Has Been
Registered Properly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Define a Medidata Rave Server
To define a Medidata Rave server, perform the following steps:
1 Log in to SAS Management Console.
2 Define a new server with the following properties:
n
For the server type, select Resource Templates  Servers  Content Servers
 HTTP Server.
n
For the base path, define a new base path that is set to the Medidata Rave Web
Services, such as /RWS.
n
For the application server type, select Medidata Rave.
n
For the authentication domain, specify a new or existing authentication domain.
Specify the application protocol as HTTPS, and enter the host name.
164 Chapter 9 / General Administration
For more information about defining a server, see the SAS Management Console online
Help.
Enable a SAS Clinical Data Integration
User to Log In to Medidata Rave
To enable a SAS Clinical Data Integration user to log in to Medidata Rave, perform the
following steps:
1 Log in to SAS Management Console as a user with permission to add server
instances and manage users and groups.
2 Add or modify a SAS Clinical Data Integration user account with the following
properties:
n
For the login information, create new login information using the user ID and
password to access the Medidata Rave server.
n
For the authentication domain, specify the same authentication domain that is
specified for the Medidata Rave server that you are using.
For more information about adding or modifying a user account, see the SAS
Management Console online Help.
Verify That the Medidata Rave Server
Has Been Registered Properly
To verify that the Medidata Rave server has been registered properly, perform the
following steps:
1 Log in to SAS Clinical Data Integration.
2 Select Tools  Medidata Rave  Servers.
Verify That the Medidata Rave Server Has Been Registered Properly
165
The Registered Rave Servers dialog box appears.
3 Verify that the Host, Services Path, and Rave User ID (the Medidata Rave user ID
for the current SAS Clinical Data Integration user) are correct.
4 Select the row for the Medidata Rave server that you just defined, and then click
Test Connection.
5 Click Close.
166 Chapter 9 / General Administration
167
10
Study Administration
Manage the Connection between a SAS Clinical
Data Integration Study and a Medidata Rave Study . . . . . . . . . . . . . 168
Create a Connection between Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
View the Mappings between Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Disconnect a SAS Clinical Data Integration
Study from a Medidata Rave Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Create a SAS Clinical Data Integration Data
Table Definition from Medidata Rave Metadata . . . . . . . . . . . . . . . . . . . 172
Manage the Medidata Rave Properties of a SAS
Clinical Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Display the Medidata Rave Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Create a Transformation Log Table for a SAS
Clinical Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
Disassociate a Log Table from a SAS Clinical
Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Specify the ODM Archive Location for a SAS
Clinical Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Managing the Codelist Table in a SAS Clinical
Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Overview: Managing the Codelist Table in a SAS
Clinical Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Create the Codelist Table for a SAS Clinical
Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
168 Chapter 10 / Study Administration
Reimport a Codelist Table into a SAS Clinical
Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Remove the Codelist Table from a SAS Clinical
Data Integration Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Review the Medidata Rave Properties of a SAS
Clinical Data Integration Data Table Definition . . . . . . . . . . . . . . . . . . . 184
Retrieving Medidata Rave Study Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Overview: Retrieving Medidata Rave Study Data . . . . . . . . . . . . . . . . 185
Notification of Potential Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Set Up the Job to Retrieve Medidata Rave Data . . . . . . . . . . . . . . . . . 186
Run the Job, and Then Check the Results . . . . . . . . . . . . . . . . . . . . . . . . 188
Ensuring No Raw Data Is Lost during Transformation . . . . . . . . . . . 189
Schedule a Job to Update Study Data from Medidata Rave . . . . 190
Deploy a Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Create and Schedule a Job Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Manage the Connection between a SAS
Clinical Data Integration Study and a
Medidata Rave Study
Create a Connection between Studies
Note: You must have Administrator access permissions to the SAS Clinical Data
Integration study.
To create a connection between studies, perform the following steps:
1 In the Folders tree, right-click a SAS Clinical Data Integration study root folder, and
then select Connect to Medidata Rave.
The Connect to a Rave Study wizard appears.
