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

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StructureMap

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StructureMap.id[0]StructureMap-PharmacogeneticTestResult-Genomics
StructureMap.url[0]https://fhir.nhs.uk/StructureMap/StructureMap-PharmacogeneticTestResult-Genomics
StructureMap.version[0]0.1.0
StructureMap.name[0]StructureMapPharmacogeneticTestResultGenomics
StructureMap.title[0]StructureMap PharmacogeneticTestResult Genomics
StructureMap.status[0]draft
StructureMap.date[0]2025-02-14T00:00:00.000Z
StructureMap.publisher[0]NHS England
StructureMap.contact[0].name[0]NHS England
StructureMap.contact[0].telecom[0].system[0]email
StructureMap.contact[0].telecom[0].value[0]interoperabilityteam@nhs.net
StructureMap.description[0]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
StructureMap.copyright[0]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.
StructureMap.structure[0].url[0]https://ckm.openehr.org/ckm/archetypes/1013.1.7066
StructureMap.structure[0].mode[0]source
StructureMap.structure[0].alias[0]PharmacogeneticTestResult
StructureMap.structure[0].documentation[0]The OpenEHR PGx logical model
StructureMap.structure[1].url[0]https://ckm.openehr.org/ckm/archetypes/1013.1.3748
StructureMap.structure[1].mode[0]source
StructureMap.structure[1].alias[0]KnowledgeBaseReference
StructureMap.structure[1].documentation[0]The OpenEHR model for citation of a digital resource
StructureMap.structure[2].url[0]https://ckm.openehr.org/ckm/archetypes/1013.1.3759
StructureMap.structure[2].mode[0]source
StructureMap.structure[2].alias[0]GenomicVariantResult
StructureMap.structure[2].documentation[0]The OpenEHR model for a variant
StructureMap.structure[3].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype
StructureMap.structure[3].mode[0]target
StructureMap.structure[3].alias[0]Genotype
StructureMap.structure[3].documentation[0]The Genotype information as a FHIR Observation
StructureMap.structure[4].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype
StructureMap.structure[4].mode[0]target
StructureMap.structure[4].alias[0]Haplotype
StructureMap.structure[4].documentation[0]The Haplotype information as a FHIR Observation
StructureMap.structure[5].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant
StructureMap.structure[5].mode[0]target
StructureMap.structure[5].alias[0]Variant
StructureMap.structure[5].documentation[0]The Variant information as a FHIR Observation
StructureMap.structure[6].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication
StructureMap.structure[6].mode[0]target
StructureMap.structure[6].alias[0]DiagnosticImplication
StructureMap.structure[6].documentation[0]The phenotypic/implication information as a FHIR Observation
StructureMap.structure[7].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence
StructureMap.structure[7].mode[0]target
StructureMap.structure[7].alias[0]MolecularConsequence
StructureMap.structure[7].documentation[0]The observed effect of variants as a FHIR Observation
StructureMap.structure[8].url[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis
StructureMap.structure[8].mode[0]target
StructureMap.structure[8].alias[0]GenomicStudyAnalysis
StructureMap.structure[8].documentation[0]Analysis metadata recorded through a profile on Procedure
StructureMap.group[0].name[0]VariantInformation
StructureMap.group[0].typeMode[0]types
StructureMap.group[0].input[0].name[0]source
StructureMap.group[0].input[0].type[0]PharmacogeneticTestResult
StructureMap.group[0].input[0].mode[0]source
StructureMap.group[0].input[1].name[0]queried
StructureMap.group[0].input[1].type[0]GenomicVariantResult
StructureMap.group[0].input[1].mode[0]source
StructureMap.group[0].input[2].name[0]target
StructureMap.group[0].input[2].type[0]Variant
StructureMap.group[0].input[2].mode[0]target
StructureMap.group[0].input[3].name[0]produced
StructureMap.group[0].input[3].type[0]GenomicStudyAnalysis
StructureMap.group[0].input[3].mode[0]target
StructureMap.group[0].rule[0].name[0]Genesymbol
StructureMap.group[0].rule[0].source[0].context[0]source
StructureMap.group[0].rule[0].source[0].min[0]1
StructureMap.group[0].rule[0].source[0].max[0]1
StructureMap.group[0].rule[0].source[0].element[0]Gene symbol
StructureMap.group[0].rule[0].source[0].variable[0]a
StructureMap.group[0].rule[0].target[0].context[0]target
StructureMap.group[0].rule[0].target[0].contextType[0]variable
StructureMap.group[0].rule[0].target[0].element[0]component
StructureMap.group[0].rule[0].target[0].variable[0]component
StructureMap.group[0].rule[0].target[1].context[0]component
StructureMap.group[0].rule[0].target[1].contextType[0]variable
StructureMap.group[0].rule[0].target[1].element[0]code
StructureMap.group[0].rule[0].target[1].variable[0]code
StructureMap.group[0].rule[0].target[1].transform[0]cc
StructureMap.group[0].rule[0].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[0].target[1].parameter[1].value[0]48018-6
StructureMap.group[0].rule[0].target[2].context[0]component
StructureMap.group[0].rule[0].target[2].contextType[0]variable
StructureMap.group[0].rule[0].target[2].element[0]value
StructureMap.group[0].rule[0].target[2].transform[0]cc
StructureMap.group[0].rule[0].target[2].parameter[0].value[0]http://www.genenames.org
StructureMap.group[0].rule[0].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[1].name[0]Bioinformaticanalysisworkflow
StructureMap.group[0].rule[1].source[0].context[0]queried
StructureMap.group[0].rule[1].source[0].max[0]1
StructureMap.group[0].rule[1].source[0].element[0]Bioinformatic analysis workflow
StructureMap.group[0].rule[1].source[0].variable[0]a
StructureMap.group[0].rule[1].target[0].context[0]produced
StructureMap.group[0].rule[1].target[0].contextType[0]variable
StructureMap.group[0].rule[1].target[0].element[0]extension
StructureMap.group[0].rule[1].target[0].variable[0]extension
StructureMap.group[0].rule[1].target[0].transform[0]create
StructureMap.group[0].rule[1].target[0].parameter[0].value[0]Extension
StructureMap.group[0].rule[1].target[1].context[0]extension
StructureMap.group[0].rule[1].target[1].contextType[0]variable
StructureMap.group[0].rule[1].target[1].element[0]url
StructureMap.group[0].rule[1].target[1].transform[0]copy
StructureMap.group[0].rule[1].target[1].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed
StructureMap.group[0].rule[1].target[2].context[0]extension
StructureMap.group[0].rule[1].target[2].contextType[0]variable
StructureMap.group[0].rule[1].target[2].element[0]value
StructureMap.group[0].rule[1].target[2].transform[0]copy
StructureMap.group[0].rule[2].name[0]Referencegenome
StructureMap.group[0].rule[2].source[0].context[0]queried
StructureMap.group[0].rule[2].source[0].min[0]1
StructureMap.group[0].rule[2].source[0].max[0]1
StructureMap.group[0].rule[2].source[0].element[0]Reference genome
StructureMap.group[0].rule[2].source[0].variable[0]a
StructureMap.group[0].rule[2].target[0].context[0]target
StructureMap.group[0].rule[2].target[0].contextType[0]variable
StructureMap.group[0].rule[2].target[0].element[0]component
StructureMap.group[0].rule[2].target[0].variable[0]component
StructureMap.group[0].rule[2].target[1].context[0]component
StructureMap.group[0].rule[2].target[1].contextType[0]variable
StructureMap.group[0].rule[2].target[1].element[0]code
StructureMap.group[0].rule[2].target[1].variable[0]code
StructureMap.group[0].rule[2].target[1].transform[0]cc
StructureMap.group[0].rule[2].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[2].target[1].parameter[1].value[0]48013-7
StructureMap.group[0].rule[2].target[2].context[0]component
StructureMap.group[0].rule[2].target[2].contextType[0]variable
StructureMap.group[0].rule[2].target[2].element[0]value
StructureMap.group[0].rule[2].target[2].transform[0]copy
StructureMap.group[0].rule[3].name[0]Variantidentification
StructureMap.group[0].rule[3].source[0].context[0]queried
StructureMap.group[0].rule[3].source[0].element[0]Variant identification
StructureMap.group[0].rule[3].source[0].variable[0]a
StructureMap.group[0].rule[3].target[0].context[0]target
StructureMap.group[0].rule[3].target[0].contextType[0]variable
