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CDISC SDTM Basics

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					   CDISC submission standard
• CDISC SDTM
  unfolding the core model that is the basis
  both for the specialised dataset templates
  (SDTM domains) optimised for medical
  reviewers
• CDISC Define.xml
  metadata describing the data exchange
  structures (domains)
   Background: CDISC SDTM’s fundamental
       model for organizing clinical data
                     General classes                 Generic structure
                                                     •Unique identifiers
                                                     •Topic variable or parameter
                                                     •Timing Variables
                                                     •Qualifiers.
                      Interventions


                        Findings       Observation


                                                      Subject              SDTM Domains
                         Events                                          (dataset structures)

                                                                                    CM
                                                                                    EX
                                                                                    EG
                                                                                    IE
                                                                                    LB
                                                                                    PE
                                                                                    AE
                                                                                    DS
                                                                                    …

The patient/subject focused information model of the clinical ‘reality’ (general classes of
observations on subjects: interventions, findings, events). This model has been developed by
CDISC/SDS team and exist today only as a text description.
             CDISC SDTM’s Domains

    Interventions             Events              Findings                 Other


        Exposure                AE             Labs        Incl Excl*       Demog


        ConMeds            Disposition         Vitals     Subj Char*      RELATES*

                                                                         SUPPQUAL*
       Subst Use*            MedHist        PhysExam         ECG          Comments*

                                                                         Study Design*
                                             QS*, MB*      CP*, DV*
   * New in Version 3                                                     Study Sum*
From CDISC SDTM Overview & Impact to AZ, 2004, by Dan Godoy, presented
at the first CDISC/SDM meeting 20 October 2004
     Basic Concepts in CDISC SDTM
       Observations and Variables
     • The SDTM provides a general framework for describing the
       organization of information collected during human and animal
       studies.
     • The model is built around the concept of observations, which
       consist of discrete pieces of information collected during a
       study. Observations normally correspond to rows in a dataset.
     • Each observation can be described by a series of named
       variables. Each variable, which normally corresponds to a
       column in a dataset, can be classified according to its Role.
     • Observations are reported in a series of domains, usually
       corresponding to data that were collected together. A domain is
       defined as a collection of observations with a topic-specific
       commonality about a subject.


From the Study Data Tabulation Model document
     Basic Concepts in CDISC/SDTM
             Variable Roles
     •   A Role determines the type of information conveyed by the variable
         about each distinct observation and how it can be used.
          – A common set of Identifier variables, which identify the study, the subject
            (individual human or animal) involved in the study, the domain, and the
            sequence number of the record.
          – Topic variables, which specify the focus of the observation (such as the
            name of a lab test), and vary according to the type of observation.
          – A common set of Timing variables, which describe the timing of an
            observation (such as start date and end date).
          – Qualifier variables, which include additional illustrative text, or numeric
            values that describe the results or additional traits of the observation (such
            as units or descriptive adjectives). The list of Qualifier variables included
            with a domain will vary considerably depending on the type of observation
            and the specific domain
          – Rule variables, which express an algorithm or executable method to define
            start, end, or looping conditions in the Trial Design model.


From the Study Data Tabulation Model document
        Example: Mapping Vital Signs




From CDISC End to End Tutorial - DIA Amsterdam 7 Nov 2004, Pierre-Yves Lastic, Sanofi-
Aventis and Philippe Verplancke, CRO24
  CDISC’s Submission standard
• Underlying Models:
  CDISC Study Data Tabulation Model
  Clinical Observations
     • General Classes: Events, Findings, Interventions
  – Trial Design Model
     • Elements, Arms, Trial Summary Parameters etc.
• Domains, submission dataset templates:
  CDISC SDTM Implementation Guide
CDISC SDTM fundamental model for organizing data collected in
clinical trials
Concept of Observations, which consist of discrete pieces of information
collected during a study described by a series of named variables.
General Classes of Observations: Events, Findings, Interventions
Variable Roles: determines the type of information conveyed by the
variable about each distinct observation: Topic variables, Identifier
variables, Timing variables, Rule variables, and Qualifiers (Grouping,
Result, Synonym, Record, Variable)
General principles and standards
       CDISC SDTM Domains
    SAS Dataset implementations
         (dataset templates)
       e.g. Vital Signs domains




Optimisations for Data Exchange per
study and for Medical Reviewers to
easier understand data
Specific principles and standards such
as ISO8601 for dates/timings, and both
Original & Standard values expected




