Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
StructureMaps
ConceptMaps to support translation from other standards into FHIR R4 (this may include translation from other versions of FHIR, other HL7 standards or standards outside HL7).
StructureMap-PharmacogeneticTestResult-Genomics
StructureMap to transform from the OpenEHR Pharmacogenetic Test Result archetype to a set of FHIR Observations, most likely attached as results to a structured DiagnosticReport. Only 1 level of references from the root PGx result archetype are explored for conciseness/readability
{
"resourceType": "StructureMap",
"id": "StructureMap-PharmacogeneticTestResult-Genomics",
"url": "https://fhir.nhs.uk/StructureMap/StructureMap-PharmacogeneticTestResult-Genomics",
"version": "0.1.0",
"name": "StructureMapPharmacogeneticTestResultGenomics",
"title": "StructureMap PharmacogeneticTestResult Genomics",
"status": "draft",
"date": "2025-02-14T00:00:00.000Z",
"publisher": "NHS England",
"contact": [
{
"name": "NHS England",
"telecom": [
{
"system": "email",
"value": "interoperabilityteam@nhs.net"
}
]
}
],
"description": "StructureMap to transform from the OpenEHR Pharmacogenetic Test Result archetype to a set of FHIR Observations, most likely attached as results to a structured DiagnosticReport. Only 1 level of references from the root PGx result archetype are explored for conciseness/readability",
"copyright": "Copyright © 2023+ NHS England Licensed under the Apache License, Version 2.0 (the \\\"License\\\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \\\"AS IS\\\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. HL7® FHIR® standard Copyright © 2011+ HL7 The HL7® FHIR® standard is used under the FHIR license. You may obtain a copy of the FHIR license at https://www.hl7.org/fhir/license.html.",
"structure": [
{
"url": "https://ckm.openehr.org/ckm/archetypes/1013.1.7066",
"mode": "source",
"alias": "PharmacogeneticTestResult",
"documentation": "The OpenEHR PGx logical model"
},
{
"url": "https://ckm.openehr.org/ckm/archetypes/1013.1.3748",
"mode": "source",
"alias": "KnowledgeBaseReference",
"documentation": "The OpenEHR model for citation of a digital resource"
},
{
"url": "https://ckm.openehr.org/ckm/archetypes/1013.1.3759",
"mode": "source",
"alias": "GenomicVariantResult",
"documentation": "The OpenEHR model for a variant"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype",
"mode": "target",
"alias": "Genotype",
"documentation": "The Genotype information as a FHIR Observation"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype",
"mode": "target",
"alias": "Haplotype",
"documentation": "The Haplotype information as a FHIR Observation"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant",
"mode": "target",
"alias": "Variant",
"documentation": "The Variant information as a FHIR Observation"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication",
"mode": "target",
"alias": "DiagnosticImplication",
"documentation": "The phenotypic/implication information as a FHIR Observation"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence",
"mode": "target",
"alias": "MolecularConsequence",
"documentation": "The observed effect of variants as a FHIR Observation"
},
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis",
"mode": "target",
"alias": "GenomicStudyAnalysis",
"documentation": "Analysis metadata recorded through a profile on Procedure"
}
],
"group": [
{
"name": "VariantInformation",
"typeMode": "types",
"input": [
{
"name": "source",
"type": "PharmacogeneticTestResult",
"mode": "source"
},
{
"name": "queried",
"type": "GenomicVariantResult",
"mode": "source"
},
{
"name": "target",
"type": "Variant",
"mode": "target"
},
{
"name": "produced",
"type": "GenomicStudyAnalysis",
"mode": "target"
}
],
"rule": [
{
"name": "Genesymbol",
"source": [
{
"context": "source",
"min": 1,
"max": "1",
"element": "Gene symbol",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48018-6"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.genenames.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Bioinformaticanalysisworkflow",
"source": [
{
"context": "queried",
"max": "1",
"element": "Bioinformatic analysis workflow",
"variable": "a"
}
],
"target": [
{
"context": "produced",
"contextType": "variable",
"element": "extension",
"variable": "extension",
"transform": "create",
"parameter": [
{
"valueString": "Extension"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "url",
"transform": "copy",
"parameter": [
{
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Referencegenome",
"source": [
{
"context": "queried",
"min": 1,
"max": "1",
"element": "Reference genome",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48013-7"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Variantidentification",
"source": [
{
"context": "queried",
"element": "Variant identification",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "81252-9"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Variant",
"source": [
{
"context": "queried",
"element": "Variant",
"max": "1",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "81290-9"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.genenames.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Structuredvariant",
"source": [
{
"context": "queried",
"element": "Structured variant",
"max": "1",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48019-4"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.sequenceontology.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Transcriptreferencesequence",
"source": [
{
"context": "queried",
"element": "Transcript reference sequence",
"variable": "a"
},
{
"context": "queried",
"element": "Best transcript candidate",
"variable": "b"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "51958-7"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "a"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "extension",
