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1© Assero Limited, 2010

Introduction to define.xml

Dave Iberson-Hurst27th May 2010ESUG Webinar

© Assero Limited, 2010


Outline


Outline

• Introduction

• Purpose of define.xml

• XML

• How define works

• FAQ

• Q&A


Introduction


Purpose


Purpose

• Describes– What is included within the data

– Where did the data come from

– Derivations, code lists, annotated PDF etc to aid understanding

• Machine Readable

• Human Readable (after processing)

• To aid/inform the reviewer, unambiguous communication


Submission & eCTD

http://www.fda.gov/ForIndustry/DataStandards/StudyDataStandards/default.htm

Revision 2, June 2008


XML


Dark Side of the Moon<CDCollection>

<CD TotalTime="45.02">

<Artist>Pink Floyd</Artist>

<Title>Dark Side of the Moon</Title>

<Track Label="1a">Speak To Me</Track>

<Track Label="1b">Breathe</Track>

<Track Label="2">On the Run</Track>

<Track Label="3">Time</Track>

<Track Label="4">The Great Gig in the Sky</Track>

<Track Label="5">Money</Track>

<Track Label="6">Us and Them</Track>

<Track Label="7">Any Colour You Like</Track>

<Track Label="8">Brain Damage</Track>

<Track Label="9">Eclipse</Track>

</CD>

</CDCollection>


Dark Side of the Moon<CDCollection>

<CD TotalTime="45.02">

<Artist>Pink Floyd</Artist>

<Title>Dark Side of the Moon</Title>

<Track Label="1a">Speak To Me</Track>

<Track Label="1b">Breathe</Track>

<Track Label="2">On the Run</Track>

<Track Label="3">Time</Track>

<Track Label="4">The Great Gig in the Sky</Track>

<Track Label="5">Money</Track>

<Track Label="6">Us and Them</Track>

<Track Label="7">Any Colour You Like</Track>

<Track Label="8">Brain Damage</Track>

<Track Label="9">Eclipse</Track>

</CD>

</CDCollection>

Element

Attribute

Structure


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


Transformations• XSL – Extensible Stylesheet Language

• Used to transform an XML document

• Requires a tool known as XSLT processor

• Focuses on presentation while XML focuses on content and structure

XSLTProcessor

<?xml version="1.0"?>

<xsl:stylesheet version="1.0" ...

XML Document New Document

XSL Document


How define.xml Works


Define Specificationhttp://www.cdisc.org/define-xml


Overall Structure

MetaDataVersion

ItemGroupDef - Domains

ItemDef - Variables

CodeList - Code lists

ODM

Study

GlobalVariables

Links and Variable Level


Overall Structure<ODM

xmlns="http://www.cdisc.org/ns/odm/v1.2"

xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xmlns:xlink="http://www.w3.org/1999/xlink"

xmlns:def="http://www.cdisc.org/ns/def/v1.0"

xsi:schemaLocation="http://www.cdisc.org/ns/odm/v1.2 define1-0-0.xsd"

FileOID="Study1234"

ODMVersion="1.2"

FileType="Snapshot"

CreationDateTime="2004-07-28T12:34:13-06:00">

<Study OID="1234">

<GlobalVariables>

<StudyName>1234</StudyName>

<StudyDescription>1234 Data Definition</StudyDescription>

<ProtocolName>1234</ProtocolName>

</GlobalVariables>

<MetaDataVersion OID="CDISC.SDTM.3.1.0"

Name="Study 1234, Data Definitions"

Description="Study 1234, Data Definitions"

def:DefineVersion="1.0.0"

def:StandardName="CDISC SDTM"

def:StandardVersion="3.1.0">

... All the content is here ...

