The Origin element is based on the def:Origin element in Define-XML v2.1 with the Trace-XML v1.0 extension. Type, Source (Description?, SourceItems?, Coding*, DocumentRef*) The SourceItems element contains SourceItem child elements that reference the source variables, if any, for a given ItemRef. SourceItem elements provide machine-readable traceability and identify specific arguments for a MethodDef, specially when used with an Origin with Type="Derived".Origin defines the source metadata, where applicable, for ODM ItemRefs or ItemGroupRefs. Origin as a child element replaces the Origin attribute in ODM v1.3 that exists for the ItemDef and ItemGroupDef elements.Element Name Origin Parent Elements ItemGroupDef, ItemRef Element XPath(s) Element Textual Value None Attributes Child Elements Usage/Business Rules
Identifies how the clinical data values were obtained. * Users are encouraged to refer to the most recent version of the CDISC Controlled Terminology (https://www.cdisc.org/standards/terminology/controlled-terminology). * Users are encouraged to refer to the most recent version of the CDISC Controlled Terminology (https://www.cdisc.org/standards/terminology/controlled-terminology).Attribute Schema Datatype or Enumeration Usage Definition Business Rule(s) Type Required Source text Optional Indicates the party responsible for the data's origin type.
Example: Origin with FHIR Resource Example
Origin with FHIR Resource Example
<ItemGroupDef OID="ODM.IG.LB.WBC" Name="WBC Lab Results with Unit" Repeating="No" Type="Section" >
<!-- Subject -->
<ItemRef ItemOID="ODM.IT.LB.SUBJID" Mandatory="Yes">
<Origin Type="Collected" Source="Investigator">
<SourceItems>
<SourceItem>
<!-- The Subject-ID is obtained from ResearchSubject.identifier -->
<Resource Type="HL7-FHIR" Name="ResearchSubject" Attribute="identifier"/>
</SourceItem>
</SourceItems>
</Origin>
</ItemRef>
<!-- Collected Leukocytes (White Blood Count) with units -->
<!-- The value itself -->
<!-- Remark the reference to the units item using UnitsItemOID -->
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRES" Mandatory="Yes" UnitsItemOID="ODM.IT.LB.WBC.LBORRESU">
<Origin Type="Collected" Source="Investigator">
<SourceItems>
<SourceItem>
<!-- The value itself is obtained from Observation.valueQuantity.value -->
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.value"/>
</SourceItem>
</SourceItems>
</Origin>
</ItemRef>
<!-- The units for the leukocytes measurement -->
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRESU" Mandatory="Yes">
<Origin Type="Collected" Source="Investigator">
<SourceItems>
<SourceItem>
<!-- The value itself is obtained from Observation.valueQuantity.unit -->
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.unit"/>
</SourceItem>
</SourceItems>
</Origin>
</ItemRef>
<!-- LOINC code of the test to be performed -->
<Coding Code="26464-8" System="http://loinc.org" SystemName="LOINC" SystemVersion="2.92"/>
</ItemGroupDef>
Example: Origin with FHIR Resource Example - alternative
Origin with FHIR Resource Example - alternative
<?xml version="1.0" encoding="UTF-8"?>
<ItemGroupDef OID="ODM.IG.LB.WBC" Name="WBC Lab Results with Unit" Repeating="No" Type="Section" >
<!-- The Subject Identifier -->
<ItemRef ItemOID="ODM.IT.SUBJID" Mandatory="Yes" />
<!-- Collected Leukocytes (White Blood Count) with units -->
<!-- The value itself -->
<!-- Remark the reference to the units item using UnitsItemOID -->
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRES" Mandatory="Yes" UnitsItemOID="ODM.IT.LB.WBC.LBORRESU" />
<!-- The units for the leukocytes measurement -->
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRESU" Mandatory="Yes" />
<!-- LOINC code of the test to be performed -->
<Coding Code="26464-8" System="http://loinc.org" SystemName="LOINC" SystemVersion="2.92"/>
<!-- Alternative way of stating the origin of the data in the group,
as coming from an Electronic Health Record using the FHIR API,
retrieved by the investigator -->
<Origin Type="Collected" Source="Investigator">
<SourceItems>
<SourceItem ItemOID="ODM.IT.LB.SUBJID">
<!-- The Subject-ID is obtained from ResearchSubject.identifier -->
<!-- The ItemOID references the ItemDef providing the metadata -->
<Resource Type="HL7-FHIR" Name="ResearchSubject" Attribute="identifier"/>
</SourceItem>
<SourceItem ItemOID="ODM.IT.LB.WBC.LBORRES">
<!-- The value itself is obtained from Observation.valueQuantity.value -->
<!-- The ItemOID references the ItemDef providing the metadata -->
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.value"/>
</SourceItem>
<SourceItem ItemOID="ODM.IT.LB.WBC.LBORRESU">
<!-- The value itself is obtained from Observation.valueQuantity.unit -->
<!-- The ItemOID references the ItemDef providing the metadata -->
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.unit"/>
</SourceItem>
</SourceItems>
</Origin>
</ItemGroupDef>
Example: HL7 FHIR eSource Example
Example highlighting the use of the HL7 FHIR standard to retrieve EHR data to use as eSource