StructureMap.group[0].rule[3].target[0].element[0]component
StructureMap.group[0].rule[3].target[0].variable[0]component
StructureMap.group[0].rule[3].target[1].context[0]component
StructureMap.group[0].rule[3].target[1].contextType[0]variable
StructureMap.group[0].rule[3].target[1].element[0]code
StructureMap.group[0].rule[3].target[1].variable[0]code
StructureMap.group[0].rule[3].target[1].transform[0]cc
StructureMap.group[0].rule[3].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[3].target[1].parameter[1].value[0]81252-9
StructureMap.group[0].rule[3].target[2].context[0]component
StructureMap.group[0].rule[3].target[2].contextType[0]variable
StructureMap.group[0].rule[3].target[2].element[0]value
StructureMap.group[0].rule[3].target[2].transform[0]copy
StructureMap.group[0].rule[4].name[0]Variant
StructureMap.group[0].rule[4].source[0].context[0]queried
StructureMap.group[0].rule[4].source[0].max[0]1
StructureMap.group[0].rule[4].source[0].element[0]Variant
StructureMap.group[0].rule[4].source[0].variable[0]a
StructureMap.group[0].rule[4].target[0].context[0]target
StructureMap.group[0].rule[4].target[0].contextType[0]variable
StructureMap.group[0].rule[4].target[0].element[0]component
StructureMap.group[0].rule[4].target[0].variable[0]component
StructureMap.group[0].rule[4].target[1].context[0]component
StructureMap.group[0].rule[4].target[1].contextType[0]variable
StructureMap.group[0].rule[4].target[1].element[0]code
StructureMap.group[0].rule[4].target[1].variable[0]code
StructureMap.group[0].rule[4].target[1].transform[0]cc
StructureMap.group[0].rule[4].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[4].target[1].parameter[1].value[0]81290-9
StructureMap.group[0].rule[4].target[2].context[0]component
StructureMap.group[0].rule[4].target[2].contextType[0]variable
StructureMap.group[0].rule[4].target[2].element[0]value
StructureMap.group[0].rule[4].target[2].transform[0]cc
StructureMap.group[0].rule[4].target[2].parameter[0].value[0]http://www.genenames.org
StructureMap.group[0].rule[4].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[5].name[0]Structuredvariant
StructureMap.group[0].rule[5].source[0].context[0]queried
StructureMap.group[0].rule[5].source[0].max[0]1
StructureMap.group[0].rule[5].source[0].element[0]Structured variant
StructureMap.group[0].rule[5].source[0].variable[0]a
StructureMap.group[0].rule[5].target[0].context[0]target
StructureMap.group[0].rule[5].target[0].contextType[0]variable
StructureMap.group[0].rule[5].target[0].element[0]component
StructureMap.group[0].rule[5].target[0].variable[0]component
StructureMap.group[0].rule[5].target[1].context[0]component
StructureMap.group[0].rule[5].target[1].contextType[0]variable
StructureMap.group[0].rule[5].target[1].element[0]code
StructureMap.group[0].rule[5].target[1].variable[0]code
StructureMap.group[0].rule[5].target[1].transform[0]cc
StructureMap.group[0].rule[5].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[5].target[1].parameter[1].value[0]48019-4
StructureMap.group[0].rule[5].target[2].context[0]component
StructureMap.group[0].rule[5].target[2].contextType[0]variable
StructureMap.group[0].rule[5].target[2].element[0]value
StructureMap.group[0].rule[5].target[2].transform[0]cc
StructureMap.group[0].rule[5].target[2].parameter[0].value[0]http://www.sequenceontology.org
StructureMap.group[0].rule[5].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[6].name[0]Transcriptreferencesequence
StructureMap.group[0].rule[6].source[0].context[0]queried
StructureMap.group[0].rule[6].source[0].element[0]Transcript reference sequence
StructureMap.group[0].rule[6].source[0].variable[0]a
StructureMap.group[0].rule[6].source[1].context[0]queried
StructureMap.group[0].rule[6].source[1].element[0]Best transcript candidate
StructureMap.group[0].rule[6].source[1].variable[0]b
StructureMap.group[0].rule[6].target[0].context[0]target
StructureMap.group[0].rule[6].target[0].contextType[0]variable
StructureMap.group[0].rule[6].target[0].element[0]component
StructureMap.group[0].rule[6].target[0].variable[0]component
StructureMap.group[0].rule[6].target[1].context[0]component
StructureMap.group[0].rule[6].target[1].contextType[0]variable
StructureMap.group[0].rule[6].target[1].element[0]code
StructureMap.group[0].rule[6].target[1].variable[0]code
StructureMap.group[0].rule[6].target[1].transform[0]cc
StructureMap.group[0].rule[6].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[6].target[1].parameter[1].value[0]51958-7
StructureMap.group[0].rule[6].target[2].context[0]component
StructureMap.group[0].rule[6].target[2].contextType[0]variable
StructureMap.group[0].rule[6].target[2].element[0]value
StructureMap.group[0].rule[6].target[2].transform[0]copy
StructureMap.group[0].rule[6].target[2].parameter[0].value[0]a
StructureMap.group[0].rule[6].target[3].context[0]component
StructureMap.group[0].rule[6].target[3].contextType[0]variable
StructureMap.group[0].rule[6].target[3].element[0]extension
StructureMap.group[0].rule[6].target[3].variable[0]extension
StructureMap.group[0].rule[6].target[3].transform[0]create
StructureMap.group[0].rule[6].target[3].parameter[0].value[0]Extension
StructureMap.group[0].rule[6].target[4].context[0]extension
StructureMap.group[0].rule[6].target[4].contextType[0]variable
StructureMap.group[0].rule[6].target[4].element[0]url
StructureMap.group[0].rule[6].target[4].transform[0]copy
StructureMap.group[0].rule[6].target[4].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[0].rule[6].target[5].context[0]extension
StructureMap.group[0].rule[6].target[5].contextType[0]variable
StructureMap.group[0].rule[6].target[5].element[0]value
StructureMap.group[0].rule[6].target[5].transform[0]copy
StructureMap.group[0].rule[6].target[5].parameter[0].value[0]b
StructureMap.group[0].rule[7].name[0]DNAregionname
StructureMap.group[0].rule[7].source[0].context[0]queried
StructureMap.group[0].rule[7].source[0].element[0]DNA region name
StructureMap.group[0].rule[7].source[0].variable[0]a
StructureMap.group[0].rule[7].source[1].context[0]queried
StructureMap.group[0].rule[7].source[1].element[0]Distance from splicing site
StructureMap.group[0].rule[7].source[1].variable[0]b
StructureMap.group[0].rule[7].target[0].context[0]target
StructureMap.group[0].rule[7].target[0].contextType[0]variable
StructureMap.group[0].rule[7].target[0].element[0]component
StructureMap.group[0].rule[7].target[0].variable[0]component
StructureMap.group[0].rule[7].target[1].context[0]component
StructureMap.group[0].rule[7].target[1].contextType[0]variable
StructureMap.group[0].rule[7].target[1].element[0]code
StructureMap.group[0].rule[7].target[1].variable[0]code
StructureMap.group[0].rule[7].target[1].transform[0]cc
StructureMap.group[0].rule[7].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[7].target[1].parameter[1].value[0]81254-5
StructureMap.group[0].rule[7].target[2].context[0]component
StructureMap.group[0].rule[7].target[2].contextType[0]variable
StructureMap.group[0].rule[7].target[2].element[0]value
StructureMap.group[0].rule[7].target[2].variable[0]range
StructureMap.group[0].rule[7].target[2].transform[0]create
StructureMap.group[0].rule[7].target[2].parameter[0].value[0]Range
StructureMap.group[0].rule[7].target[3].context[0]range
StructureMap.group[0].rule[7].target[3].contextType[0]variable
StructureMap.group[0].rule[7].target[3].element[0]low
StructureMap.group[0].rule[7].target[3].transform[0]copy
StructureMap.group[0].rule[7].target[3].parameter[0].value[0]a
StructureMap.group[0].rule[7].target[4].context[0]range
StructureMap.group[0].rule[7].target[4].contextType[0]variable
StructureMap.group[0].rule[7].target[4].element[0]high
StructureMap.group[0].rule[7].target[4].transform[0]copy
StructureMap.group[0].rule[7].target[4].parameter[0].value[0]b
StructureMap.group[0].rule[8].name[0]DNAchange
StructureMap.group[0].rule[8].source[0].context[0]queried
StructureMap.group[0].rule[8].source[0].element[0]DNA change
StructureMap.group[0].rule[8].source[0].variable[0]a
StructureMap.group[0].rule[8].target[0].context[0]target
StructureMap.group[0].rule[8].target[0].contextType[0]variable
StructureMap.group[0].rule[8].target[0].element[0]component