</MetaDataVersion>

</Study>

</ODM>


Domain Meta Data

• Dataset Name – 2 character prefix

• Description – The description for the domain

• Location – Folder and filename

• Structure – level of detail provided

• Purpose – Purpose

• Key Fields – Used to identify and index records


Domain Meta Data

<ItemGroupDef OID="DM"

Name="DM" Repeating="No"

IsReferenceData="No"

Purpose="Tabulation"

def:Label="Demographics"

def:Structure="One record per event per subject"

def:DomainKeys="STUDYID, USUBJID"

def:Class="Special Purpose"

def:ArchiveLocationID="Location.DM">

<ItemRef ItemOID="STUDYID"

OrderNumber="1" Mandatory="Yes" Role="Identifier"/>

<ItemRef ItemOID="DOMAIN"


<ItemRef ItemOID="USUBJID"


... More itemRefs Here ...

</ItemGroupDef>


Domain Meta Data

<ItemGroupDef OID="DM"

Name="DM" Repeating="No"

IsReferenceData="No"

Purpose="Tabulation"

def:Label="Demographics"

def:Structure="One record per event per subject"

def:DomainKeys="STUDYID, USUBJID"

def:Class="Special Purpose"

def:ArchiveLocationID="Location.DM">

<ItemRef ItemOID="STUDYID"


<ItemRef ItemOID="DOMAIN"


<ItemRef ItemOID="USUBJID"


... More itemRefs Here ...

</ItemGroupDef>


Variable Meta Data

• Variable Name – 8 character name• Variable Description – The description• Type – Character String or Numeric• Format – Identifies controlled terminology or

presentation• Origin – Indicator of variable origin – CRF or Derived • Role – How variable is used within a dataset (ID, Topic,

Timing, Qualifier)• Comments – Used by sponsor to assist reviewer in

interpreting the data• Label – Variable Label• References – Computational Method, Code Lists & Value

Lists


Variable Meta Data<ItemDef OID="DOMAIN"

Name="DOMAIN"

DataType="text"

Length="2"

Origin="CRF Page"

Comment="DOMAIN ABBREVIATION"

def:Label="DOMAIN ABBREVIATION">

</ItemDef>

<ItemDef OID="STUDYID"

Name="STUDYID"

DataType="text"

Length="8"

Origin="CRF Page"

Comment="Demographics CRF Page 4"

def:Label="STUDY IDENTIFIER">

</ItemDef>

<ItemDef OID="SUBJID"

Name="SUBJID"

DataType="text"

Length="60"

Origin="CRF Page"


def:Label="SUBJECT IDENTIFIER">

</ItemDef>


Variable Meta Data<ItemDef OID="DOMAIN"

Name="DOMAIN"

DataType="text"

Length="2"

Origin="CRF Page"

Comment="DOMAIN ABBREVIATION"

def:Label="DOMAIN ABBREVIATION">

</ItemDef>

<ItemDef OID="STUDYID"

Name="STUDYID"

DataType="text"

Length="8"

Origin="CRF Page"


def:Label="STUDY IDENTIFIER">

</ItemDef>

<ItemDef OID="SUBJID"

Name="SUBJID"

DataType="text"

Length="60"

Origin="CRF Page"


def:Label="SUBJECT IDENTIFIER">

</ItemDef>


Variable Meta Data <ItemDef OID="VS.VSTESTCD.FRAME“

Name="FRAME"

DataType="float“

Length="8“

SignificantDigits="1"

Origin="CRF Page“

Comment="Vital Signs CRF Page 4"

def:Label="Frame">

<CodeListRef CodeListOID="FRAME"/>

</ItemDef>

<CodeList OID="FRAME" Name="FRAME" DataType="text">

<CodeListItem CodedValue="S">

<Decode><TranslatedText xml:lang="en">Small</TranslatedText></Decode>

</CodeListItem>

<CodeListItem CodedValue="M">

<Decode><TranslatedText xml:lang="en">Medium</TranslatedText></Decode>

</CodeListItem>

<CodeListItem CodedValue="L">

<Decode><TranslatedText xml:lang="en">Large</TranslatedText></Decode>

</CodeListItem>

<CodeListItem CodedValue="XL">

<Decode><TranslatedText xml:lang="en">Extra large</TranslatedText></Decode>

</CodeListItem>

</CodeList>


Value Level Meta Data

• SDS Version 3 makes use of "Tall Skinny" structure. Findings domains consist of – Test/Result pairs (xxTESTCD/xxORRES)

