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 |
{
"resourceType" : "StructureMap",
"id" : "AllergyMap",
"language" : "en",
"text" : {
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"div" : "<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\">\r\n<span style=\"color: #cc00cc\">/// <b>url</b> = </span><span style=\"color: blue\">'http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap'</span>\r\n<span style=\"color: #cc00cc\">/// <b>name</b> = </span><span style=\"color: blue\">'AllergyMap'</span>\r\n<span style=\"color: #cc00cc\">/// <b>title</b> = </span><span style=\"color: blue\">'Mapping Allergy resource to Observation OMOP Domain'</span>\r\n<span style=\"color: #cc00cc\">/// <b>status</b> = </span><span style=\"color: blue\">'active'</span>\r\n<span style=\"color: #cc00cc\">/// <b>description</b> = </span><span style=\"color: blue\">'This mapping maps FHIR AllergyIntolerance instances to OMOP Observation Table objects.'</span>\r\n\r\n<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>\r\n<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>\r\n\r\n<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\"> {\r\n</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\"> {\r\n</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>\r\n 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\"> {\r\n</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>\r\n 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\"> {\r\n</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\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"allergyIdFromIdentifier"</i><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"allergyId"</i><span style=\"color: navy\">;</span>\r\n <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>\r\n 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\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <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>\r\n 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\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n 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\"> {\r\n</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\"> {\r\n</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\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n 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\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n 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\"> {\r\n</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\"> {\r\n</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\"> {\r\n</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>\r\n 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>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>\r\n 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>\r\n src<b> where </b><span style=\"color: navy\">(</span>src.recordedDate.empty()<span style=\"color: navy\">)</span><b> then</b><span style=\"color: navy\"> {\r\n</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>\r\n <span style=\"color: navy\">}</span> <i>"allergyDateTime"</i><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"allergyMap"</i><span style=\"color: navy\">;</span>\r\n<span style=\"color: navy\">}\r\n\r\n</span></pre></div>"
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IG © 2023+ HL7 International / Biomedical Research and Regulation.
Package hl7.fhir.uv.omop#2.0.0-ballot based on FHIR 5.0.0.
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2026-08-14
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