Data Management with FHIR
0.1.0 - ci-build

Data Management with FHIR - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

## : Mapping simple Observation laboratory resources to Measurement OMOP Domain - JSON Representation

Draft as of 2025-10-23

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    {
      "resourceType" : "StructureMap",
      "id" : "CoreSimpleObservation2OMOPMeasurement",
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Narratif généré : StructureMap CoreSimpleObservation2OMOPMeasurement</b></p><a name=\"CoreSimpleObservation2OMOPMeasurement\"> </a><a name=\"hcCoreSimpleObservation2OMOPMeasurement\"> </a><pre class=\"fml\">\r\n<b>map</b><span style=\"color: navy\"> &quot;</span>https://interop.aphp.fr/ig/fhir/dm/StructureMap/CoreSimpleObservation2OMOPMeasurement<span style=\"color: navy\">&quot; = &quot;</span>CoreSimpleObservation2OMOPMeasurement<span style=\"color: navy\">&quot;\r\n\r\n</span><span style=\"color: navy\">// </span><span style=\"color: green\">Mapping simple Observation laboratory resources to Measurement OMOP Domain</span>\r\n\r\n<b>uses</b><span style=\"color: navy\"> &quot;</span><a href=\"http://hl7.org/fhir/R4/observation.html\" title=\"Observation\">http://hl7.org/fhir/StructureDefinition/Observation</a><span style=\"color: navy\">&quot; </span><b>alias </b>LabObs <b>as </b><b>source</b>\r\n<b>uses</b><span style=\"color: navy\"> &quot;</span><a href=\"StructureDefinition-OMOPMeasurement.html\" title=\"Measurement OMOP Table\">https://interop.aphp.fr/ig/fhir/dm/StructureDefinition/OMOPMeasurement</a><span style=\"color: navy\">&quot; </span><b>alias </b>MeasurementTable <b>as </b><b>target</b>\r\n\r\n<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\"> {\r\n</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>\r\n  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\"> {\r\n</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.aphp.fr/ig/fhir/dm/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>\r\n  <span style=\"color: navy\">}</span> <i>&quot;createMeasurementConcept&quot;</i><span style=\"color: navy\">;</span>\r\n  src.effective<span style=\"color: navy\"> : </span>dateTime<b> as </b><span style=\"color: maroon\">srcDateTime</span><b> then</b><span style=\"color: navy\"> {\r\n</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>\r\n    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>\r\n  <span style=\"color: navy\">}</span> <i>&quot;SetDate&quot;</i><span style=\"color: navy\">;</span>\r\n  src.value<span style=\"color: navy\"> : </span>Quantity<b> as </b><span style=\"color: maroon\">srcValueQuantity</span><b> then</b><span style=\"color: navy\"> {\r\n</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>\r\n    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\"> {\r\n</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.aphp.fr/ig/fhir/dm/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>\r\n    <span style=\"color: navy\">}</span> <i>&quot;createComparatorConcept&quot;</i><span style=\"color: navy\">;</span>\r\n    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\"> {\r\n</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.aphp.fr/ig/fhir/dm/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>\r\n    <span style=\"color: navy\">}</span> <i>&quot;setUnitConcept&quot;</i><span style=\"color: navy\">;</span>\r\n    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>\r\n  <span style=\"color: navy\">}</span> <i>&quot;SetValue&quot;</i><span style=\"color: navy\">;</span>\r\n  src.referenceRange<b> as </b><span style=\"color: maroon\">srcRange</span><b> then</b><span style=\"color: navy\"> {\r\n</span>    srcRange.low<b> as </b><span style=\"color: maroon\">srcRangeLow</span><b> then</b><span style=\"color: navy\"> {\r\n</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>\r\n    <span style=\"color: navy\">}</span> <i>&quot;setRangeLow0&quot;</i><span style=\"color: navy\">;</span>\r\n    srcRange.high<b> as </b><span style=\"color: maroon\">srcRangeHigh</span><b> then</b><span style=\"color: navy\"> {\r\n</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>\r\n    <span style=\"color: navy\">}</span> <i>&quot;setRangeHigh0&quot;</i><span style=\"color: navy\">;</span>\r\n  <span style=\"color: navy\">}</span> <i>&quot;setRange&quot;</i><span style=\"color: navy\">;</span>\r\n  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>\r\n<span style=\"color: navy\">}\r\n\r\n</span></pre></div>"
      },
      "url" : "https://interop.aphp.fr/ig/fhir/dm/StructureMap/CoreSimpleObservation2OMOPMeasurement",
      "version" : "0.1.0",
      "name" : "CoreSimpleObservation2OMOPMeasurement",
      "title" : "Mapping simple Observation laboratory resources to Measurement OMOP Domain",
      "status" : "draft",
      "date" : "2025-10-23T20:49:03+00:00",
      "publisher" : "AP-HP",
      "contact" : [
        {
          "name" : "AP-HP",
          "telecom" : [
            {
              "system" : "url",
              "value" : "https://aphp.fr"
            }
          ]
        }
      ],
      "description" : "Mapping simple Observation laboratory resources to Measurement OMOP Domain",
