Working with CDISC Dataset-XML Files :: SAS(R) Clinical Standards Toolkit 1.7: Getting Started, Second Edition

Overview

CDISC Dataset-XML defines a standard format for transporting tabular data in XML between any two entities based on CDISC ODM XML. In addition to supporting the transport of data sets as part of a submission to the FDA, Dataset-XML can be used to exchange data between two parties. For example, the Dataset-XML data format can be used by a CRO to transmit SDTM or ADaM data sets to a sponsor organization. Dataset-XML supports SDTM, ADaM, and SEND data sets but can also be used to exchange any other type of tabular data set.

Dataset-XML and Define-XML

Dataset-XML defines a standard format for transporting tabular data set data in XML. The metadata for a data set in a Dataset-XML file must conform to the Define-XML standard. Each Dataset-XML file contains data for a single data set, but a single Define-XML file describes all the data sets included in the folder. Both Define-XML 1.0 and Define-XML 2.0 are supported for use with Dataset-XML.

Assumption

You have a library of CDISC SAS data sets from which you want to create Dataset-XML 1.0 files. You have a CRT-DDS 1.0 file or a Define-XML 2.0 file that describes the metadata for these CDISC SAS data sets.

Furthermore, you want to read the Dataset-XML files into SAS data sets and compare these SAS data sets to the original SAS data sets.

Location of Dataset-XML 1.0 Driver Programs

The Dataset-XML driver programs are located in the sample study library directory/cdisc-datasetxml-1.0.0-1.7/programs folder.

Creating Dataset-XML Files from SAS Data Sets

The sample driver program create_datasetxml_standalone.sas creates Dataset-XML files from a library of SAS data sets.

After initialization, the program runs the %DATASETXML_WRITE macro.

libname srcdata  "&studyRootPath/data";
filename srcmeta "&studyRootpathPath/xmldata/sdtm/define.xml";
libname dataxml  "&studyOutputPath/sourcexml";

%datasetxml_write(
  _cstSourceLibrary=srcdata,
  _cstOutputLibrary=dataxml,
  _cstSourceMetadataDefineFileRef=scrmeta,
  _cstCheckLengths=Y,
  _cstIndent=N,
  _cstZip=Y,
  _cstDeleteAfterZip=N
  );

The define.xml file that describes the SAS data sets must contain metadata information about all SAS data sets and all variables to convert. The Dataset-XML files by themselves do not have any information about the SAS data sets (names and labels) or the SAS variables (names, labels, data types, lengths, and display formats). When a Dataset-XML file is converted back to SAS data sets, this information must be provided by the define.xml file.

Creating SAS Data Sets from Dataset-XML Files

The sample driver program create_sas_from_datasetxml_standalone.sas creates SAS data sets from Dataset-XML files.

After initialization, the program runs the %DATASETXML_READ macro.

libname dataxml  "&studyRootPath/sourcexml";
libname sdtmdata "&studyOutputPath/data_derived";
filename defxml  "&studyOutPath/sourcexmldefine.xml";

%datasetxml_read(
  _cstSourceDatasetXMLLibrary=dataxml,
  _cstOutputLibrary=sdtmdata,
  _cstSourceMetadataDefineFileRef=defxml,
  _cstDatetimeLength=64,
  _cstAttachFormats=Y
  );

The define.xml file that describes the Dataset-XML files must contain metadata information about all Dataset-XML files and all variables to convert. The Dataset-XML files by themselves do not have any information about the SAS data sets (names and labels) or the SAS variables (names, labels, data types, lengths, and display formats).

Comparing Original SAS Data Sets to SAS Data Sets Created from Dataset-XML Files

The sample driver program create_sas_from_datasetxml_standalone.sas contains a call to the %CSTUTILCOMPAREDATASETS macro to compare the original SAS data sets to the SAS data sets that were created from the Dataset-XML files.

After initialization, the program runs the %CSTUTILCOMPAREDATASETS macro.

libname sdtmdata  "&studyOutputPath/data_derived";
libname sdtmdat0  "&studyRootPath/data";

%cstutilcomparedatasets(
  _cstLibBase=sdtmdat0,   
  _cstLibComp=sdtmdata, 
  _cstCompareLevel=0, 
  _cstCompOptions=%str(criterion=0.00000000000001),
  _cstCompDetail=Y
  );

For every SAS data set that is compared, the macro reports the error code returned by PROC COMPARE. Here are the error codes:

Error Codes Returned by PROC COMPARE

For example,

code=40 (8+32)

indicates that a format and a label are different. The following message is written to the SAS log file:

WARNING: [CSTLOGMESSAGE.CSTUTILCOMPAREDATASETS] Comparing srcdata.adqs and
trgdata.adqs  - Differences: FORMAT/LABEL (SysInfo=40)

When converting SAS data sets to Dataset-XML files and then converting them back to SAS data sets, here are differences to expect:

The lengths of date- and time-related columns are not defined in the Define-XML metadata.

Specify a length to assign in the macro (for example, _cstdatetimeLength=64). The length is used to create date- and time-related columns but can be different from the original lengths.
SAS numeric variables are created with a length of 8 to avoid loss of precision, even when the original length or the length specified in the define.xml file is less than 8.
The length of a character variable (DataType="text") that is not specified in the define.xml file is created with a length of 200.
Small differences in precision can be expected around the machine precision for numeric variables that represent real numbers.
Character data that contains leading spaces or trailing spaces loses the leading spaces and trailing spaces.

By specifying PROC COMPARE options with the _cstCompOptions parameter, you can specify that the comparison be less precise (for example, _cstCompOptions=%str(criterion=0.00000000000001)). Less precision prevents differences close to machine precision from being reported as errors.