Manage the Connection between a SAS Clinical Data Integration Study and a Medidata Rave
Study 169
2 Select a server from the Registered Rave Servers table.
3 (Optional) Test the connection to the server.
4 Click Next.
The Rave Studies page appears.
170 Chapter 10 / Study Administration
5 Select a study from the Select a Rave Study table, and then click Finish.
6 (Optional) Verify the connection by performing the following steps:
a In the Folders tree, right-click the study root folder, and then select Properties.
The Properties dialog box appears.
b Click the Medidata Rave tab.
The Medidata Rave tab contains a table with entries that specify the properties
of the Medidata Rave study associated with the SAS Clinical Data Integration
study. This information includes the Medidata Rave server information (name,
host, base path, and user name) and the Medidata Rave study information (OID,
study name, and protocol name).
c Click OK.
Manage the Connection between a SAS Clinical Data Integration Study and a Medidata Rave
Study 171
View the Mappings between Studies
To view the mappings between studies, perform the following steps:
1 Select Tools  Medidata Rave  Study Mappings.
The CDI-Rave Study Mappings dialog box appears.
Each row of the table shows a mapping between a SAS Clinical Data Integration
study and a Medidata Rave study on a specific Medidata Rave server.
2 Review the mappings, and then click Close.
Disconnect a SAS Clinical Data Integration
Study from a Medidata Rave Study
To disconnect a SAS Clinical Data Integration study from a Medidata Rave study, in the
Folders tree, right-click a mapped SAS Clinical Data Integration study root folder, and
then select Disconnect from Medidata Rave.
Note: When you disconnect the studies, the data and objects are not deleted.
However, all metadata properties specific to the Medidata Rave connection are deleted
from the objects.
172 Chapter 10 / Study Administration
Create a SAS Clinical Data Integration
Data Table Definition from Medidata
Rave Metadata
Note: You must have Administrator access permissions to the SAS Clinical Data
Integration study.
Before you can populate a SAS Clinical Data Integration study with data extracted from
a Medidata Rave study, you must create at least one data table definition.
To create a SAS Clinical Data Integration data table definition from Medidata Rave
metadata, perform the following steps:
1 In the Folders tree, navigate to the SAS Clinical Data Integration study root folder
that is mapped to a Medidata Rave study.
For information, see “Create a Connection between Studies” on page 168.
2 Right-click a SAS Clinical Data Integration study folder, and then select Import
Medidata Rave Table Definitions.
A progress indicator appears, and then the Import Medidata Rave Table Definitions
wizard appears.
Create a SAS Clinical Data Integration Data Table Definition from Medidata Rave Metadata
173
All Medidata Rave table definitions for the study and the study version are listed.
Note: The list does not contain table definitions that have no columns.
3 Select one or more tables to import.
4 Click Next.
If you select a Medidata Rave table that has been previously imported into the target
folder, a warning appears. You must select a different table. Or, you can exit the
wizard, and delete the table from the target folder.
The SAS Library page appears.
174 Chapter 10 / Study Administration
5 Using the standard SAS Data Integration Studio library controls, select a library, or
create a library definition.
Note: You must have Create access permission to the library that you select.
For help with using these controls, see the SAS Data Integration Studio: User's
Guide or the SAS Data Integration Studio online Help.
6 Click Finish.
The tables are imported.
A SAS Data Integration Studio physical table appears in the folder for each imported
Medidata Rave table.
Note: The data table definition has been created, but the data table has no data at
this point.
The name of the SAS Data Integration Studio table is the same as the Medidata
Rave table name, except that any characters in the Medidata Rave table name that
are not valid for a SAS table name are removed.
Manage the Medidata Rave Properties of a SAS Clinical Data Integration Study
175
See Also
n
“Review the Medidata Rave Properties of a SAS Clinical Data Integration Data Table
Definition” on page 184
n
“Retrieving Medidata Rave Study Data” on page 185
Manage the Medidata Rave Properties
of a SAS Clinical Data Integration Study
Display the Medidata Rave Properties
To display the Medidata Rave properties, perform the following steps:
1 In the Folders tree, navigate to the SAS Clinical Data Integration study root folder
that is mapped to a Medidata Rave study.
