FHIR to OMOP FHIR IG
1.0.0 - INFORMATIVE 1
FHIR to OMOP FHIR IG
1.0.0 - INFORMATIVE 1
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 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: Informative | Maturity Level: 1 |
@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:StructureMap ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "AllergyMap"] ; #
fhir:language [ fhir:v "en"] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div [ fhir:v "<div xml:lang=\"en\" xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: StructureMap AllergyMap</b></p><a name=\"AllergyMap\"> </a><a name=\"hcAllergyMap\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Language: en</p></div><pre class=\"fml\">#xD;\n<span style=\"color: #cc00cc\">/// <b>url</b> = </span><span style=\"color: blue\">'http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap'</span>#xD;\n<span style=\"color: #cc00cc\">/// <b>name</b> = </span><span style=\"color: blue\">'AllergyMap'</span>#xD;\n<span style=\"color: #cc00cc\">/// <b>title</b> = </span><span style=\"color: blue\">'Mapping Allergy resource to Observation OMOP Domain'</span>#xD;\n<span style=\"color: #cc00cc\">/// <b>status</b> = </span><span style=\"color: blue\">'draft'</span>#xD;\n#xD;\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>#xD;\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>#xD;\n#xD;\n<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\"> {#xD;\n</span> src.id<span style=\"color: navy\"><b> -> </b></span>tgt.observation_id = <span style=\"color: blue\">'1'</span><span style=\"color: navy\">;</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>#xD;\n src.patient<span style=\"color: navy\"><b> -> </b></span>tgt.person_id = <span style=\"color: blue\">'1'</span><span style=\"color: navy\">;</span> <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>#xD;\n src.encounter<span style=\"color: navy\"><b> -> </b></span>tgt.visit_occurrence_id = <span style=\"color: blue\">'1'</span><span style=\"color: navy\">;</span> <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>#xD;\n src.type<b> as </b><span style=\"color: maroon\">s</span><span style=\"color: navy\"><b> -> </b></span><span style=\"color: maroon\">tgt</span><b> then</b><span style=\"color: navy\"> {#xD;\n</span> s.coding<b> as </b><span style=\"color: maroon\">sc</span><span style=\"color: navy\"><b> -> </b></span><span style=\"color: maroon\">tgt</span><b> then</b><span style=\"color: navy\"> {#xD;\n</span> sc.code<b> as </b><span style=\"color: maroon\">code</span><b> where </b>(code = 'allergy')<b> then</b><span style=\"color: navy\"> {#xD;\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>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\n src.code<b> as </b><span style=\"color: maroon\">code</span><b> where </b>(code = 'intolerance')<b> then</b><span style=\"color: navy\"> {#xD;\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>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\n src.code<b> as </b><span style=\"color: maroon\">s</span><span style=\"color: navy\"><b> -> </b></span><span style=\"color: maroon\">tgt</span><b> then</b><span style=\"color: navy\"> {#xD;\n</span> s.coding<b> as </b><span style=\"color: maroon\">sc</span><span style=\"color: navy\"><b> -> </b></span><span style=\"color: maroon\">tgt</span><b> then</b><span style=\"color: navy\"> {#xD;\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>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\n <span style=\"color: navy\">}</span><span style=\"color: navy\">;</span>#xD;\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>#xD;\n<span style=\"color: navy\">}#xD;\n#xD;\n</span></pre></div>"^^rdf:XMLLiteral ]
] ; #
fhir:extension ( [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-wg> ] ;
fhir:value [
a fhir:Code ;
fhir:v "brr" ]
] [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm> ] ;
fhir:value [
a fhir:Integer ;
fhir:v 1 ;
( fhir:extension [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom> ] ;
fhir:value [
a fhir:Canonical ;
fhir:v "http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop> ] ] ) ]
] [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status> ] ;
fhir:value [
a fhir:Code ;
fhir:v "informative" ;
( fhir:extension [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom> ] ;
fhir:value [
a fhir:Canonical ;
fhir:v "http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop> ] ] ) ]
] ) ; #
fhir:url [
fhir:v "http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/omop/StructureMap/AllergyMap>
] ; #
fhir:version [ fhir:v "1.0.0"] ; #
fhir:name [ fhir:v "AllergyMap"] ; #
fhir:title [ fhir:v "Mapping Allergy resource to Observation OMOP Domain"] ; #
fhir:status [ fhir:v "draft"] ; #
fhir:date [ fhir:v "2026-04-02T22:51:15+00:00"^^xsd:dateTime] ; #
fhir:publisher [ fhir:v "HL7 International / Biomedical Research and Regulation"] ; #
fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Biomedical Research and Regulation" ] ;
( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/rcrim" ] ] )
] ) ; #
fhir:description [ fhir:v "This mapping maps FHIR AllergyIntolerance instances to OMOP Observation Table objects."] ; #
fhir:jurisdiction ( [
( fhir:coding [
fhir:system [
fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ;
fhir:l <http://unstats.un.org/unsd/methods/m49/m49.htm> ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ] ] )
] ) ; #
fhir:structure ( [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/AllergyIntolerance"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/AllergyIntolerance> ] ;
