FHIR to OMOP FHIR IG
1.0.0-ballot - INFORMATIVE 1 - Ballot International flag

This page is part of the Vulcan FHIR to OMOP FHIR Implementation Guide (v1.0.0-ballot: INFORMATIVE 1 Ballot 1) based on FHIR (HL7® FHIR® Standard) v5.0.0. No current official version has been published yet. For a full list of available versions, see the Directory of published versions

: Mapping Observation resource to Observation OMOP Domain - XML Representation

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<StructureMap xmlns="http://hl7.org/fhir">
  <id value="ObservationMap"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: StructureMap ObservationMap</b></p><a name="ObservationMap"> </a><a name="hcObservationMap"> </a><pre class="fml">
<span style="color: #cc00cc">/// <b>url</b> = </span><span style="color: blue">'http://hl7.org/fhir/uv/omop/StructureMap/ObservationMap'</span>
<span style="color: #cc00cc">/// <b>name</b> = </span><span style="color: blue">'ObservationMap'</span>
<span style="color: #cc00cc">/// <b>title</b> = </span><span style="color: blue">'Mapping Observation 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/observation.html" title="Observation">http://hl7.org/fhir/StructureDefinition/Observation</a><span style="color: navy">&quot; </span><b>alias </b>Observation <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>ObsTable <b>as </b><b>target</b>

<b>group </b>Observe<span style="color: navy">(</span><b>source</b> <span style="color: maroon">src</span><span style="color: navy"> : </span>Observation, <b>target</b> <span style="color: maroon">tgt</span><span style="color: navy"> : </span>ObsTable<span style="color: navy">)</span><span style="color: navy"> {
</span>  src<b> where </b>('social-history' | 'imaging' | 'survey' | 'exam' | 'therapy' | 'activity' | 'procedure').supersetOf(Observation.category.coding.code)<b> then</b><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<b> as </b><span style="color: maroon">a</span><span style="color: navy"><b> -&gt; </b></span>tgt.observation_concept_id = <span style="color: maroon">a</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: green">src.id as id -&gt; tgt.observation_id = cast(id, &quot;integer&quot;);</span>
    src.effective<span style="color: navy"> : </span>dateTime<b> as </b><span style="color: maroon">a</span><span style="color: navy"><b> -&gt; </b></span> tgt.observation_datetime = <span style="color: maroon">a</span><span style="color: navy">, </span> tgt.observation_date = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">a</span><span style="color: navy">, </span><span style="color: blue">'date'</span><span style="color: navy">)</span><span style="color: navy">;</span> <span style="color: navy">// </span><span style="color: green">src.subject as s -&gt; tgt then {</span>
    src.effective<span style="color: navy"> : </span>instant<b> as </b><span style="color: maroon">einst</span><span style="color: navy"><b> -&gt; </b></span> tgt.observation_datetime = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">einst</span><span style="color: navy">, </span><span style="color: blue">'dateTime'</span><span style="color: navy">)</span><span style="color: navy">, </span> tgt.observation_date = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">einst</span><span style="color: navy">, </span><span style="color: blue">'date'</span><span style="color: navy">)</span><span style="color: navy">;</span>
    src.effective<span style="color: navy"> : </span>Period<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.start<b> as </b><span style="color: maroon">ss</span><span style="color: navy"><b> -&gt; </b></span> tgt.observation_datetime = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">ss</span><span style="color: navy">, </span><span style="color: blue">'dateTime'</span><span style="color: navy">)</span><span style="color: navy">, </span> tgt.observation_date = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">ss</span><span style="color: navy">, </span><span style="color: blue">'date'</span><span style="color: navy">)</span><span style="color: navy">;</span>
    <span style="color: navy">}</span><span style="color: navy">;</span>
    src.issued<b> as </b><span style="color: maroon">s</span><b> where </b>(s.toDate != src.effectiveDate)<span style="color: navy"><b> -&gt; </b></span>tgt.observation_source_value = <b>cast</b><span style="color: navy">(</span><span style="color: maroon">s</span><span style="color: navy">, </span><span style="color: blue">'string'</span><span style="color: navy">)</span><span style="color: navy">;</span>
    src.value<span style="color: navy"> : </span>Quantity<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.value<b> as </b><span style="color: maroon">a</span><span style="color: navy"><b> -&gt; </b></span>tgt.value_as_number = <span style="color: maroon">a</span><span style="color: navy">;</span>