For information, see “Create a Connection between Studies” on page 168.
2 Right-click the SAS Clinical Data Integration study root folder, and then select
Properties.
The Properties dialog box appears.
176 Chapter 10 / Study Administration
3 Click the Medidata Rave tab.
Manage the Medidata Rave Properties of a SAS Clinical Data Integration Study
177
4 Modify the properties, and then click OK.
Create a Transformation Log Table for a SAS
Clinical Data Integration Study
Note: The primary purpose of the Medidata Rave transformation log table is to debug
and provide technical support. Do not alter this table in any way.
To create a Medidata Rave transformation log table for a SAS Clinical Data Integration
study, perform the following steps:
1 Display the Medidata Rave properties.
For information, see “Display the Medidata Rave Properties” on page 175.
2 Click New adjacent to the Transformation Log Table field.
The New Rave Transformation Log Table wizard appears.
3 Enter a name and optional description, and then click Next.
178 Chapter 10 / Study Administration
Note: The name must be a valid SAS table name.
The SAS Library page appears.
4 Using the standard SAS Data Integration Studio library controls, select a library, or
create a library definition.
Note: You must have Create access permission to the library that you select.
For help with using these controls, see the SAS Data Integration Studio: User's
Guide or the SAS Data Integration Studio online Help.
5 Click Finish.
The log table is created directly beneath the study root folder.
Manage the Medidata Rave Properties of a SAS Clinical Data Integration Study
179
Disassociate a Log Table from a SAS Clinical
Data Integration Study
To disassociate a log table from a SAS Clinical Data Integration study, perform the
following steps:
1 Display the Medidata Rave properties.
For information, see “Display the Medidata Rave Properties” on page 175.
2 Click Remove adjacent to the Transformation Log Table field.
Specify the ODM Archive Location for a SAS
Clinical Data Integration Study
To specify the Operational Data Model (ODM) archive location for a SAS Clinical Data
Integration study, perform the following steps:
1 Display the Medidata Rave properties.
For information, see “Display the Medidata Rave Properties” on page 175.
2 Click Browse adjacent to the ODM Document Archive Folder field.
3 If you are prompted to log in to the SAS Foundation server, log on so that you can
access the SAS Foundation server’s file system.
4 In the ODM Archive Folder dialog box, select a folder to which you have Read and
Write access permissions, and then click OK.
180 Chapter 10 / Study Administration
Managing the Codelist Table in a SAS
Clinical Data Integration Study
Overview: Managing the Codelist Table in a
SAS Clinical Data Integration Study
When you import a codelist table, SAS Clinical Data Integration imports the codelist
table only for the study versions that currently have or that could have (in the future)
enrolled subjects. These study versions are considered non-retired versions.
A non-retired version is the desired version set for a specific study environment. This
version set contains all study versions which, for that study environment, contain at
least one enrolled subject. The most recent version for an environment or site is
included in the set for any environment or site in that study. As a result, the most recent
version is always available for the forward migration of subject data, even if no subjects
are currently enrolled in the most recent version.
Limiting the codelist table in this way ensures that the codelist table does not include
data for versions that will never be referenced.
The structure of a SAS data set required to store Medidata Rave codelist table
information is the same across all versions. Therefore, the data in a SAS data set for a
codelist table can be reimported without data mismatch or metadata mismatch.
Create the Codelist Table for a SAS Clinical
Data Integration Study
To create the codelist table for a SAS Clinical Data Integration study, perform the
following steps:
1 Display the Medidata Rave properties.
For information, see “Display the Medidata Rave Properties” on page 175.
2 Click New adjacent to the Codelist Table field.
Managing the Codelist Table in a SAS Clinical Data Integration Study
The New Rave Codelist Table wizard appears.
3 Enter a name and optional description, and then click Next.
Note: The name must be a valid SAS table name.
The SAS Library page appears.
