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The Implementation of “Define.xml: Metadata for SAS-Based Clinical Data. Tang Li. Overview of the eCTD CDISC Data. What is define.xml?.

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Presentation Transcript
what is define xml
What is define.xml?
  • The Define.xml describes the submitted Case Report Tabulation (SAS) datasets and variables in a machine-readable format, and it replaces the older specification called the “Define.pdf”.
xml schemals informal
XML Schemals (informal)

W3C xml schema

Extend

CDISC ODM schema

Extend

CDISC define.xml schema

We are here

slide5

Implementation of Define.xml in Cephalon

.xpt

anBlankcrf

Defxmldata

Defxml

cephCDISC DB

defxx

Define.xml

Defxmldat:

VLVariables

CLVariables

CTLCMN

Define1-0-0.xsl

the structure of define xml
The Structure of Define.xml
  • ODM
    • Study
      • GlobalVariables
        • Study Name
        • Study Description
        • ProtocolName
        • MetaDataVersion
          • Def:AnnotatedCRF
          • Def:ValueListDef
          • ItemGroupDef
          • ItemDef
          • CodeList
itemgroupdef
ItemGroupDef
  • An ItemGroupDef describes the properties of a domain, including the attributes of a domain, e.g. name , domain keys, and purpose,
  • and its corresponding variables, of which each one is referred to one ItemRef.
itemgroupdef example

<ItemGroupDef OID="VS"

Name="VS"

Repeating="Yes"

IsReferenceData="No"

Purpose="Tabulation"

def:Label="Vital Signs"

def:Structure="One record per vital sign measurement per timepoint per subject"

def:DomainKeys="STUDYID, USUBJID, VSTESTCD, VISITNUM, VSTPTNUM"

def:Class="Findings"

def:ArchiveLocationID="Location.VS"

>

Attributes of VS Domain

<ItemRef ItemOID="VS.STUDYID"

Role="Identifier" Mandatory="Yes"

OrderNumber="1" />

<ItemRef ItemOID="VS.DOMAIN"

Role="Identifier" Mandatory="Yes"

OrderNumber="2" />

Variables in VS Domain

ItemGroupDef (example)
itemdef
ItemDef
  • An ItemDef describes a variable, e.g. USUBJID, within a study. One variable one ItemDef
  • The properties of a variable include name, datatype, origin, or codelist restrictions, etc.
itemdef examples

<ItemDef OID="AE.STUDYID" Name="STUDYID"

Origin="CRF Pages 26.01" Comment="" DataType="text"

def:Label="Study Identifier" Length="48" />

Variable Without

Code List

<ItemDef OID="DM.ARMCD" Name="ARMCD"

Origin="Derived" Comment="" DataType="text"

def:Label="Planned Arm Code" Length="60">

<CodeListRef CodeListOID="CL.$ARMCD" />

</ItemDef>

Variable With

Code List

ItemDef (examples)
valuelistdef
ValueListDef
  • A value list is to show the list of “subvariables” in the vertical structure of a specific variable.
  • ValueListDef describes the values in a vertical structure, which could be a true value list (e.g. VSTESTCD)or a list of supplemental qualifies (e.g. values in QNAM of a SUPPxx domain).
valuelistdef example 1

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

<ItemRef ItemOID="VS.VSTESTCD.DIABP"

OrderNumber="1" Mandatory="No" />

<ItemRef ItemOID="VS.VSTESTCD.HEIGHT"

OrderNumber="2" Mandatory="No" />

</def:ValueListDef>

Value List

VSTESTCD

Subvariable OIDs MUST match

<ItemDef OID="VS.VSTESTCD.DIABP" Name="DIABP"

Origin="CRF Pages 8,15,19,23,99.03" Comment="" DataType="integer"

def:Label="DIASTOLIC BLOOD PRESSURE" Length="8" />

<ItemDef OID="VS.VSTESTCD.HEIGHT" Name="HEIGHT"

Origin="CRF Pages 99.03" Comment="" DataType="float"

def:Label="HEIGHT" Length="8" />

ValueListDef (example 1)
valuelistdef example 2

<def:ValueListDef OID="SUPPAE.QNAM">

<ItemRef ItemOID="SUPPAE.QNAM.HLT“

OrderNumber="1" Mandatory="No" />

<ItemRef ItemOID="SUPPAE.QNAM.LLT"

OrderNumber="2" Mandatory="No" />

</def:ValueListDef>

A List of Supplemental

Qualifiers (SUPPAE.QNAM)

SuppQual OIDs MUST match

<ItemDef OID="SUPPAE.QNAM.HLT" Name="HLT"

Origin="Derived" Comment="" DataType="text"

def:Label="Higher Level Term" Length="8" />

<ItemDef OID="SUPPAE.QNAM.LLT" Name="LLT"

Origin="Derived" Comment="" DataType="text"

def:Label="Lower Level Term" Length="8" />

ValueListDef (example 2)
codelist
CodeList
  • CodeList defines a discrete set of permitted values for an item. The definition can be an explicit list of values or a reference to an externally defined codelist.
codelist example

<ItemDef OID="DM.ARMCD" Name="ARMCD"

Origin="Derived" Comment="" DataType="text"

def:Label="Planned Arm Code" Length="60">

<CodeListRef CodeListOID="CL.$ARMCD" />

</ItemDef>

<CodeList OID="CL.$ARMCD" SASFormatName="$ARMCD"

Name="$ARMCD" DataType="text">

<CodeListItem CodedValue='1'>

<Decode>

<TranslatedText xml:lang="en"> A B C</TranslatedText>

</Decode>

</CodeListItem>

<CodeListItem CodedValue='2'>

<Decode>

<TranslatedText xml:lang="en">B C A </TranslatedText>

</Decode>

</CodeListItem>

</CodeList>

CodeList

CL.$ARMCD

CodeList (example)
validation of define xml
Validation of define.xml
  • The Define.xml file has to be validated using an xml editor, e.g. oXygen, Xmlspy etc. The validation is based on the syntax of xml schemas. However, the validation can only check the syntax. The semantics MUST be reviewed by human being.
issues
Issues
  • Value List
  • Value or subvariable
  • Questionnaire Domain
  • xxTESTCD
issue value list
Issue:Value List
  • Value list is a debatable and complicated concept. It intends to present the metadata of a vertical structure, like VSTESTCD. Syntactically, it describes the value level metadata. The challenge is the semantics. Not all vertical structures are value lists. For example, QSTESTCD is not a value list.
issue value or subvariable
Issue: Value or subvariable
  • This is related to value list issue. Weight is a value of variable VSTESTCD. However, weight is also qualified as a “variable” in the value list and defined by ItemDef. To describe this type of variables, “subvariable” is a suitable one. This may be used to identified the TRUE value lists. That is if the values of a variable are qualified as a subvariables, such a variable is a value list. QSTESTCD is not a source variable for a value list since its values are simply the questionnaire numbers.
issue questionnaire domain
Issue: Questionnaire Domain
  • QS domain is semantically complicated, including questions in CRF and eDiary. Each set of questions may be significantly different, leading to subdomains.
  • The values of the vertical structure QSTESTCD of QS domain is simply the question IDs, which are not qualified as subvariables.
issue xxtestcd
Issue: xxTESTCD
  • The variables of xxTESTCD in different domains are vertical structures containing the values which may be treated as “subvariables”. Their corresponding values of xxTEST serve as “labels” of the these “subvariables”.