SAS Clinical Standards Toolkit: define.xml and Value Level ... · lang: CHAR(128)...
Transcript of SAS Clinical Standards Toolkit: define.xml and Value Level ... · lang: CHAR(128)...
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS® Clinical Standards Toolkit: define.xml and Value Level Metadata
Lex Jansen, presented by Gene Lightfoot SAS Institute Inc.
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Agenda
§ What is define.xml (CRT-DDS)?
§ The CRT-DDS SAS Data Model
§ What is SAS Clinical Standards Toolkit (CST)?
§ Create define.xml from SDTM 3.1.2 metadata
§ Implementing Value Level Metadata
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What is the define.xml (CRT-DDS)? § Case Report Tabulation Data Specification (CRT-DDS,
or define.xml): Production version: 1.0.0 CRT-DDS 1.0.0 is the only production version right now
§ Extension of the CDISC Operational Data Model (ODM), an XML specification to facilitate the archival and interchange of the metadata and data for clinical research
§ Maintained by CDISC’s XML Technologies Team (formerly known as the ODM team)
§ New Define-XML v2.0 released soon with additional metadata support (based on ODM 1.3.1)
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the define.xml (CRT-DDS)?
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What is the define.xml (CRT-DDS)? The specifications
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What is the define.xml (CRT-DDS)?
Metadata Submission Guidelines
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What is the define.xml (CRT-DDS)? XML Schemas in Simple Terms § Defines elements, attributes, data types etc. and their
relationships § Provides the specification for an XML document
§ Enables validation of XML documents
§ Important: an XML schema is not able to verify all business rules in the specification!!
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the define.xml (CRT-DDS)?
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Copyright © 2011, SAS Institute Inc. All rights reserved.
define.xml – content - metadata
§ Domain Level metadata § Variable Level metadata § Value Level metadata § Code List metadata § Computational Methods metadata § Documents metadata (aCRF)
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Copyright © 2011, SAS Institute Inc. All rights reserved.
define.xml – Domain level metadata
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define.xml – Variable level metadata
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What is the define.xml (CRT-DDS)? • define.xml contains metadata and is machine readable • define.xml becomes human readable with a stylesheet • The stylesheet is for display, but is not the standard.
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the define.xml (CRT-DDS)? define.xml becomes human readable with an XSL stylesheet
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What is the define.xml (CRT-DDS)? … and looks even fancier with a different stylesheet
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Copyright © 2011, SAS Institute Inc. All rights reserved.
The CRT-DDS SAS Data Model
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The CRT-DDS SAS Data Model
§ define.xml has a deep hierarchy
§ define.xml contains many relations
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The CRT-DDS SAS Data Model § SAS provides data model that represents CRT-DDS
Version 1.0 format in 39 SAS data sets 20 of these are typically used for the define.xml (*)
§ Patterned to match the XML element and attribute structure of the define.xml file
§ XML element à SAS dataset XML attribute à SAS variable
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Copyright © 2011, SAS Institute Inc. All rights reserved.
The CRT-DDS SAS Data Model
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The CRT-DDS SAS Data Model
DefineDocument
