SAS Clinical Standards Toolkit 1.2

SAS Clinical Standards Toolkit 1.2
®
SAS Clinical
Standards Toolkit 1.2
Quick Start for SDTM Validation for
SAS 9.2 and SAS 9.1.3
®
The correct bibliographic citation for this manual is as follows: SAS Institute Inc. 2009. SAS Clinical
Standards Toolkit 1.2: Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3. Cary, NC: SAS
Institute Inc.
SAS® Clinical Standards Toolkit 1.2: Quick Start for SDTM Validation for SAS 9.2 and
SAS 9.1.3
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SAS® Clinical Standards Toolkit 1.2
Quick Start for SDTM Validation
for SAS 9.2 and SAS 9.1.3
Contents
Getting Started.............................................................................................................................................. 2
Overview ................................................................................................................................................... 2
Tutorial Goal and Exercises ....................................................................................................................... 2
Install this Tutorial ........................................................................................................................................ 2
Default Directories and Installation .......................................................................................................... 3
Exercise 1 – Prepare Study Data and Metadata ........................................................................................... 4
Exercise 1A – Prepare Data ....................................................................................................................... 4
Exercise 1B – Prepare Format Catalogs .................................................................................................... 5
Exercise 1C – Prepare Metadata Files ....................................................................................................... 5
Exercise 2 – Step by Step .............................................................................................................................. 6
Exercise 2A – Create a SAS References data set ....................................................................................... 6
Exercise 2B – Select the Validation Checks ............................................................................................... 6
Exercise 2C – Run Validation ..................................................................................................................... 7
Exercise 3 – All in One ................................................................................................................................... 8
Summary ....................................................................................................................................................... 8
Document Last Revised: 2009-08-25
SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
Getting Started
This version of the SAS® Clinical Standards Toolkit 1.2 – Quick Start Tutorial for SDTM Validation is for
use with SAS 9.2 and SAS 9.1.3.
Overview
SAS® Clinical Standards Toolkit 1.2 (CST) is a powerful and flexible product. This tutorial provides a quick
introduction to CST. Using this tutorial, you will walk through the main tasks required to use CST to
validate CDISC SDTM 3.1.1 data. When you have completed this tutorial, you will understand how to
configure CST to run CDISC SDTM 3.1.1 validations against your own data. While this tutorial specifically
discusses CDISC SDTM 3.1.1 validation, many of the concepts apply to using CST to perform other tasks.
This tutorial is intended to show you the basic steps for using CST. It is not intended to provide
comprehensive training in CST, the capabilities of CST, or the best practices. The goal is to present what
the SAS code is doing. For example, the tutorial avoids using unnecessary SAS macros or SAS macro
variables and all paths are hard-coded. The comments within the SAS programs provide additional
information about the tasks being performed.
One of the biggest challenges you will face when using CST is the preparation of your own data and
metadata. By definition, this data must be in CDISC SDTM 3.1.1 SAS data sets. The steps required to get
your data into CDISC SDTM 3.1.1 SAS data sets is beyond the scope of this tutorial.
This tutorial uses a small number of the many options available within CST. To understand all the
options provided by CST, see the SAS Clinical Standards Toolkit 1.2: User’s Guide.
Tutorial Goal and Exercises
This tutorial walks you through the main steps that you need to use CST to validate your own data. Your
own data will be represented as the fictitious study, MyStudy. The challenge is to test how well MyStudy
complies with the CDISC SDTM 3.1.1 standard.
The tutorial consists of the following four steps:
1.
2.
3.
4.
Install this tutorial.
Exercise 1: Prepare the study data and metadata.
Exercise 2: Walk through the steps needed to setup CST to run a CDISC SDTM 3.1.1 Validation.
Exercise 3: Consolidate and simplify the steps from Exercise 2 into a single program.
Install this Tutorial
In this section, you will install the directories and files provided in this tutorial. To set up the tutorial,
extract the following applicable file into the c:\ directory:
For SAS 9.2
For SAS 9.1.3
cstQuickStartSDTMValidation.zip
cstQuickStartSDTMValidation913.zip
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
The extraction creates the following directory which contains all of the subdirectories and files required
by this tutorial:
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart
c:\cstQuickStart913
The subdirectories and files are described in the following table.
Table 1. Quick Start Tutorial Folder Structure
Contains the data and metadata that are specific to a
study.
MyData
o Study data in CDISC SDTM 3.1.1 SAS data set
format.
MyFormats
o Format catalogs including coding dictionaries.
MyMetadata
o SAS data sets that describe the tables and
columns that are used to store the data in
MyData, for example, the study data’s
metadata.
Exercise1_PrepareStudyData
Three SAS programs that create the data and metadata
that comprise MyStudy. Technically, these programs are
not part of CST. The programs are included in the
tutorial because you might need to perform similar
tasks.
Exercise2_StepByStep
Three SAS programs that walk through the set up and
execution of the CST CDISC SDTM 3.1.1 validation.
Exercise3_AllInOne
One SAS program that combines the steps outlined in
Exercise 2.
