FHIR to OMOP FHIR IG
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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 1.0.0-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

: Mapping Allergy resource to Observation OMOP Domain - XML Representation

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<StructureMap xmlns="http://hl7.org/fhir">
  <id value="AllergyMap"/>
  <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">'draft'</span>

<b>uses</b><span style="color: navy"> &quot;</span><a href="http://hl7.org/fhir/R5/allergyintolerance.html" title="AllergyIntolerance">http://hl7.org/fhir/StructureDefinition/AllergyIntolerance</a><span style="color: navy">&quot; </span><b>alias </b>Allergy <b>as </b><b>source</b>
<b>uses</b><span style="color: navy"> &quot;</span><a href="StructureDefinition-Observation.html" title="Observation OMOP Table">http://hl7.org/fhir/uv/omop/StructureDefinition/Observation</a><span style="color: navy">&quot; </span><b>alias </b>ObservationTable <b>as </b><b>target</b>

<b>group </b>Observation<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.code<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>    s.coding<b> as </b><span style="color: maroon">sc</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>      sc.code<span style="color: navy"><b> -&gt; </b></span> tgt.observation_concept_id<span style="color: navy">, </span> tgt.observation_source_value<span style="color: navy">, </span> tgt.observation_source_concept_id<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: green">src.id as id -&gt; tgt.observation_id = cast(id, &quot;integer&quot;);</span>
  src.onset<span style="color: navy"> : </span>dateTime<b> as </b><span style="color: maroon">osd</span><span style="color: navy"><b> -&gt; </b></span> tgt.observation_date = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">osd</span><span style="color: navy">, </span><span style="color: blue">'date'</span><span style="color: navy">)</span><span style="color: navy">, </span> tgt.observation_datetime = <span style="color: maroon">osd</span><span style="color: navy">;</span> <span style="color: navy">// </span><span style="color: green">src.patient as s -&gt; tgt then {</span>
  src.reaction<b> as </b><span style="color: maroon">s</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>    s.manifestation<b> as </b><span style="color: maroon">sman</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>      sman.concept<b> as </b><span style="color: maroon">smanc</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>        smanc.coding<b> as </b><span style="color: maroon">sc</span><span style="color: navy"><b> -&gt; </b></span><span style="color: maroon">tgt</span><b> then</b><span style="color: navy"> {
</span>          sc.code<span style="color: navy"><b> -&gt; </b></span> tgt.value_as_concept_id<span style="color: navy">, </span> tgt.value_source_value<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><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="1">
      <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="informative">
      <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"/>
  <version value="1.0.0-ballot"/>
  <name value="AllergyMap"/>
  <title value="Mapping Allergy resource to Observation OMOP Domain"/>
  <status value="draft"/>
  <date value="2025-07-29T17:40:15+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="Observation"/>
    <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="code"/>
      <source>
        <context value="src"/>
        <element value="code"/>
        <variable value="s"/>
      </source>
      <target>
        <transform value="copy"/>
        <parameter>
          <valueId value="tgt"/>
        </parameter>
      </target>
      <rule>
        <name value="coding"/>
        <source>
          <context value="s"/>
          <element value="coding"/>
          <variable value="sc"/>
        </source>
        <target>
          <transform value="copy"/>
          <parameter>
            <valueId value="tgt"/>
          </parameter>
        </target>
        <rule>
          <name value="code"/>
          <source>
            <context value="sc"/>
            <element value="code"/>
          </source>
          <target>
            <context value="tgt"/>
            <element value="observation_concept_id"/>
          </target>
          <target>
            <context value="tgt"/>
            <element value="observation_source_value"/>
          </target>
          <target>
            <context value="tgt"/>
            <element value="observation_source_concept_id"/>
          </target>
        </rule>
      </rule>
      <documentation
                     value="src.id as id -&gt; tgt.observation_id = cast(id, &quot;integer&quot;);"/>
    </rule>
    <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="cast"/>
        <parameter>
          <valueId value="osd"/>
        </parameter>
        <parameter>
          <valueString value="date"/>
        </parameter>
      </target>
      <target>
        <context value="tgt"/>
        <element value="observation_datetime"/>
        <transform value="copy"/>
        <parameter>
          <valueId value="osd"/>
        </parameter>
      </target>
      <documentation value="src.patient as s -&gt; tgt then {"/>
    </rule>
    <rule>
      <name value="reaction"/>
      <source>
        <context value="src"/>
        <element value="reaction"/>
        <variable value="s"/>
      </source>
      <target>
        <transform value="copy"/>
        <parameter>
          <valueId value="tgt"/>
        </parameter>
      </target>
      <rule>
        <name value="manifestation"/>
        <source>
          <context value="s"/>
          <element value="manifestation"/>
          <variable value="sman"/>
        </source>
        <target>
          <transform value="copy"/>
          <parameter>
            <valueId value="tgt"/>
          </parameter>
        </target>
        <rule>
          <name value="concept"/>
          <source>
            <context value="sman"/>
            <element value="concept"/>
            <variable value="smanc"/>
          </source>
          <target>
            <transform value="copy"/>
            <parameter>
              <valueId value="tgt"/>
            </parameter>
          </target>
          <rule>
            <name value="coding"/>
            <source>
              <context value="smanc"/>
              <element value="coding"/>
              <variable value="sc"/>
            </source>
            <target>
              <transform value="copy"/>
              <parameter>
                <valueId value="tgt"/>
              </parameter>
            </target>
            <rule>
              <name value="code"/>
              <source>
                <context value="sc"/>
                <element value="code"/>
              </source>
              <target>
                <context value="tgt"/>
                <element value="value_as_concept_id"/>
              </target>
              <target>
                <context value="tgt"/>
                <element value="value_source_value"/>
              </target>
            </rule>
          </rule>
        </rule>
      </rule>
    </rule>
  </group>
</StructureMap>