*PK FileOID: CHAR(128) CreationDateTime: CHAR(24) Archival: CHAR(3) AsOfDateTime: CHAR(24) Description: CHAR(2000)* FileType: CHAR(13) Granularity: CHAR(15) Id: CHAR(128) ODMVersion: CHAR(2000) Originator: CHAR(2000) PriorFileOID: CHAR(128) SourceSystem: CHAR(2000) SourceSystemVersion: CHAR(2000)
+ PK_DefineDocument(FileOID)
Study
*PK OID: CHAR(128)* StudyName: CHAR(128)* StudyDescription: CHAR(2000)* ProtocolName: CHAR(128)*FK FK_DefineDocument: CHAR(128)
+ FK_Study_DefineDocument(FK_DefineDocument)+ PK_Study(OID)
MeasurementUnits
*PK OID: CHAR(128)* Name: CHAR(128)*FK FK_Study: CHAR(128)
+ FK_MeasurementUnits_Study(FK_Study)+ PK_MeasurementUnits(OID)
MUTranslatedText
TranslatedText: CHAR(2000) lang: CHAR(128)*FK FK_MeasurementUnits: CHAR(128)
+ FK_MUTranslatedT_MeasurementUn(FK_MeasurementUnits)
MetaDataVersion
*PK OID: CHAR(128)* Name: CHAR(128) Description: CHAR(2000) IncludedOID: CHAR(128) IncludedStudyOID: CHAR(128)* DefineVersion: CHAR(2000)* StandardName: CHAR(2000)* StandardVersion: CHAR(2000)*FK FK_Study: CHAR(128)
+ FK_MetaDataVersion_Study(FK_Study)+ PK_MetaDataVersion(OID)
AnnotatedCRFs
DocumentRef: CHAR(2000)*FK leafID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_AnnotatedCRFs_MDVLeaf(leafID)+ FK_AnnotatedCRFs_MetaDataVers(FK_MetaDataVersion)
SupplementalDocs
DocumentRef: CHAR(2000)*FK leafID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_SupplementalD_MetaDataVersi(FK_MetaDataVersion)+ FK_SupplementalDocs_MDVLeaf(leafID)
MDVLeaf
*PK ID: CHAR(128) href: CHAR(512)*FK FK_MetaDataVersion: CHAR(128)
+ FK_MDVLeaf_MetaDataVersion(FK_MetaDataVersion)+ PK_MDVLeaf(ID)
MDVLeafTitles
title: CHAR(2000)*FK FK_MDVLeaf: CHAR(128)
+ FK_MDVLeafTitles_MDVLeaf(FK_MDVLeaf)
ComputationMethods
*PK OID: CHAR(128) method: CHAR(2000)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ComputationMe_MetaDataVersi(FK_MetaDataVersion)+ PK_ComputationMethods(OID)
ValueLists
*PK OID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ValueLists_MetaDataVersion(FK_MetaDataVersion)+ PK_ValueLists(OID) ValueListItemRefs
*FK ItemOID: CHAR(128) OrderNumber: NUMBER(8,2)* Mandatory: CHAR(3) KeySequence: NUMBER(8,2) FK ImputationMethodOID: CHAR(128) Role: CHAR(128) FK RoleCodeListOID: CHAR(128)*FK FK_ValueLists: CHAR(128)
+ FK_ValueListItem_ImputationMet(ImputationMethodOID)+ FK_ValueListItemRefs_ItemDefs(ItemOID)+ FK_ValueListItemRef_ValueLists(FK_ValueLists)+ FK_ValueListItemRefs_CodeLists(RoleCodeListOID)
ProtocolEventRefs
* Mandatory: CHAR(3) OrderNumber: NUMBER(8,2)*FK StudyEventOID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ProtocolEvent_MetaDataVersi(FK_MetaDataVersion)+ FK_ProtocolEvent_StudyEventDef(StudyEventOID)
StudyEventDefs
*PK OID: CHAR(128) Category: CHAR(2000)* Name: CHAR(128)* Repeating: CHAR(3)* Type: CHAR(11)*FK FK_MetaDataVersion: CHAR(128)
+ FK_StudyEventDef_MetaDataVersi(FK_MetaDataVersion)+ PK_StudyEventDefs(OID)
StudyEventFormRefs
*FK FormOID: CHAR(128)* Mandatory: CHAR(3) OrderNumber: NUMBER(8,2)*FK FK_StudyEventDefs: CHAR(128)
+ FK_StudyEventFor_StudyEventDef(FK_StudyEventDefs)+ FK_StudyEventFormRefs_FormDefs(FormOID)
FormDefs
*PK OID: CHAR(128)* Name: CHAR(128)* Repeating: CHAR(3)*FK FK_MetaDataVersion: CHAR(128)
+ FK_FormDefs_MetaDataVersion(FK_MetaDataVersion)+ PK_FormDefs(OID)
FormDefItemGroupRefs
*FK ItemGroupOID: CHAR(128)* Mandatory: CHAR(3) OrderNumber: NUMBER(8,2)*FK FK_FormDefs: CHAR(128)
+ FK_FormDefItemGr_ItemGroupDefs(ItemGroupOID)+ FK_FormDefItemGroupRe_FormDefs(FK_FormDefs)+ PK_FormDefItemGroupDefs(ItemGroupOID)
FormDefArchLayouts
*PK OID: CHAR(128)* PdfFileName: CHAR(512) FK PresentationOID: CHAR(128)*FK FK_FormDefs: CHAR(128)
+ FK_FormDefArchLay_Presentation(PresentationOID)+ FK_FormDefArchLayouts_FormDefs(FK_FormDefs)+ PK_FormDefArchLayouts(OID)
ItemGroupDefs
*PK OID: CHAR(128)* Name: CHAR(128)* Repeating: CHAR(3) IsReferenceData: CHAR(3) SASDatasetName: CHAR(8) Domain: CHAR(2000) Origin: CHAR(2000) Role: CHAR(128) Purpose: CHAR(2000) Comment: CHAR(2000)* Label: CHAR(2000) Class: CHAR(2000) Structure: CHAR(2000) DomainKeys: CHAR(2000)* ArchiveLocationID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ItemGroupDefs_MetaDataVers(FK_MetaDataVersion)+ PK_ItemGroupDefs(OID)
