What's New

Overview

The following are some of the new capabilities in SAS Clinical Standards Toolkit 1.3:
  • The CDISC SDTM 3.1.1 validation checks are updated to reflect WebSDM 3.0 updates revised June 29, 2009. There are 10 new validation checks, eight modified validation checks, and five deprecated validation checks in SAS Clinical Standards Toolkit 1.3.
  • The SAS implementation of the CDISC SDTM 3.1.2 reference standard is published. This reference standard now includes 32 domains (with seven new domains). SDTM 3.1.2 domain validation includes the WebSDM 3.0 updates revised June 29, 2009, and applicable checks published by the open source community OpenCDISC.
  • A new snapshot of the National Cancer Institute (NCI) Enterprise Vocabulary Services (EVS) Thesaurus controlled terminology for CDISC is captured as the CDISC-Terminology-201003 reference standard. This cumulative snapshot includes 60 distinct code lists, many of which support CDISC SDTM 3.1.2 validation.
  • There is an initial implementation of the CDISC ODM 1.3.0 reference standard, which is targeted specifically at translating the (study) metadata and ClinicalData sections of an odm.xml file into the SAS representation of the CDISC ODM standard.
  • Updated sample reports that offer more user-friendly views of SAS Clinical Standards Toolkit process results are provided. Comprehensive views of validation check metadata for those standards that support validation are available.
  • Sample driver programs that streamline and standardize setup tasks associated with SAS Clinical Standards Toolkit processes are updated. These driver programs support 17 distinct tasks across the CDISC SDTM, CDISC CRT-DDS, and CDISC ODM models.
  • The SAS Clinical Standards Toolkit metadata and code base are significantly updated. These changes are discussed in a following section.

Changes to Metadata and Code Base

Framework Changes

The following autocall macros are new. These macros can be found in the !sasroot/cstframework/sasmacro directory:
  • cstcheck_notimplemented is a placeholder validation check macro that documents in the Results data set that a specific check has not yet been implemented in SAS Clinical Standards Toolkit.
  • cstcheckutil_formatlookup is used in the CDISC SDTM 3.1.2 Validation Master data set in the check metadata codelogic field to evaluate value-level compliance with CDISC terminology.
  • cstutil_createmetadatareport is a driver macro that generates report output based on all available check metadata information.
  • cstutil_createreport is a driver macro that generates report output summarizing SAS Clinical Standards Toolkit process results.
  • cstutil_createunixsubdir is used in sample SAS Clinical Standards Toolkit driver modules for UNIX users to create work subdirectories to support process write operations.
  • cstutil_processsetup is used in sample SAS Clinical Standards Toolkit driver modules to perform necessary setup operations, including library and file allocations.
  • cstutil_reportgeneralprocess is called by the cstutil_createreport macro to create the General Process Reporting panel.
  • cstutil_reportinputsoutputs is called by the cstutil_createreport macro to create the Process Inputs/Outputs panel.
  • cstutil_reportprocessmetrics is called by the cstutil_createreport macro to create the Process Metrics panel.
  • cstutil_reportprocessresults is called by the cstutil_createreport macro to create the Process Results panel.
  • cstutil_reportprocesssummary is called by the cstutil_createreport macro to create the Process Summary panel.
  • cstutil_reportsetup interprets information from either a SAS Clinical Standards Toolkit Results data set or a SASReferences data set to perform setup functions for SAS Clinical Standards Toolkit reporting.
  • cstutil_reporttabledata is called by the cstutil_reportprocessmetrics and cstutil_reportprocessresults macros to facilitate reporting by domain.
  • cstutil_saveresults performs the common task of saving process results based on SASReferences data set settings.
The following autocall macros have been modified. These macros are located in the !sasroot/cstframework/sasmacro directory:
  • cstcheck_metamismatch
  • cstutil_getsasreference
The following framework properties have been modified. The properties can be found in <global standards library directory>/standards/cst-framework-1.3/programs/initialize.properties:
  • The _cstSASRefsLoc=, _cstSASRefsName=, and _cstSASRefs=work._cstsasrefs properties were moved from the CDISC SDTM initialize.properties file. The default value for _cstSASRefsLoc was changed to &workpath.
  • The default value for the _cstFMTLibraries properties was changed from WORK to <blank>.
Eight type/subtype combinations were added and five type/subtype combinations were removed from the Standardlookup data set. The data set can be found in <global standards library directory>/standards/cst-framework-1.3/control/standardlookup.sas7bdat.
The CST0009, CST0024, and CST0025 messages have been added to the Messages data set.
The productRevision column has been added to standards.sas7bdat. The column is blank for standards installed with SAS Clinical Standards Toolkit 1.2. The column value is 1.3 for standards added with SAS Clinical Standards Toolkit 1.3 or when SAS Clinical Standards Toolkit 1.3 is allowed to overwrite any standard installed with SAS Clinical Standards Toolkit 1.2. It can be found in <global standards library directory>/metadata/standards.sas7bdat.
The codetype, uniqueid, and comment columns were added to the Validation Master data set. The checkno column was removed. The data set can be found in <global standards library directory>/standards/cst-framework-1.3/templates/validation_master.sas7bdat.
The SAS Note 37164, “An error can occur if you run the macro %CSTUTIL_ALLOCATESASREFERENCES in SAS® Clinical Standards Toolkit more than once in the same SAS® session,” is available on http://support.sas.com.
The SAS Note 38421, “SAS® Clinical Standards Toolkit folder is missing in SAS® 9.2,” was added. The <global standards library directory>/standards/<standard-version>/programs/development directory for each standard that is provided by SAS should no longer be available for any SAS version.

