Mapping Corporate Data Standards to the CDISC Model. David Parker, AstraZeneca UK Ltd, Manchester, UK

Transcription

1 Mapping Corporate Data Standards to the CDISC Model David Parker, AstraZeneca UK Ltd, Manchester, UK

2 Introduction Discuss CDISC Case Report Tabulations Data Definition, Study Data Tabulation Model, Operational Data Model and mapping strategies from existing standards Why do we need to map Could we make more use of XML

3 Standards in the Industry Need for Standards, ( Compare Past with vision of the Future) Use of SAS Use of XML

4 Discussing Implementation Options Kenny & Litzsinger PharmaSug 2005 Parallel Method DBMS Extract SDTM Domains Analysis Datasets Retrospective Development DBMS extract Analysis Datasets SDTM Domains Linear Method DBMS Extract SDTM Domains Analysis Datasets Hybrid Method DBMS Extract SDTM Draft Domain Analysis DataSets SDTM Final Domains

5 Parallel Algorithms ETL SDTM Domains Database Algorithms Advantages Disadvantages Analysis Data Sets STDM and ADaM Independent SDTM created at Time of Submission Parallel Project Teams Minimum re-engineering of existing processes Documentation different for each dataset and decreased efficiency. ADaM derived variables do not reference SDTM Regulators do not have original extracts for ADaM derived variables. Analysis Programs submitted to Regulators do not point to raw data Validation between SDTM and ADaM needed

6 Retrospective ETL Algorithms Database RAW CRTs Analysis Data Sets Advantages SDTM created at Time of Submission Enhancements/new releases of SDTM are not affected Disadvantages SDTM Regulators do not have original extracts for ADaM derived variables. Analysis Programs submitted to Regulators do not point to raw data Date imputation have to be undone to match SDTM data standard All CRF variables in the SDTM would have to be retained in the analysis datasets. Validation between SDTM and source needed Analysis Datasets needed before SDTM

7 Linear ETL Algorithms Algorithms Database RAW CRTs SDTM Advantages Disadvantages Analysis Data Sets Analysis programs utilise the SDTM SDTM domains facilitate standardisation of Analysis Datasets Logical Flow of Software Development (A to B to C) Development of Analysis Datasets depend on completion of SDTM SDTM domain created for all studies regardless of whether part of submission Potential Outsourcing problems

8 Hybrid ETL Algorithms Algorithms Database RAW CRTs Draft SDTM Advantages Disadvantages Final SDTM SDTM created at the time of submission. SDTM domains facilitate standardisation of Analysis Datasets Analysis programs submitted to the Agency are useable and informative to the reviewer as SDTM input. Creation of baseline or population flags in harmony SDTM vs ADaM Development of Analysis Datasets depend on completion of SDTM SDTM domain created for all studies regardless of whether part of submission Potential Outsourcing problems

9 SDTM Modelling

10 Modelling a Mapping Process (Common issues in mapping dummy corporate standards to CDISC standards ) Character variables defined as Numeric and vice versa Variables collected without an obvious corresponding domain in the CDISC SDTM mapping. So must go into SUPPQUAL Several corporate modules that map to one corresponding domain in CDISC SDTM. Dictionary codes not in SDTM parent module, so if needed must be collected in SUPPQUAL Core SDTM is a subset of the existing corporate standards Different structure of data Lab CDISC Domain e.g. baseline flag, Vitals Horizontal vs Vertical Additional Metadata needed to describe the source in SUPPQUAL; also metadata needed to laboratory data standardization. Dates combining date and times; partial dates. Data collapsing issues e.g. Adverse Events and Concomitant Medications, Adverse Events maximum intensity.