181
182 Chapter 10 / Study Administration
4 Using the standard SAS Data Integration Studio library controls, select a library, or
create a library definition.
Note: You must have Create access permission to the library that you select.
For help with using these controls, see the SAS Data Integration Studio: User's
Guide or the SAS Data Integration Studio online Help.
5 Click Next.
The Codelists page appears.
Managing the Codelist Table in a SAS Clinical Data Integration Study
183
The table lists the codelist tables that are registered to active Medidata Rave studies
to which the SAS Clinical Data Integration study is mapped.
Each row in the table represents one declared codelist table to import. The same
codelist table can appear multiple times, once for each study version.
6 (Optional) Click a column heading to reorder the table.
Note: The information in this table is read-only. You cannot select a row.
7 Click Finish.
A codelist table with the specified name and description is created directly beneath
the study root folder. The codelist table contains the necessary columns and is
associated with the SAS library that you selected.
Reimport a Codelist Table into a SAS Clinical
Data Integration Study
To reimport a codelist table into a study, perform the following step:
184 Chapter 10 / Study Administration
In the Folders tree, right-click on a codelist table, and then select Import Codelists
from Medidata Rave.
Remove the Codelist Table from a SAS
Clinical Data Integration Study
To remove the codelist table from a study, perform the following steps:
1 Display the Medidata Rave properties.
For information, see “Display the Medidata Rave Properties” on page 175.
The Codelist Table field displays the name of the codelist table associated with the
study.
2 Click Remove adjacent to the Codelist Table field.
Although the codelist table is no longer associated with the study, the codelist table
still exists in its original location and retains its data.
Review the Medidata Rave Properties of
a SAS Clinical Data Integration Data
Table Definition
To review the Medidata Rave properties of a SAS Clinical Data Integration data table
definition, perform the following steps:
1 In the Folders tree, right-click a SAS Clinical Data Integration data table definition
that was imported from Medidata Rave, and then select Properties.
The Properties dialog box appears.
2 Click the Medidata Rave tab, and then review the properties of the Medidata Rave
data table definition.
3 Click the Columns tab, right-click on a column, and then select Properties.
Retrieving Medidata Rave Study Data
185
The Properties dialog box appears.
4 Click the Medidata Rave tab, and then review the properties of the Medidata Rave
table column.
5 Click OK.
See Also
“Create a SAS Clinical Data Integration Data Table Definition from Medidata Rave
Metadata” on page 172
Retrieving Medidata Rave Study Data
Overview: Retrieving Medidata Rave Study
Data
After you have created the SAS Clinical Data Integration data table definitions from
Medidata Rave metadata, you can populate the SAS Clinical Data Integration study with
data extracted from a Medidata Rave study. There are two transformations to retrieve
study data from Medidata Rave.
The Extract Medidata Rave Data transformation deletes all Medidata Rave data from
the specified data tables in the associated SAS Clinical Data Integration study. Then,
the transformation inserts the Medidata Rave study data into the specified data tables.
You specify the data tables when you set up the job.
The Update from Medidata Data Rave transformation updates the Medidata Rave study
data in the specified data tables with data that has changed since the study data was
last retrieved. You specify the data tables when you set up the job.
If you run the Update from Medidata Data Rave transformation on a SAS Clinical Data
Integration data table that has not been populated using either of these two
transformations, the Update from Medidata Data Rave transformation populates the
study just as the Extract Medidata Rave Data transformation does.
186 Chapter 10 / Study Administration
See Also
“Create a SAS Clinical Data Integration Data Table Definition from Medidata Rave
Metadata” on page 172
Notification of Potential Changes
When you retrieve study data from Medidata Rave, it is possible that the Medidata Rave
table metadata has changed since the data table definition was initially imported. You
can choose how to handle a potential change. You can attempt to retrieve the changed
data, or you can skip the retrieval of study data for any data table with Medidata Rave
table metadata that might have changed. And, you can choose to notify one or more
users via e-mail if the transformation detects potential table metadata changes.
The value that you specify for the e-mail address can be a single address, a mailing list,
or any other value that is valid for your default e-mail client. The transformation passes
the value to the e-mail client without any validation.