StructureMap.group[0].rule[8].target[0].variable[0]component
StructureMap.group[0].rule[8].target[1].context[0]component
StructureMap.group[0].rule[8].target[1].contextType[0]variable
StructureMap.group[0].rule[8].target[1].element[0]code
StructureMap.group[0].rule[8].target[1].variable[0]code
StructureMap.group[0].rule[8].target[1].transform[0]cc
StructureMap.group[0].rule[8].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[8].target[1].parameter[1].value[0]48004-6
StructureMap.group[0].rule[8].target[2].context[0]component
StructureMap.group[0].rule[8].target[2].contextType[0]variable
StructureMap.group[0].rule[8].target[2].element[0]value
StructureMap.group[0].rule[8].target[2].transform[0]cc
StructureMap.group[0].rule[8].target[2].parameter[0].value[0]http://www.genenames.org
StructureMap.group[0].rule[8].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[9].name[0]Aminoacidchange
StructureMap.group[0].rule[9].source[0].context[0]queried
StructureMap.group[0].rule[9].source[0].element[0]Amino acid change
StructureMap.group[0].rule[9].source[0].variable[0]a
StructureMap.group[0].rule[9].target[0].context[0]target
StructureMap.group[0].rule[9].target[0].contextType[0]variable
StructureMap.group[0].rule[9].target[0].element[0]component
StructureMap.group[0].rule[9].target[0].variable[0]component
StructureMap.group[0].rule[9].target[1].context[0]component
StructureMap.group[0].rule[9].target[1].contextType[0]variable
StructureMap.group[0].rule[9].target[1].element[0]code
StructureMap.group[0].rule[9].target[1].variable[0]code
StructureMap.group[0].rule[9].target[1].transform[0]cc
StructureMap.group[0].rule[9].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[9].target[1].parameter[1].value[0]48005-3
StructureMap.group[0].rule[9].target[2].context[0]component
StructureMap.group[0].rule[9].target[2].contextType[0]variable
StructureMap.group[0].rule[9].target[2].element[0]value
StructureMap.group[0].rule[9].target[2].transform[0]cc
StructureMap.group[0].rule[9].target[2].parameter[0].value[0]http://www.genenames.org
StructureMap.group[0].rule[9].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[10].name[0]Aminoacidchangetype
StructureMap.group[0].rule[10].source[0].context[0]queried
StructureMap.group[0].rule[10].source[0].element[0]Amino acid change type
StructureMap.group[0].rule[10].source[0].variable[0]a
StructureMap.group[0].rule[10].target[0].context[0]target
StructureMap.group[0].rule[10].target[0].contextType[0]variable
StructureMap.group[0].rule[10].target[0].element[0]component
StructureMap.group[0].rule[10].target[0].variable[0]component
StructureMap.group[0].rule[10].target[1].context[0]component
StructureMap.group[0].rule[10].target[1].contextType[0]variable
StructureMap.group[0].rule[10].target[1].element[0]code
StructureMap.group[0].rule[10].target[1].variable[0]code
StructureMap.group[0].rule[10].target[1].transform[0]cc
StructureMap.group[0].rule[10].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[10].target[1].parameter[1].value[0]48006-1
StructureMap.group[0].rule[10].target[2].context[0]component
StructureMap.group[0].rule[10].target[2].contextType[0]variable
StructureMap.group[0].rule[10].target[2].element[0]value
StructureMap.group[0].rule[10].target[2].transform[0]cc
StructureMap.group[0].rule[10].target[2].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[10].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[11].name[0]RNAchange
StructureMap.group[0].rule[11].source[0].context[0]queried
StructureMap.group[0].rule[11].source[0].element[0]RNA change
StructureMap.group[0].rule[11].source[0].variable[0]a
StructureMap.group[0].rule[11].target[0].context[0]target
StructureMap.group[0].rule[11].target[0].contextType[0]variable
StructureMap.group[0].rule[11].target[0].element[0]component
StructureMap.group[0].rule[11].target[0].variable[0]component
StructureMap.group[0].rule[11].target[1].context[0]component
StructureMap.group[0].rule[11].target[1].contextType[0]variable
StructureMap.group[0].rule[11].target[1].element[0]code
StructureMap.group[0].rule[11].target[1].variable[0]code
StructureMap.group[0].rule[11].target[1].transform[0]cc
StructureMap.group[0].rule[11].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[11].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[11].target[1].parameter[2].value[0]RNA change
StructureMap.group[0].rule[11].target[2].context[0]component
StructureMap.group[0].rule[11].target[2].contextType[0]variable
StructureMap.group[0].rule[11].target[2].element[0]value
StructureMap.group[0].rule[11].target[2].transform[0]cc
StructureMap.group[0].rule[11].target[2].parameter[0].value[0]http://www.genenames.org
StructureMap.group[0].rule[11].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[12].name[0]Genename
StructureMap.group[0].rule[12].source[0].context[0]queried
StructureMap.group[0].rule[12].source[0].element[0]Gene name
StructureMap.group[0].rule[12].source[0].variable[0]a
StructureMap.group[0].rule[12].target[0].context[0]target
StructureMap.group[0].rule[12].target[0].contextType[0]variable
StructureMap.group[0].rule[12].target[0].element[0]component
StructureMap.group[0].rule[12].target[0].variable[0]component
StructureMap.group[0].rule[12].target[1].context[0]component
StructureMap.group[0].rule[12].target[1].contextType[0]variable
StructureMap.group[0].rule[12].target[1].element[0]code
StructureMap.group[0].rule[12].target[1].variable[0]code
StructureMap.group[0].rule[12].target[1].transform[0]cc
StructureMap.group[0].rule[12].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[12].target[1].parameter[1].value[0]48018-6
StructureMap.group[0].rule[12].target[2].context[0]component
StructureMap.group[0].rule[12].target[2].contextType[0]variable
StructureMap.group[0].rule[12].target[2].element[0]value
StructureMap.group[0].rule[12].target[2].transform[0]copy
StructureMap.group[0].rule[13].name[0]Copynumberoverlap
StructureMap.group[0].rule[13].source[0].context[0]queried
StructureMap.group[0].rule[13].source[0].element[0]Copy number overlap
StructureMap.group[0].rule[13].source[0].variable[0]a
StructureMap.group[0].rule[13].target[0].context[0]target
StructureMap.group[0].rule[13].target[0].contextType[0]variable
StructureMap.group[0].rule[13].target[0].element[0]component
StructureMap.group[0].rule[13].target[0].variable[0]component
StructureMap.group[0].rule[13].target[1].context[0]component
StructureMap.group[0].rule[13].target[1].contextType[0]variable
StructureMap.group[0].rule[13].target[1].element[0]code
StructureMap.group[0].rule[13].target[1].variable[0]code
StructureMap.group[0].rule[13].target[1].transform[0]cc
StructureMap.group[0].rule[13].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[13].target[1].parameter[1].value[0]82155-3
StructureMap.group[0].rule[13].target[2].context[0]component
StructureMap.group[0].rule[13].target[2].contextType[0]variable
StructureMap.group[0].rule[13].target[2].element[0]value
StructureMap.group[0].rule[13].target[2].transform[0]qty
StructureMap.group[0].rule[13].target[2].parameter[0].value[0]a
StructureMap.group[0].rule[13].target[2].parameter[1].value[0]{ratio}
StructureMap.group[0].rule[13].target[2].parameter[2].value[0]http://unitsofmeasure.org
StructureMap.group[0].rule[14].name[0]Partoffusion
StructureMap.group[0].rule[14].source[0].context[0]queried
StructureMap.group[0].rule[14].source[0].element[0]Part of fusion
StructureMap.group[0].rule[14].source[0].variable[0]a
StructureMap.group[0].rule[14].target[0].context[0]target
StructureMap.group[0].rule[14].target[0].contextType[0]variable
StructureMap.group[0].rule[14].target[0].element[0]component
StructureMap.group[0].rule[14].target[0].variable[0]component
StructureMap.group[0].rule[14].target[1].context[0]component
StructureMap.group[0].rule[14].target[1].contextType[0]variable
StructureMap.group[0].rule[14].target[1].element[0]code
StructureMap.group[0].rule[14].target[1].variable[0]code
StructureMap.group[0].rule[14].target[1].transform[0]cc
StructureMap.group[0].rule[14].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[14].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[14].target[1].parameter[2].value[0]Part of fusion
StructureMap.group[0].rule[14].target[2].context[0]component
