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" : "MeasurementMap",
"language" : "en",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: StructureMap MeasurementMap</b></p><a name=\"MeasurementMap\"> </a><a name=\"hcMeasurementMap\"> </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/MeasurementMap'</span>\r\n<span style=\"color: #cc00cc\">/// <b>name</b> = </span><span style=\"color: blue\">'MeasurementMap'</span>\r\n<span style=\"color: #cc00cc\">/// <b>title</b> = </span><span style=\"color: blue\">'Mapping Observation resource to Measurement 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 Observation instances that are considered measurements to OMOP Measurement Table objects. Currently, this is done by considering the category code and mapping \\'vital-signs\\' and \\'laboratory\\' Observations.'</span>\r\n\r\n<b>uses</b><span style=\"color: navy\"> "</span><a href=\"http://hl7.org/fhir/R5/observation.html\" title=\"Observation\">http://hl7.org/fhir/StructureDefinition/Observation</a><span style=\"color: navy\">" </span><b>alias </b>Observation <b>as </b><b>source</b>\r\n<b>uses</b><span style=\"color: navy\"> "</span><a href=\"StructureDefinition-Measurement.html\" title=\"Measurement OMOP Table\">http://hl7.org/fhir/uv/omop/StructureDefinition/Measurement</a><span style=\"color: navy\">" </span><b>alias </b>MeasureTable <b>as </b><b>target</b>\r\n\r\n<b>group </b>Measures<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>MeasureTable<span style=\"color: navy\">)</span><span style=\"color: navy\"> {\r\n</span> src<b> where </b><span style=\"color: navy\">(</span>src.category.coding.code contains 'laboratory'<span style=\"color: navy\">)</span><b> then</b><span style=\"color: navy\"> {\r\n</span> src<b> where </b><span style=\"color: navy\">(</span>src.effective.empty().not()<span style=\"color: navy\">)</span><b> then</b><span style=\"color: navy\"> {\r\n</span> 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.measurement_id = <b>cast</b><span style=\"color: navy\">(</span><span style=\"color: maroon\">id</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> <i>"measureID"</i><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.code<b> as </b><span style=\"color: maroon\">a</span><span style=\"color: navy\"><b> -> </b></span>tgt.measurement_concept_id = <span style=\"color: maroon\">a</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>"MeasurementConcept"</i><span style=\"color: navy\">;</span>\r\n src.subject<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 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.effective<span style=\"color: navy\"> : </span>dateTime<b> as </b><span style=\"color: maroon\">edt</span><span style=\"color: navy\"><b> -> </b></span> tgt.measurement_datetime = <span style=\"color: maroon\">edt</span><span style=\"color: navy\">, </span> tgt.measurement_date = <span style=\"color: navy\">(</span>edt.toString().substring(0, 10)<span style=\"color: navy\">)</span><span style=\"color: navy\">;</span>\r\n src.effective<span style=\"color: navy\"> : </span>instant<b> as </b><span style=\"color: maroon\">einst</span><span style=\"color: navy\"><b> -> </b></span> tgt.measurement_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> <span style=\"color: navy\">(</span>einst.toString().substring(0, 10)<span style=\"color: navy\">)</span><span style=\"color: navy\">;</span>\r\n src.effective<span style=\"color: navy\"> : </span>Period<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.start<b> as </b><span style=\"color: maroon\">eps</span><span style=\"color: navy\"><b> -> </b></span> tgt.measurement_datetime = <b>cast</b><span style=\"color: navy\">(</span><span style=\"color: maroon\">eps</span><span style=\"color: navy\">, </span><span style=\"color: blue\">'dateTime'</span><span style=\"color: navy\">)</span><span style=\"color: navy\">, </span> tgt.measurement_date = <span style=\"color: navy\">(</span>eps.toString().substring(0, 10)<span style=\"color: navy\">)</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"MeasurementDate"</i><span style=\"color: navy\">;</span>\r\n <span style=\"color: #b36b00\" title=\"This element was not defined prior to R5\">// src.issued as s where (src.issued.toDate() != src.effective) -> tgt.measurement_source_value = (s.toString());</span>\r\n src.category<span style=\"color: navy\"><b> -> </b></span>tgt.measurement_type_concept_id = <span style=\"color: blue\">32817</span> <i>"EHR"</i><span style=\"color: navy\">;</span>\r\n src.performer<b> as </b><span style=\"color: maroon\">performer</span><span style=\"color: navy\"><b> -> </b></span>tgt<b> then</b><span style=\"color: navy\"> {\r\n</span> performer.reference<b> as </b><span style=\"color: maroon\">p</span><span style=\"color: navy\"><b> -> </b></span>tgt.provider_id = <span style=\"color: navy\">(</span>%p.substring(%p.