      "jurisdiction" : [
        {
          "coding" : [
            {
              "system" : "urn:iso:std:iso:3166",
              "code" : "FR",
              "display" : "France"
            }
          ]
        }
      ],
      "structure" : [
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          "url" : "http://hl7.org/fhir/StructureDefinition/Observation",
          "mode" : "source",
          "alias" : "LabObs"
        },
        {
          "url" : "https://interop.aphp.fr/ig/fhir/dm/StructureDefinition/OMOPMeasurement",
          "mode" : "target",
          "alias" : "MeasurementTable"
        }
      ],
      "group" : [
        {
          "name" : "SimpleObservation",
          "typeMode" : "none",
          "input" : [
            {
              "name" : "src",
              "type" : "LabObs",
              "mode" : "source"
            },
            {
              "name" : "tgt",
              "type" : "MeasurementTable",
              "mode" : "target"
            }
          ],
          "rule" : [
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              "name" : "setSubject",
              "source" : [
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                  "context" : "src",
                  "element" : "subject",
                  "variable" : "srcSubject"
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              ],
              "target" : [
                {
                  "context" : "tgt",
                  "contextType" : "variable",
                  "element" : "person_id",
                  "transform" : "copy",
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                      "valueId" : "srcSubject"
                    }
                  ]
                }
              ],
              "documentation" : "reference impropre dans le monde OMOP mais permet d'illustrer l'information qui doit être utilisée pour retrouver la bonne OMOPPerson"
            },
            {
              "name" : "createMeasurementConcept",
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                {
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                  "element" : "code",
                  "variable" : "srcCode"
                }
              ],
              "target" : [
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                  "contextType" : "variable",
                  "element" : "measurement_concept_id",
                  "variable" : "tgtReference",
                  "transform" : "create",
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                    }
                  ]
                }
              ],
              "rule" : [
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                  "name" : "setMeasurementConcept",
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                      "context" : "srcCode",
                      "element" : "coding",
                      "variable" : "srcCoding"
                    }
                  ],
                  "target" : [
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                      "variable" : "measurementCode",
                      "transform" : "translate",
                      "parameter" : [
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                        },
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                          "valueString" : "https://interop.aphp.fr/ig/fhir/dm/ConceptMap/LabAnalyses"
                        },
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                        }
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                        },
                        {
                          "valueId" : "measurementCode"
                        }
                      ]
                    }
                  ]
                }
              ]
            },
            {
              "name" : "SetDate",
              "source" : [
                {
                  "context" : "src",
                  "type" : "dateTime",
                  "element" : "effective",
                  "variable" : "srcDateTime"
                }
              ],
              "rule" : [
                {
                  "name" : "setDateTime",
                  "source" : [
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                      "context" : "srcDateTime"
                    }
                  ],
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                      "contextType" : "variable",
                      "element" : "measurement_datetime",
                      "transform" : "copy",
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                        }
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                }
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                      "source" : [
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                          "variable" : "srcRangeLowValue"
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            }
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