      s.unit<b> as </b><span style="color: maroon">b</span><span style="color: navy"><b> -&gt; </b></span>tgt.unit_concept_id = <span style="color: maroon">b</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.performer as s -&gt; tgt then {</span>
    src.value<span style="color: navy"> : </span>CodeableConcept<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<b> as </b><span style="color: maroon">a</span><span style="color: navy"><b> -&gt; </b></span>tgt.value_as_concept_id = <span style="color: maroon">a</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.value<span style="color: navy"> : </span>string<b> as </b><span style="color: maroon">b</span><span style="color: navy"><b> -&gt; </b></span>tgt.value_as_string = <span style="color: maroon">b</span><span style="color: navy">;</span>
    src.note<b> as </b><span style="color: maroon">d</span><span style="color: navy"><b> -&gt; </b></span>tgt.observation_source_value = <span style="color: maroon">d</span><span style="color: navy">;</span>
  <span style="color: navy">}</span> <i>&quot;OnlyObs&quot;</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="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/ObservationMap"/>
  <version value="1.0.0-ballot"/>
  <name value="ObservationMap"/>
  <title value="Mapping Observation resource to  Observation OMOP Domain"/>
  <status value="draft"/>
  <date value="2025-07-29T21:03:04+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 Observation instances that are NOT considered measurements to OMOP Observation Table objects.  Currently, this is done by considering the category code and mapping 'social-history', 'imaging', 'survey', 'exam', 'therapy', 'activity', and 'procedure' Observations."/>
  <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/Observation"/>
    <mode value="source"/>
    <alias value="Observation"/>
  </structure>
  <structure>
    <url value="http://hl7.org/fhir/uv/omop/StructureDefinition/Observation"/>
    <mode value="target"/>
    <alias value="ObsTable"/>
  </structure>
  <group>
    <name value="Observe"/>
    <input>
      <name value="src"/>
      <type value="Observation"/>
      <mode value="source"/>
    </input>
    <input>
      <name value="tgt"/>
      <type value="ObsTable"/>
      <mode value="target"/>
    </input>
    <rule>
      <name value="OnlyObs"/>
      <source>
        <context value="src"/>
        <condition
                   value="('social-history' | 'imaging' | 'survey' | 'exam' | 'therapy' | 'activity' | 'procedure').supersetOf(Observation.category.coding.code)"/>
      </source>
      <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"/>
              <variable value="a"/>
            </source>
            <target>
              <context value="tgt"/>
              <element value="observation_concept_id"/>
              <transform value="copy"/>
              <parameter>
                <valueId value="a"/>
              </parameter>
            </target>
          </rule>
        </rule>
        <documentation
                       value="src.id as id -&gt; tgt.observation_id = cast(id, &quot;integer&quot;);"/>
      </rule>
      <rule>
        <name value="effectiveDateTime"/>
        <source>
          <context value="src"/>
          <type value="dateTime"/>
          <element value="effective"/>
          <variable value="a"/>
        </source>
        <target>
          <context value="tgt"/>
          <element value="observation_datetime"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="a"/>
          </parameter>
        </target>
        <target>
          <context value="tgt"/>
          <element value="observation_date"/>
          <transform value="cast"/>
          <parameter>
            <valueId value="a"/>
          </parameter>
          <parameter>
            <valueString value="date"/>
          </parameter>
        </target>
        <documentation value="src.subject as s -&gt; tgt then {"/>
      </rule>
      <rule>
        <name value="effectiveInstant"/>
        <source>
          <context value="src"/>
          <type value="instant"/>
          <element value="effective"/>
          <variable value="einst"/>
        </source>
        <target>
          <context value="tgt"/>
          <element value="observation_datetime"/>
          <transform value="cast"/>
          <parameter>
            <valueId value="einst"/>
          </parameter>
          <parameter>
            <valueString value="dateTime"/>
          </parameter>
        </target>
        <target>
          <context value="tgt"/>
          <element value="observation_date"/>
          <transform value="cast"/>
          <parameter>
            <valueId value="einst"/>