StructureMap.group[0].rule[14].target[2].contextType[0]variable
StructureMap.group[0].rule[14].target[2].element[0]value
StructureMap.group[0].rule[14].target[2].transform[0]copy
StructureMap.group[0].rule[15].name[0]Fusionexon
StructureMap.group[0].rule[15].source[0].context[0]queried
StructureMap.group[0].rule[15].source[0].element[0]Fusion exon
StructureMap.group[0].rule[15].source[0].variable[0]a
StructureMap.group[0].rule[15].target[0].context[0]target
StructureMap.group[0].rule[15].target[0].contextType[0]variable
StructureMap.group[0].rule[15].target[0].element[0]component
StructureMap.group[0].rule[15].target[0].variable[0]component
StructureMap.group[0].rule[15].target[1].context[0]component
StructureMap.group[0].rule[15].target[1].contextType[0]variable
StructureMap.group[0].rule[15].target[1].element[0]code
StructureMap.group[0].rule[15].target[1].variable[0]code
StructureMap.group[0].rule[15].target[1].transform[0]cc
StructureMap.group[0].rule[15].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[15].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[15].target[1].parameter[2].value[0]Fusion exon
StructureMap.group[0].rule[15].target[2].context[0]component
StructureMap.group[0].rule[15].target[2].contextType[0]variable
StructureMap.group[0].rule[15].target[2].element[0]value
StructureMap.group[0].rule[15].target[2].transform[0]copy
StructureMap.group[0].rule[16].name[0]ConservationScore
StructureMap.group[0].rule[16].source[0].context[0]queried
StructureMap.group[0].rule[16].source[0].element[0]Score
StructureMap.group[0].rule[16].source[0].variable[0]a
StructureMap.group[0].rule[16].source[1].context[0]queried
StructureMap.group[0].rule[16].source[1].element[0]Conservation score knowledge base
StructureMap.group[0].rule[16].source[1].variable[0]b
StructureMap.group[0].rule[16].target[0].context[0]target
StructureMap.group[0].rule[16].target[0].contextType[0]variable
StructureMap.group[0].rule[16].target[0].element[0]component
StructureMap.group[0].rule[16].target[0].variable[0]component
StructureMap.group[0].rule[16].target[1].context[0]component
StructureMap.group[0].rule[16].target[1].contextType[0]variable
StructureMap.group[0].rule[16].target[1].element[0]code
StructureMap.group[0].rule[16].target[1].variable[0]code
StructureMap.group[0].rule[16].target[1].transform[0]cc
StructureMap.group[0].rule[16].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[16].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[16].target[1].parameter[2].value[0]Conservation Score
StructureMap.group[0].rule[16].target[2].context[0]component
StructureMap.group[0].rule[16].target[2].contextType[0]variable
StructureMap.group[0].rule[16].target[2].element[0]value
StructureMap.group[0].rule[16].target[2].transform[0]copy
StructureMap.group[0].rule[16].target[2].parameter[0].value[0]a
StructureMap.group[0].rule[16].target[3].context[0]component
StructureMap.group[0].rule[16].target[3].contextType[0]variable
StructureMap.group[0].rule[16].target[3].element[0]extension
StructureMap.group[0].rule[16].target[3].variable[0]extension
StructureMap.group[0].rule[16].target[3].transform[0]create
StructureMap.group[0].rule[16].target[3].parameter[0].value[0]Extension
StructureMap.group[0].rule[16].target[4].context[0]extension
StructureMap.group[0].rule[16].target[4].contextType[0]variable
StructureMap.group[0].rule[16].target[4].element[0]url
StructureMap.group[0].rule[16].target[4].transform[0]copy
StructureMap.group[0].rule[16].target[4].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[0].rule[16].target[5].context[0]extension
StructureMap.group[0].rule[16].target[5].contextType[0]variable
StructureMap.group[0].rule[16].target[5].element[0]value
StructureMap.group[0].rule[16].target[5].transform[0]copy
StructureMap.group[0].rule[16].target[5].parameter[0].value[0]b
StructureMap.group[0].rule[17].name[0]Readdepth
StructureMap.group[0].rule[17].source[0].context[0]queried
StructureMap.group[0].rule[17].source[0].max[0]1
StructureMap.group[0].rule[17].source[0].element[0]Read depth
StructureMap.group[0].rule[17].source[0].variable[0]a
StructureMap.group[0].rule[17].target[0].context[0]target
StructureMap.group[0].rule[17].target[0].contextType[0]variable
StructureMap.group[0].rule[17].target[0].element[0]component
StructureMap.group[0].rule[17].target[0].variable[0]component
StructureMap.group[0].rule[17].target[1].context[0]component
StructureMap.group[0].rule[17].target[1].contextType[0]variable
StructureMap.group[0].rule[17].target[1].element[0]code
StructureMap.group[0].rule[17].target[1].variable[0]code
StructureMap.group[0].rule[17].target[1].transform[0]cc
StructureMap.group[0].rule[17].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[17].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[17].target[1].parameter[2].value[0]Read depth
StructureMap.group[0].rule[17].target[2].context[0]component
StructureMap.group[0].rule[17].target[2].contextType[0]variable
StructureMap.group[0].rule[17].target[2].element[0]value
StructureMap.group[0].rule[17].target[2].transform[0]copy
StructureMap.group[0].rule[18].name[0]Alleledepth
StructureMap.group[0].rule[18].source[0].context[0]queried
StructureMap.group[0].rule[18].source[0].max[0]1
StructureMap.group[0].rule[18].source[0].element[0]Allele depth
StructureMap.group[0].rule[18].source[0].variable[0]a
StructureMap.group[0].rule[18].target[0].context[0]target
StructureMap.group[0].rule[18].target[0].contextType[0]variable
StructureMap.group[0].rule[18].target[0].element[0]component
StructureMap.group[0].rule[18].target[0].variable[0]component
StructureMap.group[0].rule[18].target[1].context[0]component
StructureMap.group[0].rule[18].target[1].contextType[0]variable
StructureMap.group[0].rule[18].target[1].element[0]code
StructureMap.group[0].rule[18].target[1].variable[0]code
StructureMap.group[0].rule[18].target[1].transform[0]cc
StructureMap.group[0].rule[18].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[18].target[1].parameter[1].value[0]82121-5
StructureMap.group[0].rule[18].target[2].context[0]component
StructureMap.group[0].rule[18].target[2].contextType[0]variable
StructureMap.group[0].rule[18].target[2].element[0]value
StructureMap.group[0].rule[18].target[2].transform[0]copy
StructureMap.group[0].rule[19].name[0]Allelefrequency
StructureMap.group[0].rule[19].source[0].context[0]queried
StructureMap.group[0].rule[19].source[0].max[0]1
StructureMap.group[0].rule[19].source[0].element[0]Allele frequency
StructureMap.group[0].rule[19].source[0].variable[0]a
StructureMap.group[0].rule[19].target[0].context[0]target
StructureMap.group[0].rule[19].target[0].contextType[0]variable
StructureMap.group[0].rule[19].target[0].element[0]component
StructureMap.group[0].rule[19].target[0].variable[0]component
StructureMap.group[0].rule[19].target[1].context[0]component
StructureMap.group[0].rule[19].target[1].contextType[0]variable
StructureMap.group[0].rule[19].target[1].element[0]code
StructureMap.group[0].rule[19].target[1].variable[0]code
StructureMap.group[0].rule[19].target[1].transform[0]cc
StructureMap.group[0].rule[19].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[19].target[1].parameter[1].value[0]81258-6
StructureMap.group[0].rule[19].target[2].context[0]component
StructureMap.group[0].rule[19].target[2].contextType[0]variable
StructureMap.group[0].rule[19].target[2].element[0]value
StructureMap.group[0].rule[19].target[2].transform[0]copy
StructureMap.group[0].rule[20].name[0]Populationallelefrequencydetails
StructureMap.group[0].rule[20].source[0].context[0]queried
StructureMap.group[0].rule[20].source[0].element[0]Population allele frequency knowledge base
StructureMap.group[0].rule[20].source[0].variable[0]a
StructureMap.group[0].rule[20].source[1].context[0]queried
StructureMap.group[0].rule[20].source[1].element[0]Population allele frequency
StructureMap.group[0].rule[20].source[1].variable[0]b
StructureMap.group[0].rule[20].target[0].context[0]target
StructureMap.group[0].rule[20].target[0].contextType[0]variable
StructureMap.group[0].rule[20].target[0].element[0]component
StructureMap.group[0].rule[20].target[0].variable[0]component
