FHIR to OMOP FHIR IG
2.0.0-ballot - STU 1 Ballot
FHIR to OMOP FHIR IG
2.0.0-ballot - STU 1 Ballot
FHIR to OMOP FHIR IG, published by HL7 International / Biomedical Research and Regulation. This guide is not an authorized publication; it is the continuous build for version 2.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-omop-ig/ and changes regularly. See the Directory of published versions
| Page standards status: Trial-use | Maturity Level: 2 |
<StructureMap xmlns="http://hl7.org/fhir">
<id value="AllergyMap"/>
<language value="en"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: StructureMap AllergyMap</b></p><a name="AllergyMap"> </a><a name="hcAllergyMap"> </a><pre class="fml">
<span style="color: #cc00cc">/// <b>url</b> = </span><span style="color: blue">'http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap'</span>
<span style="color: #cc00cc">/// <b>name</b> = </span><span style="color: blue">'AllergyMap'</span>
<span style="color: #cc00cc">/// <b>title</b> = </span><span style="color: blue">'Mapping Allergy resource to Observation OMOP Domain'</span>
<span style="color: #cc00cc">/// <b>status</b> = </span><span style="color: blue">'active'</span>
<span style="color: #cc00cc">/// <b>description</b> = </span><span style="color: blue">'This mapping maps FHIR AllergyIntolerance instances to OMOP Observation Table objects.'</span>
<b>uses</b><span style="color: navy"> "</span><a href="http://hl7.org/fhir/R5/allergyintolerance.html" title="AllergyIntolerance">http://hl7.org/fhir/StructureDefinition/AllergyIntolerance</a><span style="color: navy">" </span><b>alias </b>Allergy <b>as </b><b>source</b>
<b>uses</b><span style="color: navy"> "</span><a href="StructureDefinition-Observation.html" title="Observation OMOP Table">http://hl7.org/fhir/uv/omop/StructureDefinition/Observation</a><span style="color: navy">" </span><b>alias </b>ObservationTable <b>as </b><b>target</b>
<b>group </b>Allergy<span style="color: navy">(</span><b>source</b> <span style="color: maroon">src</span><span style="color: navy"> : </span>Allergy, <b>target</b> <span style="color: maroon">tgt</span><span style="color: navy"> : </span>ObservationTable<span style="color: navy">)</span><span style="color: navy"> {
</span> src<b> where </b><span style="color: navy">(</span>src.recordedDate.empty().not() | src.onset.empty().not()<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> <span style="color: navy">// </span><span style="color: green">OMOP Observation ID would be a map from FHIR ID to an external key</span>
src<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> s.id<b> as </b><span style="color: maroon">id</span><span style="color: navy"><b> -> </b></span>tgt.observation_id = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">id</span><span style="color: navy">, </span><span style="color: blue">'integer'</span><span style="color: navy">)</span><span style="color: navy">;</span>
src<b> as </b><span style="color: maroon">s</span><b> where </b><span style="color: navy">(</span>src.id.empty()<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> s.identifier<b> as </b><span style="color: maroon">i</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> i.value<b> as </b><span style="color: maroon">id</span><span style="color: navy"><b> -> </b></span>tgt.observation_id = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">id</span><span style="color: navy">, </span><span style="color: blue">'integer'</span><span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">}</span> <i>"allergyIdFromIdentifier"</i><span style="color: navy">;</span>
<span style="color: navy">}</span> <i>"allergyId"</i><span style="color: navy">;</span>
<span style="color: navy">// </span><span style="color: green">OMOP Person ID would be a map from the FHIR Allergy Patient reference to an external key</span>
src.patient<b> as </b><span style="color: maroon">subject</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> subject.reference<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -> </b></span>tgt.person_id = <span style="color: navy">(</span>%s.substring(%s.indexOf('/') + 1)<span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">// </span><span style="color: green">OMOP Visit Occurrence ID would be a map from the FHIR Allergy Encounter reference to an external key</span>