11 Operational Data Model (ODM) ODM used for Data Interchange Map Data from SAS to the ODM structure Use of XSLT Stylesheet to subset the XML dataset

12 XML file of SAS Data

13 SDTM view of the Data

14 Global Ordering Of Elements Case Report Tabulation Data Definition Specification (define.xml) Standards Version CDISC Page 44 of 45 ODM Study Global Variables MetDataVersion ItemGroupDef ItemRef Def:leaf Def:title Def:ValueListRef ItemDef CodeListRef CodeList CodeListItem Decode TranslatedText ExternalCodeList

15 ItemGroupDef <xs:element name="itemgroupdef" type="odmcomplextypedefinition-itemgroupdef"> <xs:complextype name="odmcomplextypedefinition-itemgroupdef"> <xs:sequence> <xs:element ref="itemref" maxoccurs="unbounded"/> <xs:element ref="alias" minoccurs="0" maxoccurs="unbounded"/> <xs:group ref="itemgroupdefelementextension" minoccurs="0" maxoccurs="unbounded"/> </xs:sequence> <xs:attributegroup ref="itemgroupdefattributedefinition"/> <xs:attributegroup ref="itemgroupdefattributeextension"/> </xs:complextype>

16 ItemGroupDefAttributeDefinition <xs:attributegroup name="itemgroupdefattributedefinition"> <xs:attribute name="oid" type="oid" use="required"/> <xs:attribute name="name" type="name" use="required"/> <xs:attribute name="repeating" type="yesorno" use="required"/> <xs:attribute name="isreferencedata" type="yesorno"/> <xs:attribute name="sasdatasetname" type="sasname"/> <xs:attribute name="domain" type="text"/> <xs:attribute name="origin" type="text"/> <xs:attribute name="role" type="name"/> <xs:attribute name="purpose" type="text"/> <xs:attribute name="comment" type="text"/> </xs:attributegroup>

17 ItemGroupDefAttributeDefinition <ItemGroupDef> <ID>1</ID> <OID>Demographics</OID> <Name>DM</Name> <Repeating>No</Repeating> <IsReferenceData>No</IsReferenceData> <Purpose>Tabulation</Purpose> <def_x003a_label>demographics</def_x003a_label> <def_x003a_structure>one record per subject</def_x003a_structure> <def_x003a_domainkeys>studyid,usubjid</def_x003a_domainkeys> <def_x003a_class>special Purpose Domains</def_x003A_Class> <def_x003a_archivelocation>dm.xpt</def_x003a_archivelocation> </ItemGroupDef>

18 ItemGroupDefDefinition

19 Global Ordering Of Elements Case Report Tabulation Data Definition Specification (define.xml) Standards Version CDISC Page 44 of 45 ODM Study Global Variables MetDataVersion ItemGroupDef ItemRef Def:leaf Def:title Def:ValueListRef ItemDef CodeListRef CodeList CodeListItem Decode TranslatedText ExternalCodeList

20 ITEMDEF <xs:element name="itemdef" type="odmcomplextypedefinition-itemdef"/> <xs:complextype name="odmcomplextypedefinition-itemdef"> <xs:sequence> <xs:element ref="question" minoccurs="0"/> <xs:element ref="externalquestion" minoccurs="0"/> <xs:element ref="measurementunitref" minoccurs="0" maxoccurs="unbounded"/> <xs:element ref="rangecheck" minoccurs="0" maxoccurs="unbounded"/> <xs:element ref="codelistref" minoccurs="0"/> <xs:element ref="role" minoccurs="0" maxoccurs="unbounded"/> <xs:element ref="alias" minoccurs="0" maxoccurs="unbounded"/> <xs:group ref="itemdefelementextension" minoccurs="0" maxoccurs="unbounded"/> </xs:sequence> <xs:attributegroup ref="itemdefattributedefinition"/> <xs:attributegroup ref="itemdefattributeextension"/> </xs:complextype>

21 ItemDefAttributeDefinition <xs:attributegroup name="itemdefattributedefinition"> <xs:attribute name="oid" type="oid" use="required"/> <xs:attribute name="name" type="name" use="required"/> <xs:attribute name="datatype" type="datatype" use="required"/> <xs:attribute name="length" type="integer"/> <xs:attribute name="significantdigits" type="integer"/> <xs:attribute name="sasfieldname" type="sasname"/> <xs:attribute name="sdsvarname" type="sasname"/> <xs:attribute name="origin" type="text"/> <xs:attribute name="comment" type="text"/> </xs:attributegroup>

