A HOW-TO GUIDE FOR EXTENDING
CONTROLLED TERMINOLOGY USING SAS
CLINICAL DATA INTEGRATION
MELISSA R. MARTINEZ
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
AGENDA
• 
• 
• 
• 
• 
What is Controlled Terminology?
Adding a New CDISC Controlled Terminology Version
Extending CDISC Controlled Terminology Codelists
Customizing Controlled Terminology for a Study
External Data Dictionaries
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
2
WHAT IS
CONTROLLED
TERMINOLOGY?
CDISC definition: Set of
standard value lists that are
used throughout the clinical
research process
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
3
WHAT IS
CONTROLLED
TERMINOLOGY?
Set of possible
values for your study
within a codelist
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
4
WHAT IS
CONTROLLED
TERMINOLOGY?
Set of possible
values for your study
within a codelist
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
5
WHAT IS
CONTROLLED
TERMINOLOGY?
WHO Drug Dictionary – Dictionary of medicinal product information
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
6
WHAT IS
CONTROLLED
TERMINOLOGY?
MedDRA - Validated medical terminology
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
7
A NOTE BEFORE
DISCLAIMER ALERT
PROCEEDING
Please read full paper for complete details,
available in the conference proceedings.
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
8
A NOTE BEFORE
DISCLAIMER ALERT
PROCEEDING
Please read my full paper for complete details,
available in the conference proceedings.
This paper was
developed for
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
9
FOUR WAYS OF
EXTENDING
CONTROLLED
TERMINOLOGY
Copyright © 2013, SAS Institute Inc. All rights reserved.
External
Data
Dictionary
Add New
Version
Customize
Extend
Codelist
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
10
ADDING A NEW
CDISC CONTROLLED
TERMINOLOGY
VERSION
Add New
Version
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
11
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
WHY?
CDISC releases new versions
frequently
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
12
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
WHY?
CDISC releases new versions
frequently
Too long until planned CDI
upgrade
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
13
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
WHY?
CDISC releases new versions
frequently
Too long until planned CDI
upgrade
Take advantage of new terms
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
14
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
15
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
16
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
17
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
18
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
19
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
20
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
21
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
22
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
23
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
24
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
25
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
26
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
27
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
28
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
29
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
30
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
31
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
32
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
33
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RAW CDISC CONTROLLED TERMINOLOGY FILE
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
34
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RESTRUCTURED CDISC CONTROLLED TERMINOLOGY
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
35
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
RESTRUCTURED CDISC CONTROLLED TERMINOLOGY
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
36
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
REGISTER AND IMPORT NEW CONTROLLED
TERMINOLOGY VERSION
• 
Update standardsubtypes data set
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
37
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
REGISTER AND IMPORT NEW CONTROLLED
TERMINOLOGY VERSION
• 
Update standardsubtypes data set
See Paper!
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
38
ADDING A NEW
CDISC
CONTROLLED
TERMINOLOGY
VERSION
REGISTER AND IMPORT NEW CONTROLLED
TERMINOLOGY VERSION
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Update standardsubtypes data set
New CDISC Controlled Terminology version available
in the Data Standards Import Wizard
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
39
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
Extend
Codelist
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
40
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
WHY?
Some codelists are extensible
so that sponsors may add new,
non-duplicate values
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
41
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
WHY?
Some codelists are extensible
so that sponsors may add new,
non-duplicate values
Add custom terms needed for
a study
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
42
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
WHY?
Some codelists are extensible
so that sponsors may add new,
non-duplicate values
Add custom terms needed for
a study
Incorporate standard terms
from a newer CDISC
terminology release
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
43
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
EXAMPLE: FRM CODELIST
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Pharmaceutical Dosage Form
Study Drug is a Caplet
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
44
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
Copyright © 2013, SAS Institute Inc. All rights reserved.
HOW-TO
• 
Make a new folder for the extended controlled
terminology data set
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
45
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
HOW-TO
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the extended controlled
terminology data set
Insert new terms using data step programming
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
46
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
HOW-TO
• 
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the extended controlled
terminology data set
Insert new terms using data step programming
Register the new controlled terminology data set in
standardsubtypes dataset
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
47
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
HOW-TO
• 
• 
• 
Make a new folder for the extended controlled
terminology data set
Insert new terms using data step programming
Register the new controlled terminology data set in
standardsubtypes dataset
See Paper!