src.encounter<b> as </b><span style="color: maroon">encounter</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> encounter.reference<b> as </b><span style="color: maroon">e</span><span style="color: navy"><b> -> </b></span>tgt.visit_occurrence_id = <span style="color: navy">(</span>%e.substring(%e.indexOf('/') + 1)<span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
src.type<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> s.coding<b> as </b><span style="color: maroon">sc</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> sc.code<b> as </b><span style="color: maroon">code</span><b> where </b><span style="color: navy">(</span>code = 'allergy'<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> src.category<b> as </b><span style="color: maroon">category</span><span style="color: navy"><b> -> </b></span>tgt.observation_concept_id = <b>translate</b><span style="color: navy">(</span><span style="color: maroon">category</span><span style="color: navy">, </span><span style="color: blue">'http://hl7.org/fhir/uv/omop/ConceptMap/AllergyType'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
sc.code<b> as </b><span style="color: maroon">code</span><b> where </b><span style="color: navy">(</span>code = 'intolerance'<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> src.category<b> as </b><span style="color: maroon">category</span><span style="color: navy"><b> -> </b></span>tgt.observation_concept_id = <b>translate</b><span style="color: navy">(</span><span style="color: maroon">category</span><span style="color: navy">, </span><span style="color: blue">'http://hl7.org/fhir/uv/omop/ConceptMap/IntoleranceType'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
src.code<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> s.coding<b> as </b><span style="color: maroon">sc</span><span style="color: navy"><b> -> </b></span>tgt<b> then</b><span style="color: navy"> {
</span> sc.system<b> as </b><span style="color: maroon">s</span><b> where </b><span style="color: navy">(</span>s = 'http://snomed.info/sct'<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> sc.code<b> as </b><span style="color: maroon">code</span><span style="color: navy"><b> -> </b></span> tgt.value_as_concept_id = <b>translate</b><span style="color: navy">(</span><span style="color: maroon">code</span><span style="color: navy">, </span><span style="color: blue">'http://hl7.org/fhir/uv/omop/ConceptMap/AllergySubstanceType'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><span style="color: navy">, </span> tgt.value_source_value = <span style="color: maroon">code</span><span style="color: navy">;</span>
sc.display<b> as </b><span style="color: maroon">display</span><span style="color: navy"><b> -> </b></span>tgt.value_as_string = <span style="color: maroon">display</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
<span style="color: navy">}</span><span style="color: navy">;</span>
src.recordedDate<span style="color: navy"> : </span>dateTime<b> as </b><span style="color: maroon">osd</span><span style="color: navy"><b> -> </b></span> tgt.observation_date = <span style="color: navy">(</span>src.recordedDate.toString().substring(0, 10)<span style="color: navy">)</span><span style="color: navy">, </span> tgt.observation_datetime = <span style="color: maroon">osd</span><span style="color: navy">;</span>
src<b> where </b><span style="color: navy">(</span>src.recordedDate.empty()<span style="color: navy">)</span><b> then</b><span style="color: navy"> {
</span> src.onset<span style="color: navy"> : </span>dateTime<b> as </b><span style="color: maroon">osd</span><span style="color: navy"><b> -> </b></span> tgt.observation_date = <span style="color: navy">(</span>src.onset.toString().substring(0, 10)<span style="color: navy">)</span><span style="color: navy">, </span> tgt.observation_datetime = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">osd</span><span style="color: navy">, </span><span style="color: blue">'dateTime'</span><span style="color: navy">)</span><span style="color: navy">;</span>
<span style="color: navy">}</span> <i>"allergyDateTime"</i><span style="color: navy">;</span>
<span style="color: navy">}</span> <i>"allergyMap"</i><span style="color: navy">;</span>
<span style="color: navy">}
</span></pre></div>
</text>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="brr"/>
