Creating a define.xml File from CDISC SDTM 3.1.3 Source Data :: SAS(R) Clinical Standards Toolkit 1.5: Getting Started

Overview

The SAS Clinical Standards Toolkit supports the currently published CDISC CRT-DDS 1.0 (define.xml) submission standard, which supports representation of the CDISC SDTM 3.1.1, 3.1.2, and 3.1.3 tabulation data sets and ADaM 2.1 analysis data sets in metadata form.

Assumption

You have a library of CDISC SDTM SAS data sets (which are not read by this process) from which a set of metadata (in the form of source_study, source_tables, source_columns, source_values, and source_documents data sets) has been created. This metadata must contain the expected, correctly typed columns created for the sample study provided by SAS.

Location of CRT-DDS Driver Modules

The CRT-DDS driver modules are located in this directory:

sample study library directory/cdisc-crtdds-1.0-1.5/programs

Step 1: Extract Available SDTM Metadata into CRT-DDS Metadata Files

The initial task is to extract available SDTM metadata into CRT-DDS metadata files. The SAS representation of CRT-DDS involves 39 data sets, but only 19 of these derive directly from the SDTM metadata. The sample driver create_crtdds_from_sdtm.sas, modified to point to your specific SDTM study, should be submitted to extract the SDTM metadata. This process builds all 39 data sets but populates only 19 (depending on your study).

Note: The key input (source) files are the SDTM metadata files (source_study, source_tables, source_columns, source_values, and source_documents), not the SDTM domain data sets.

Step 2: (Optional) Populate the Remaining CRT-DDS Data Sets

Note: If you do not have additional metadata, you can skip this step.

None of the remaining 39 data sets must be populated to create a viable define.xml file using the SAS Clinical Standards Toolkit. However, they might be needed to further populate the remaining CRT-DDS data sets using your own metadata sources and methods.

For more discussion of this step, see FAQ How Do I Add Supplemental Data (Not Directly Derivable from Other Standards Such as CDISC SDTM) Used to Create a define.xml File?. For a discussion of the data sets most critical for successful derivation of the define.xml file, see “Special Topic: A Round Trip Exercise Involving the CDISC CRT-DDS Standard: Importing and Exporting the define.xml File” in Chapter 8, “XML-Based Standards,” in the SAS Clinical Standards Toolkit: User's Guide.

Step 3: Create the define.xml File

At this point, all available content for the define.xml file has been captured in the SAS representation (39 data sets) of the CDISC CRT-DDS standard. The SAS Clinical Standards Toolkit provides a sample driver module, create_crtdds_define.sas. This module builds and validates the define.xml file. Submit the create_crtdds_define.sas driver module.

In this driver, the call to the primary task macro requests that the default style sheet provided by SAS (source: CDISC) be copied to the folder location containing the generated define.xml file. The macro is located in the global standards library directory/standards/cdisc-crtdds-1.0-1.5/macros directory.

Here is the macro:

%crtdds_write(_cstCreateDisplayStyleSheet=1);

Here is a portion of the define.xml file, as rendered by this default style sheet. Hyperlinks among tables, columns, codelists, and other file elements are provided.

Partial Sample define.xml File (as Rendered by the Default Style Sheet)

Step 4: Validate the Generated define.xml File

The final step is to validate the generated define.xml file. As discussed in Chapter 8, “XML-Based Standards,” in the SAS Clinical Standards Toolkit: User's Guide, the SAS Clinical Standards Toolkit offers two complementary validation methodologies.

The first methodology relies on the definition of a master set of validation checks as described in the previous example. This method uses SAS files and SAS code to validate the SAS representation of the standard. Example checks include the assessment of foreign key relationships across data sets and value conformance to a set of expected values.
The second methodology involves verification that the XML file is valid structurally and syntactically according to the XML schema.

The final task in the sample create_crtdds_define.sas driver is to call the crtdds_xmlvalidate() macro to perform the schema validation.

Here is a sample Results data set produced by the validation process:

Partial Sample Results Data Set (CDISC CRT-DDS 1.0 Create Process)

The Results data set provides process information and the location of the generated define.xml file. The Results data set confirms that no problems were found with the file following validation of the file.

Note: The SAS validation of file content was not run in this example.