HL7 FHIR eSource Example
<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v2.0"
xmlns:xlink="http://www.w3.org/1999/xlink"
ODMVersion="2.0"
FileOID="FHIR-examples"
FileType="Snapshot"
CreationDateTime="2020-09-02T11:20:00">
<Study OID="fhir-odm-esource-study" StudyName="FHIR eSource" ProtocolName="FHIR-eSource-Demo-01">
<Description>
<TranslatedText xml:lang="en" Type="text/plain">FHIR eSource Demo Study</TranslatedText>
</Description>
<MetaDataVersion OID="MDV.fhir-odm" Name="FHIR eSource MDV">
<ItemGroupDef OID="ODM.IG.COMMON" Name="Common" Repeating="No" Type="Form">
<ItemRef ItemOID="ODM.IT.Common.StudyID" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.Common.SiteID" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.Common.SubjectID" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.Common.Visit" Mandatory="Yes"/>
</ItemGroupDef>
<ItemGroupDef OID="ODM.IG.LB" Name="LAB Measurements" Repeating="No" Type="Form">
<ItemRef ItemOID="ODM.IT.LB.LBDTC" Mandatory="Yes"/>
<ItemGroupRef ItemGroupOID="ODM.IG.LB.WBC" Mandatory="Yes" MethodOID="ODM.MT.LB.LBORRES"/>
<ItemRef ItemOID="ODM.IT.LB.ALB.LBORRES" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.LB.ALB.LBORRESU" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.LB.GLUC.LBORRES" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.LB.GLUC.LBORRESU" Mandatory="Yes"/>
</ItemGroupDef>
<ItemGroupDef OID="ODM.IG.LB.WBC" Name="WBC Lab Results with Unit" Repeating="No" Type="Form">
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRES" UnitsItemOID="ODM.IT.LB.WBC.LBORRESU" Mandatory="Yes"/>
<ItemRef ItemOID="ODM.IT.LB.WBC.LBORRESU" Mandatory="Yes"/>
<Origin Type="EHR" Source="Investigator">
<Description>
<TranslatedText xml:lang="en" Type="text/plain">Lab values retrieved from EHR using FHIR</TranslatedText>
</Description>
<SourceItems>
<SourceItem>
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.value" Label="value">
<Selection Path="Resource/@Name='Observation' and Resource/@Attribute='valueQuantity.value"/>
</Resource>
</SourceItem>
<SourceItem>
<Resource Type="HL7-FHIR" Name="Observation" Attribute="valueQuantity.unit" Label="unit">
<Selection Path="Resource/@Name='Observation' and Resource/@Attribute='valueQuantity.unit"/>
</Resource>
</SourceItem>
<Coding Code="26464-8" System="http://loinc.org" SystemName="LOINC" SystemVersion="2.61" Label="loinc_code"/>
</SourceItems>
</Origin>
</ItemGroupDef>
<ItemDef OID="ODM.IT.LB.WBC.LBORRES" Name="WBC" DataType="float" Length="3">
<Description>
<TranslatedText xml:lang="en" Type="text/plain">Result of the measurement or finding as originally received or collected.</TranslatedText>
</Description>
<Question>
<TranslatedText xml:lang="en" Type="text/plain">Result</TranslatedText>
</Question>
<Coding Code="26464-8" System="http://loinc.org" SystemName="LOINC" SystemVersion="2.61"/>
<Alias Context="SAS" Name="LBORRES"/>
</ItemDef>
<ItemDef OID="ODM.IT.LB.WBC.LBORRESU" Name="LBORRESU" DataType="text" Length="6">
<Description>
<TranslatedText xml:lang="en" Type="text/plain">WBC</TranslatedText>
</Description>
<CodeListRef CodeListOID="CL.LBORRESU"/>
<Coding Code="26464-8" System="http://loinc.org" SystemName="LOINC" SystemVersion="2.61"/>
<Alias Context="SAS" Name="LBORRESU"/>
</ItemDef>
<CodeList OID="CL.LBORRESU" Name="Unit (LBRESU)" DataType="text">
<CodeListItem CodedValue="10^9/L">
<Alias Name="C67255" Context="nci:ExtCodeID"/>
</CodeListItem>
<Alias Name="C71620" Context="nci:ExtCodeID"/>
</CodeList>
<MethodDef OID="ODM.MT.LB.LBORRES" Name="Retrieve Lab Result using FHIR" Type="Preload">
<Description><TranslatedText xml:lang="en" Type="text/plain">FHIR API call definition to retrieve lab result</TranslatedText></Description>
<MethodSignature>
<Parameter Name="value" Definition="Lab Result" DataType="text"/>
<Parameter Name="unit" Definition="Result Unit" DataType="text"/>
<Parameter Name="loinc_code" Definition="LOINC Code" DataType="text"/>
<ReturnValue Name="LBORRES" Definition="Lab result from the EHR system" DataType="text"/>
<ReturnValue Name="LBORRESU" Definition="Lab result from the EHR system" DataType="text"/>
</MethodSignature>
<FormalExpression Context="Python 3.7">
<!-- assumes have access to study state (e.g. subjectid, studyid, etc) and can retrieve patient_id using ResearchSubject -->
<!-- assumes libraries have been imported: "from fhirclient import client" and "import fhirclient.models.observation as ob" -->
<Code>
smart = client.FHIRClient(settings={'app_id': 'rof_adapter', 'api_base': 'https://api.logicahealth.org/STU301withSynthea/open'})
search_obs = ob.Observation.where(struct=dict(patient=patient_id, code=loinc_code))
value = ""
unit = ""
if search_obs.perform_resources(smart.server):
obs = search_obs.perform_resources(smart.server).pop().as_json()
lborres = obs[value.split(".")[0]][value.split(".")[1]]
lborresu = obs[unit.split(".")[0]][unit.split(".")[1]]
return lborres, lborresu
</Code>
</FormalExpression>
</MethodDef>
</MetaDataVersion>
</Study>
</ODM>