StructureMap.group[0].rule[20].target[1].context[0]component
StructureMap.group[0].rule[20].target[1].contextType[0]variable
StructureMap.group[0].rule[20].target[1].element[0]code
StructureMap.group[0].rule[20].target[1].variable[0]code
StructureMap.group[0].rule[20].target[1].transform[0]cc
StructureMap.group[0].rule[20].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[20].target[1].parameter[1].value[0]92821-8
StructureMap.group[0].rule[20].target[2].context[0]component
StructureMap.group[0].rule[20].target[2].contextType[0]variable
StructureMap.group[0].rule[20].target[2].element[0]value
StructureMap.group[0].rule[20].target[2].transform[0]copy
StructureMap.group[0].rule[20].target[2].parameter[0].value[0]b
StructureMap.group[0].rule[20].target[3].context[0]component
StructureMap.group[0].rule[20].target[3].contextType[0]variable
StructureMap.group[0].rule[20].target[3].element[0]extension
StructureMap.group[0].rule[20].target[3].variable[0]extension
StructureMap.group[0].rule[20].target[3].transform[0]create
StructureMap.group[0].rule[20].target[3].parameter[0].value[0]Extension
StructureMap.group[0].rule[20].target[4].context[0]extension
StructureMap.group[0].rule[20].target[4].contextType[0]variable
StructureMap.group[0].rule[20].target[4].element[0]url
StructureMap.group[0].rule[20].target[4].transform[0]copy
StructureMap.group[0].rule[20].target[4].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[0].rule[20].target[5].context[0]extension
StructureMap.group[0].rule[20].target[5].contextType[0]variable
StructureMap.group[0].rule[20].target[5].element[0]value
StructureMap.group[0].rule[20].target[5].transform[0]copy
StructureMap.group[0].rule[20].target[5].parameter[0].value[0]a
StructureMap.group[0].rule[21].name[0]VCFqualityfilter
StructureMap.group[0].rule[21].source[0].context[0]queried
StructureMap.group[0].rule[21].source[0].element[0]Filter name
StructureMap.group[0].rule[21].source[0].variable[0]a
StructureMap.group[0].rule[21].source[1].context[0]queried
StructureMap.group[0].rule[21].source[1].element[0]Description
StructureMap.group[0].rule[21].source[1].variable[0]b
StructureMap.group[0].rule[21].source[2].context[0]queried
StructureMap.group[0].rule[21].source[2].element[0]Filter passed
StructureMap.group[0].rule[21].source[2].variable[0]c
StructureMap.group[0].rule[21].target[0].context[0]target
StructureMap.group[0].rule[21].target[0].contextType[0]variable
StructureMap.group[0].rule[21].target[0].element[0]component
StructureMap.group[0].rule[21].target[0].variable[0]component
StructureMap.group[0].rule[21].target[1].context[0]component
StructureMap.group[0].rule[21].target[1].contextType[0]variable
StructureMap.group[0].rule[21].target[1].element[0]code
StructureMap.group[0].rule[21].target[1].variable[0]code
StructureMap.group[0].rule[21].target[1].transform[0]cc
StructureMap.group[0].rule[21].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[21].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[21].target[1].parameter[2].value[0]a
StructureMap.group[0].rule[21].target[2].context[0]code
StructureMap.group[0].rule[21].target[2].contextType[0]variable
StructureMap.group[0].rule[21].target[2].element[0]coding
StructureMap.group[0].rule[21].target[2].variable[0]coding
StructureMap.group[0].rule[21].target[3].context[0]coding
StructureMap.group[0].rule[21].target[3].contextType[0]variable
StructureMap.group[0].rule[21].target[3].element[0]display
StructureMap.group[0].rule[21].target[3].transform[0]append
StructureMap.group[0].rule[21].target[3].parameter[0].value[0]b
StructureMap.group[0].rule[21].target[4].context[0]component
StructureMap.group[0].rule[21].target[4].contextType[0]variable
StructureMap.group[0].rule[21].target[4].element[0]value
StructureMap.group[0].rule[21].target[4].transform[0]copy
StructureMap.group[0].rule[21].target[4].parameter[0].value[0]c
StructureMap.group[0].rule[22].name[0]Strandbiasratio
StructureMap.group[0].rule[22].source[0].context[0]queried
StructureMap.group[0].rule[22].source[0].max[0]1
StructureMap.group[0].rule[22].source[0].element[0]Strand bias ratio
StructureMap.group[0].rule[22].source[0].variable[0]a
StructureMap.group[0].rule[22].target[0].context[0]target
StructureMap.group[0].rule[22].target[0].contextType[0]variable
StructureMap.group[0].rule[22].target[0].element[0]component
StructureMap.group[0].rule[22].target[0].variable[0]component
StructureMap.group[0].rule[22].target[1].context[0]component
StructureMap.group[0].rule[22].target[1].contextType[0]variable
StructureMap.group[0].rule[22].target[1].element[0]code
StructureMap.group[0].rule[22].target[1].variable[0]code
StructureMap.group[0].rule[22].target[1].transform[0]cc
StructureMap.group[0].rule[22].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[22].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[22].target[1].parameter[2].value[0]Strand bias ratio
StructureMap.group[0].rule[22].target[2].context[0]component
StructureMap.group[0].rule[22].target[2].contextType[0]variable
StructureMap.group[0].rule[22].target[2].element[0]value
StructureMap.group[0].rule[22].target[2].transform[0]copy
StructureMap.group[0].rule[23].name[0]Strandbiaspvalue
StructureMap.group[0].rule[23].source[0].context[0]queried
StructureMap.group[0].rule[23].source[0].max[0]1
StructureMap.group[0].rule[23].source[0].element[0]Strand bias p-value
StructureMap.group[0].rule[23].source[0].variable[0]a
StructureMap.group[0].rule[23].target[0].context[0]target
StructureMap.group[0].rule[23].target[0].contextType[0]variable
StructureMap.group[0].rule[23].target[0].element[0]component
StructureMap.group[0].rule[23].target[0].variable[0]component
StructureMap.group[0].rule[23].target[1].context[0]component
StructureMap.group[0].rule[23].target[1].contextType[0]variable
StructureMap.group[0].rule[23].target[1].element[0]code
StructureMap.group[0].rule[23].target[1].variable[0]code
StructureMap.group[0].rule[23].target[1].transform[0]cc
StructureMap.group[0].rule[23].target[1].parameter[0].value[0]''
StructureMap.group[0].rule[23].target[1].parameter[1].value[0]''
StructureMap.group[0].rule[23].target[1].parameter[2].value[0]Strand bias p-value
StructureMap.group[0].rule[23].target[2].context[0]component
StructureMap.group[0].rule[23].target[2].contextType[0]variable
StructureMap.group[0].rule[23].target[2].element[0]value
StructureMap.group[0].rule[23].target[2].transform[0]copy
StructureMap.group[0].rule[24].name[0]Allelicstate
StructureMap.group[0].rule[24].source[0].context[0]queried
StructureMap.group[0].rule[24].source[0].max[0]1
StructureMap.group[0].rule[24].source[0].element[0]Allelic state
StructureMap.group[0].rule[24].source[0].variable[0]a
StructureMap.group[0].rule[24].target[0].context[0]target
StructureMap.group[0].rule[24].target[0].contextType[0]variable
StructureMap.group[0].rule[24].target[0].element[0]component
StructureMap.group[0].rule[24].target[0].variable[0]component
StructureMap.group[0].rule[24].target[1].context[0]component
StructureMap.group[0].rule[24].target[1].contextType[0]variable
StructureMap.group[0].rule[24].target[1].element[0]code
StructureMap.group[0].rule[24].target[1].variable[0]code
StructureMap.group[0].rule[24].target[1].transform[0]cc
StructureMap.group[0].rule[24].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[24].target[1].parameter[1].value[0]53034-5
StructureMap.group[0].rule[24].target[2].context[0]component
StructureMap.group[0].rule[24].target[2].contextType[0]variable
StructureMap.group[0].rule[24].target[2].element[0]value
StructureMap.group[0].rule[24].target[2].transform[0]cc
StructureMap.group[0].rule[24].target[2].parameter[0].value[0]http://loinc.org
StructureMap.group[0].rule[24].target[2].parameter[1].value[0]a
StructureMap.group[0].rule[25].name[0]Additionaldetails
StructureMap.group[0].rule[25].source[0].context[0]queried
StructureMap.group[0].rule[25].source[0].element[0]Additional details
StructureMap.group[0].rule[25].source[0].variable[0]a
StructureMap.group[0].rule[25].target[0].context[0]target
StructureMap.group[0].rule[25].target[0].contextType[0]variable
StructureMap.group[0].rule[25].target[0].element[0]note
StructureMap.group[0].rule[25].target[0].transform[0]copy
