Creating a Define-XML 2.0 define.xml File from ADaM Source Data :: SAS(R) Clinical Standards Toolkit 1.7: Getting Started, Second Edition

Overview

The SAS Clinical Standards Toolkit supports the currently published CDISC Analysis Results Metadata 1.0 extension for the Define-XML 2.0 submission standard, which supports representation of the ADaM 2.1 analysis data sets in metadata form, including Analysis Results Metadata.

Assumption

You have a library of CDISC ADaM 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_codelists, source_values, source_documents, and source_analysisresults data sets) has been created. This metadata must contain the expected, correctly typed columns created for the sample study provided by SAS. The source_study, source_tables, and source_columns data sets are the minimally required SAS data sets to create a Define-XML 2.0 file.

Location of Define-XML 2.0 Driver Programs

The Define-XML driver programs are located in the sample study library directory/cdisc-definexml-2.0-1.7/programs directory.

Step 1: Extract Available ADaM Source Metadata into the SAS Representation of Define-XML 2.0 Metadata

The initial task is to extract the available ADaM metadata into Define-XML 2.0 metadata files. The complete SAS representation of Define-XML 2.0 involves 54 data sets, but only 31 of these are typically used to create of a Define-XML 2.0 file. The other 23 data sets contain Operational Data Model (ODM) metadata or Analysis Results metadata, which are extensions of the Define-XML 2.0 model.

The sample driver program create_definexml_from_source_adam.sas, modified to point to your specific ADaM study metadata, must be submitted to create the SAS representation of Define-XML 2.0 metadata. This process builds 39 data sets in the SAS WORK library, but it might not populate all of the data sets (depending on the completeness of the metadata of your study). The 39 data sets consist of the 31 core Define-XML 2.0 data sets and eight data sets related to Analysis Results metadata.

The sample driver program runs the following macro:

%define_sourcetodefine(
  _cstOutLib=srcdata,
  _cstSourceStudy=sampdata.source_study,
  _cstSourceTables=sampdata.source_tables,
  _cstSourceColumns=sampdata.source_columns,
  _cstSourceCodeLists=sampdata.source_codelists,
  _cstSourceValues=sampdata.source_values,
  _cstSourceDocuments=sampdata.source_documents,
  _cstSourceAnalysisResults=sampdata.source_analysisresults,
  _cstFullModel=N,
  _cstCheckLengths=Y,
  _cstLang=en
  );

The macro is located in the global standards library directory/standards/cdisc-definexml-2.0-1.7/macros directory.

Note: The key input files (source files) are the ADaM metadata files (source_study, source_tables, source_columns, source_codelists, source_values, source_documents, and source_analysisresults), not the ADaM domain data sets. The metadata files (source files) to create a Define-XML 2.0 file have a different structure than the metadata files (source files) that are used to create a CRT-DDS 1.0 file.

In the sample study, the source metadata files for the ADaM 2.1 study are located in the

sample study library directory/cdisc-definexml-2.0-1.7/
                     sascstdemodata/cdisc-adam-2.1/metadata

directory.

Step 2: 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 Define-XML 2.0 standard. The next step is to build and validate the define-adam-2.1.xml file.

In the driver program, the call to the %DEFINE_WRITE macro requests that the default style sheet provided by SAS (based on the CDISC style sheet) be copied to the folder location that contains the generated define-adam-2.1.xml file. The macro is located in the global standards library directory/standards/cdisc-definexml-2.0-1.7/macros directory.

Here is the macro:

%define_write(_cstCreateDisplayStyleSheet=1,
               _cstHeaderComment=%str(Produced from SAS data using the SAS
               Clinical Standards Toolkit &_cstVersion));

Here is a portion of the define-adam-2.1.xml file, as rendered by the default style sheet in a browser. Links among tables, columns, codelists, and other file elements are provided.

Partial Sample define-adam-2.1.xml File (as Rendered by the Default Style Sheet)

The next task in the sample create_definexml_from_source_adam.sas driver program is to call the %CSTUTILXMLVALIDATE macro to perform the schema validation. This involves verifying that the Define-XML file is valid both structurally and syntactically, according to the XML schema.

The sample create_definexml_from_source_adam.sas driver program also contains SAS code to create the HTML rendition define-adam-2.1.html of the define-adam-2.1.xml using the define2-0-0.xsl style sheet:

proc xsl
  in=extxml
  xsl=xslt01
  out="&studyOutputPath/sourcexml/%sysfunc(tranwrd(&_cstDefineFile, %str(.xml), %str(.html)))";
  parameter 'nCodeListItemDisplay'=5 'displayMethodsTable'=1 'displayCommentsTable'=1;
 run;

If the style sheet parameters displayMethodsTable and displayCommentsTable were set to 0, the resulting HTML file would not have the separate tables for methods and comments.

Note: The SAS Clinical Standards Toolkit 1.7 does not contain validation checks to validate the SAS representation of the Define-XML 2.0 standard. The only methodology included in the SAS Clinical Standards Toolkit 1.7 to validate a Define-XML 2.0 file is XML schema validation.

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

Partial Sample Results Data Set (CDISC Define-XML 2.0 Create Process)

The Results data set provides process information and the location of the generated define-adam-2.1.xml file. The Results data set confirms that no problems were found with the file following validation of the file.