Note: When created, some directories are empty. The tutorial exercises will add content to these
directories.
MyStudy
The tutorial zip file is located on the SAS download page. If you need help locating this file, search the
SAS support Web site (http://support.sas.com) or contact your SAS Administrator for assistance. A copy
of this document is provided within the tutorial zip file.
Default Directories and Installation
This tutorial and the supporting SAS programs and SAS data sets all assume that you have extracted
them into their default directories.
Table 2. Installed Software and the Associated Default Directory
Installed Software
Tutorial
SAS Software
Version
For SAS 9.2
For SAS 9.1.3
Default Directory
c:\cstQuickStart
c:\cstQuickStart913
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
SAS
For SAS 9.2
c:\Program Files\SAS\SASFoundation\9.2
For SAS 9.1.3
c:\Program Files\SAS\SAS 9.1
Note: This directory also is known as the SAS Root folder.
SAS Clinical Standards
Toolkit
For SAS 9.2
c:\Program Files\SAS
For SAS 9.1.3
c:\Program Files\SAS
Note: This directory also is known as the SAS Home folder.
SAS Clinical Standards
Toolkit’s Global Library
For SAS 9.2
c:\cstGlobalLibrary
For SAS 9.1.3
c:\cstGlobalLibrary
Note: Because this directory sometimes is shared by multiple users, it is
the most likely installed in a non-default directory.
It is not required that you install SAS, CST, or this tutorial in their respective default directories.
However, if you choose to install any of this software into a different directory, then you must modify
the paths in:
•
•
all of the SAS programs
in the SAS References data set
The SAS References data set is created in Exercise 2A and updated in Exercise 3.
Exercise 1 – Prepare Study Data and Metadata
In this section you will generate the data and metadata for the fictitious study called MyStudy. Your data
must be in CDISC SDTM 3.1.1-formatted SAS data sets. Also, you must have the supporting metadata
files that describe the tables and columns for the domains. Therefore, one of the most critical parts of
using CST is the preparation of your own data and metadata.
The preparation can vary depending on your organization’s requirements, data, metadata, tools,
capabilities, policies, and procedures. You might have everything you need already in place and the
preparations are complete or it might take you and your co-workers months to prepare. To assist you
with preparing your data and metadata, SAS Institute provides SAS® Clinical Data Integration. Clinical
Data Integration integrates seamlessly with CST.
The exercises in this section are intended to give you a general idea about the kinds of tasks you must
perform to generate your data and metadata for use with CST.
Exercise 1A – Prepare Data
To simulate the process of creating your data, copy the data from the sample study.
 Edit the following applicable SAS program and update any paths if needed.
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise1_PrepareStudyData\Exercise1A_PrepareMyStudyData.sas
c:\cstQuickStart913\ Exercise1_PrepareStudyData\Exercise1A_PrepareMyStudyData.sas
 Submit the edited SAS program.
This program copies several study data sets into the MyData subdirectory. Each data set represents one
SDTM domain.
Exercise 1B – Prepare Format Catalogs
To simulate the process of creating SAS formats, which can include controlled terminology, copy the SAS
catalogs from the sample study.
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise1_PrepareStudyData\Exercise1B_PrepareMyStudyFormats.sas
c:\cstQuickStart913\ Exercise1_PrepareStudyData\Exercise1B_PrepareMyStudyFormats.sas
 Submit the edited SAS program.
This program copies several SAS catalogs to the MyFormats subdirectory.
Exercise 1C – Prepare Metadata Files
To simulate the process of creating the metadata files that are specific to MyStudy (that is, the source
metadata), copy the SAS standardized set of metadata (that is, the reference metadata).
The purpose of study-level metadata (source metadata) is to enable you to use a modified version of the
SDTM formats (for example, SDTM+) or your own internal standards.
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise1_PrepareStudyData\Exercise1C_PrepareMyStudyMetadata.sas
c:\cstQuickStart913\ Exercise1_PrepareStudyData\ Exercise1C_PrepareMyStudyMetadata.sas
 Submit the edited SAS program.
This program copies two SAS data sets into the MyMetadata subdirectory. The
MyTableMetadata.sas7bdat file contains the metadata required to define the tables (domains) for the
given study. The MyColumnMetadata.sas7bdat file contains the metadata required to define the
columns within the tables (domains.)
Unlike the earlier steps, you made some changes to the contents of these two data sets rather than
copying them unchanged. These changes represent the minimum required to use a copy of the CST
reference metadata as your source metadata.
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
If you are validating against the standard SAS CDISC SDTM 3.1.1 format, then the process shown in the
Exercise1C_PrapreMyStudyMetadata.sas program might be all that you require for validation.
Exercise 2 – Step by Step
In this exercise, you will explore the tasks required to run a CST validation program. You will complete
the steps necessary to execute a CST SDTM validation against the data that was configured in Exercise 1.
See the SAS Clinical Standards Toolkit 1.2: User’s Guide for more information about each of these steps.
Exercise 2A – Create a SAS References data set
The SAS References data set is used to pass parameters to CST. It defines the SAS libraries, data sets, and
other files that CST requires. The SAS References data set must contain a row that references itself.