                               CDISC SDTM fundamental model for organizing data collected in
                               clinical trials
                               Concept of Observations, which consist of discrete pieces of information
                               collected during a study described by a series of named variables.
                               General Classes of Observations: Events, Findings, Interventions
                               Variable Roles: determines the type of information conveyed by the
                               variable about each distinct observation: Topic variables, Identifier
                               variables, Timing variables, Rule variables, and Qualifiers (Grouping,
                               Result, Synonym, Record, Variable)
                               General principles and standards
       CDISC SDTM Domains
    SAS Dataset implementations                            Decoded format, that is, the
         (dataset templates)                               textual interpretation of
       e.g. Vital Signs domains                            whichever code was
                                                           selected from the code list.



Optimisations for Data Exchange per          Identifiers of records
study and for Medical Reviewers to           per dataset and study
easier understand data
Specific principles and standards such
as ISO8601 for dates/timings, and both
Original & Standard values expected




                               CDISC SDTM fundamental model for organizing data collected in
                               clinical trials
                               Concept of Observations, which consist of discrete pieces of information
                               collected during a study described by a series of named variables.
                               General Classes of Observations: Events, Findings, Interventions
                               Variable Roles: determines the type of information conveyed by the
                               variable about each distinct observation: Topic variables, Identifier
                               variables, Timing variables, Rule variables, and Qualifiers (Grouping,
                               Result, Synonym, Record, Variable)
                               General principles and standards
                                              Controlled Terminologies
       CDISC SDTM Domains
                                              CT Packages for SDTM
    SAS Dataset implementations
                                              e.g. Codelist Patient
         (dataset templates)
                                              Positiion and proposed
       e.g. Vital Signs domains
                                              terms for VSTESTCD




Optimisations for Data Exchange per
study and for Medical Reviewers to
easier understand data
Specific principles and standards such
as ISO8601 for dates/timings, and both
Original & Standard values expected




                               CDISC SDTM fundamental model for organizing data collected in
                               clinical trials
                               Concept of Observations, which consist of discrete pieces of information
                               collected during a study described by a series of named variables.
                               General Classes of Observations: Events, Findings, Interventions
                               Variable Roles: determines the type of information conveyed by the
                               variable about each distinct observation: Topic variables, Identifier
                               variables, Timing variables, Rule variables, and Qualifiers (Grouping,
                               Result, Synonym, Record, Variable)
                               General principles and standards
                                                          Controlled Terminologies
          CDISC SDTM Domains
                                                          CT Packages for SDTM
       SAS Dataset implementations
                                                          e.g. Codelist Patient
            (dataset templates)
                                                          Positiion and proposed
          e.g. Vital Signs domains
                                                          terms for VSTESTCD

 CDISC Codelist Specification                                                  CDISC Codelist Values
                                                                               Codelist_Nam e        Controlled Term s                         Com m ent
 Codelist_Nam e          VSTEST                                                                      --TESTCD       --TEST
                         Vital Exchange per
  Optimisations for Data Signs Test Name
 Codelist_Label                                                                 VSTEST               WEIGHT         Weight
                         Y
 Upper_Case for Medical Reviewers to
  study and                                                                     VSTEST               HEIGHT         Height
 Restriction_8char       Y                                                      VSTEST               HR             Heart Rate
  easier understand data
 Extensible_NY           Y                                                      VSTEST               PULSE          Pulse Rate
  Specific principles Organization Name: CDISC
 Reference_Description and standards such                                       VSTEST               SYSBP          Systolic Blood Pressure
                         Document Title: Study Data
  as ISO8601 for dates/timings, and both Tabulation Model
                         Implementation Guide: Human Clinical Trials
  Original & Standard values expected
                         Document Version: 1.01
                         Date: 2004-07-14
CDISC Codelist SpecificationVital Signs Test Codes CDISC Codelist Values
                         Chapter:10.3.3
Codelist_Nam e           Page: 169
                            VSRESU                               Codelist_Nam e  Controlled Term s   Com m ent
 Reference_URL
Codelist_Label           http://www.cdisc.org/models/sds/v3.1/index.html VSTEST
                            Units for Vital Signs Results        VSRESU                              DIABP          Diastolic Blood Pressure
                                                                                         kg
Upper_Case                    N                                  VSRESU                  lb
Restriction_8char             N                                  VSRESU                 VSTEST             RESP           Respiratory Rate
                                                                                         cm
Extensible_NY                              Specification VSRESU
                  CDISC Codelist CDISC SDTM fundamental model for
                              Y
                                                                                        VSTESTorganizing TEMP collected in Values
                                                                                         in
                                                                                                             CDISC Codelist
                                                                                                            data          Temperature
                  Codelist_Name applicable       RACE                                   VSTEST               Codelist Controlled Size s
                                                                                                           FRMSIZE        Frame Term             SIZECD    Com m ent
Reference_Description         Not         clinical trials        VSRESU                  mmHG
                                                                                        VSTEST             BMI            Body Mass Index
Reference_URL                 Not
                  Codelist_Label applicable                      VSRESU                  beats/min
                                                                                        VSTEST             BSA            Body INDIAN Area
                                          Concept of Observations, which consist of discrete pieces of AMERICAN SurfaceOR ALASKA NATIVE
                                                 Race                                                        RACE     information                          FDA code
                                                                 VSRESU                  kg/m2series of named variables.
                                                                                        VSTEST             BODYFAT        Body Fat
                  Upper_Case              collected during a study described by a
                                                 Y                                                           RACE     ASIAN                                FDA code
                                                                 VSRESU                 VSTEST
                                                                                         m2                MAP            Mean Arterial Pressure