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.value<span style=\"color: navy\"> : </span>Quantity<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.value<b> as </b><span style=\"color: maroon\">a</span><span style=\"color: navy\"><b> -> </b></span>tgt.value_as_number = <b>cast</b><span style=\"color: navy\">(</span><span style=\"color: maroon\">a</span><span style=\"color: navy\">, </span><span style=\"color: blue\">'decimal'</span><span style=\"color: navy\">)</span><span style=\"color: navy\">;</span>\r\n s.unit<b> as </b><span style=\"color: maroon\">b</span><span style=\"color: navy\"><b> -> </b></span>tgt.unit_concept_id = <span style=\"color: maroon\">b</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"QuantityValue"</i><span style=\"color: navy\">;</span>\r\n src.value<span style=\"color: navy\"> : </span>CodeableConcept<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\">a</span><span style=\"color: navy\"><b> -> </b></span>tgt.value_as_concept_id = <span style=\"color: maroon\">a</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>"CodeableConceptValue"</i><span style=\"color: navy\">;</span>\r\n src.value<span style=\"color: navy\"> : </span>string<b> as </b><span style=\"color: maroon\">b</span><span style=\"color: navy\"><b> -> </b></span>tgt.value_source_value = <span style=\"color: maroon\">b</span><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"OnlyMeasures"</i><span style=\"color: navy\">;</span>\r\n <span style=\"color: navy\">}</span> <i>"measurementMap"</i><span style=\"color: navy\">;</span>\r\n<span style=\"color: navy\">}\r\n\r\n</span></pre></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "brr"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger" : 2,
"_valueInteger" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical" : "http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"
}
]
}
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode" : "trial-use",
"_valueCode" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
"valueCanonical" : "http://hl7.org/fhir/uv/omop/ImplementationGuide/hl7.fhir.uv.omop"
}
]
}
}
],
"url" : "http://hl7.org/fhir/uv/omop/StructureMap/MeasurementMap",
"identifier" : [
{
"system" : "urn:ietf:rfc:3986",
"value" : "urn:oid:2.16.840.1.113883.4.642.40.77.43.6"
}
],
"version" : "2.0.0-ballot",
"name" : "MeasurementMap",
"title" : "Mapping Observation resource to Measurement OMOP Domain",
"status" : "active",
"date" : "2026-08-14T16:09:20+00:00",
"publisher" : "HL7 International / Biomedical Research and Regulation",
"contact" : [
{
"name" : "HL7 International / Biomedical Research and Regulation",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/rcrim"
}
]
}
],
"description" : "This mapping maps FHIR Observation instances that are considered measurements to OMOP Measurement Table objects. Currently, this is done by considering the category code and mapping 'vital-signs' and 'laboratory' Observations.",
"jurisdiction" : [
{
"coding" : [
{
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"structure" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/Observation",
"mode" : "source",
"alias" : "Observation"
},
{
"url" : "http://hl7.org/fhir/uv/omop/StructureDefinition/Measurement",
"mode" : "target",
"alias" : "MeasureTable"
}
],
"group" : [
{
"name" : "Measures",
"input" : [
{
"name" : "src",
"type" : "Observation",
"mode" : "source"
},
{
"name" : "tgt",
"type" : "MeasureTable",
"mode" : "target"
}
],
"rule" : [
{
"name" : "measurementMap",
"source" : [
{
"context" : "src",
"condition" : "src.category.coding.code contains 'laboratory'"
}
],
"rule" : [
{
"name" : "OnlyMeasures",
"source" : [
{
"context" : "src",
"condition" : "src.effective.empty().not()"
}
],
"rule" : [
{
"name" : "measureID",
"source" : [
{
"context" : "src",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "id",
"source" : [
{
"context" : "s",
"element" : "id",
"variable" : "id"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_id",
"transform" : "cast",
"parameter" : [
{
"valueId" : "id"
},
{
"valueString" : "code"
}
]
}
]
}
]
},
{
"name" : "MeasurementConcept",
"source" : [
{
"context" : "src",
"element" : "code",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "coding",
"source" : [
{
"context" : "s",
"element" : "coding",
"variable" : "sc"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "code",
"source" : [
{
"context" : "sc",
"element" : "code",
"variable" : "a"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_concept_id",
"transform" : "copy",
"parameter" : [
{