The full details of the SAS References data set are beyond the scope of this document. See the SAS
Clinical Standards Toolkit 1.2: User’s Guide for more information.
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\Exercise2A_CreateSASReferences.sas
c:\cstQuickStart913\Exercise2_StepByStep\Exercise2A_CreateSASReferences.sas
 Submit the edited SAS program.
The SAS References data set is written to the study-level directory in the following file:
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\ SASReferences.sas7bdat
c:\cstQuickStart913\Exercise2_StepByStep\ SASReferences.sas7bdat
You will reuse this SAS References data set in Exercise 3.
Exercise 2B – Select the Validation Checks
In this exercise, you will select the validation checks that you wish to run against the MyStudy data. The
validation_master data set contains the complete list of checks that the CST predefines. One row is
equal to one check. When running a validation job, you create a subset of the validation_master data
set. This resulting data set is called the validation_control data set.
The validation_control data set contains the list of checks that are executed by the validation job. The
validation_master is not used directly by the validation process itself.
Some rows in the validation_master data set appear to conduct the same validation check, that is, some
of the tests performed by the checks are repeated by multiple checks. However, upon close review, you
can see that these rows do differ in other details. The differences often occur in the source of the check
(for example, WebSDM orJANUS) or in the level of severity that is reported when the data fails the check
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
(for example, WARNING or ERROR.) This enables greater flexibility in choosing which checks you want
to run. For example, you can choose to run all of the JANUS checks and only the JANUS checks.
Note: You also can add your own checks to CST, but this capability is beyond the scope of this tutorial.
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\Exercise2B_ChooseChecks.sas
c:\cstQuickStart913\Exercise2_StepByStep\Exercise2B_ChooseChecks.sas
 Submit the edited SAS program.
The SAS References data set is written to the study-level directory in the following file:
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\checkstorun.sas7bdat
c:\cstQuickStart913\Exercise2_StepByStep\checkstorun.sas7bdat
This data set contains two rows that are similar. Both rows test for the same condition. However, one
check is defined by JANUS , which reports the condition as a note. The other check is defined by
WebSDM, which reports the condition as warning. Typically, in a production system, you would choose
to run only one of these checks.
Exercise 2C – Run Validation
In this exercise, you will validate MyStudy data against CDISC SDTM 3.1.1.
When reviewing the SAS code, notice several lines that are referencing properties. In addition to the SAS
References and Control data sets, you can pass parameters into CST using properties. Properties are
options that impact how CST performs various tasks. For the purposes of this tutorial, you will use only
default values. However, the tutorial does include an example properties file, MyValidation.properties,
in the MyStudy folder. For more information about properties, see the SAS Clinical Standards Toolkit 1.2:
User’s Guide.
To run the validation, complete the following steps:
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\Exercise2C_RunValidation.sas
c:\cstQuickStart913\Exercise2_StepByStep\Exercise2C_RunValidation.sas
 Submit the edited SAS program.
The SAS References data set is written to the study-level directory in the following file:
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\validationresult.sas7bdat
c:\cstQuickStart913\Exercise2_StepByStep\validationresult.sas7bdat
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SAS® Clinical Standards Toolkit 1.2 – Quick Start for SDTM Validation for SAS 9.2 and SAS 9.1.3
The results data set contains the findings reported by the validation process.
The following data set file contains some information about the validation process itself, for example,
the number of checks the process ran:
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise2_StepByStep\validationmetrics.sas7bdat
c:\cstQuickStart913\Exercise2_StepByStep\ validationmetrics.sas7bdat
Exercise 3 – All in One
In this exercise, you will combine all of the steps from Exercise 2 into a single program.
The SAS References data set created in Exercise 2A is very close to what you need in this exercise. You
will update the data set by changing a few values.
This program also demonstrates how to run all of the JANUS checks, but for the purposes of this
exercise, you will run only the first few JANUS checks.
 Edit the following applicable SAS program and update any paths if needed.
For SAS 9.2
For SAS 9.1.3
c:\cstQuickStart\Exercise3_AllInOne\Exercise3_RunCSTValidation.sas
c:\cstQuickStart913\Exercise3_AllInOne\Exercise3_RunCSTValidation.sas
 Submit the edited SAS program.
The following job-specific files are written to the Exercise3_AllInOne subdirectory:
•
•
CST CDISC SDTM 3.1.1 validation job-specific input:
o The SAS references data set file sasreferences.sas7bdat
o The control checks data set file checks.sas7bdat
CST CDISC SDTM 3.1.1 validation job-specific output:
o The results data set file results.sas7bdat
o The metrics data set file metrics.sas7bdat
Summary
This Quick Start tutorial provided an overview so you could learn the basic process for using Clinical
Standards Toolkit. While this tutorial focused on CDISC SDTM 3.1.1 validation, other CST tasks, such as
CDISC CRT-DDS validation, use a similar process. For detailed information, see the SAS Clinical Standards
Toolkit 1.2: User’s Guide.
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