StructureMap.group[1].name[0]GenotypeInformation
StructureMap.group[1].typeMode[0]types
StructureMap.group[1].input[0].name[0]source
StructureMap.group[1].input[0].type[0]PharmacogeneticTestResult
StructureMap.group[1].input[0].mode[0]source
StructureMap.group[1].input[1].name[0]queried
StructureMap.group[1].input[1].type[0]KnowledgeBaseReference
StructureMap.group[1].input[1].mode[0]source
StructureMap.group[1].input[2].name[0]target
StructureMap.group[1].input[2].type[0]Genotype
StructureMap.group[1].input[2].mode[0]target
StructureMap.group[1].rule[0].name[0]Diplotype
StructureMap.group[1].rule[0].source[0].context[0]source
StructureMap.group[1].rule[0].source[0].max[0]1
StructureMap.group[1].rule[0].source[0].element[0]Diplotype
StructureMap.group[1].rule[0].source[0].variable[0]a
StructureMap.group[1].rule[0].target[0].context[0]target
StructureMap.group[1].rule[0].target[0].contextType[0]variable
StructureMap.group[1].rule[0].target[0].element[0]value
StructureMap.group[1].rule[0].target[0].transform[0]copy
StructureMap.group[1].rule[1].name[0]Overallactivityscore
StructureMap.group[1].rule[1].source[0].context[0]source
StructureMap.group[1].rule[1].source[0].max[0]1
StructureMap.group[1].rule[1].source[0].element[0]Overall activity score
StructureMap.group[1].rule[1].source[0].variable[0]a
StructureMap.group[1].rule[1].target[0].context[0]target
StructureMap.group[1].rule[1].target[0].contextType[0]variable
StructureMap.group[1].rule[1].target[0].element[0]component
StructureMap.group[1].rule[1].target[0].variable[0]component
StructureMap.group[1].rule[1].target[1].context[0]component
StructureMap.group[1].rule[1].target[1].contextType[0]variable
StructureMap.group[1].rule[1].target[1].element[0]code
StructureMap.group[1].rule[1].target[1].variable[0]code
StructureMap.group[1].rule[1].target[1].transform[0]cc
StructureMap.group[1].rule[1].target[1].parameter[0].value[0]''
StructureMap.group[1].rule[1].target[1].parameter[1].value[0]''
StructureMap.group[1].rule[1].target[1].parameter[2].value[0]Overall activity score
StructureMap.group[1].rule[1].target[2].context[0]component
StructureMap.group[1].rule[1].target[2].contextType[0]variable
StructureMap.group[1].rule[1].target[2].element[0]value
StructureMap.group[1].rule[1].target[2].transform[0]copy
StructureMap.group[1].rule[2].name[0]Genomicregion
StructureMap.group[1].rule[2].source[0].context[0]source
StructureMap.group[1].rule[2].source[0].element[0]Genomic region
StructureMap.group[1].rule[2].source[0].variable[0]a
StructureMap.group[1].rule[2].source[1].context[0]source
StructureMap.group[1].rule[2].source[1].element[0]Allele covered
StructureMap.group[1].rule[2].source[1].variable[0]b
StructureMap.group[1].rule[2].source[2].context[0]queried
StructureMap.group[1].rule[2].source[2].element[0]Knowledge base URI
StructureMap.group[1].rule[2].source[2].variable[0]c
StructureMap.group[1].rule[2].source[3].context[0]queried
StructureMap.group[1].rule[2].source[3].element[0]Item name
StructureMap.group[1].rule[2].source[3].variable[0]d
StructureMap.group[1].rule[2].target[0].context[0]target
StructureMap.group[1].rule[2].target[0].contextType[0]variable
StructureMap.group[1].rule[2].target[0].element[0]component
StructureMap.group[1].rule[2].target[0].variable[0]component
StructureMap.group[1].rule[2].target[1].context[0]component
StructureMap.group[1].rule[2].target[1].contextType[0]variable
StructureMap.group[1].rule[2].target[1].element[0]code
StructureMap.group[1].rule[2].target[1].variable[0]code
StructureMap.group[1].rule[2].target[1].transform[0]cc
StructureMap.group[1].rule[2].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[1].rule[2].target[1].parameter[1].value[0]48018-6
StructureMap.group[1].rule[2].target[2].context[0]component
StructureMap.group[1].rule[2].target[2].contextType[0]variable
StructureMap.group[1].rule[2].target[2].element[0]value
StructureMap.group[1].rule[2].target[2].transform[0]copy
StructureMap.group[1].rule[2].target[2].parameter[0].value[0]a
StructureMap.group[1].rule[2].target[3].context[0]component
StructureMap.group[1].rule[2].target[3].contextType[0]variable
StructureMap.group[1].rule[2].target[3].element[0]value
StructureMap.group[1].rule[2].target[3].transform[0]append
StructureMap.group[1].rule[2].target[3].parameter[0].value[0]b
StructureMap.group[1].rule[2].target[4].context[0]component
StructureMap.group[1].rule[2].target[4].contextType[0]variable
StructureMap.group[1].rule[2].target[4].element[0]extension
StructureMap.group[1].rule[2].target[4].variable[0]extension
StructureMap.group[1].rule[2].target[4].transform[0]create
StructureMap.group[1].rule[2].target[4].parameter[0].value[0]Extension
StructureMap.group[1].rule[2].target[5].context[0]extension
StructureMap.group[1].rule[2].target[5].contextType[0]variable
StructureMap.group[1].rule[2].target[5].element[0]url
StructureMap.group[1].rule[2].target[5].transform[0]copy
StructureMap.group[1].rule[2].target[5].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[1].rule[2].target[6].context[0]extension
StructureMap.group[1].rule[2].target[6].contextType[0]variable
StructureMap.group[1].rule[2].target[6].element[0]value
StructureMap.group[1].rule[2].target[6].transform[0]copy
StructureMap.group[1].rule[2].target[6].parameter[0].value[0]c
StructureMap.group[1].rule[2].target[7].context[0]extension
StructureMap.group[1].rule[2].target[7].contextType[0]variable
StructureMap.group[1].rule[2].target[7].element[0]value
StructureMap.group[1].rule[2].target[7].transform[0]append
StructureMap.group[1].rule[2].target[7].parameter[0].value[0]d
StructureMap.group[1].rule[3].name[0]Genotype
StructureMap.group[1].rule[3].source[0].context[0]queried
StructureMap.group[1].rule[3].source[0].max[0]1
StructureMap.group[1].rule[3].source[0].element[0]Genotype
StructureMap.group[1].rule[3].source[0].variable[0]a
StructureMap.group[1].rule[3].target[0].context[0]target
StructureMap.group[1].rule[3].target[0].contextType[0]variable
StructureMap.group[1].rule[3].target[0].element[0]value
StructureMap.group[1].rule[3].target[0].transform[0]append
StructureMap.group[1].rule[3].target[0].parameter[0].value[0]a
StructureMap.group[1].rule[4].name[0]Genotypequality
StructureMap.group[1].rule[4].source[0].context[0]queried
StructureMap.group[1].rule[4].source[0].max[0]1
StructureMap.group[1].rule[4].source[0].element[0]Genotype quality
StructureMap.group[1].rule[4].source[0].variable[0]a
StructureMap.group[1].rule[4].target[0].context[0]target
StructureMap.group[1].rule[4].target[0].contextType[0]variable
StructureMap.group[1].rule[4].target[0].element[0]component
StructureMap.group[1].rule[4].target[0].variable[0]component
StructureMap.group[1].rule[4].target[1].context[0]component
StructureMap.group[1].rule[4].target[1].contextType[0]variable
StructureMap.group[1].rule[4].target[1].element[0]code
StructureMap.group[1].rule[4].target[1].variable[0]code
StructureMap.group[1].rule[4].target[1].transform[0]cc
StructureMap.group[1].rule[4].target[1].parameter[0].value[0]''
StructureMap.group[1].rule[4].target[1].parameter[1].value[0]''
StructureMap.group[1].rule[4].target[1].parameter[2].value[0]Genotype quality
StructureMap.group[1].rule[4].target[2].context[0]component
StructureMap.group[1].rule[4].target[2].contextType[0]variable
StructureMap.group[1].rule[4].target[2].element[0]value
StructureMap.group[1].rule[4].target[2].transform[0]copy
StructureMap.group[1].rule[5].name[0]Genotypeprobability
StructureMap.group[1].rule[5].source[0].context[0]queried
StructureMap.group[1].rule[5].source[0].max[0]1
StructureMap.group[1].rule[5].source[0].element[0]Genotype probability
StructureMap.group[1].rule[5].source[0].variable[0]a
StructureMap.group[1].rule[5].target[0].context[0]target
StructureMap.group[1].rule[5].target[0].contextType[0]variable
StructureMap.group[1].rule[5].target[0].element[0]component
StructureMap.group[1].rule[5].target[0].variable[0]component
StructureMap.group[1].rule[5].target[1].context[0]component
StructureMap.group[1].rule[5].target[1].contextType[0]variable
StructureMap.group[1].rule[5].target[1].element[0]code
StructureMap.group[1].rule[5].target[1].variable[0]code
