Validation Checks by Standard
ADaM 2.1
The SAS Clinical Standards
Toolkit 1.4 provides 159 unique ADaM 2.1 validation checks. These
validation checks are derived from the SAS interpretation of the CDISC
ADaM Validation Checks Version 1.0 (final production version dated
September 20, 2010), and the CDISC ADaM Validation Checks Version
1.1 Maintenance Release (dated and released January 21, 2011 to correct
errors and remove duplicate checks). These documents are available
in the members only area at http://www.cdisc.org/adam.
Information
about the 159 records in the CDISC ADaM 2.1 Validation Master data
set is in Validation Checks. Only selected columns are listed
in the appendix.
Consider the
interrelationships among the SAS Clinical Standards Toolkit validation
check metadata. All run-time Validation Control data sets, any programs
that build or derive from these data sets, corresponding Messages
data sets, and the Validation_StdRef data set are examples of how
interconnected many SAS Clinical Standards Toolkit metadata files
are. For more information about the Messages data set, see Messages.
CDISC ODM 1.3.0
The SAS Clinical Standards
Toolkit provides check macros that validate the data in the SAS data
sets representing CDISC ODM 1.3.0 data. The structure of this data
is similar to CDISC CRT-DDS. Therefore, the process for validating
the data is similar. The goal of these check macros is to ensure that
all data is correctly specified, and that referential integrity is
maintained. As a result, a standards-compliant CDISC define.xml file
can be produced from these data sets.
As in CRT-DDS, the validity
of ODM data is determined by the standard in the form of XML schema
definitions. These XML schema definitions must be translated into
checks appropriate for the relational and tabular formats.
The SAS Clinical Standards
Toolkit 1.4 provides 179 unique ODM 1.3.0 validation checks. These
validation checks were developed by SAS and are based on ODM implementation
experience and careful review of the CDISC ODM Implementation
Guide, with special emphasis on the occurrence of “should”
within the Implementation Guide.
Information
about the 179 records in the CDISC ODM 1.3.0 Validation Master data
set is in Validation Checks. Only selected columns are listed
in the appendix.
Consider the
interrelationships among the SAS Clinical Standards Toolkit validation
check metadata. All run-time Validation Control data sets, any programs
that build or derive from these data sets, corresponding Messages
data sets, and the Validation_StdRef data set are examples of how
interconnected many SAS Clinical Standards Toolkit metadata files
are. For more information about the Messages data set, see Messages.
By default, the Validation
Master data set is located in the
<global standards library directory>/standards/cdisc-odm-1.3.0-1.4/validation/control folder.
ODM Validation Check Types lists the types of checks for ODM
data.
Each check type is assumed
to operate on data that exists in a source column in a source data
set. A check type can reference one or more parameters that validate
the source column data. A parameter can be a character string or a
representation of a column other than the source column against which
the source column data must be compared.
All character comparisons
are case sensitive. Character data is assumed to have been trimmed
of leading and trailing white space.
ODM Validation Check Types
-
Structural checks deal with relationships and data integrity between tables. An example is foreign key enforcement. Structural conditions must be met for the successful generation of an ODM XML file. You might want to defer structural checks until later in the process when populating the ODM data sets. This is because foreign key relationships require that the data is made available in a particular order (that is, a referenced key must be available before the foreign key to it can exist).
The CDISC ODM
validation checks that are listed in ODM Validation Checks Using Expected Values are performed by comparing the
data against a set of expected values. The expected values are stored
in a format catalog (odmct.sas7bcat) and a data set (odmct.sas7bdat).
They are located in the
<global
standards library directory>/standards/cdisc-odm-1.3.0-1.4/formats folder.
The methodology ensures
case-sensitivity compliance, which is required by the XML schema validation.
For example, ItemRangeChecks has a Comparator variable whose values
are controlled by the Comp Enumeration ("EQ", "GE", "GT", "IN", "LE",
"LT", "NE", and "NOTIN"). If mixed case or lowercase values are detected,
then this validation check reports an error. The validation check
is ODM0114 (see ODM Validation Check Types), and it uses
the Comp SAS format to report this as an error.
The SASReferences data
set needs to contain a row for fmtsearch, with SAS libref set to
odmfmt and the Filename set to odmct.sas7bcat.