                  Restriction_8char       General Classes of Observations: Events, Findings, InterventionsAFRICAN AMERICAN
                                                 N               VSRESU                  C                   RACE     BLACK OR                             FDA code
                                                                 VSRESU                  F
                  Extensible_NY                                                                                       by the
                                          Variable Roles: determines the type of information conveyed NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
                                                 N                                                           RACE                                          FDA code
                                                                 VSRESU                  breath/min
                                          variable about each distinct observation: Topic variables, Identifier
                                                                 VSRESU
                                                 Organization Name: FDA                  g                   RACE
                  Reference_Description variables, Timing variables, Rule variables, and Qualifiers (Grouping,        WHITE                                FDA code
                                                                 VSRESU                  %
                                                 Document Title: Draft Guidance for Industry Collection of
                                                                 Record,
                                          Result, Synonym, VSRESU Variable)
                                                                                         Ohm
                                                 Race and Ethnicity Data in Clinical Trials
                                             Date: January 2003
                                        General principles and standards
                                               Chapter: III COLLECTING RACE AND ETHNICITY DATA IN
                                               CLINICAL TRIALS
                                               Codelist_Name: Race
                                               Page: 5
                  Reference_URL                http://www.fda.gov/cder/guidance/5054dft.pdf
                                              Controlled Terminologies
       CDISC SDTM Domains
                                              CT Packages for SDTM
    SAS Dataset implementations
                                              e.g. Codelist Patient
         (dataset templates)
                                              Positiion and proposed
       e.g. Vital Signs domains
                                              terms for VSTESTCD




Optimisations for Data Exchange per
study and for Medical Reviewers to
easier understand data
Specific principles and standards such
as ISO8601 for dates/timings, and both
Original & Standard values expected




                               CDISC SDTM fundamental model for organizing data collected in
                               clinical trials
                               Concept of Observations, which consist of discrete pieces of information
                               collected during a study described by a series of named variables.
                               General Classes of Observations: Events, Findings, Interventions
                               Variable Roles: determines the type of information conveyed by the
                               variable about each distinct observation: Topic variables, Identifier
                               variables, Timing variables, Rule variables, and Qualifiers (Grouping,
                               Result, Synonym, Record, Variable)
                               General principles and standards

  define.xml
  Case Report Tabulation Data Definition Specification
  to submit the Data Definition Document (submission
  dataset metadata) in a machine-readable format
                                          Controlled Terminologies
      CDISC SDTM Domains
                                          CT Packages for SDTM
   SAS Dataset implementations
                                          e.g. Codelist Patient
        (dataset templates)
                                          Positiion and proposed
      e.g. Vital Signs domains
                                          terms for VSTESTCD