StructureMap.group[1].rule[5].target[1].transform[0]cc
StructureMap.group[1].rule[5].target[1].parameter[0].value[0]''
StructureMap.group[1].rule[5].target[1].parameter[1].value[0]''
StructureMap.group[1].rule[5].target[1].parameter[2].value[0]Genotype probability
StructureMap.group[1].rule[5].target[2].context[0]component
StructureMap.group[1].rule[5].target[2].contextType[0]variable
StructureMap.group[1].rule[5].target[2].element[0]value
StructureMap.group[1].rule[5].target[2].transform[0]copy
StructureMap.group[1].rule[6].name[0]Specimenidentifier
StructureMap.group[1].rule[6].source[0].context[0]queried
StructureMap.group[1].rule[6].source[0].max[0]1
StructureMap.group[1].rule[6].source[0].element[0]Specimen identifier
StructureMap.group[1].rule[6].source[0].variable[0]a
StructureMap.group[1].rule[6].target[0].context[0]target
StructureMap.group[1].rule[6].target[0].contextType[0]variable
StructureMap.group[1].rule[6].target[0].element[0]specimen
StructureMap.group[1].rule[6].target[0].transform[0]pointer
StructureMap.group[1].rule[6].target[0].parameter[0].value[0]a
StructureMap.group[2].name[0]DiagnosticImplicationInformation
StructureMap.group[2].typeMode[0]types
StructureMap.group[2].input[0].name[0]source
StructureMap.group[2].input[0].type[0]PharmacogeneticTestResult
StructureMap.group[2].input[0].mode[0]source
StructureMap.group[2].input[1].name[0]queried
StructureMap.group[2].input[1].type[0]GenomicVariantResult
StructureMap.group[2].input[1].mode[0]source
StructureMap.group[2].input[2].name[0]target
StructureMap.group[2].input[2].type[0]DiagnosticImplication
StructureMap.group[2].input[2].mode[0]target
StructureMap.group[2].rule[0].name[0]Phenotype
StructureMap.group[2].rule[0].source[0].context[0]source
StructureMap.group[2].rule[0].source[0].element[0]Phenotype
StructureMap.group[2].rule[0].source[0].variable[0]a
StructureMap.group[2].rule[0].target[0].context[0]target
StructureMap.group[2].rule[0].target[0].contextType[0]variable
StructureMap.group[2].rule[0].target[0].element[0]component
StructureMap.group[2].rule[0].target[0].variable[0]component
StructureMap.group[2].rule[0].target[1].context[0]component
StructureMap.group[2].rule[0].target[1].contextType[0]variable
StructureMap.group[2].rule[0].target[1].element[0]code
StructureMap.group[2].rule[0].target[1].variable[0]code
StructureMap.group[2].rule[0].target[1].transform[0]cc
StructureMap.group[2].rule[0].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[2].rule[0].target[1].parameter[1].value[0]81259-4
StructureMap.group[2].rule[0].target[2].context[0]component
StructureMap.group[2].rule[0].target[2].contextType[0]variable
StructureMap.group[2].rule[0].target[2].element[0]value
StructureMap.group[2].rule[0].target[2].transform[0]copy
StructureMap.group[2].rule[1].name[0]ACMGclassification
StructureMap.group[2].rule[1].source[0].context[0]source
StructureMap.group[2].rule[1].source[0].element[0]ACMG classification
StructureMap.group[2].rule[1].source[0].variable[0]a
StructureMap.group[2].rule[1].target[0].context[0]target
StructureMap.group[2].rule[1].target[0].contextType[0]variable
StructureMap.group[2].rule[1].target[0].element[0]component
StructureMap.group[2].rule[1].target[0].variable[0]component
StructureMap.group[2].rule[1].target[1].context[0]component
StructureMap.group[2].rule[1].target[1].contextType[0]variable
StructureMap.group[2].rule[1].target[1].element[0]code
StructureMap.group[2].rule[1].target[1].variable[0]code
StructureMap.group[2].rule[1].target[1].transform[0]cc
StructureMap.group[2].rule[1].target[1].parameter[0].value[0]http://loinc.org
StructureMap.group[2].rule[1].target[1].parameter[1].value[0]53037-8
StructureMap.group[2].rule[1].target[2].context[0]component
StructureMap.group[2].rule[1].target[2].contextType[0]variable
StructureMap.group[2].rule[1].target[2].element[0]value
StructureMap.group[2].rule[1].target[2].transform[0]cc
StructureMap.group[2].rule[1].target[2].parameter[0].value[0]http://loinc.org
StructureMap.group[2].rule[1].target[2].parameter[1].value[0]a
StructureMap.group[3].name[0]HaplotypeInformation
StructureMap.group[3].typeMode[0]types
StructureMap.group[3].input[0].name[0]source
StructureMap.group[3].input[0].type[0]PharmacogeneticTestResult
StructureMap.group[3].input[0].mode[0]source
StructureMap.group[3].input[1].name[0]target
StructureMap.group[3].input[1].type[0]Haplotype
StructureMap.group[3].input[1].mode[0]target
StructureMap.group[3].rule[0].name[0]Allelehaplotype
StructureMap.group[3].rule[0].source[0].context[0]source
StructureMap.group[3].rule[0].source[0].element[0]Allele haplotype
StructureMap.group[3].rule[0].source[0].variable[0]a
StructureMap.group[3].rule[0].target[0].context[0]target
StructureMap.group[3].rule[0].target[0].contextType[0]variable
StructureMap.group[3].rule[0].target[0].element[0]value
StructureMap.group[3].rule[0].target[0].transform[0]copy
StructureMap.group[3].rule[1].name[0]Activityvalue
StructureMap.group[3].rule[1].source[0].context[0]source
StructureMap.group[3].rule[1].source[0].element[0]Activity value
StructureMap.group[3].rule[1].source[0].variable[0]a
StructureMap.group[3].rule[1].target[0].context[0]target
StructureMap.group[3].rule[1].target[0].contextType[0]variable
StructureMap.group[3].rule[1].target[0].element[0]component
StructureMap.group[3].rule[1].target[0].variable[0]component
StructureMap.group[3].rule[1].target[1].context[0]component
StructureMap.group[3].rule[1].target[1].contextType[0]variable
StructureMap.group[3].rule[1].target[1].element[0]code
StructureMap.group[3].rule[1].target[1].variable[0]code
StructureMap.group[3].rule[1].target[1].transform[0]cc
StructureMap.group[3].rule[1].target[1].parameter[0].value[0]''
StructureMap.group[3].rule[1].target[1].parameter[1].value[0]''
StructureMap.group[3].rule[1].target[1].parameter[2].value[0]Activity value
StructureMap.group[3].rule[1].target[2].context[0]component
StructureMap.group[3].rule[1].target[2].contextType[0]variable
StructureMap.group[3].rule[1].target[2].element[0]value
StructureMap.group[3].rule[1].target[2].transform[0]copy
StructureMap.group[4].name[0]MolecularConsequenceInformation
StructureMap.group[4].typeMode[0]types
StructureMap.group[4].input[0].name[0]queried
StructureMap.group[4].input[0].type[0]GenomicVariantResult
StructureMap.group[4].input[0].mode[0]source
StructureMap.group[4].input[1].name[0]target
StructureMap.group[4].input[1].type[0]MolecularConsequence
StructureMap.group[4].input[1].mode[0]target
StructureMap.group[4].rule[0].name[0]Predictedimpactknowledgebase
StructureMap.group[4].rule[0].source[0].context[0]queried
StructureMap.group[4].rule[0].source[0].element[0]Predicted impact knowledge base
StructureMap.group[4].rule[0].source[0].variable[0]a
StructureMap.group[4].rule[0].target[0].context[0]target
StructureMap.group[4].rule[0].target[0].contextType[0]variable
StructureMap.group[4].rule[0].target[0].element[0]component
StructureMap.group[4].rule[0].target[0].variable[0]component
StructureMap.group[4].rule[0].target[1].context[0]component
StructureMap.group[4].rule[0].target[1].contextType[0]variable
StructureMap.group[4].rule[0].target[1].element[0]code
StructureMap.group[4].rule[0].target[1].variable[0]code
StructureMap.group[4].rule[0].target[1].transform[0]cc
StructureMap.group[4].rule[0].target[1].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
StructureMap.group[4].rule[0].target[1].parameter[1].value[0]feature-consequence
StructureMap.group[4].rule[0].target[2].context[0]component
StructureMap.group[4].rule[0].target[2].contextType[0]variable
StructureMap.group[4].rule[0].target[2].element[0]extension
StructureMap.group[4].rule[0].target[2].variable[0]extension
StructureMap.group[4].rule[0].target[2].transform[0]create
StructureMap.group[4].rule[0].target[2].parameter[0].value[0]Extension
StructureMap.group[4].rule[0].target[3].context[0]extension
StructureMap.group[4].rule[0].target[3].contextType[0]variable
StructureMap.group[4].rule[0].target[3].element[0]url
StructureMap.group[4].rule[0].target[3].transform[0]copy
StructureMap.group[4].rule[0].target[3].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[4].rule[0].target[4].context[0]extension