Note: Notification does not apply to the Medidata Rave Comments table. The structure
of the Comments table cannot change across study versions. Therefore, omitting
notification prevents unnecessary notifications.
Set Up the Job to Retrieve Medidata Rave
Data
To set up the job to retrieve Medidata Rave data, perform the following steps:
1 In the Folders tree, navigate to a SAS Clinical Data Integration study that is mapped
to Medidata Rave, and create a job.
2 In the Transformations tree, expand Clinical.
3 Drag the Extract Medidata Rave Data transformation or the Update from
Medidata Rave Data transformation onto the job, and then double-click the
transformation.
The Properties dialog box appears.
4 To select a Medidata Rave data table definition, perform the following steps:
Retrieving Medidata Rave Study Data
187
a Click the Tables tab, select a clinical study, and then select one or more
Medidata Rave data table definitions.
Note the selected data table definitions.
Note: You can select a Medidata Rave data table definition that contains no
data.
b Click OK.
5 To notify users of potential changes to the Medidata Rave table metadata, perform
the following steps:
a Click the Notifications tab.
b Select the Send Email on Potential Table Metadata Mismatch check box.
c In the Address field, enter a valid e-mail address or e-mail group.
188 Chapter 10 / Study Administration
d Specify what action to take when a potential mismatch is detected, and then click
OK.
6 Confirm that there is a green check mark in the lower right corner of the
transformation.
If the green check mark is not there, click on the transformation to display a
message that indicates any problems.
Run the Job, and Then Check the Results
To update data table data from Medidata Rave, perform the following steps:
1 Run the job
After the job runs, there should be no errors or warnings in the log. If there are,
debug them, and run the job again.
2 Save and close the job.
3 Select the transformation log table, and open it.
There is a record per selected table.
4 Close the transformation log table.
5 For each data table that was selected for processing, perform the following steps:
a In the Folders tree, right-click a table, and then select Open.
The View Data page appears.
b Confirm that the data is correct.
c Compare the values in the regular data columns to the _RAW data columns to
ensure that no raw data was lost.
For more information, see “Ensuring No Raw Data Is Lost during Transformation”
on page 189.
Retrieving Medidata Rave Study Data
189
If the Medidata Rave data tables contain data, the tables selected for processing
contain data. If the Medidata Rave data tables do not contain data, the tables
selected for processing do not contain data.
Note: It is possible that a table will not have data in it if there are no records in the
data entry system.
Ensuring No Raw Data Is Lost during
Transformation
When the Medidata Rave Web Services transforms raw data into regular data, some
data might fail validation or transformation. Failure during validation or transformation is
the result of flawed raw data in Medidata Rave. To ensure that this flawed raw data is
not lost during transformation, you can examine in SAS Clinical Data Integration the raw
data that was used during the transformation. The ability to examine the raw data helps
you prevent submitting null data to a regulatory body when flawed data was entered in
Medidata Rave.
The raw data is included in the SAS Clinical Data Integration data set so that you can
examine the data and correct it.
For every _RAW data column definition in a Medidata Rave data table definition, there
is a corresponding regular data column with the same name, minus the _RAW
designation. For example, the IT_SEVERE_RAW data column has a corresponding
regular data column named IT_SEVERE.
If the raw data was validated or transformed without error, the values in both the regular
data column and the _RAW data column will be identical.
If the raw data was not validated or transformed without error, the value in the regular
data column will be empty, and the _RAW data column will contain the raw, invalid
value that was in Medidata Rave.
190 Chapter 10 / Study Administration
Schedule a Job to Update Study Data
from Medidata Rave
Deploy a Job
To deploy a job to update study data from Medidata Rave, perform the following steps:
1 Select the job that will retrieve data from Medidata Rave.
2 In the Folders tree, right-click the job, and then select Scheduling  Deploy.
The Deploy a job for scheduling dialog box appears.