          </parameter>
          <parameter>
            <valueString value="date"/>
          </parameter>
        </target>
      </rule>
      <rule>
        <name value="effectivePeriod"/>
        <source>
          <context value="src"/>
          <type value="Period"/>
          <element value="effective"/>
          <variable value="s"/>
        </source>
        <target>
          <transform value="copy"/>
          <parameter>
            <valueId value="tgt"/>
          </parameter>
        </target>
        <rule>
          <name value="start"/>
          <source>
            <context value="s"/>
            <element value="start"/>
            <variable value="ss"/>
          </source>
          <target>
            <context value="tgt"/>
            <element value="observation_datetime"/>
            <transform value="cast"/>
            <parameter>
              <valueId value="ss"/>
            </parameter>
            <parameter>
              <valueString value="dateTime"/>
            </parameter>
          </target>
          <target>
            <context value="tgt"/>
            <element value="observation_date"/>
            <transform value="cast"/>
            <parameter>
              <valueId value="ss"/>
            </parameter>
            <parameter>
              <valueString value="date"/>
            </parameter>
          </target>
        </rule>
      </rule>
      <rule>
        <name value="issued"/>
        <source>
          <context value="src"/>
          <element value="issued"/>
          <variable value="s"/>
          <condition value="(s.toDate != src.effectiveDate)"/>
        </source>
        <target>
          <context value="tgt"/>
          <element value="observation_source_value"/>
          <transform value="cast"/>
          <parameter>
            <valueId value="s"/>
          </parameter>
          <parameter>
            <valueString value="string"/>
          </parameter>
        </target>
      </rule>
      <rule>
        <name value="valueQuantity"/>
        <source>
          <context value="src"/>
          <type value="Quantity"/>
          <element value="value"/>
          <variable value="s"/>
        </source>
        <target>
          <transform value="copy"/>
          <parameter>
            <valueId value="tgt"/>
          </parameter>
        </target>
        <rule>
          <name value="value"/>
          <source>
            <context value="s"/>
            <element value="value"/>
            <variable value="a"/>
          </source>
          <target>
            <context value="tgt"/>
            <element value="value_as_number"/>
            <transform value="copy"/>
            <parameter>
              <valueId value="a"/>
            </parameter>
          </target>
        </rule>
        <rule>
          <name value="unit"/>
          <source>
            <context value="s"/>
            <element value="unit"/>
            <variable value="b"/>
          </source>
          <target>
            <context value="tgt"/>
            <element value="unit_concept_id"/>
            <transform value="copy"/>
            <parameter>
              <valueId value="b"/>
            </parameter>
          </target>
        </rule>
        <documentation value="src.performer as s -&gt; tgt then {"/>
      </rule>
      <rule>
        <name value="valueCodeableConcept"/>
        <source>
          <context value="src"/>
          <type value="CodeableConcept"/>
          <element value="value"/>
          <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"/>
              <variable value="a"/>
            </source>
            <target>
              <context value="tgt"/>
              <element value="value_as_concept_id"/>
              <transform value="copy"/>
              <parameter>
                <valueId value="a"/>
              </parameter>
            </target>
          </rule>
        </rule>
      </rule>
      <rule>
        <name value="valueString"/>
        <source>
          <context value="src"/>
          <type value="string"/>
          <element value="value"/>
          <variable value="b"/>
        </source>
        <target>
          <context value="tgt"/>
          <element value="value_as_string"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="b"/>
          </parameter>
        </target>
      </rule>
      <rule>
        <name value="note"/>
        <source>
          <context value="src"/>
          <element value="note"/>
          <variable value="d"/>
        </source>
        <target>
          <context value="tgt"/>
          <element value="observation_source_value"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="d"/>
          </parameter>
        </target>
      </rule>
    </rule>
  </group>
</StructureMap>