ItemGroupDefitemRefs
*FK ItemOID: CHAR(128)* Mandatory: CHAR(3) OrderNumber: NUMBER(8,2) KeySequence: NUMBER(8,2) FK ImputationMethodOID: CHAR(128) Role: CHAR(128) FK RoleCodeListOID: CHAR(128)*FK FK_ItemGroupDefs: CHAR(128)
+ FK_ItemGroupDefi_ImputationMet(ImputationMethodOID)+ FK_ItemGroupDefi_ItemGroupDefs(FK_ItemGroupDefs)+ FK_ItemGroupDefitemR_CodeLists(RoleCodeListOID)+ FK_ItemGroupDefitemRef_ItemDefs(ItemOID)
ItemGroupAliases
* Context: CHAR(2000)* Name: CHAR(2000)*FK FK_ItemGroupDefs: CHAR(128)
+ FK_ItemGroupAlia_ItemGroupDefs(FK_ItemGroupDefs)
ItemGroupLeaf
*PK ID: CHAR(128) href: CHAR(512)*FK FK_ItemGroupDefs: CHAR(128)
+ FK_ItemGroupLeaf_ItemGroupDefs(FK_ItemGroupDefs)+ PK_ItemGroupLeaf(ID)
ItemGroupLeafTitles
title: CHAR(2000)*FK FK_ItemGroupLeaf: CHAR(128)
+ FK_ItemGroupLeaf_ItemGroupLeaf(FK_ItemGroupLeaf)
ItemDefs
*PK OID: CHAR(128)* Name: CHAR(128)* DataType: CHAR(8) Length: NUMBER(8,2) SignificantDigits: NUMBER(8,2) SASFieldName: CHAR(8) SDSVarName: CHAR(8) Origin: CHAR(2000) Comment: CHAR(2000) FK CodeListRef: CHAR(128) Label: CHAR(2000) DisplayFormat: CHAR(2000) FK ComputationMethodOID: CHAR(128)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ItemDefs_CodeLists(CodeListRef)+ FK_ItemDefs_ComputationMethods(ComputationMethodOID)+ FK_ItemDefs_MetaDataVersion(FK_MetaDataVersion)+ PK_ItemDefs(OID)
ItemQuestionTranslatedText
TranslatedText: CHAR(2000) lang: CHAR(17)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemQuestionTransl_ItemDefs(FK_ItemDefs)
ItemQuestionExternal
Dictionary: CHAR(2000) Version: CHAR(2000) Code: CHAR(2000)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemQuestionExtern_ItemDefs(FK_ItemDefs)
ItemMURefs
*FK MeasurementUnitOID: CHAR(128)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemMURefs_ItemDefs(FK_ItemDefs)+ FK_ItemMURefs_MeasurementUnits(MeasurementUnitOID)
ItemRangeChecks
*PK OID: CHAR(128)* Comparator: CHAR(5)* SoftHard: CHAR(4) FK MURefOID: CHAR(128)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemRangeChec_MeasurementUn(MURefOID)+ FK_ItemRangeChecks_ItemDefs(FK_ItemDefs)+ PK_ItemRangeChecks(OID)
ItemRangeCheckValues
CheckValue: CHAR(512)*FK FK_ItemRangeChecks: CHAR(128)
+ FK_ItemRangeChec_ItemRangeChec(FK_ItemRangeChecks)
RCErrorTranslatedText
TranslatedText: CHAR(2000) lang: CHAR(17)*FK FK_ItemRangeChecks: CHAR(128)
+ FK_RCErrorTransl_ItemRangeChec(FK_ItemRangeChecks)
ItemRole
Name: CHAR(2000)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemRole_ItemDefs(FK_ItemDefs)
ItemAliases
* Context: CHAR(2000)* Name: CHAR(2000) FK FK_ItemDefs: CHAR(128)
+ FK_ItemAliases_ItemDefs(FK_ItemDefs)
ItemValueListRefs
*FK ValueListOID: CHAR(128)*FK FK_ItemDefs: CHAR(128)
+ FK_ItemValueListRef_ValueLists(ValueListOID)+ FK_ItemValueListRefs_ItemDefs(FK_ItemDefs)
CodeLists
*PK OID: CHAR(128)* Name: CHAR(128)* DataType: CHAR(7) SASFormatName: CHAR(8)*FK FK_MetaDataVersion: CHAR(128)
+ FK_CodeLists_MetaDataVersion(FK_MetaDataVersion)+ PK_CodeLists(OID)
ExternalCodeLists
Dictionary: CHAR(2000) Version: CHAR(2000)*FK FK_CodeLists: CHAR(128)
+ FK_ExternalCodeLists_CodeLists(FK_CodeLists)
CodeListItems
*PK OID: CHAR(128)* CodedValue: CHAR(512)*FK FK_CodeLists: CHAR(128) Rank: NUMBER(8,2)
+ FK_CodeListItems_CodeLists(FK_CodeLists)+ PK_CodeListItems(OID)
CLItemDecodeTranslatedText
TranslatedText: CHAR(2000) lang: CHAR(17)*FK FK_CodeListItems: CHAR(128)
+ FK_CLItemDecodeT_CodeListItems(FK_CodeListItems)
ImputationMethods
*PK OID: CHAR(128) method: CHAR(2000)*FK FK_MetaDataVersion: CHAR(128)
+ FK_ImputationMet_MetaDataVersi(FK_MetaDataVersion)+ PK_ImputationMethods(OID)
Presentation
*PK OID: CHAR(128) presentation: CHAR(2000) lang: CHAR(17)*FK FK_MetaDataVersion: CHAR(128)
+ FK_Presentation_MetaDataVersi(FK_MetaDataVersion)+ PK_Presentation(OID)
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the SAS Clinical Standards Toolkit (CST)?