"variable": "extension",
"transform": "create",
"parameter": [
{
"valueString": "Extension"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "url",
"transform": "copy",
"parameter": [
{
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "b"
}
]
}
]
},
{
"name": "DNAregionname",
"source": [
{
"context": "queried",
"element": "DNA region name",
"variable": "a"
},
{
"context": "queried",
"element": "Distance from splicing site",
"variable": "b"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "81254-5"
}
]
},
{
"context": "component",
"contextType": "variable",
"variable": "range",
"element": "value",
"transform": "create",
"parameter": [
{
"valueString": "Range"
}
]
},
{
"context": "range",
"contextType": "variable",
"element": "low",
"transform": "copy",
"parameter": [
{
"valueId": "a"
}
]
},
{
"context": "range",
"contextType": "variable",
"element": "high",
"transform": "copy",
"parameter": [
{
"valueId": "b"
}
]
}
]
},
{
"name": "DNAchange",
"source": [
{
"context": "queried",
"element": "DNA change",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48004-6"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.genenames.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Aminoacidchange",
"source": [
{
"context": "queried",
"element": "Amino acid change",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48005-3"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.genenames.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Aminoacidchangetype",
"source": [
{
"context": "queried",
"element": "Amino acid change type",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48006-1"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "RNAchange",
"source": [
{
"context": "queried",
"element": "RNA change",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "''"
},
{
"valueString": "''"
},
{
"valueString": "RNA change"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "cc",
"parameter": [
{
"valueString": "http://www.genenames.org"
},
{
"valueId": "a"
}
]
}
]
},
{
"name": "Genename",
"source": [
{
"context": "queried",
"element": "Gene name",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "48018-6"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Copynumberoverlap",
"source": [
{
"context": "queried",
"element": "Copy number overlap",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "82155-3"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "qty",
"parameter": [
{
"valueId": "a"
},
{
"valueString": "{ratio}"
},
{
"valueString": "http://unitsofmeasure.org"
}
]
}
]
},
{
"name": "Partoffusion",
"source": [
{
"context": "queried",
"element": "Part of fusion",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "''"
},
{
"valueString": "''"
},
{
"valueString": "Part of fusion"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Fusionexon",
"source": [
{
"context": "queried",
"element": "Fusion exon",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "''"
},
{
"valueString": "''"
},
{
"valueString": "Fusion exon"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "ConservationScore",
"source": [
{
"context": "queried",
"element": "Score",
"variable": "a"
},
{
"context": "queried",
"element": "Conservation score knowledge base",
"variable": "b"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "''"
},
{
"valueString": "''"
},
{
"valueString": "Conservation Score"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "a"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "extension",
"variable": "extension",
"transform": "create",
"parameter": [
{
"valueString": "Extension"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "url",
"transform": "copy",
"parameter": [
{
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "b"
}
]
}
]
},
{
"name": "Readdepth",
"source": [
{
"context": "queried",
"max": "1",
"element": "Read depth",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "''"
},
{
"valueString": "''"
},
{
"valueString": "Read depth"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Alleledepth",
"source": [
{
"context": "queried",
"max": "1",
"element": "Allele depth",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "82121-5"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Allelefrequency",
"source": [
{
"context": "queried",
"max": "1",
"element": "Allele frequency",
"variable": "a"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "81258-6"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Populationallelefrequencydetails",
"source": [
{
"context": "queried",
"element": "Population allele frequency knowledge base",
"variable": "a"
},
{
"context": "queried",
"element": "Population allele frequency",
"variable": "b"
}
],
"target": [
{
"context": "target",
"contextType": "variable",
"element": "component",
"variable": "component"
},
{
"context": "component",
"contextType": "variable",
"element": "code",
"variable": "code",
"transform": "cc",
"parameter": [
{
"valueString": "http://loinc.org"
},
{
"valueString": "92821-8"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "b"
}
]
},
{
"context": "component",
"contextType": "variable",
"element": "extension",
"variable": "extension",
"transform": "create",
"parameter": [
{
"valueString": "Extension"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "url",
"transform": "copy",
"parameter": [
{
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
}
]
},
{
"context": "extension",
"contextType": "variable",
"element": "value",
"transform": "copy",
"parameter": [
{
"valueId": "a"
}
]
}
]
},
{
"name": "VCFqualityfilter",
"source": [
{
"context": "queried",
"element": "Filter name",
"variable": "a"
},
{
"context": "queried",
"element": "Description",
"variable": "b"
},
{
"context": "queried",
"element": "Filter passed",
"variable": "c"
}
],
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