{
"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",
"_filename": "examples/StructureMap-PharmacogeneticTestResult-Genomics.json",
"package_name": "uk.nhsengland.genomics.r4",
"date": "2025-02-14T00:00:00.000Z",
"group": [ {
"name": "VariantInformation",
"rule": [ {
"name": "Genesymbol",
"source": [ {
"max": "1",
"min": 1,
"context": "source",
"element": "Gene symbol",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48018-6"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.genenames.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Bioinformaticanalysisworkflow",
"source": [ {
"max": "1",
"context": "queried",
"element": "Bioinformatic analysis workflow",
"variable": "a"
} ],
"target": [ {
"context": "produced",
"element": "extension",
"variable": "extension",
"parameter": [ {
"valueString": "Extension"
} ],
"transform": "create",
"contextType": "variable"
}, {
"context": "extension",
"element": "url",
"parameter": [ {
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "extension",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Referencegenome",
"source": [ {
"max": "1",
"min": 1,
"context": "queried",
"element": "Reference genome",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48013-7"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Variantidentification",
"source": [ {
"context": "queried",
"element": "Variant identification",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "81252-9"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Variant",
"source": [ {
"max": "1",
"context": "queried",
"element": "Variant",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "81290-9"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.genenames.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Structuredvariant",
"source": [ {
"max": "1",
"context": "queried",
"element": "Structured variant",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48019-4"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.sequenceontology.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Transcriptreferencesequence",
"source": [ {
"context": "queried",
"element": "Transcript reference sequence",
"variable": "a"
}, {
"context": "queried",
"element": "Best transcript candidate",
"variable": "b"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "51958-7"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueId": "a"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "component",
"element": "extension",
"variable": "extension",
"parameter": [ {
"valueString": "Extension"
} ],
"transform": "create",
"contextType": "variable"
}, {
"context": "extension",
"element": "url",
"parameter": [ {
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "extension",
"element": "value",
"parameter": [ {
"valueId": "b"
} ],
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "DNAregionname",
"source": [ {
"context": "queried",
"element": "DNA region name",
"variable": "a"
}, {
"context": "queried",
"element": "Distance from splicing site",
"variable": "b"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "81254-5"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"variable": "range",
"parameter": [ {
"valueString": "Range"
} ],
"transform": "create",
"contextType": "variable"
}, {
"context": "range",
"element": "low",
"parameter": [ {
"valueId": "a"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "range",
"element": "high",
"parameter": [ {
"valueId": "b"
} ],
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "DNAchange",
"source": [ {
"context": "queried",
"element": "DNA change",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48004-6"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.genenames.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Aminoacidchange",
"source": [ {
"context": "queried",
"element": "Amino acid change",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48005-3"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.genenames.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Aminoacidchangetype",
"source": [ {
"context": "queried",
"element": "Amino acid change type",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48006-1"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "RNAchange",
"source": [ {
"context": "queried",
"element": "RNA change",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "RNA change"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://www.genenames.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Genename",
"source": [ {
"context": "queried",
"element": "Gene name",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48018-6"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Copynumberoverlap",
"source": [ {
"context": "queried",
"element": "Copy number overlap",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "82155-3"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueId": "a"
}, {
"valueString": "{ratio}"
}, {
"valueString": "http://unitsofmeasure.org"
} ],
"transform": "qty",
"contextType": "variable"
} ]
}, {
"name": "Partoffusion",
"source": [ {
"context": "queried",
"element": "Part of fusion",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Part of fusion"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Fusionexon",
"source": [ {
"context": "queried",
"element": "Fusion exon",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Fusion exon"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "ConservationScore",
