Guide d'implémentation du GT Standards et Interopérabilité pour les EDS
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: Mapping simple Observation laboratory resources to Measurement OMOP Domain - XML Representation

Draft as of 2024-10-08

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<StructureMap xmlns="http://hl7.org/fhir">
  <id value="SimpleObservation"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: StructureMap SimpleObservation</b></p><a name="SimpleObservation"> </a><a name="hcSimpleObservation"> </a><a name="SimpleObservation-fr-FR"> </a><pre class="fml">
<b>map</b><span style="color: navy"> &quot;</span>https://interop.esante.gouv.fr/ig/fhir/eds/StructureMap/SimpleObservation<span style="color: navy">&quot; = &quot;</span>SimpleObservation<span style="color: navy">&quot;

</span><span style="color: navy">// </span><span style="color: green">Mapping simple Observation laboratory resources to Measurement OMOP Domain</span>

<b>uses</b><span style="color: navy"> &quot;</span><a href="StructureDefinition-EDSObservationLaboratoryGeneric.html" title="Résultat de laboratoire">https://interop.esante.gouv.fr/ig/fhir/eds/StructureDefinition/EDSObservationLaboratoryGeneric</a><span style="color: navy">&quot; </span><b>alias </b>LabObs <b>as </b><b>source</b>
<b>uses</b><span style="color: navy"> &quot;</span><a href="StructureDefinition-OMOPMeasurement.html" title="Measurement OMOP Table">https://interop.esante.gouv.fr/ig/fhir/eds/StructureDefinition/OMOPMeasurement</a><span style="color: navy">&quot; </span><b>alias </b>MeasurementTable <b>as </b><b>target</b>

<b>group </b>SimpleObservation<span style="color: navy">(</span><b>source</b> <span style="color: maroon">src</span><span style="color: navy"> : </span>LabObs, <b>target</b> <span style="color: maroon">tgt</span><span style="color: navy"> : </span>MeasurementTable<span style="color: navy">)</span><span style="color: navy"> {
</span>  src.subject<b> as </b><span style="color: maroon">srcSubject</span><span style="color: navy"><b> -&gt; </b></span>tgt.person_id = <span style="color: maroon">srcSubject</span> <i>&quot;setSubject&quot;</i><span style="color: navy">;</span> <span style="color: navy">// </span><span style="color: green">reference impropre dans le monde OMOP mais permet d'illustrer l'information qui doit être utilisée pour retrouver la bonne OMOPPerson</span>
  src.code<b> as </b><span style="color: maroon">srcCode</span><span style="color: navy"><b> -&gt; </b></span>tgt.measurement_concept_id = <b>create</b><span style="color: navy">(</span><span style="color: blue">'Reference'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">tgtReference</span><b> then</b><span style="color: navy"> {
</span>    srcCode.coding<b> as </b><span style="color: maroon">srcCoding</span><span style="color: navy"><b> -&gt; </b></span> <b>translate</b><span style="color: navy">(</span><span style="color: maroon">srcCoding</span><span style="color: navy">, </span><span style="color: blue">'https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabAnalyses'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">measurementCode</span><span style="color: navy">, </span> tgtReference.reference = <b>append</b><span style="color: navy">(</span><span style="color: blue">'Concept/'</span><span style="color: navy">, </span><span style="color: maroon">measurementCode</span><span style="color: navy">)</span> <i>&quot;setMeasurementConcept&quot;</i><span style="color: navy">;</span>
  <span style="color: navy">}</span> <i>&quot;createMeasurementConcept&quot;</i><span style="color: navy">;</span>
  src.effective<span style="color: navy"> : </span>dateTime<b> as </b><span style="color: maroon">srcDateTime</span><b> then</b><span style="color: navy"> {
</span>    srcDateTime<span style="color: navy"><b> -&gt; </b></span>tgt.measurement_datetime = <span style="color: maroon">srcDateTime</span> <i>&quot;setDateTime&quot;</i><span style="color: navy">;</span>
    srcDateTime<span style="color: navy"><b> -&gt; </b></span>tgt.measurement_date = <span style="color: navy">(</span>%srcDateTime.toString().substring(0, 10)<span style="color: navy">)</span> <i>&quot;setDateNotTime&quot;</i><span style="color: navy">;</span>
  <span style="color: navy">}</span> <i>&quot;SetDate&quot;</i><span style="color: navy">;</span>
  src.value<span style="color: navy"> : </span>Quantity<b> as </b><span style="color: maroon">srcValueQuantity</span><b> then</b><span style="color: navy"> {
</span>    srcValueQuantity.value<b> as </b><span style="color: maroon">srcResultValue</span><span style="color: navy"><b> -&gt; </b></span>tgt.value_as_number = <span style="color: maroon">srcResultValue</span> <i>&quot;setResultValue&quot;</i><span style="color: navy">;</span>
    srcValueQuantity<span style="color: navy"><b> -&gt; </b></span>tgt.operator_concept_id = <b>create</b><span style="color: navy">(</span><span style="color: blue">'Reference'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">tgtReference</span><b> then</b><span style="color: navy"> {
