HCLS/ClinicalObservationsInteroperability/CDISC

ODM as RDF

Taking Jozef Aerts' HL7-in-ODM example (complete example)

The general structure of ODM is:

<ODM>
  <Study OID="SomeStudy">
    <MetadataVersion Name="SomeStudy_Metadata">
      <ItemGroupDef Name="e.g. Physical Exam">
	<ItemRef itemOID="measured item, e.g. I_HEIGHT"/>
	<ItemRef itemOID="measured item, e.g. I_WEIGHT"/>
      </ItemGroupDef>
      <ItemDef DataType="integer" Length="3" Name="Height" OID="I_HEIGHT" SASFieldName="HEIGHT" SDSVarName="VSORRES">
	<Question><TranslatedText>Height</TranslatedText></Question>
	<range Comparator="LT"><val>220</val><unit>MU_CM</unit></range>
	<range Comparator="LT"><val>90</val><unit>MU_IN</unit></range>
      </ItemDef>
    </MetadataVersion>
  </Study>

  <ReferenceData StudyOID="SomeStudy" MetaDataVersionOID="SomeStudy_Metadata">
    <ItemGroupData ItemGroupOID="IG_PE_BASE">
      <ItemData ItemOID="I_HEIGHT" Value="193" units="MU_CM"/>
      <ItemData ItemOID="I_WEIGHT" Value="90" units="MU_KG"/>
    </ItemGroupData>
  </ReferenceData>

  <ClinicalData>
    <SubjectData SubjectKey="Bob">
      <StudyEventData StudyEventOID="SomeStudy_Event1">
	<FormData FormOID="F_WEEK_1_2">
	  <ItemGroupData ItemGroupOID="IG_COMMON">
	    <ItemData ItemOID="I_SITE" Value="23" />
	    <ItemData ItemOID="I_SUBJECTID" Value="001" />
	    <ItemData ItemOID="I_VISIT" Value="2010-03-13" />
	    <ItemData ItemOID="I_VISITTIME" Value="09:12:28" />
	  </ItemGroupData>
	  <ItemGroupData ItemGroupOID="IG_PE_WEEK">
	    <ItemData ItemOID="I_HEIGHT" Value="193">
	      <MeasurementUnitRef MeasurementUnitOID="MU_CM"/>
	    </ItemData>
	  </ItemGroupData>
	</FormData>
      </StudyEventData>
    </SubjectData>
  </ClinicalData>
</ODM>

path	purpose	RDF class
Study/MetadataVersion/ItemGroupDef	list of variables	odm:VariableList
...ItemRef	Variable	odm:Variable
Study/MetadataVersion/ItemGroupDef/ItemDev	description of a variable	odm:Input
ReferenceData/ItemGroupData	list of reference values	odm:ReferenceValueList
...ItemData	reference value	odm:ReferenceValue
ClinicalData/SubjectData/StudyEventData/FormData	list of captured values	odm:CapturedValueGroupList
...ItemGroupData	collection of values	odm:CapturedValueGroup
...ItemData	captured value	odm:CapturedValue

Presentations at CDISC Europe Interchange

• 2012, in Stockholm, joint presentation Frederik Malfait, Roche, and Kerstin Forsberg, AstraZeneca Semantic Models for CDISC based standards and metadata management.

• 2011, in Brussels, Kerstin Forsberg, AstraZeneca Linking Clinical Data Standards and Frederik Malfait Roche Integration of Clinical Trial Data Standards Part II. Models and Applications.

Presentations to US FDA

CDER 5 Nov 2012: call Kerstin's blog comments position paper, slides

Discussion

Semantic models for CDISC based standard and metadata management (slides)

Linking Clinical Data Standards

Kerstin Forsberg's call to respond to US FDA call for study data exchange standards and resulting HCLS IG thread.

Related

CDER

Tools

• CMap COE - represent mindmaps as OWL ontologies. (Note article on mindmaps as RDF.)