ODM Validation Checks Using Expected Values
|
Controlled by the two-letter
codes from the ISO 3166-1 standard for country codes. The values
are available from this Web site: http://www.iso.org/iso/country_codes/iso_3166_code_lists.htm
|
CDISC SDTM 3.1.1
The SAS Clinical Standards
Toolkit 1.4 provides 150 unique SDTM 3.1.1 validation checks. These
checks are derived from four sources.
The CDISC SDTM 3.1.1
Validation Master data set, as defined in the SAS Clinical Standards
Toolkit 1.4, contains 257 records. Even though the SAS Clinical Standards
Toolkit provides 150 unique CDISC SDTM 3.1.1 checks, there are 257
records in the Validation Master data set. The Validation Master data
set is built with multiple instances of the checks. This better supports
check selection by version or checksource (that is, WebSDM, Janus,
or customer-defined checks), and enables unique check logic and messaging
by version or checksource. Of these 257 checks, three are inactive,
and 12 are deprecated. Deprecated CDISC SDTM checks generally reflect
changes in the WebSDM specifications over time.
Note: The validation check data
set column checkstatus is designed to provide an indication of the
“state” of each check. It says whether the check is
ready to be run in its current defined state, or should it be run
based on some external criteria. Valid values are 1 (active), 0 (inactive),
-1 (deprecated), and -2 (not yet implemented). Values are extensible
to meet your given requirements. No SAS Clinical Standards Toolkit
code requires specific values. You can elect to use other values such
as 0 (draft), 1 (test), and 2 (production). If a check is included
in the run-time validation control data set, the SAS Clinical Standards
Toolkit attempts to run the check as defined, regardless of the value
of the checkstatus column.
This table provides
the distribution of all 257 CDISC SDTM validation checks by the original
source of the check (the Validation Master checksource field).
Distribution of CDISC SDTM 3.1.1 Validation Checks
This does not mean that
the SAS Clinical Standards Toolkit 1.4 supports 114 different WebSDM
checks or 32 unique SAS checks. There are multiple instances of specific
checks to handle different sets of SDTM domains. For example, check
SDTM0604 assesses whether the sequence numbers (**SEQ) are consecutively
numbered. For most domains, this is assessed within each patient (USUBJID).
However, the trial summary (TS) domain does not contain patient-level
data, so the check logic differs. The Validation Master metadata differs
for these two instances of the SDTM0604 check, but reports the same
error message for the check.
Information
about the 257 records in the CDISC SDTM 3.1.1 Validation Master data
set is itemized in CDISC SDTM Validation Checks. Only selected columns are listed
in the appendix. For a full
description of a sample Validation Master data set for the CDISC SDTM
standard, see Sample CDISC SDTM 3.1.2 Validation Master Data Set Record.
Consider the
interrelationships among the SAS Clinical Standards Toolkit validation
check metadata. All run-time Validation Control data sets, any programs
that build or derive from these data sets, corresponding Messages
data sets, and the Validation_StdRef data set are examples of how
interconnected many SAS Clinical Standards Toolkit metadata files
are. For more information about the Messages data set, see Messages.
By default, the Validation_StdRef
data set is found in the
<global
standards library directory>/standards/cdisc-sdtm-3.1.1-1.4/validation/control folder.
Note: Currently, the SAS Clinical
Standards Toolkit does not fully support all WebSDM checks. Checks
that are not supported require a comparison between SDTM metadata
and an associated define.xml file. Loads into the Janus repository
require the existence and use of a define.xml file. However, the SAS
Clinical Standards Toolkit 1.4 does not require an associated define.xml
file for SDTM validation. For more information, see the SAS site
support.sas.com for SAS Notes, other usage notes, and their
current status.
CDISC SDTM 3.1.2
The SAS Clinical Standards
Toolkit 1.4 provides 243 unique SDTM 3.1.2 validation checks. These
checks are derived from four sources.
The CDISC SDTM 3.1.2
Validation Master data set, as defined in the SAS Clinical Standards
Toolkit 1.4, contains 247 records. Even though the SAS Clinical Standards
Toolkit provides 243 unique CDISC SDTM 3.1.1 checks, there are 247
records in the Validation Master data set. Of these 247 checks, one
is inactive, eight are deprecated, and 18 are not implemented. Deprecated
CDISC SDTM checks generally reflect changes in the WebSDM specifications
over time. Checks that are not implemented generally involve a comparison
of the CDISC SDTM data, metadata, or both with an associated define.xml
file. Such cross-standard validation is not supported in the current
release of the SAS Clinical Standards Toolkit. In the SAS Clinical
Standards Toolkit 1.4, the Janus and JanusFR checks were dropped for
SDTM 3.1.2.