</span>      srcValueQuantity.comparator<b> as </b><span style="color: maroon">srcValueComparator</span><span style="color: navy"><b> -&gt; </b></span> <b>translate</b><span style="color: navy">(</span><span style="color: maroon">srcValueComparator</span><span style="color: navy">, </span><span style="color: blue">'https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabComparator'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">comparatorCode</span><span style="color: navy">, </span> tgtReference.reference = <b>append</b><span style="color: navy">(</span><span style="color: blue">'Concept/'</span><span style="color: navy">, </span><span style="color: maroon">comparatorCode</span><span style="color: navy">)</span> <i>&quot;setComparatorConcept&quot;</i><span style="color: navy">;</span>
    <span style="color: navy">}</span> <i>&quot;createComparatorConcept&quot;</i><span style="color: navy">;</span>
    srcValueQuantity<span style="color: navy"><b> -&gt; </b></span>tgt.unit_concept_id = <b>create</b><span style="color: navy">(</span><span style="color: blue">'Reference'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">tgtReference</span><b> then</b><span style="color: navy"> {
</span>      srcValueQuantity.code<b> as </b><span style="color: maroon">srcValueCode</span><span style="color: navy"><b> -&gt; </b></span> <b>translate</b><span style="color: navy">(</span><span style="color: maroon">srcValueCode</span><span style="color: navy">, </span><span style="color: blue">'https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabUnit'</span><span style="color: navy">, </span><span style="color: blue">'code'</span><span style="color: navy">)</span><b> as </b><span style="color: maroon">unitCode</span><span style="color: navy">, </span> tgtReference.reference = <b>append</b><span style="color: navy">(</span><span style="color: blue">'Concept/'</span><span style="color: navy">, </span><span style="color: maroon">unitCode</span><span style="color: navy">)</span> <i>&quot;createUnitConcept&quot;</i><span style="color: navy">;</span>
    <span style="color: navy">}</span> <i>&quot;setUnitConcept&quot;</i><span style="color: navy">;</span>
    srcValueQuantity.code<b> as </b><span style="color: maroon">srcValueCode</span><span style="color: navy"><b> -&gt; </b></span>tgt.unit_source_value = <span style="color: maroon">srcValueCode</span> <i>&quot;setUnitSourceValue&quot;</i><span style="color: navy">;</span>
  <span style="color: navy">}</span> <i>&quot;SetValue&quot;</i><span style="color: navy">;</span>
  src.referenceRange<b> as </b><span style="color: maroon">srcRange</span><b> then</b><span style="color: navy"> {
</span>    srcRange.low<b> as </b><span style="color: maroon">srcRangeLow</span><b> then</b><span style="color: navy"> {
</span>      srcRangeLow.value<b> as </b><span style="color: maroon">srcRangeLowValue</span><span style="color: navy"><b> -&gt; </b></span>tgt.range_low = <span style="color: maroon">srcRangeLowValue</span> <i>&quot;setRangeLow1&quot;</i><span style="color: navy">;</span>
    <span style="color: navy">}</span> <i>&quot;setRangeLow0&quot;</i><span style="color: navy">;</span>
    srcRange.high<b> as </b><span style="color: maroon">srcRangeHigh</span><b> then</b><span style="color: navy"> {
</span>      srcRangeHigh.value<b> as </b><span style="color: maroon">srcRangeHighValue</span><span style="color: navy"><b> -&gt; </b></span>tgt.range_high = <span style="color: maroon">srcRangeHighValue</span> <i>&quot;setRangeHigh1&quot;</i><span style="color: navy">;</span>
    <span style="color: navy">}</span> <i>&quot;setRangeHigh0&quot;</i><span style="color: navy">;</span>
  <span style="color: navy">}</span> <i>&quot;setRange&quot;</i><span style="color: navy">;</span>
  src.performer<b> as </b><span style="color: maroon">srcPerformer</span><span style="color: navy"><b> -&gt; </b></span>tgt.provider_id = <span style="color: maroon">srcPerformer</span> <i>&quot;setPerformer&quot;</i><span style="color: navy">;</span> <span style="color: navy">// </span><span style="color: green">reference impropre dans le monde OMOP mais permet d'illustrer l'information qui doit être utilisée pour retrouver le bon OMOPProvider</span>
<span style="color: navy">}

</span></pre></div>
  </text>
  <url
       value="https://interop.esante.gouv.fr/ig/fhir/eds/StructureMap/SimpleObservation"/>
  <version value="0.1.0"/>
  <name value="SimpleObservation"/>
  <title
         value="Mapping simple Observation laboratory resources to Measurement OMOP Domain"/>
  <status value="draft"/>
  <date value="2024-10-08T09:22:03+00:00"/>
  <publisher value="ANS"/>
  <contact>
    <name value="ANS"/>
    <telecom>
      <system value="url"/>
      <value value="https://esante.gouv.fr"/>
    </telecom>
  </contact>
  <description
               value="Mapping simple Observation laboratory resources to Measurement OMOP Domain"/>
  <jurisdiction>
    <coding>
      <system value="urn:iso:std:iso:3166"/>
      <code value="FR"/>
      <display value="France"/>
    </coding>
  </jurisdiction>
  <structure>
    <url
         value="https://interop.esante.gouv.fr/ig/fhir/eds/StructureDefinition/EDSObservationLaboratoryGeneric"/>
    <mode value="source"/>
    <alias value="LabObs"/>