    CRTDDS              =       Case Report Tabulation Data Description
                                Specification (= an ODM extension, formerly
study and for Medical Reviewers called „define.xml“) will replace define.pdf in e-CTD
Optimisations for Data Exchange per
                                to
                                                               ValueList (in an item)
    <ItemDef OID="SU.SUTRT.SMKCLASS" Name="SMKCLASS" DataType="integer" Length="8“
easier understand data
                        Item                 Item
         principles and standards Comment="Substance Use CRF Page 4" def:Label="Smoking classification">
SpecificOrigin="CRF Page" such
            <CodeListRef and both
as ISO8601 for dates/timings, CodeListOID="SMKCLAS" />
     </ItemDef>
Original & Standard values expected
    <CodeList OID="SMKCLAS" Name="SMKCLAS" DataType="integer">
      <CodeListItem CodedValue="1">
        <Decode>
          <TranslatedText xml:lang="en">NEVER SMOKED</TranslatedText>
   ItemGroup
        </Decode>
                                                                                              Item
                                         define.XML as organizing data collected in
      </CodeListItem> CDISC SDTM fundamental model for machine-readable replacement for define.pdf
                       clinical trials
      <CodeListItem CodedValue=“2"> prevoius called Data Defintion Tables in item 11)
                                         (=
        <Decode>       Concept of Observations, which consist of discrete pieces of information
   ItemGroup                              study described by a series of named variables. Item
          <TranslatedText xml:lang="en">SMOKER</TranslatedText>
                       collected during a> Needs complete syntax to reference external lists
        </Decode>
                       General Classes of Observations: Events, Findings, Interventions
      </CodeListItem>                    From Randy Levins presentation, see
      <CodeListItem CodedValue=“3">
                       Variable Roles: determines the type of information conveyed by the
        <Decode>
   ItemGroup                             http://www.cdisc.org/publications/interchange2005/se
                       variable about each distinct observation: Topic variables, Identifier
                                                                                             Item
                                         variables, Rule variables, and Qualifiers (Grouping,
                       variables, Timing ssion8/JANUS2005.pdf
          <TranslatedText xml:lang="en">EX SMOKER</TranslatedText>
        </Decode>      Result, Synonym, Record, Variable)
                                         > And to reference sponsor defined code lists cross studies
      </CodeListItem> General principles and standards

 define.xml
 Case Report Tabulation Data Definition Specification
 to submit the Data Definition Document (submission
 dataset metadata) in a machine-readable format
       CDISC SDTM Domains
    SAS Dataset implementations
         (dataset templates)
       e.g. Vital Signs domains


                                                                                    SDTM fundemantal mode is also the basis for:
                                                                                    • SEND Domains for Nonclinical Data (generated
Optimisations for Data Exchange per                                                 from animal toxicity studies)
study and for Medical Reviewers to
easier understand data                                                              • Future domains of derived data, capturing
Specific principles and standards such
                                                                                    metadata to describe derivations and analyses.
as ISO8601 for dates/timings, and both
Original & Standard values expected




                               CDISC SDTM fundamental model for organizing data collected in
                               clinical trials
                               Concept of Observations, which consist of discrete pieces of information
                               collected during a study described by a series of named variables.
                               General Classes of Observations: Events, Findings, Interventions
                               Variable Roles: determines the type of information conveyed by the
                               variable about each distinct observation: Topic variables, Identifier
                               variables, Timing variables, Rule variables, and Qualifiers (Grouping,
                               Result, Synonym, Record, Variable)
                               General principles and standards
     Basic Concepts in CDISC/SDTM
         Subclasses of Qualifiers
     •   Grouping Qualifiers are used to group together a collection of observations within the
         same domain.
          –   Examples include --CAT, --SCAT, --GRPID, --SPEC, --LOT, and --NAM. The latter three grouping qualifiers can
              be used to tie a set of observations to a common source (i.e., specimen, drug lot, or laboratory name,
              respectively).
     •   Synonym Qualifiers specify an alternative name for a particular variable in an
         observation.
          –   Examples include --MODIFY and --DECOD, which are equivalent terms for a --TRT or --TERM topic variable,
              and --LOINC which is an equivalent term for a --TEST and --TESTCD.
     •   Result Qualifiers describe the specific results associated with the topic variable for a
         finding. It is the answer to the question raised by the topic variable.
          –   Examples include --ORRES, --STRESC, and --STRESN.
     •   Variable Qualifiers are used to further modify or describe a specific variable within an
         observation and is only meaningful in the context of the variable they qualify.
          –   Examples include --ORRESU, --ORNHI, and --ORNLO, all of which are variable qualifiers of --ORRES: and --
              DOSU, --DOSFRM, and --DOSFRQ, all of which are variable qualifiers of --DOSE. observation and is
     •   Record Qualifiers define additional attributes of the observation record as a whole
         (rather than describing a particular variable within a record).
          –   Examples include --REASND, AESLIFE, and allother SAE flag variables in the AE domain; and --BLFL, --POS
              and --LOC.