</extension>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
<valueInteger value="2">
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
<valueCanonical
value="http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"/>
</extension>
</valueInteger>
</extension>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use">
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
<valueCanonical
value="http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"/>
</extension>
</valueCode>
</extension>
<url value="http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap"/>
<identifier>
<system value="urn:ietf:rfc:3986"/>
<value value="urn:oid:2.16.840.1.113883.4.642.40.77.43.1"/>
</identifier>
<version value="2.0.0-ballot"/>
<name value="AllergyMap"/>
<title value="Mapping Allergy resource to Observation OMOP Domain"/>
<status value="active"/>
<date value="2026-08-14T16:09:20+00:00"/>
<publisher value="HL7 International / Biomedical Research and Regulation"/>
<contact>
<name value="HL7 International / Biomedical Research and Regulation"/>
<telecom>
<system value="url"/>
<value value="http://www.hl7.org/Special/committees/rcrim"/>
</telecom>
</contact>
<description
value="This mapping maps FHIR AllergyIntolerance instances to OMOP Observation Table objects."/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<structure>
<url value="http://hl7.org/fhir/StructureDefinition/AllergyIntolerance"/>
<mode value="source"/>
<alias value="Allergy"/>
</structure>
<structure>
<url value="http://hl7.org/fhir/uv/omop/StructureDefinition/Observation"/>
<mode value="target"/>
<alias value="ObservationTable"/>
</structure>
<group>
<name value="Allergy"/>
<input>
<name value="src"/>
<type value="Allergy"/>
<mode value="source"/>
</input>
<input>
<name value="tgt"/>
<type value="ObservationTable"/>
<mode value="target"/>
</input>
<rule>
<name value="allergyMap"/>
<source>
<context value="src"/>
<condition
value="src.recordedDate.empty().not() | src.onset.empty().not()"/>
</source>
<rule>
<name value="allergyId"/>
<source>
<context value="src"/>
<variable value="s"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="id"/>
<source>
<context value="s"/>
<element value="id"/>
<variable value="id"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_id"/>
<transform value="cast"/>
<parameter>
<valueId value="id"/>
</parameter>
<parameter>
<valueString value="integer"/>
</parameter>
</target>
</rule>
<rule>
<name value="allergyIdFromIdentifier"/>
<source>
<context value="src"/>
<variable value="s"/>
<condition value="src.id.empty()"/>
</source>
<rule>
<name value="identifier"/>
<source>
<context value="s"/>
<element value="identifier"/>
<variable value="i"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="value"/>
<source>
<context value="i"/>
<element value="value"/>
<variable value="id"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_id"/>
<transform value="cast"/>
<parameter>
<valueId value="id"/>
</parameter>
<parameter>
<valueString value="integer"/>
</parameter>
</target>
</rule>
</rule>
</rule>
<documentation
value="OMOP Observation ID would be a map from FHIR ID to an external key"/>
</rule>
<rule>
<name value="patient"/>
<source>
<context value="src"/>
<element value="patient"/>
<variable value="subject"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="reference"/>
<source>
<context value="subject"/>
<element value="reference"/>
<variable value="s"/>
</source>
<target>
<context value="tgt"/>
<element value="person_id"/>
<transform value="evaluate"/>
<parameter>
<valueString value="%s.substring(%s.indexOf('/') + 1)"/>
</parameter>
</target>
</rule>
<documentation
value="OMOP Person ID would be a map from the FHIR Allergy Patient reference to an external key"/>
</rule>
<rule>
<name value="encounter"/>
<source>
<context value="src"/>
<element value="encounter"/>
<variable value="encounter"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="reference"/>
<source>
<context value="encounter"/>
<element value="reference"/>
<variable value="e"/>
</source>
<target>
<context value="tgt"/>
<element value="visit_occurrence_id"/>
<transform value="evaluate"/>
<parameter>
<valueString value="%e.substring(%e.indexOf('/') + 1)"/>
</parameter>
</target>
</rule>
<documentation
value="OMOP Visit Occurrence ID would be a map from the FHIR Allergy Encounter reference to an external key"/>