fhir:mode [ fhir:v "source" ] ;
fhir:alias [ fhir:v "Allergy" ]
] [
fhir:url [
fhir:v "http://hl7.org/fhir/uv/omop/StructureDefinition/Observation"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/omop/StructureDefinition/Observation> ] ;
fhir:mode [ fhir:v "target" ] ;
fhir:alias [ fhir:v "ObservationTable" ]
] ) ; #
fhir:group ( [
fhir:name [ fhir:v "Observation" ] ;
( fhir:input [
fhir:name [ fhir:v "src" ] ;
fhir:type [ fhir:v "Allergy" ] ;
fhir:mode [ fhir:v "source" ] ] [
fhir:name [ fhir:v "tgt" ] ;
fhir:type [ fhir:v "ObservationTable" ] ;
fhir:mode [ fhir:v "target" ] ] ) ;
( fhir:rule [
fhir:name [ fhir:v "id" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "id" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "observation_id" ] ;
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:String ;
fhir:v "1" ] ] ) ] ) ;
fhir:documentation [ fhir:v "OMOP Observation ID would be a map from FHIR ID to an external key" ] ] [
fhir:name [ fhir:v "patient" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "patient" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "person_id" ] ;
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:String ;
fhir:v "1" ] ] ) ] ) ;
fhir:documentation [ fhir:v "OMOP Person ID would be a map from the FHIR Allergy Patient reference to an external key" ] ] [
fhir:name [ fhir:v "encounter" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "encounter" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "visit_occurrence_id" ] ;
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:String ;
fhir:v "1" ] ] ) ] ) ;
fhir:documentation [ fhir:v "OMOP Visit Occurrence ID would be a map from the FHIR Allergy Encounter reference to an external key" ] ] [
fhir:name [ fhir:v "type" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "type" ] ;
fhir:variable [ fhir:v "s" ] ] ) ;
( fhir:target [
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "tgt" ] ] ) ] ) ;
( fhir:rule [
fhir:name [ fhir:v "coding" ] ;
( fhir:source [
fhir:context [ fhir:v "s" ] ;
fhir:element [ fhir:v "coding" ] ;
fhir:variable [ fhir:v "sc" ] ] ) ;
( fhir:target [
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "tgt" ] ] ) ] ) ;
( fhir:rule [
fhir:name [ fhir:v "code" ] ;
( fhir:source [
fhir:context [ fhir:v "sc" ] ;
fhir:element [ fhir:v "code" ] ;
fhir:variable [ fhir:v "code" ] ;
fhir:condition [ fhir:v "(code = 'allergy')" ] ] ) ;
( fhir:rule [
fhir:name [ fhir:v "category" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "category" ] ;
fhir:variable [ fhir:v "category" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "observation_concept_id" ] ;
fhir:transform [ fhir:v "translate" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "category" ] ] [
fhir:value [
a fhir:String ;
fhir:v "http://hl7.org/fhir/uv/omop/ConceptMap/AllergyType" ] ] [
fhir:value [
a fhir:String ;
fhir:v "code" ] ] ) ] ) ] ) ] [
fhir:name [ fhir:v "code" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "code" ] ;
fhir:variable [ fhir:v "code" ] ;
fhir:condition [ fhir:v "(code = 'intolerance')" ] ] ) ;
( fhir:rule [
fhir:name [ fhir:v "category" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "category" ] ;
fhir:variable [ fhir:v "category" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "observation_concept_id" ] ;
fhir:transform [ fhir:v "translate" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "category" ] ] [
fhir:value [
a fhir:String ;
fhir:v "http://hl7.org/fhir/uv/omop/ConceptMap/IntoleranceType" ] ] [
fhir:value [
a fhir:String ;
fhir:v "code" ] ] ) ] ) ] ) ] ) ] ) ] [
fhir:name [ fhir:v "code" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:element [ fhir:v "code" ] ;
fhir:variable [ fhir:v "s" ] ] ) ;
( fhir:target [
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "tgt" ] ] ) ] ) ;
( fhir:rule [
fhir:name [ fhir:v "coding" ] ;
( fhir:source [
fhir:context [ fhir:v "s" ] ;
fhir:element [ fhir:v "coding" ] ;
fhir:variable [ fhir:v "sc" ] ] ) ;
( fhir:target [
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "tgt" ] ] ) ] ) ;
( fhir:rule [
fhir:name [ fhir:v "code" ] ;
( fhir:source [
fhir:context [ fhir:v "sc" ] ;
fhir:element [ fhir:v "code" ] ;
fhir:variable [ fhir:v "code" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "value_as_concept_id" ] ;
fhir:transform [ fhir:v "translate" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "code" ] ] [
fhir:value [
a fhir:String ;
fhir:v "http://hl7.org/fhir/uv/omop/ConceptMap/AllergySubstanceType" ] ] [
fhir:value [
a fhir:String ;
fhir:v "code" ] ] ) ] [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "value_source_value" ] ;
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "code" ] ] ) ] ) ] ) ] ) ] [
fhir:name [ fhir:v "recordedDateDateTime" ] ;
( fhir:source [
fhir:context [ fhir:v "src" ] ;
fhir:type [ fhir:v "dateTime" ] ;
fhir:element [ fhir:v "recordedDate" ] ;
fhir:variable [ fhir:v "osd" ] ] ) ;
( fhir:target [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "observation_date" ] ;
fhir:transform [ fhir:v "evaluate" ] ;
( fhir:parameter [
fhir:value [
a fhir:String ;
fhir:v "src.recordedDate.toString().substring(0, 10)" ] ] ) ] [
fhir:context [ fhir:v "tgt" ] ;
fhir:element [ fhir:v "observation_datetime" ] ;
fhir:transform [ fhir:v "copy" ] ;
( fhir:parameter [
fhir:value [
a fhir:Id ;
fhir:v "osd" ] ] ) ] ) ] )
] ) . #
IG © 2023+ HL7 International / Biomedical Research and Regulation.
Package hl7.fhir.uv.omop#1.0.0 based on FHIR 5.0.0.
Generated
2026-04-02
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