• Interpretation of information in the Results depends on the value of xxTESTCD

• Results for different tests may have different data types, formats, labels, etc



<def:ValueListDef OID="ValueList.VS.VSTESTCD">

<ItemRef ItemOID="VS.VSTESTCD.FRAME"

OrderNumber="10" Mandatory="No"/>

<ItemRef ItemOID="VS.VSTESTCD.HTRAW"


<ItemRef ItemOID="VS.VSTESTCD.WTRAW"


<ItemRef ItemOID="VS.VSTESTCD.MEANBP"


</def:ValueListDef>



<def:ValueListDef OID="ValueList.VS.VSTESTCD">

<ItemRef ItemOID="VS.VSTESTCD.FRAME"


<ItemRef ItemOID="VS.VSTESTCD.HTRAW"


<ItemRef ItemOID="VS.VSTESTCD.WTRAW"


<ItemRef ItemOID="VS.VSTESTCD.MEANBP"


</def:ValueListDef>


Additional Information

• Annotated CRF – Link to file containing annotated CRF

• See draft Meta Data Guidelines (draft) at http://www.cdisc.org/msg-draft

http://www.cdisc.org/msg-draft




Annotated CRF

<def:AnnotatedCRF>

<def:DocumentRef leafID="blankcrf"/>

</def:AnnotatedCRF>

<def:leaf ID="blankcrf" xlink:href="blankcrf.pdf">

<def:title>Annotated Case Report Form</def:title>

</def:leaf>


Exampleshttp://www.cdisc.org/define-xml


FAQ


Define is an ODM Extension?

• Define.xml is built from the components used by CDISC to build the Operational Data Model (ODM)

• The ODM is used to transport Case Report Form (CRF) data

• Define.xnl is used to transport tabulation metadata

• They are quite different use cases


Same Components, Different Use


Define is an ODM Extension?


Define is Machine Readable?

• Define.xml is built using XML technology

• A computer can consume and process (and understand) the information within the define.xml file


Define is Machine Readable?


Define is Human Readable?

• As we said, define.xml is built using XML technology

• A computer can consume and process (and understand) the information within the define.xml file

• But using style sheet technology we can also transform the XML into a form that humans can understand


Define is Human Readable?


What tools do I use with define.xml?

http://www.cdisc.org/define-xml


What tools do I use with define.xml?

Slide courtesy of Formedix Limited


Tools• OpenCDISC

– Validator– http://www.opencdisc.org/

• XML4Pharma – CDISC Define.xml Checker– http://www.xml4pharma.com/CDISC_Define_Checker/index.html

• SAS tool set– http://www.sas.com/industry/pharma/cdisc/

• Formedix– Origin Submission Modeller– http://www.formedix.com/cms/index.php?option=com_content&task=view&i

d=28&Itemid=53

• Entimo– entmICE DARE– http://www.entimo.com/solution/entimICE_DARE.html

• Octagon– Checkpoint– http://www.octagonresearch.com/checkpoint-data-validation.html

http://www.opencdisc.org/

http://www.xml4pharma.com/CDISC_Define_Checker/index.html

http://www.sas.com/industry/pharma/cdisc/

http://www.formedix.com/cms/index.php?option=com_content&task=view&id=28&Itemid=53

http://www.formedix.com/cms/index.php?option=com_content&task=view&id=28&Itemid=53

http://www.entimo.com/solution/entimICE_DARE.html

http://www.octagonresearch.com/checkpoint-data-validation.html






CDISC Plans

• New release of define Q3/Q4 2010

• Support ADaM metadata

• Support SDTM V3.1.2


Summary


Purpose

• Describes– What is included within the data

– Where did the data come from

– Derivations, code lists, annotated PDF etc to aid understanding

• Machine Readable

• Human Readable (after processing)

• To aid/inform the reviewer, unambiguous communication


Q&A

[email protected]

[email protected]

mailto:[email protected]




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