22 <ItemOID>VISITNUM</ItemOID> <Name>VISITNUM</Name> <DataType>Num</DataType> <Origin>CRF </Origin> <Comment>Vital Signs CRF Page x</comment> <def_x003a_label>visit Number</def_x003A_Label> <def_x003a_displayformat>8</def_x003a_displayformat> </ItemDef>

23 Global Ordering Of Elements Case Report Tabulation Data Definition Specification (define.xml) Standards Version CDISC Page 44 of 45 ODM Study Global Variables MetDataVersion ItemGroupDef ItemRef Def:leaf Def:title Def:ValueListRef ItemDef CodeListRef CodeList CodeListItem Decode TranslatedText ExternalCodeList

24 ITEMREF <xs:element name="itemref" type="odmcomplextypedefinition-itemref"/> <xs:complextype name="odmcomplextypedefinition-itemref"> <xs:sequence> <xs:group ref="itemrefelementextension" minoccurs="0" maxoccurs="unbounded"/> </xs:sequence> <xs:attributegroup ref="itemrefattributedefinition"/> <xs:attributegroup ref="itemrefattributeextension"/> </xs:complextype>

25 ItemRefAttributeDefinition <xs:attributegroup name="itemrefattributedefinition"> <xs:attribute name="itemoid" type="oidref" use="required"/> <xs:attribute name="ordernumber" type="integer"/> <xs:attribute name="mandatory" type="yesorno" use="required"/> <xs:attribute name="keysequence" type="integer"/> <xs:attribute name="imputationmethodoid" type="oidref"/> <xs:attribute name="role" type="xs:nmtokens"/> <xs:attribute name="rolecodelistoid" type="oidref"/> </xs:attributegroup> <ItemRef> <ID>1</ID> <ItemOID>USUBJID</ItemOID> <OrderNumber>1</OrderNumber> <Mandatory>Yes</Mandatory> <Role>Identifier</Role> </ItemRef> <

26 <ItemRef> <ID>1</ID> <ItemOID>USUBJID</ItemOID> <OrderNumber>1</OrderNumber> <Mandatory>Yes</Mandatory> <Role>Identifier</Role> </ItemRef> <

27 <xs:attributegroup name="itemdataattributedefinition"> <xs:attribute name="itemoid" type="oidref" use="required"/> <xs:attribute name="transactiontype" type="transactiontype"/> <xs:attribute name="value" type="value"/> <xs:attribute name="isnull" type="yesonly"/> </xs:attributegroup> ITEMDATA <xs:element name="itemdata" type="odmcomplextypedefinition-itemdata"/> <xs:complextype name="odmcomplextypedefinition-itemdata"> <xs:sequence> <xs:element ref="auditrecord" minoccurs="0"/> <xs:element ref="signature" minoccurs="0"/> <xs:element ref="measurementunitref" minoccurs="0"/> <xs:element ref="annotation" minoccurs="0" maxoccurs="unbounded"/> <xs:group ref="itemdataelementextension" minoccurs="0" maxoccurs="unbounded"/> </xs:sequence> <xs:attributegroup ref="itemdataattributedefinition"/> <xs:attributegroup ref="itemdataattributeextension"/> </xs:complextype>

28 And Finally the Data <VIT> <STUDYID>1234C00001</STUDYID> <SITEID>1</SITEID> <USUBJID>18</USUBJID> <VISITNUM>1</VISITNUM> <VSDTC> T00:00:00</VSDTC> <VSTESTCD>HRSUP</VSTESTCD> <Field7>100</Field7> <DOMAIN>VIT</DOMAIN> </VIT>

29 XML Mapping

30 Summary and Questions Mapping Options Common Problems Potential further use of XML