CDISC SDTM Changes

CDISC SDTM 3.1.2 is the default for new SAS Clinical Standards Toolkit 1.3 installations. For more information about upgrades from SAS Clinical Standards Toolkit 1.2, see Framework.
The following CDISC SDTM 3.1.1 macros are new. These macros are also available with the CDISC SDTM 3.1.2 standard. These macros can be found in the <global standards library directory>/standards/cdisc-sdtm-3.1.1-1.3/macros directory:
  • sdtmutil_createformatsfromcrtdds is a utility macro that creates a SAS format catalog from CDISC CRT-DDS define.xml codelists.
  • sdtmutil_createsasdatafromxpt is utility macro that creates SAS (SDTM) data sets from reachable CDISC CRT-DDS define.xml referenced SAS transport files.
  • sdtmutil_createsrcmetafromcrtdds is a utility macro that creates SAS (SDTM) source metadata (study, table, column) from CDISC CRT-DDS define.xml metadata.
  • sdtmutil_createsrcmetafromsaslib is utility macro that creates SAS (SDTM) source metadata (study, table, column) from a library of CDISC SDTM domains.
The CDISC SDTM 3.1.1 validation checks have been updated to reflect WebSDM 3.0 updates revised June 29, 2009. This includes 10 new, eight modified, and five deprecated validation checks. The modified checks have a UNIQUEID value that includes an effective date substring that is not equal to ‘2009-05-13’.
The SAS Note 36343, “SAS Clinical Standards Toolkit sample data set needs to be updated,” has been added. This note provides corrected paths in the sample SASReferences data set.
The SAS Note 37853, “SAS Clinical Standards Toolkit validation master list contains an error,” has been added. This note provides the corrected value for the CHECKID=SDTM0651 record in the Validation Master data set. The column value for SOURCEID should be IR4140.

CDISC CRT-DDS Changes

The following CDISC CRT-DDS macros are new. These macros can be found in the <global standards library directory>/standards/cdisc-crtdds-1.0-1.3/macros directory:
  • crtdds_computationmethods is called by the crtdds_sdtm311todefine10 macro to populate the CDISC CRT-DDS ComputationMethods data set from the CDISC SDTM column metadata.
  • crtdds_itemgroupleaf is called by the crtdds_sdtm311todefine10 macro to populate the CDISC CRT-DDS ItemGroupLeaf data set from the CDISC SDTM table metadata.
  • crtdds_itemgroupleaftitles is called by the crtdds_sdtm311todefine10 macro to populate the CDISC CRT-DDS ItemGroupLeafTitles data set from the CDISC SDTM table metadata.
  • crtdds_read translates a define.xml file into the SAS representation of CDISC CRT-DDS 1.0. The representation included 39 tables, table metadata, and column metadata.
  • crtdds_buildchecktablelist is a utility macro that identifies the domains to be validated by each check. The check is based on the contents of the tableScope and columnScope check metadata columns in the Validation Master data set.
CDISC CRT-DDS column length and label metadata have been updated. This metadata can be found in <global standards library directory>/standards/cdisc-crtdds-1.0-1.3/metadata/reference_columns.sas7bdat, !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.3/sample/cdisc-crtdds-1.0/data, and !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.3/sample/cdisc-crtdds-1.0/metadata/source_columns.sas7bdat. These metadata updates include:
  • All *OID and FK* that reference *OIDs have been reset to a length of 128.
  • Column labels have been added to some files.
SAS Note 38149, “%CRTDDS_XMLVALIDATE() macro might generate errors with logging levels above 'Info',” has been added.

CDISC-Terminology Changes

201003 is the default CDISC-Terminology standard version for new SAS Clinical Standards Toolkit 1.3 installations. For more information about upgrades from SAS Clinical Standards Toolkit 1.2, see Framework. This version can be found in the <global standards library directory>/metadata Standard data set. It fully supports CDISC SDTM 3.1.2.

CDISC SDTM, CDISC ODM, and CDISC CRT-DDS Changes

The use of cstutil_saveresults was added to standardize the persistence of process results to honor SASReferences type=results records. If there are no such records (by default), results are written to work._cstresults.