  </structure>
  <structure>
    <url
         value="https://interop.esante.gouv.fr/ig/fhir/eds/StructureDefinition/OMOPMeasurement"/>
    <mode value="target"/>
    <alias value="MeasurementTable"/>
  </structure>
  <group>
    <name value="SimpleObservation"/>
    <typeMode value="none"/>
    <input>
      <name value="src"/>
      <type value="LabObs"/>
      <mode value="source"/>
    </input>
    <input>
      <name value="tgt"/>
      <type value="MeasurementTable"/>
      <mode value="target"/>
    </input>
    <rule>
      <name value="setSubject"/>
      <source>
        <context value="src"/>
        <element value="subject"/>
        <variable value="srcSubject"/>
      </source>
      <target>
        <context value="tgt"/>
        <contextType value="variable"/>
        <element value="person_id"/>
        <transform value="copy"/>
        <parameter>
          <valueId value="srcSubject"/>
        </parameter>
      </target>
      <documentation
                     value="reference impropre dans le monde OMOP mais permet d'illustrer l'information qui doit être utilisée pour retrouver la bonne OMOPPerson"/>
    </rule>
    <rule>
      <name value="createMeasurementConcept"/>
      <source>
        <context value="src"/>
        <element value="code"/>
        <variable value="srcCode"/>
      </source>
      <target>
        <context value="tgt"/>
        <contextType value="variable"/>
        <element value="measurement_concept_id"/>
        <variable value="tgtReference"/>
        <transform value="create"/>
        <parameter>
          <valueString value="Reference"/>
        </parameter>
      </target>
      <rule>
        <name value="setMeasurementConcept"/>
        <source>
          <context value="srcCode"/>
          <element value="coding"/>
          <variable value="srcCoding"/>
        </source>
        <target>
          <contextType value="variable"/>
          <variable value="measurementCode"/>
          <transform value="translate"/>
          <parameter>
            <valueId value="srcCoding"/>
          </parameter>
          <parameter>
            <valueString
                         value="https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabAnalyses"/>
          </parameter>
          <parameter>
            <valueString value="code"/>
          </parameter>
        </target>
        <target>
          <context value="tgtReference"/>
          <contextType value="variable"/>
          <element value="reference"/>
          <transform value="append"/>
          <parameter>
            <valueString value="Concept/"/>
          </parameter>
          <parameter>
            <valueId value="measurementCode"/>
          </parameter>
        </target>
      </rule>
    </rule>
    <rule>
      <name value="SetDate"/>
      <source>
        <context value="src"/>
        <type value="dateTime"/>
        <element value="effective"/>
        <variable value="srcDateTime"/>
      </source>
      <rule>
        <name value="setDateTime"/>
        <source>
          <context value="srcDateTime"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="measurement_datetime"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="srcDateTime"/>
          </parameter>
        </target>
      </rule>
      <rule>
        <name value="setDateNotTime"/>
        <source>
          <context value="srcDateTime"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="measurement_date"/>
          <transform value="evaluate"/>
          <parameter>
            <valueString value="%srcDateTime.toString().substring(0, 10)"/>
          </parameter>
        </target>
      </rule>
    </rule>
    <rule>
      <name value="SetValue"/>
      <source>
        <context value="src"/>
        <type value="Quantity"/>
        <element value="value"/>
        <variable value="srcValueQuantity"/>
      </source>
      <rule>
        <name value="setResultValue"/>
        <source>
          <context value="srcValueQuantity"/>
          <element value="value"/>
          <variable value="srcResultValue"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="value_as_number"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="srcResultValue"/>
          </parameter>
        </target>
      </rule>
      <rule>
        <name value="createComparatorConcept"/>
        <source>
          <context value="srcValueQuantity"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="operator_concept_id"/>
          <variable value="tgtReference"/>
          <transform value="create"/>
          <parameter>
            <valueString value="Reference"/>
          </parameter>
        </target>
        <rule>
          <name value="setComparatorConcept"/>
          <source>
            <context value="srcValueQuantity"/>
            <element value="comparator"/>
            <variable value="srcValueComparator"/>
          </source>
          <target>
            <contextType value="variable"/>
            <variable value="comparatorCode"/>
            <transform value="translate"/>
            <parameter>
              <valueId value="srcValueComparator"/>
            </parameter>