</rule>
<rule>
<name value="type"/>
<source>
<context value="src"/>
<element value="type"/>
<variable value="s"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="coding"/>
<source>
<context value="s"/>
<element value="coding"/>
<variable value="sc"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="code"/>
<source>
<context value="sc"/>
<element value="code"/>
<variable value="code"/>
<condition value="code = 'allergy'"/>
</source>
<rule>
<name value="category"/>
<source>
<context value="src"/>
<element value="category"/>
<variable value="category"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_concept_id"/>
<transform value="translate"/>
<parameter>
<valueId value="category"/>
</parameter>
<parameter>
<valueString
value="http://hl7.org/fhir/uv/omop/ConceptMap/AllergyType"/>
</parameter>
<parameter>
<valueString value="code"/>
</parameter>
</target>
</rule>
</rule>
<rule>
<name value="code"/>
<source>
<context value="sc"/>
<element value="code"/>
<variable value="code"/>
<condition value="code = 'intolerance'"/>
</source>
<rule>
<name value="category"/>
<source>
<context value="src"/>
<element value="category"/>
<variable value="category"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_concept_id"/>
<transform value="translate"/>
<parameter>
<valueId value="category"/>
</parameter>
<parameter>
<valueString
value="http://hl7.org/fhir/uv/omop/ConceptMap/IntoleranceType"/>
</parameter>
<parameter>
<valueString value="code"/>
</parameter>
</target>
</rule>
</rule>
</rule>
</rule>
<rule>
<name value="code"/>
<source>
<context value="src"/>
<element value="code"/>
<variable value="s"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="coding"/>
<source>
<context value="s"/>
<element value="coding"/>
<variable value="sc"/>
</source>
<target>
<context value="tgt"/>
</target>
<rule>
<name value="system"/>
<source>
<context value="sc"/>
<element value="system"/>
<variable value="s"/>
<condition value="s = 'http://snomed.info/sct'"/>
</source>
<rule>
<name value="code"/>
<source>
<context value="sc"/>
<element value="code"/>
<variable value="code"/>
</source>
<target>
<context value="tgt"/>
<element value="value_as_concept_id"/>
<transform value="translate"/>
<parameter>
<valueId value="code"/>
</parameter>
<parameter>
<valueString
value="http://hl7.org/fhir/uv/omop/ConceptMap/AllergySubstanceType"/>
</parameter>
<parameter>
<valueString value="code"/>
</parameter>
</target>
<target>
<context value="tgt"/>
<element value="value_source_value"/>
<transform value="copy"/>
<parameter>
<valueId value="code"/>
</parameter>
</target>
</rule>
<rule>
<name value="display"/>
<source>
<context value="sc"/>
<element value="display"/>
<variable value="display"/>
</source>
<target>
<context value="tgt"/>
<element value="value_as_string"/>
<transform value="copy"/>
<parameter>
<valueId value="display"/>
</parameter>
</target>
</rule>
</rule>
</rule>
</rule>
<rule>
<name value="recordedDateDateTime"/>
<source>
<context value="src"/>
<type value="dateTime"/>
<element value="recordedDate"/>
<variable value="osd"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_date"/>
<transform value="evaluate"/>
<parameter>
<valueString
value="src.recordedDate.toString().substring(0, 10)"/>
</parameter>
</target>
<target>
<context value="tgt"/>
<element value="observation_datetime"/>
<transform value="copy"/>
<parameter>
<valueId value="osd"/>
</parameter>
</target>
</rule>
<rule>
<name value="allergyDateTime"/>
<source>
<context value="src"/>
<condition value="src.recordedDate.empty()"/>
</source>
<rule>
<name value="onsetDateTime"/>
<source>
<context value="src"/>
<type value="dateTime"/>
<element value="onset"/>
<variable value="osd"/>
</source>
<target>
<context value="tgt"/>
<element value="observation_date"/>
<transform value="evaluate"/>
<parameter>
<valueString value="src.onset.toString().substring(0, 10)"/>
</parameter>
</target>
<target>
<context value="tgt"/>
<element value="observation_datetime"/>
<transform value="cast"/>
<parameter>
<valueId value="osd"/>
</parameter>
<parameter>
<valueString value="dateTime"/>
</parameter>
</target>
</rule>
</rule>
</rule>
</group>
</StructureMap>
IG © 2023+ HL7 International / Biomedical Research and Regulation.
Package hl7.fhir.uv.omop#2.0.0-ballot based on FHIR 5.0.0.
Generated
2026-08-14
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