Changes between SAS Clinical Standards Toolkit 1.2 and SAS Clinical Standards Toolkit 1.3

Global Changes

The validation check data set structure was modified. The following are the new column details:
  • codetype defines whether to use codelogic and what type of codelogic can be used in the validation code. Valid values include:
    • 0—No codelogic used.
    • 1—DATA step statement level. (For example, if &_cstColumn <0 then _cstError=1.)
    • 2—Full DATA step, PROC SQL step, or multiple steps.
    • 3—Calls a SAS macro or %include that can contain only DATA step statement level code. (For example, codetype=1.)
    • 4—Calls a SAS macro or %include that can contain only full DATA step or PROC SQL step code. (For example, codetype=2.)
    This column is required.
  • uniqueid ensures uniqueness in the data set and in SAS Clinical Standards Toolkit. This column allows any shipped or derived check to be uniquely identifiable over time. This column is required. An example is SDTM000100CST120SDTM3112009-05-12T12:00:00CDI. In the legend, characters 1 through 8 are checkid, characters 9 through 10 are checkid repeat indicator, characters 11 through 16 are the SAS Clinical Standards Toolkit version, characters 17 through 23 are standard version, characters 24 through 42 are implementation datetime, and characters 43 through 48 are assigning authority.
  • comment contains additional information for the check. This column is optional.
  • checkno column was removed.
  • All template, master (Validation Master), and run-specific (Validation Control) data sets for all standards that support validation have been changed to include or exclude these columns. For more information, see Column Descriptions of the Validation Master Data Set.
The Results data set output for most primary SAS Clinical Standards Toolkit tasks was modified. Results data sets now include records that report on the following process metadata:
  • PROCESS STANDARD (example: CDISC SDTM)
  • PROCESS STANDARDVERSION (example: 3.1.2)
  • PROCESS DRIVER (example: SDTM_VALIDATE)
  • PROCESS DATE (example: 2010-07-16T13:25:11)
  • PROCESS TYPE (example: VALIDATION)
  • PROCESS SASREFERENCES (example: c:/…/_cstsasrefs.sas7bdat)
  • PROCESS STUDYROOTPATH (example: c:/myStudy)
  • PROCESS GLOBALLIBRARY (example: c:/cstGlobalLibrary)
  • PROCESS CSTVERSION (example: 1.3)

Framework Changes

The following properties were modified:
  • The installed location for properties is <global standards library directory>/standards/cst-framework-1.3/programs/initialize.properties.
  • You should reset the default value for _cstFMTLibraries from WORK to <blank>. For any SAS Clinical Standards Toolkit process, to include formats built in the SAS Work directory in the format search path, you should:
    1. Reset the property to WORK.<catalog>.
    2. Issue %let _cstFMTLibraries=WORK.<catalog> after the call to cst_setStandardProperties and before the call to cstutil_processsetup.
    3. Issue the OPTIONS FMTSEARCH statement to include WORK.<catalog> at the right point in the job stream.
The Standardlookup data set contents were modified.
  • The installed location for the data set is <global standards library directory>/standards/cst-framework-1.3/control/standardlookup.sas7bdat.
  • This data set serves as the primary lookup to perform basic validation of each SASReferences data set. Any type and subtype values found in a SASReferences data set must be registered in the Standardlookup data set.
    • type=referencecontrol, subtype=validation These values point to the standard-specific Validation Master data set.
    • type=referencexml, subtype=map For XML-based standards, these values reference a SAS XML map file that interprets an interim XML file that was generated by SAS for any process reading from or writing to XML.
    • type=report
    • type=report, subtype=library
    • type=report, subtype=outputfile For reporting processes, subtype=library points to a destination library for report output, and subtype=outputfile points to a file location for a specific report output file.
    • type=sourcemetadata, subtype=study These values facilitate conversions to and from CDISC CRT-DDS define.xml files, which contain metadata information that is associated with the <Study> element.
    • type=targetdata This value points to an output library where derived or target data is to be written. For example, reading a define.xml file generates data sets comprising the SAS representation of CDISC CRT-DDS files.
    • type=transport This value points to a library of SAS transport files as referenced in CDISC CRT-DDS define.xml files.
The autocall macros were modified.
  • The installed location for autocall macros is !sasroot/cstframework/sasmacro.
  • cstcheck_metamismatch: In codeLogic, you can produce two possible data sets that are processed in the check macro. These data sets are work._cstnonmatch (mismatches that prevent assessment) and work._cstmatch (reportable problems found).
  • cstutil_getsasreference: A new parameter is available: _cstAllowZeroObs. If set to 1, then it allows SASReferences to operate without warnings when a row that is requested is not found and returns zero observations. The default value is 0. This default value creates a warning when zero observations are encountered.
The Messages data set was modified. The following messages were added:
  • CST0009: &_cstparm1 macro variable was not defined (error).
  • CST0024: The column &_cstparm1 was not found in &_cstparm2. Compliance was not assessed (warning: check incomplete).
  • CST0025: Data set was not found in reference standard. Compliance was not assessed (warning: check incomplete).

CDISC CRT-DDS Changes

A parameter was added to the crtdds_write macro.
  • The installed location for the autocall macros is <global standards library directory>/standards/cdisc-crtdds-1.0-1.3/macros.
  • The new parameter is _cstLogLevel. This parameter is optional. It identifies the level of error reporting. Valid values are Info, Warning, Error, and Fatal Error.
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