This table provides
the distribution of all 247 CDISC SDTM validation checks by the original
source of the check (the Validation Master checksource field).
Distribution of CDISC SDTM 3.1.2 Validation Checks
Note: The SAS Clinical Standards
Toolkit allows multiple invocations of the same validation check.
Multiple invocations for four checks account for the difference between
the 243 unique checks and 247 records in the Validation Master data
set. For example, check SDTM0604 assesses whether the sequence numbers
(**SEQ) are consecutively numbered. For most domains, this is assessed
within each patient (USUBJID). However, the trial summary (TS) domain
does not contain patient-level data, so the check logic differs. The
Validation Master metadata differs for these two instances of the
SDTM0604 check, but reports the same error message for the check.
Information
about the 247 records in the CDISC SDTM 3.1.2 Validation Master data
set is itemized in CDISC SDTM Validation Checks. Only selected columns are listed
in the appendix.
Consider the
interrelationships among the SAS Clinical Standards Toolkit validation
check metadata. All run-time Validation Control data sets, any programs
that build or derive from these data sets, corresponding Messages
data sets, and the Validation_StdRef data set are examples of how
interconnected many SAS Clinical Standards Toolkit metadata files
are. For more information about the Messages data set, see Messages.
By default, the Validation_StdRef
data set is found in the
<global
standards library directory>/standards/cdisc-sdtm-3.1.2-1.4/validation/control folder.
Note: Currently, the SAS Clinical
Standards Toolkit does not fully support all WebSDM checks. Checks
that are not supported require a comparison between SDTM metadata
and an associated define.xml file. Loads into the Janus repository
require the existence and use of a define.xml file. However, the SAS
Clinical Standards Toolkit 1.4 does not require an associated define.xml
file for SDTM validation. For more information, see the SAS site at
support.sas.com for SAS Notes, other usage notes, and their
current status.
CDISC CRT-DDS 1.0
The SAS Clinical Standards
Toolkit provides check macros that validate the data in the SAS data
sets representing CDISC CRT-DDS data. The goal of these check macros
is to ensure that all data is correctly specified and that referential
integrity is maintained. As a result, a standards-compliant CDISC
define.xml file can be produced from these data sets.
The validity of CRT-DDS
data is determined by the standard in the form of XML schema definitions.
These XML schema definitions must be translated into checks appropriate
for the relational and tabular format.
CRT-DDS Validation Check Types lists the types of checks for CRT-DDS
data.
Each check type is assumed
to operate on data that exists in a source column in a source data
set. A check type can reference one or more parameters that validate
the source column data. A parameter can be a character string or a
representation of some column other than the source column against
which the source column data must be compared.
All character comparisons
are case sensitive. Character data is assumed to have been trimmed
of leading or trailing white space.
CRT-DDS Validation Check Types
Each check type belongs
to one of two categories.
-
Data checks have no dependencies on data outside of the source table. An example is ensuring that a value exists in a column in which values cannot be missing.
-
Structural checks deal with relationships and data integrity between tables. Foreign key enforcement is an example of a structural check. Structural conditions must be met for the successful generation of a define.xml file. You might want to defer structural checks until later in the process of populating the CRT-DDS data sets. This is because foreign key relationships require that the data be made available in a particular order (that is, a referenced key must be available before the foreign key to it can exist).
The CDISC
CRT-DDS validation checks that are listed in CRT-DDS Validation Checks are performed by comparing the data against a set of expected
values. The expected values have been stored in a format catalog (crtddsct.sas7bcat)
and a data set (crtddsct.sas7bdat). They are in the
<global standards library directory>/standards/cdisc-crtdds-1.0-1.4/formats folder.
This table lists the
format names and values that are used during CRT-DDS validation. This
methodology ensures case-sensitivity compliance required by the XML
schema validation. For example, the ItemRangeChecks data set requires
an enumeration edit for values such as LT and LE. If mixed case or
lowercase values are detected, then the validation check reports an
error. In this case, the validation check is CRT0114, (see CRT-DDS Validation Checks) and it uses
the Comp format to report this as an error.
Enumeration Validation Format Values*