3 Specify the information for deployment, and then click OK.
Create and Schedule a Job Flow
To create and schedule a job flow, log in to SAS Management Console. Create a flow,
and select Platform Process Manager as the scheduling server.
Note: You must log in to SAS Management Console as the same user who created
and deployed the job in SAS Clinical Data Integration.
For more information about creating and scheduling a job flow, see the SAS
Management Console online Help.
191
Part 6
Appendixes
Appendix 1
Addition of Users to the Clinical Administrator Group . . . . . 193
Appendix 2
Repair of Clinical Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Appendix 3
SAS Clinical Data Integration Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
192
193
Appendix 1
Addition of Users to the Clinical
Administrator Group
Overview: Adding Users to the Clinical
Administrators Group
Only users in the Clinical Administrators group have permission to see the Clinical
Administration tree in SAS Data Integration Studio. Significant features and functions
are available through the Clinical Administration tree.
The default security model for SAS Clinical Data Integration is described in the following
table. Depending on the level of security required in your organization, users can modify
security after installation. Contact your system administrator to determine how security
is implemented in your organization.
Table A1.1 Default Users, Groups, Roles, and Descriptions
User, Group, or Role
Description
SAS Administrators
Default SAS Metadata Server administration group. This group
should not be removed from any object in the metadata. Very few
users should be added to this group.
Clinical Administrators
Members of this group can use the Clinical Administration tree
and are responsible for managing data standards, studies or
submissions, and controlled terminology.
194 Appendix 1 / Addition of Users to the Clinical Administrator Group
User, Group, or Role
Description
SASUSERS
All authenticated users belong to this group. These users are
responsible for defining content such as creating domains, jobs,
and output. Users are assigned to this group by default.
Add a User to the Clinical Administrators
User Group
To add a user to the Clinical Administrators user group, perform the following steps:
1 Start SAS Management Console, and then connect to the SAS Metadata Server as
an unrestricted user.
For more information, see SAS Management Console: Guide to Users and
Permissions.
2 On the Plug-ins tab, expand Environment Management, and then select User
Manager.
3 In the right pane, right-click Clinical Administrators, and then select Properties.
The Clinical Administrators Properties dialog box appears.
Adding Users to the Clinical Administrators Group
195
4 Click the Groups and Roles tab.
5 Use the arrows to move one or more users or user groups between the Available
Groups and Roles list and the Member of list.
6 Click OK.
196 Appendix 1 / Addition of Users to the Clinical Administrator Group
197
Appendix 2
Repair of Clinical Objects
Overview: Repairing Clinical Objects
When a clinical object is damaged and must be repaired, you receive a message.
These are the objects that you might need to repair:
n
data standard
n
domain template
n
column group
n
controlled terminology package
n
study or submission
n
domain or domain column
Note: A clinical object can be damaged when you export data standards or controlled
terminology packages using Export  SAS Package or Export  Metadata in SAS
Data Integration Studio. These methods are not recommended. Instead, create the data
standard or controlled terminology package using SAS Clinical Data Integration.
198 Appendix 2 / Repair of Clinical Objects
Repair a Domain Template, Column Group, or
Controlled Terminology Package
To repair a domain template, column group, or controlled terminology package, perform
the following steps:
1 In the Folders tree or in the Clinical Administration tree, navigate to a domain
template, column group, or controlled terminology package.
2 Right-click the item, and then select Repair.
A message appears when the repair is completed.
3 If no problems are found, click OK.
4 To review the analysis report for a domain template or column group, click Details.
If you choose to repair the problems, a progress indicator appears. A message
appears when the repair is completed.
Repair a Copy of a Data Standard, Study, or
Submission
To repair a copy of a data standard, study, or submission, perform the following steps:
1 In the Folders tree, navigate to a data standard, study, or submission.
2 Right-click the item, and then select Repair Copy.
The Repair Copy wizard appears.
3 In the New Name field, accept the default name, or enter a new name.
4 Click Next.
5 Review the summary, and then click Finish.
Repairing Clinical Objects
199
Repairs are made. The Folders tree or the Clinical Administration tree is updated
with new information.