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
48
EXTENDING CDISC
CONTROLLED
TERMINOLOGY
CODELISTS
HOW-TO
• 
• 
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the extended controlled
terminology data set
Insert new terms using data step programming
Register the new controlled terminology data set in
standardsubtypes dataset
Import controlled terminology into CDI
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
49
CUSTOMIZING
CONTROLLED
TERMINOLOGY FOR
A STUDY
Customize
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
50
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
WHY?
Codelists should contain only
possible values for a study
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
51
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
WHY?
Codelists should contain only
possible values for a study
Catch invalid values accurately
with compliance checks
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
52
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
WHY?
Codelists should contain only
possible values for a study
Catch invalid values accurately
with compliance checks
Create a better, more accurate
define.xml
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
53
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
Copyright © 2013, SAS Institute Inc. All rights reserved.
EXAMPLE: COUNTRY CODELIST
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
54
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
Copyright © 2013, SAS Institute Inc. All rights reserved.
HOW-TO
• 
Make a new folder for the study-specific controlled
terminology data set
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
55
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
HOW-TO
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the study-specific controlled
terminology data set
Remove unneeded terms using data step
programming
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
56
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
HOW-TO
• 
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the study-specific controlled
terminology data set
Remove unneeded terms using data step
programming
Register the study-specific controlled terminology data
set in standardsubtypes dataset
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
57
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
HOW-TO
• 
• 
• 
Make a new folder for the study-specific controlled
terminology data set
Remove unneeded terms using data step
programming
Register the study-specific controlled terminology data
set in standardsubtypes dataset
See Paper!
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
58
CUSTOMIZING
CONTROLLED
TERMINOLOGY
FOR A STUDY
HOW-TO
• 
• 
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Make a new folder for the study-specific controlled
terminology data set
Remove unneeded terms using data step
programming
Register the study-specific controlled terminology data
set in standardsubtypes dataset
Import controlled terminology into CDI
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
59
EXTERNAL DATA
DICTIONARIES
External
Data
Dictionary
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
60
EXTERNAL DATA
DICTIONARIES
WHY?
Perform one more quality
check on data values through
compliance checks
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
61
EXTERNAL DATA
DICTIONARIES
WHY?
Perform one more quality
check on data values through
compliance checks
Ability to use several different
data dictionaries
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
62
EXTERNAL DATA
DICTIONARIES
WHY?
Perform one more quality
check on data values through
compliance checks
Ability to use several different
data dictionaries
Ability to use several versions
of a dictionary
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
63
EXTERNAL DATA
DICTIONARIES
Copyright © 2013, SAS Institute Inc. All rights reserved.
EXAMPLE: MEDDRA
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
64
EXTERNAL DATA
DICTIONARIES
HOW-TO
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Convert raw data file to SAS data set
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
65
EXTERNAL DATA
DICTIONARIES
HOW-TO
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Convert raw data file to SAS data set
Register table in CDI
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
66
EXTERNAL DATA
DICTIONARIES
HOW-TO
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Convert raw data file to SAS data set
Register table in CDI
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
67
EXTERNAL DATA
DICTIONARIES
HOW-TO
• 
• 
• 
Copyright © 2013, SAS Institute Inc. All rights reserved.
Convert raw data file to SAS data set
Register table in CDI
Add to a terminology package
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
68
CONCLUSION
Copyright © 2013, SAS Institute Inc. All rights reserved.
External
Data
Dictionary
Add New
Version
Customize
Extend
Codelist
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
69
CONCLUSION
• 
• 
• 
Increase data quality in submission data sets
Make define.xml file more complete and accurate
Please read full paper for complete details, available in the conference
proceedings
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
70
MELISSA R. MARTINEZ
SAS INSTITUTE, INC.
[email protected]
Copyright © 2013, SAS Institute Inc. All rights reserved.
This information is confidential and covered under the terms of any SAS agreements as executed by customer and SAS Institute Inc.
www.SAS.com