"valueId" : "a"
}
]
}
]
}
]
}
]
},
{
"name" : "subject",
"source" : [
{
"context" : "src",
"element" : "subject",
"variable" : "subject"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "reference",
"source" : [
{
"context" : "subject",
"element" : "reference",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt",
"element" : "person_id",
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "%s.substring(%s.indexOf('/') + 1)"
}
]
}
]
}
]
},
{
"name" : "encounter",
"source" : [
{
"context" : "src",
"element" : "encounter",
"variable" : "encounter"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "reference",
"source" : [
{
"context" : "encounter",
"element" : "reference",
"variable" : "e"
}
],
"target" : [
{
"context" : "tgt",
"element" : "visit_occurrence_id",
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "%e.substring(%e.indexOf('/') + 1)"
}
]
}
]
}
]
},
{
"name" : "effectiveDateTime",
"source" : [
{
"context" : "src",
"type" : "dateTime",
"element" : "effective",
"variable" : "edt"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_datetime",
"transform" : "copy",
"parameter" : [
{
"valueId" : "edt"
}
]
},
{
"context" : "tgt",
"element" : "measurement_date",
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "edt.toString().substring(0, 10)"
}
]
}
]
},
{
"name" : "effectiveInstant",
"source" : [
{
"context" : "src",
"type" : "instant",
"element" : "effective",
"variable" : "einst"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_datetime",
"transform" : "cast",
"parameter" : [
{
"valueId" : "einst"
},
{
"valueString" : "dateTime"
}
]
},
{
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "einst.toString().substring(0, 10)"
}
]
}
]
},
{
"name" : "MeasurementDate",
"source" : [
{
"context" : "src",
"type" : "Period",
"element" : "effective",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "start",
"source" : [
{
"context" : "s",
"element" : "start",
"variable" : "eps"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_datetime",
"transform" : "cast",
"parameter" : [
{
"valueId" : "eps"
},
{
"valueString" : "dateTime"
}
]
},
{
"context" : "tgt",
"element" : "measurement_date",
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "eps.toString().substring(0, 10)"
}
]
}
]
}
]
},
{
"name" : "EHR",
"source" : [
{
"context" : "src",
"element" : "category"
}
],
"target" : [
{
"context" : "tgt",
"element" : "measurement_type_concept_id",
"transform" : "copy",
"parameter" : [
{
"valueInteger" : 32817
}
]
}
],
"documentation" : "src.issued as s where (src.issued.toDate() != src.effective) -> tgt.measurement_source_value = (s.toString());"
},
{
"name" : "performer",
"source" : [
{
"context" : "src",
"element" : "performer",
"variable" : "performer"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "reference",
"source" : [
{
"context" : "performer",
"element" : "reference",
"variable" : "p"
}
],
"target" : [
{
"context" : "tgt",
"element" : "provider_id",
"transform" : "evaluate",
"parameter" : [
{
"valueString" : "%p.substring(%p.indexOf('/') + 1)"
}
]
}
]
}
]
},
{
"name" : "QuantityValue",
"source" : [
{
"context" : "src",
"type" : "Quantity",
"element" : "value",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "value",
"source" : [
{
"context" : "s",
"element" : "value",
"variable" : "a"
}
],
"target" : [
{
"context" : "tgt",
"element" : "value_as_number",
"transform" : "cast",
"parameter" : [
{
"valueId" : "a"
},
{
"valueString" : "decimal"
}
]
}
]
},
{
"name" : "unit",
"source" : [
{
"context" : "s",
"element" : "unit",
"variable" : "b"
}
],
"target" : [
{
"context" : "tgt",
"element" : "unit_concept_id",
"transform" : "copy",
"parameter" : [
{
"valueId" : "b"
}
]
}
]
}
]
},
{
"name" : "CodeableConceptValue",
"source" : [
{
"context" : "src",
"type" : "CodeableConcept",
"element" : "value",
"variable" : "s"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "coding",
"source" : [
{
"context" : "s",
"element" : "coding",
"variable" : "sc"
}
],
"target" : [
{
"context" : "tgt"
}
],
"rule" : [
{
"name" : "code",
"source" : [
{
"context" : "sc",
"element" : "code",
"variable" : "a"
}
],
"target" : [
{
"context" : "tgt",
"element" : "value_as_concept_id",
"transform" : "copy",
"parameter" : [
{
"valueId" : "a"
}
]
}
]
}
]
}
]
},
{
"name" : "valueString",
"source" : [
{
"context" : "src",
"type" : "string",
"element" : "value",
"variable" : "b"
}
],
"target" : [
{
"context" : "tgt",
"element" : "value_source_value",
"transform" : "copy",
"parameter" : [
{
"valueId" : "b"
}
]
}
]
}
]
}
]
}
]
}
]
}
IG © 2023+ HL7 International / Biomedical Research and Regulation.
Package hl7.fhir.uv.omop#2.0.0-ballot based on FHIR 5.0.0.
Generated
2026-08-14
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change