Repair a Domain or Domain Column
To repair a domain or domain column, perform the following steps:
1 In the Folders tree or in the Clinical Administration tree, navigate to a domain or a
domain column.
2 Right-click the domain or domain column, and then select Repair.
3 If no problems are found, click OK.
4 To review the analysis report, click Details.
If you choose to repair the problems, a progress indicator appears. A message
appears when the repair is completed.
200 Appendix 2 / Repair of Clinical Objects
201
Appendix 3
SAS Clinical Data Integration Icons
The Folders Tree
The following icons represent objects in the Folders tree that are provided by SAS
Clinical Data Integration. All other icons are standard SAS Data Integration icons.
Icon
Description
Root folder of a submission
Root folder of a study
SAS Clinical Data Integration study that is
connected to a Medidata Rave study
Clinical domain
Submission
Study
Medidata Rave table
Medidata Rave codelist
Medidata Rave log
Analysis data set
202 Appendix 3 / SAS Clinical Data Integration Icons
The Clinical Administration Tree
The following icons represent objects in the Clinical Administration tree that are
provided by SAS Clinical Data Integration. All other icons are standard SAS Data
Integration icons.
Icon
Description
Study
Submission
203
Index
A
ADAE data sets 114
ADaM data sets
ADAE 114
ADSL 114
BDS 114
create 120
create from define.xml 126
create user-defined 130
creating 118
promoting to be user-defined
template 128
transforming into define.xml
file 138
types 114
wildcard variables 117
xx parameters 115
xx, y, and zz variable
parameters 115
y parameters 115
zz parameters 117
ADaM data standard
assessing compliance 132
ADSL data sets 114
annotated CRF metadata
adding to define.xml file 145
B
BDS data sets 114
C
CDISC SDTM data standard
validating domains for
compliance with 108
CDISC SDTM target files
converting study data into 105
CDISC-Define Creation
transformation 138
create define.xml from
customized data 150
saving data from 142
CDISC-Define Validation
transformation 152
Clinical Administration tree
permissions for 193
Clinical Administrators group
adding users to 193
clinical domains
validating 31
clinical objects
repairing 197
clinical programmers and data
managers 5
204 Index
codelist tables
create for a study 180
re-import 183
remove from a study 184
column groups 87
repair 198
column properties
edit multiple in data standards
20
edit multiple in studies 73
edit multiple in submissions
73
columns
add to domains 96
edit domain column properties
98
repair domain columns 199
common property models 18
compliance
assessing ADaM compliance
132
assessing CDISC SDTM
compliance 108
compliance checks
change the status of 41
create 35
delete 41
edit 35
managing 31
status of 31
viewing 34
conditional column groups 87
controlled terminology 23
See also terminology
packages
import 24
controlled terminology
packages
repair 198
CRT-DDS standard format
transforming ADAM data set
to 138
transforming CDISC-SDTM
format to 138
custom domains
automatically create key 100
create 90
create from existing domain
93
creating 86
creating from existing domains
87
D
data
loading into domains 105
saving from CDISC-Define
Creation transformation
142
data sets
create ADaM data set 120
create ADaM data set from
define.xml 126
create user-defined ADaM
data set 130
creating ADaM data set 118
validating for compliance with
ADaM 132
Index
data standard column
properties
edit multiple 20
data standard table properties
edit multiple 21
data standards
assessing ADaM compliance
132
assessing CDISC SDTM
compliance 108
customizing domain templates
23
customizing properties 18
defining studies with 11
edit multiple column properties
20
edit multiple table properties
21
importing metdata 11
managing compliance checks
31
promoting custom ADaM data
set to 128
promoting domains to 42
repair copies of 198
data standards administration
10
data standards administrators 5
define.xml
create ADaM data set from
126
create from customized data
150
create study from 69
define.xml file 138
See also define.xml file
adding annotated CRF and
value-level metadata to
145
adding value-level metadata
to 145
validating 152
domain columns
repair 199
domain properties
edit 97
domain tables
importing 103
domain templates
creating standard domains 88
customizing, for data
standards 23