"source": [ {
"context": "queried",
"element": "Score",
"variable": "a"
}, {
"context": "queried",
"element": "Conservation score knowledge base",
"variable": "b"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Conservation Score"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueId": "a"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "component",
"element": "extension",
"variable": "extension",
"parameter": [ {
"valueString": "Extension"
} ],
"transform": "create",
"contextType": "variable"
}, {
"context": "extension",
"element": "url",
"parameter": [ {
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "extension",
"element": "value",
"parameter": [ {
"valueId": "b"
} ],
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Readdepth",
"source": [ {
"max": "1",
"context": "queried",
"element": "Read depth",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Read depth"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Alleledepth",
"source": [ {
"max": "1",
"context": "queried",
"element": "Allele depth",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "82121-5"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Allelefrequency",
"source": [ {
"max": "1",
"context": "queried",
"element": "Allele frequency",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "81258-6"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Populationallelefrequencydetails",
"source": [ {
"context": "queried",
"element": "Population allele frequency knowledge base",
"variable": "a"
}, {
"context": "queried",
"element": "Population allele frequency",
"variable": "b"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "92821-8"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueId": "b"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "component",
"element": "extension",
"variable": "extension",
"parameter": [ {
"valueString": "Extension"
} ],
"transform": "create",
"contextType": "variable"
}, {
"context": "extension",
"element": "url",
"parameter": [ {
"valueString": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent"
} ],
"transform": "copy",
"contextType": "variable"
}, {
"context": "extension",
"element": "value",
"parameter": [ {
"valueId": "a"
} ],
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "VCFqualityfilter",
"source": [ {
"context": "queried",
"element": "Filter name",
"variable": "a"
}, {
"context": "queried",
"element": "Description",
"variable": "b"
}, {
"context": "queried",
"element": "Filter passed",
"variable": "c"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "code",
"element": "coding",
"variable": "coding",
"contextType": "variable"
}, {
"context": "coding",
"element": "display",
"parameter": [ {
"valueId": "b"
} ],
"transform": "append",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueId": "c"
} ],
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Strandbiasratio",
"source": [ {
"max": "1",
"context": "queried",
"element": "Strand bias ratio",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Strand bias ratio"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Strandbiaspvalue",
"source": [ {
"max": "1",
"context": "queried",
"element": "Strand bias p-value",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Strand bias p-value"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Allelicstate",
"source": [ {
"max": "1",
"context": "queried",
"element": "Allelic state",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "53034-5"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueId": "a"
} ],
"transform": "cc",
"contextType": "variable"
} ]
}, {
"name": "Additionaldetails",
"source": [ {
"context": "queried",
"element": "Additional details",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "note",
"transform": "copy",
"contextType": "variable"
} ]
} ],
"input": [ {
"mode": "source",
"name": "source",
"type": "PharmacogeneticTestResult"
}, {
"mode": "source",
"name": "queried",
"type": "GenomicVariantResult"
}, {
"mode": "target",
"name": "target",
"type": "Variant"
}, {
"mode": "target",
"name": "produced",
"type": "GenomicStudyAnalysis"
} ],
"typeMode": "types"
}, {
"name": "GenotypeInformation",
"rule": [ {
"name": "Diplotype",
"source": [ {
"max": "1",
"context": "source",
"element": "Diplotype",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Overallactivityscore",
"source": [ {
"max": "1",
"context": "source",
"element": "Overall activity score",
"variable": "a"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "''"
}, {
"valueString": "''"
}, {
"valueString": "Overall activity score"
} ],
"transform": "cc",
"contextType": "variable"
}, {
"context": "component",
"element": "value",
"transform": "copy",
"contextType": "variable"
} ]
}, {
"name": "Genomicregion",
"source": [ {
"context": "source",
"element": "Genomic region",
"variable": "a"
}, {
"context": "source",
"element": "Allele covered",
"variable": "b"
}, {
"context": "queried",
"element": "Knowledge base URI",
"variable": "c"
}, {
"context": "queried",
"element": "Item name",
"variable": "d"
} ],
"target": [ {
"context": "target",
"element": "component",
"variable": "component",
"contextType": "variable"
}, {
"context": "component",
"element": "code",
"variable": "code",
"parameter": [ {
"valueString": "http://loinc.org"
}, {
"valueString": "48018-6"
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