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>