repair 198
domains
add columns to 96
analyzing usage information
42
creating custom domains 86
creating custom domains from
existing domains 87
creating standard domains 88
edit column properties 98
edit properties 97
loading data into 105
monitoring status of 78
promoting 42
promoting domains 42
refreshing metadata in
standard domain 80
repairing 199
205
206 Index
transforming from CDISC
SDTM standard format to
CRT-DDS standard format
138
validating clinical domains 31
validating for compliance with
CDISC SDTM 108
library template 60
delete 64
view and modify properties 63
library templates
create 62
librefs
consistent use of 60
loading data into domains 105
F
M
folder templates 55
create 57
create folder in 58
duplicate 58
view and modify properties 59
I
icons
Medidata Rave 202
SAS Clinical Data Integration
201
J
jobs
schedule to update study data
from Medidata Rave 190
L
libraries 86
Medidata Rave icons 202
Medidata Rave properties
SAS Clinical Data Integration
data table definition 184
Medidata Rave server
define 163
test 164
Medidata Rave studies
connect SAS Clinical Data
Integration study 168
disconnect SAS Clinical Data
Integration study 171
view mapping to SAS Clinical
Data Integration study 171
Medidata Rave table metadata
notification of potential
changes 186
Medidata Rave transformation
log tables
create 177
disassociate from a study 179
metadata
Index
adding annotated CRF and
value-level metadata to
define.xml file 145
adding value-level metadata
to define.xml file 145
importing, for data standards
11
O
ownership 5
P
permissions
for Clinical Administration tree
193
properties
customizing data standard
properties 18
edit domain column properties
98
edit study or submission 72
editing domain properties 97
view and modify folder
template properties 59
view and modify library
template properties 63
R
reports 47
run and save 48
S
SAS Clinical Data Integration 3
workflow 4
SAS Clinical Data Integration
data table definitions
create for Medidata Rave
metadata 172
Medidata Rave properties
184
SAS Clinical Data Integration
icons 201
SAS Clinical Data Integration
studies
connect Medidata Rave study
168
disconnect Medidata Rave
study 171
view mapping to Medidata
Rave study 171
SDTM domains
transforming into define.xml
file 138
security model 193
sequence numbers 105
standard domains
create 88
creating 88
refreshing 80
status
change, for compliance
checks 41
of compliance checks 31
studies
consistent use of librefs 60
207
208 Index
create 66
create folder in folder template
58
create folder template 57
create from define.xml 69
creating 64
defining with data standard 11
delete 76
edit multiple column properties
73
edit multiple table properties
75
edit properties 72
folder templates 55
managing 54
monitoring domain status 78
repair copies of 198
view and modify folder
template properties 59
study column properties
edit multiple 73
study data
schedule a job to update 190
study table properties
edit multiple 75
Subject Sequence Generator
transformation 105
submission column properties
edit multiple 73
submission table properties
edit multiple 75
submissions
consistent use of librefs 60
create 66
create folder in folder template
58
create folder template 57
creating 64
delete 76
edit multiple column properties
73
edit multiple table properties
75
edit properties 72
folder templates 55
managing 54
monitoring domain status 78
repair copies of 198
view and modify folder
template properties 59
T
table properties
edit multiple in data standards
21
edit multiple in studies 75
edit multiple in submissions
75
target files
converting study data into 105
templates
See folder templates
See library template
terminology
See controlled terminology
terminology data sets
importing 24
Index
terminology packages 23
create 26
edit 28
repair 198
terminology tables 23
trial manager 5
wildcard 117
W
wildcard variables 117
workflow owners 5
workflows 4
U
unique records 105
usage information
analyzing 42
user-defined template
create from ADaM data set
128
users
adding to Clinical
Administrators group 193
X
xx parameters 115
xx, y, and zz variable
parameters 115
Y
y parameters 115
y variable parameters 115
V
value-level metadata
adding to define.xml file 145
variable parameters
xx, y, and zz 115
variables
Z
zz parameters 117
zz variable parameters 115
209
210 Index
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