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the SAS Clinical Standards Toolkit?
§ Framework to primarily support clinical research activities.
§ Initially focusing on standards as defined by CDISC, but not limited to CDISC.
§ A collection of “tools”, providing an initial set of standards and functionality that is evolving and growing with updates and releases.
§ Designed as an integral part of Clinical Data Integration (CDI), but is available to all SAS users as open source SAS Macros.
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Copyright © 2011, SAS Institute Inc. All rights reserved.
What is the SAS Clinical Standards Toolkit?
§ CDISC SDTM models available 3.1.1 and 3.1.2
§ ADaM support
§ Controlled Terminology (NCI)
§ CRT-DDS (define.xml) capability
§ ODM 1.3 import/export
§ Flexible: customizable to fit various standards (there is no 'magic bullet' !)
§ Available at no additional charge for SAS/Base customers
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SDTM metadata à define.xml
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CST typical program § Define global macro variables ("properties")
§ %cst_setStandardProperties(_cstStandard=CST-FRAMEWORK,_cstSubType=initialize);
§ Define inputs / outputs (libnames, filenames, SAS autocall macros, …) § 1. Create SASReferences dataset § 2. %cstutil_processsetup();
(default: use WORK.SASReferences
§ Run process specific macro: %crtdds_sdtmtodefine %crtdds_validate %crtdds_write %crtdds_xmlvalidate %crtdds_read
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CRT-DDS macros for creating define.xml § %crtdds_sdtmtodefine –
Create empty CRT-DDS SAS data sets and populates them based on SDTM sourcemetadata
§ %crtdds_validate – Validate CRT-DDS SAS data sets
§ %crtdds_write – Create define.xml from CRT-DDS SAS data sets
§ %crtdds_xmlvalidate – Validate define.xml against XML schema
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CRT-DDS macros for creating define.xml
§ %crtdds_sdtmtodefine – Create 39 empty CRT-DDS SAS data sets and populates a selection of them based on SDTM sourcemetadata
§ 20 of the 39 CRT-DDS datasets are needed for creating the define.xml for submission
§ CST 1.4: %crtdds_sdtmtodefine will populate 12 of these data sets (no Value Level Metadata)
§ CST 1.5: %crtdds_sdtmtodefine will populate all of the 20 data sets using more SDTM source metadata (including Value Level Metadata)
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SDTM to define.xml
SAS representation of
CRT-DDS
(39 SAS data sets)
Table Study
Metadata
SDTM Study Data
Column Study
Metadata
Other Study
Metadata
- Value Level Metadata - aCRF reference
…
Validation Process
XML Validation Process
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SDTM to define.xml – Source metadata
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Value Level Metadata
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Value Level Metadata § Update the CRT-DDS SAS datasets to get Value level metadata
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Value Level Metadata
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SDTM to define.xml
SAS representation of
CRT-DDS
(39 SAS data sets)
Table Study
Metadata
SDTM Study Data
Column Study
Metadata
Other Study
Metadata
- Value Level Metadata - aCRF reference
…
Validation Process
Adding Value Level Metadata from source_values SAS data set
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Value Level Metadata § Update the CRT-DDS SAS datasets:
» Value level metadata
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Value Level Metadata § Update the CRT-DDS SAS datasets to get Value level metadata
» Manual process in 1.4 » Automated in 1.5
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Clinical Standards Toolkit: resources http://support.sas.com/rnd/base/cdisc/cst/index.html
CST 1.4 Value Level Metadata example code
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Clinical Standards Toolkit: resources http://support.sas.com/rnd/base/cdisc/cst/index.html
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Clinical Standards Toolkit: resources
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Copyright © 2011, SAS Institute Inc. All rights reserved.
SAS Clinical Standards Toolkit: resources
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Copyright © 2011, SAS Institute Inc. All rights reserved.
Questions ?