            <parameter>
              <valueString
                           value="https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabComparator"/>
            </parameter>
            <parameter>
              <valueString value="code"/>
            </parameter>
          </target>
          <target>
            <context value="tgtReference"/>
            <contextType value="variable"/>
            <element value="reference"/>
            <transform value="append"/>
            <parameter>
              <valueString value="Concept/"/>
            </parameter>
            <parameter>
              <valueId value="comparatorCode"/>
            </parameter>
          </target>
        </rule>
      </rule>
      <rule>
        <name value="setUnitConcept"/>
        <source>
          <context value="srcValueQuantity"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="unit_concept_id"/>
          <variable value="tgtReference"/>
          <transform value="create"/>
          <parameter>
            <valueString value="Reference"/>
          </parameter>
        </target>
        <rule>
          <name value="createUnitConcept"/>
          <source>
            <context value="srcValueQuantity"/>
            <element value="code"/>
            <variable value="srcValueCode"/>
          </source>
          <target>
            <contextType value="variable"/>
            <variable value="unitCode"/>
            <transform value="translate"/>
            <parameter>
              <valueId value="srcValueCode"/>
            </parameter>
            <parameter>
              <valueString
                           value="https://interop.esante.gouv.fr/ig/fhir/eds/ConceptMap/LabUnit"/>
            </parameter>
            <parameter>
              <valueString value="code"/>
            </parameter>
          </target>
          <target>
            <context value="tgtReference"/>
            <contextType value="variable"/>
            <element value="reference"/>
            <transform value="append"/>
            <parameter>
              <valueString value="Concept/"/>
            </parameter>
            <parameter>
              <valueId value="unitCode"/>
            </parameter>
          </target>
        </rule>
      </rule>
      <rule>
        <name value="setUnitSourceValue"/>
        <source>
          <context value="srcValueQuantity"/>
          <element value="code"/>
          <variable value="srcValueCode"/>
        </source>
        <target>
          <context value="tgt"/>
          <contextType value="variable"/>
          <element value="unit_source_value"/>
          <transform value="copy"/>
          <parameter>
            <valueId value="srcValueCode"/>
          </parameter>
        </target>
      </rule>
    </rule>
    <rule>
      <name value="setRange"/>
      <source>
        <context value="src"/>
        <element value="referenceRange"/>
        <variable value="srcRange"/>
      </source>
      <rule>
        <name value="setRangeLow0"/>
        <source>
          <context value="srcRange"/>
          <element value="low"/>
          <variable value="srcRangeLow"/>
        </source>
        <rule>
          <name value="setRangeLow1"/>
          <source>
            <context value="srcRangeLow"/>
            <element value="value"/>
            <variable value="srcRangeLowValue"/>
          </source>
          <target>
            <context value="tgt"/>
            <contextType value="variable"/>
            <element value="range_low"/>
            <transform value="copy"/>
            <parameter>
              <valueId value="srcRangeLowValue"/>
            </parameter>
          </target>
        </rule>
      </rule>
      <rule>
        <name value="setRangeHigh0"/>
        <source>
          <context value="srcRange"/>
          <element value="high"/>
          <variable value="srcRangeHigh"/>
        </source>
        <rule>
          <name value="setRangeHigh1"/>
          <source>
            <context value="srcRangeHigh"/>
            <element value="value"/>
            <variable value="srcRangeHighValue"/>
          </source>
          <target>
            <context value="tgt"/>
            <contextType value="variable"/>
            <element value="range_high"/>
            <transform value="copy"/>
            <parameter>
              <valueId value="srcRangeHighValue"/>
            </parameter>
          </target>
        </rule>
      </rule>
    </rule>
    <rule>
      <name value="setPerformer"/>
      <source>
        <context value="src"/>
        <element value="performer"/>
        <variable value="srcPerformer"/>
      </source>
      <target>
        <context value="tgt"/>
        <contextType value="variable"/>
        <element value="provider_id"/>
        <transform value="copy"/>
        <parameter>
          <valueId value="srcPerformer"/>
        </parameter>
      </target>
      <documentation
                     value="reference impropre dans le monde OMOP mais permet d'illustrer l'information qui doit être utilisée pour retrouver le bon OMOPProvider"/>
    </rule>
  </group>
</StructureMap>