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Creating Define-XML version 2 including Analysis Results Metadata
with the SAS® Clinical Standards ToolkitLex Jansen
Principal Software Developer @ SAS
PharmaSUG 2016
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Agenda
Why Analysis Results Metadata?
Analysis Results Metadata in Detail
SAS Support for Analysis Results Metadata
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• Traceability is a fundamental principle in ADaM:• It enables the reader to understand the data flow from collection to
SDTM and ADaM to Analysis Results• Analysis Results Metadata provides traceability from results
in a statistical display to the data in the analysis datasets• Analysis Results Metadata includes:
• Identification of critical analysis displays and particular results• Details on analysis performed (reason, underlying analysis dataset(s),
analysis variables, selection criteria, documentation, programming statements)
• Facilitates documentation and reproduction of the analysis results
• Not needed - or advisable - for every analysis in a submission
Why Analysis Results Metadata ?
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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2005 - CRT-DDS v1.0Focus on SDTM metadata
2008 - CDISC SDTM/ADaM Pilot Project
2009 - ADaM v2.1 Model ADaM specific metadata requirements(Parameter VLM, Analysis Results Metadata)
2009 - CDISC/FDA Integrated Data Pilot2013 - Updated CDISC SDTM/ADaM Pilot
2013: Define-XML v2.0officially applicable for ADaM)2015 - Analysis Results Metadata v1.0 for Define-XML v2
Including draft Analysis Results Metadata
based on CRT-DDS v1.0)
Including draft Analysis Results Metadata
based on CRT-DDS v1.0)
ADaM Metadata and Define-XML History
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ADaM Results Metadata – Pilot 1 (2008)
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ADaM Results Metadata – Pilot 2 (2009)
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ADaM Results Metadata – Pilot 1 Update (2013)
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• No formal specification• Draft XML schemas (or no schema at all)• Based on CRT-DDS 1.0 (Define-XML 1.0)
• Limited document referencing capabilities• No WhereClause support• Limited comment support
ADaM Results Metadata – Pilots
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ADaM Results Metadata – 3 Pilots – 3 XML formats
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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• Formal Technical Specifications
ADaM Results Metadata v1 for Define-XML v2
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• For Define-XML v2 only• Utilizes various Define-XML v2 constructs
• WhereClause• Document reference support• Comment support
• It is recommended to move to Define-XML v2
ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2ODM
Study
GlobalVariables
MetaDataVersion
def:SupplementalDoc
def:ValueListDef
def:WhereClauseDef
ItemGroupDef
ItemDef
CodeList
MethodDef
def:CommentDef
def:leaf
arm:AnalysisResultDisplays
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• Updated Define-XML v2 XSL Stylesheet• Works for ADaM, SDTM, SEND (with or without Results
Metadata)• Bug fixes• Many improvements for linking to external PDF documents with
physical page references or named destinations
ADaM Results Metadata v1 for Define-XML v2
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PMDA – New Study Data Technical Conformance Guide (April 27, 2015) *
* PMDA Technical conformance guide (in Japanese) http://www.pmda.go.jp/files/000204728.pdfProvisional Translation (as of July 2015) http://www.pmda.go.jp/files/000206449.pdf
• In order for the review of clinical study data to progress smoothly, it is important that the relationship between the analysis results shown in the application documents and the analysis datasets is easily understandable. Therefore, the definition documents of the ADaM datasets should preferably include Analysis Results Metadata ...
• For the format of the Analysis Results Metadata, the applicant should refer to the Analysis Results Metadata Specification for Define-XML by CDISC to the extent possible, but if it is difficult to include it into the definition document, it is possible to submit it as a separated file in PDF format.
ADaM Results Metadata v1 for Define-XML v2
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What’s Next?
• The ADaM Metadata Team is developing validation checks for The Analysis Results Metadata extension
• These can then be implemented by validating applications (Pinnacle 21, ...)
• But you can already validate your Define-XML v2 (+ ARM) against the XML Schema (you should!)
• Implementations (SAS Clinical Standards Toolkit 1.7.1 – HotFix)
• FDA reference in the Data Standards Catalog?
ADaM Results Metadata v1 for Define-XML v2
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Analysis Results Metadata for Define-XML v2in Detail
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• Display Identifier• Display name• Result Identifier• Parameter (Code/Decode)• Analysis Variable• Reason• Dataset• Selection Criteria• Documentation• Programming Statements
* Version 2.1 of the Analysis Data Model (ADaM) Document, December 17, 2009
ADaM Results Metadata in the ADaM Model (2009)
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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ADaM Results Metadata v1 for Define-XML v2
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SAS Support for Analysis Results Metadata for Define-XML v2
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SAS Clinical Standards Toolkit 1.7
Introduction
• Framework to primarily support Clinical Research
activities (CDISC).
• Designed as an integral part of Clinical Data Integration
(CDI)
• Available to all licensed SAS customers as open source
SAS Macros and metadata at no additional charge.