From the Study Data Tabulation Model document
        Basic Concepts in CDISC/SDTM
                Variable Roles
        •     Topic variables                       •   Grouping qualifiers
              which specify the focus of the            are used to group together a collection of observations
              observation (such as the name of          within the same domain.
              a lab test), and vary according to            –   Examples include --CAT, --SCAT, --GRPID, --SPEC, --LOT,
              the type of observation.                          and --NAM. The latter three grouping qualifiers can be used
                                                                to tie a set of observations to a common source (i.e.,
                                                                specimen, drug lot, or laboratory name, respectively)

                                                    •   Synonym Qualifiers
                                                        specify an alternative name for a particular variable in
                                                        an observation.
                                                            –   Examples include --MODIFY and --DECOD, which are
                                                                equivalent terms for a --TRT or --TERM topic variable,
                                                                                                                 Qualifier
Observation                                                     and --LOINC which is an equivalent term for      variables
  Record                                                        a --TEST and --TESTCD.



                                         Grouping Synonym
         Topic
                                           Qual     Qual



  From the Study Data Tabulation Model document
        Basic Concepts in CDISC/SDTM
                Variable Roles
        •     Identifier variables                    •   Result Qualifiers
              which identify the study, the subject       describe the specific results associated
              (individual human or animal) involved       with the topic variable for a finding. It is the
              in the study, the domain, and the           answer to the question raised by the topic
              sequence number of the record.
                                                          variable. Depending on the type of result
        •     Timing variables                            (numeric or character) different variables
              which describe the timing of an             are being used. Includes variables for both
              observation (such as start date and
                                                          original (as supplied values) and for
              end date).
                                                          standardised values (for uniformity).
                                                           –   Examples include --ORRES,
                                                               --STRESC, and --STRESN.                  Qualifier
Observation                                                                                             variables
  Record



                                                                 Result
         Topic    Identifier   Timing
                                                                 Qual



  From the Study Data Tabulation Model document
        Basic Concepts in CDISC/SDTM
                Variable Roles
                                             •    Variable Qualifiers
                                                  are used to further modify or describe a specific
                                                  variable within an observation and is only
                                                  meaningful in the context of the variable they
                                                  qualify.
                                                   – Examples include --ORRESU, --ORNHI,
                                                       and --ORNLO, all of which are variable
                                                       qualifiers of --ORRES: and --DOSU, --
                                                       DOSFRM, and --DOSFRQ, all of which are
                                                       variable qualifiers of --DOSE.
                                                   – Indictors where the results falls with respect
                                                       to reference range                          Qualifier
Observation                                                                                        variables
  Record



                                                         Result             Variable
         Topic   Identifier   Timing
                                                         Qual                Qual



  From the Study Data Tabulation Model document
        Basic Concepts in CDISC/SDTM
                Variable Roles
                                             •    Record Qualifiers
                                                  define additional attributes of the observation
                                                  record as a whole (rather than describing a
                                                  particular variable within a record).
                                                   –   Examples include --REASND, AESLIFE, and
                                                       allother SAE flag variables in the AE domain; and
                                                       --BLFL, --POS and --LOC.




                                                                                                       Qualifier
Observation                                                                                            variables
  Record



                                                         Result               Variable        Record
         Topic   Identifier   Timing                                                           Qual
                                                         Qual                  Qual



  From the Study Data Tabulation Model document
     Basic Concepts in CDISC/SDTM
         Subclasses of Qualifiers
     •   Topic variables                      •   Qualifier variables
     •   Identifier variables                         –   Grouping Qualifiers
     •   Timing variables                             –   Result Qualifiers
                                                      –   Synonym Qualifiers
     •   Rule variables
                                                      –   Record Qualifiers
                                                      –   Variable Qualifiers




     Observation Record




                                   Grouping Synonym         Result        Variable   Record
     Topic   Identifier   Timing                                                      Qual
                                     Qual     Qual          Qual           Qual



From the Study Data Tabulation Model document
                                 Qual
                                     Qual     Qual          Qual            Qual



From the Study Data Tabulation Model document

				
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