• Framework: designed to customize and extend
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SAS Clinical Standards Toolkit 1.7
Introduction
• A collection of metadata and "tools", providing an initial
set of standards and functionality that is evolving and
growing with updates and releases.
• Provides SAS representation of published standards as
SAS data sets and catalogs• Contents standards: SDTM, ADaM, SEND
• XML standards: Define-XML, Dataset-XML and ODM
• Controlled Terminology (CDISC/NCI)
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SAS Clinical Standards Toolkit 1.7
Introduction
• Supported CDISC standards in Toolkit 1.7:• SDTM 3.1.2, 3.1.3 and 3.2
• ADaM 2.1 (ADSL, Basic Data Structure, ADAE and ADTTE)
• CDASH 1.1 Domain definitions
• SEND 3.0 (initial implementation)
• CRT-DDS 1.0 (Define-XML - Create / Import / Validate)
• Define-XML 2.0 (Create / Import / Validate)
• Dataset-XML 1.0 (Create / Import / Validate)
• ODM 1.3.0, 1.3.1 - Read / Write / Validate
• NCI CDISC Controlled Terminology (June 2014)
(import/export of ODM XML through CT 1.0 standard)
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SAS Clinical Standards Toolkit 1.7
Introduction
• Hotfix for Toolkit 1.7 (CST 1.7.1):• Support for Analysis Results Metadata v1.0 for Define-XML v2
• Implemented as an update to the existing CDISC-DEFINE-XML
2.0.0 standard
• CST 1.7.1 expected availability May/June 2016.
• CST is available at no additional charge to currently
licensed SAS customers.
• Contact your SAS Account Representative concerning
availability
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SAS Clinical StandardsToolkit 1.7
SAS Data Model for Define-XML
• SAS Clinical Standards Toolkit v1.7 provides a data model that represents the Define-XML v2 format in SAS data sets
• Patterned to match the XML element and attribute structure of the ODM XML format• XML element table• XML attribute column
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SAS Clinical Standards
Toolkit 1.7.1SAS Data Model for Define-XML
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Define.xml
cube
39 Define-XMLSAS data sets
XML Map
JavaObj
JavaObj
Data _null_
SAS Clinical Standards Toolkit and Define-XML - Process Flow
7 Source MetadataSAS data sets
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SAS Clinical Standards
Toolkit 1.7.1From Study Source Metadata to Define-XML v2
Internal SAS representation of
Define-XML
(54 SAS data sets*)
StudyMetadata
Table Metadata
Column Metadata
Value Level Metadata
CodelistMetadata
Document Metadata
Analysis Results
Metadata
XMLValidation Process
*Define-XML v2 uses 39 data sets
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SAS Clinical Standards
Toolkit 1.7.1From Study Source Metadata to Define-XML v2
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SAS Clinical Standards
Toolkit 1.7.1
Creating Source Metadata for Define-XML v2:Mapping your Metadata
Internal SAS representation of Define-XML
StudyMetadata
Table Metadata
Column Metadata
Value Level
Metadata CodelistMetadata
Document Metadata
Analysis Results
Metadata
Excel
MDR
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SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_study- One record per study
ADaM example
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SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_tables- One record per table
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SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_columns- One record per table, column
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SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_values- One record per table, column, whereclause
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SAS Clinical Standards
Toolkit 1.7.1
WhereClausesSyntax defined with Railroad DiagramChecked in CST with a Regular Expression
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1
WhereClausesSyntax defined with Railroad DiagramChecked in CST with a Regular Expression
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_codelists- One record per CodeList, Item
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_analysisresults (ADaM)- One record per DisplayIdentifier, ResultIdentifier, Table
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1
Source Metadata - source_analysisresults (ADaM)- One record per DisplayIdentifier, ResultIdentifier, Table
Whitespace and "\n" or Carriage Return ('0D'x) in Code metada will be honored in Define-XML file and HTML display.
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1Source Metadata - source_documents (ADaM)- One record per table, column, whereclauseor- One record per DisplayIdentifier, ResultIdentifier
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1Creating Source Metadata for Define-XML v2
• %define_createsrcmetafromsaslib - derives initial source metadata files from a data library that contains SAS study domain data sets.Uses SDTM/ADaM/SEND standards metadata to fill in gaps.• Can not create study metadata like: Origin, Derivation, Comment, Value
Level Metadata• %define_createsrcmetafromdefine - derives source metadata files
from a data library that contains the SAS representation from Define-XML V2.0 file, imported via %define_read.
• %cstutilmigratecrtdds2define - migrates source metadata data sets from CRT-DDS v1.0 to Define-XML v2.0
• %cstutilgetncimetadata - create the source_codelists dataset from• a list of format catalogs that define the study formats• a SAS data set that contains CDISC/NCI codelist metadata (imported from
CDISC/NCI ODM XML file)
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Copyright © 2014, SAS Institute Inc. All rights reserved.
SAS Clinical Standards
Toolkit 1.7.1Define-XML v2 with Analysis Results Metadata
http://blueballfixed.ytmnd.com/
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