StructureMap.group[4].rule[0].target[4].contextType[0]variable
StructureMap.group[4].rule[0].target[4].element[0]value
StructureMap.group[4].rule[0].target[4].transform[0]copy
StructureMap.group[4].rule[1].name[0]score
StructureMap.group[4].rule[1].source[0].context[0]queried
StructureMap.group[4].rule[1].source[0].element[0]score
StructureMap.group[4].rule[1].source[0].variable[0]a
StructureMap.group[4].rule[1].target[0].context[0]target
StructureMap.group[4].rule[1].target[0].contextType[0]variable
StructureMap.group[4].rule[1].target[0].element[0]value
StructureMap.group[4].rule[1].target[0].transform[0]copy
StructureMap.group[4].rule[2].name[0]Qualitativeprediction
StructureMap.group[4].rule[2].source[0].context[0]queried
StructureMap.group[4].rule[2].source[0].element[0]Qualitative prediction
StructureMap.group[4].rule[2].source[0].variable[0]a
StructureMap.group[4].rule[2].target[0].context[0]target
StructureMap.group[4].rule[2].target[0].contextType[0]variable
StructureMap.group[4].rule[2].target[0].element[0]interpretation
StructureMap.group[4].rule[2].target[0].transform[0]copy
StructureMap.group[4].rule[3].name[0]Impact
StructureMap.group[4].rule[3].source[0].context[0]queried
StructureMap.group[4].rule[3].source[0].element[0]Impact
StructureMap.group[4].rule[3].source[0].variable[0]a
StructureMap.group[4].rule[3].source[1].context[0]queried
StructureMap.group[4].rule[3].source[1].element[0]Source
StructureMap.group[4].rule[3].source[1].variable[0]b
StructureMap.group[4].rule[3].target[0].context[0]target
StructureMap.group[4].rule[3].target[0].contextType[0]variable
StructureMap.group[4].rule[3].target[0].element[0]component
StructureMap.group[4].rule[3].target[0].variable[0]component
StructureMap.group[4].rule[3].target[1].context[0]component
StructureMap.group[4].rule[3].target[1].contextType[0]variable
StructureMap.group[4].rule[3].target[1].element[0]code
StructureMap.group[4].rule[3].target[1].variable[0]code
StructureMap.group[4].rule[3].target[1].transform[0]cc
StructureMap.group[4].rule[3].target[1].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
StructureMap.group[4].rule[3].target[1].parameter[1].value[0]functional-effect
StructureMap.group[4].rule[3].target[2].context[0]component
StructureMap.group[4].rule[3].target[2].contextType[0]variable
StructureMap.group[4].rule[3].target[2].element[0]value
StructureMap.group[4].rule[3].target[2].transform[0]cc
StructureMap.group[4].rule[3].target[2].parameter[0].value[0]http://www.sequenceontology.org
StructureMap.group[4].rule[3].target[2].parameter[1].value[0]a
StructureMap.group[4].rule[3].target[3].context[0]component
StructureMap.group[4].rule[3].target[3].contextType[0]variable
StructureMap.group[4].rule[3].target[3].element[0]extension
StructureMap.group[4].rule[3].target[3].variable[0]extension
StructureMap.group[4].rule[3].target[3].transform[0]create
StructureMap.group[4].rule[3].target[3].parameter[0].value[0]Extension
StructureMap.group[4].rule[3].target[4].context[0]extension
StructureMap.group[4].rule[3].target[4].contextType[0]variable
StructureMap.group[4].rule[3].target[4].element[0]url
StructureMap.group[4].rule[3].target[4].transform[0]copy
StructureMap.group[4].rule[3].target[4].parameter[0].value[0]http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent
StructureMap.group[4].rule[3].target[5].context[0]extension
StructureMap.group[4].rule[3].target[5].contextType[0]variable
StructureMap.group[4].rule[3].target[5].element[0]value
StructureMap.group[4].rule[3].target[5].transform[0]copy
StructureMap.group[4].rule[3].target[5].parameter[0].value[0]b

XML View

<StructureMap xmlns="http://hl7.org/fhir">
<id value="StructureMap-PharmacogeneticTestResult-Genomics" />
<url value="https://fhir.nhs.uk/StructureMap/StructureMap-PharmacogeneticTestResult-Genomics" />
<version value="0.1.0" />
<name value="StructureMapPharmacogeneticTestResultGenomics" />
<title value="StructureMap PharmacogeneticTestResult Genomics" />
<status value="draft" />
<date value="2025-02-14T00:00:00.000Z" />
<publisher value="NHS England" />
<contact>
<name value="NHS England" />
<telecom>
<system value="email" />
<value value="interoperabilityteam@nhs.net" />
</telecom>
</contact>
<description value="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 value="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 value="https://ckm.openehr.org/ckm/archetypes/1013.1.7066" />
<mode value="source" />
<alias value="PharmacogeneticTestResult" />
<documentation value="The OpenEHR PGx logical model" />
</structure>
<structure>
<url value="https://ckm.openehr.org/ckm/archetypes/1013.1.3748" />
<mode value="source" />
<alias value="KnowledgeBaseReference" />
<documentation value="The OpenEHR model for citation of a digital resource" />
</structure>
<structure>
<url value="https://ckm.openehr.org/ckm/archetypes/1013.1.3759" />
<mode value="source" />
<alias value="GenomicVariantResult" />
<documentation value="The OpenEHR model for a variant" />
</structure>
<structure>
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<alias value="Genotype" />
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<url value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype" />
<mode value="target" />
<alias value="Haplotype" />
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<mode value="target" />
<alias value="Variant" />
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<mode value="target" />
<alias value="DiagnosticImplication" />
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<mode value="target" />
<alias value="MolecularConsequence" />
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<mode value="target" />
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<type value="PharmacogeneticTestResult" />
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<name value="produced" />
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<context value="source" />
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<variable value="component" />
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<contextType value="variable" />
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<valueId value="a" />
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<variable value="component" />
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<context value="component" />
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<context value="target" />
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<variable value="component" />
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<context value="component" />
<contextType value="variable" />
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<valueId value="a" />
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<context value="queried" />
<element value="Best transcript candidate" />
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<context value="target" />
<contextType value="variable" />
<element value="component" />
<variable value="component" />
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<context value="queried" />
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<context value="queried" />
<element value="Distance from splicing site" />
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<variable value="component" />
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<context value="range" />
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<context value="target" />
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<valueId value="b" />
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<context value="component" />
<contextType value="variable" />
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<transform value="copy" />
<parameter>
<valueId value="c" />
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<rule>
<name value="Strandbiasratio" />
<source>
<context value="queried" />
<max value="1" />
<element value="Strand bias ratio" />
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</source>
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<context value="target" />
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<variable value="component" />
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<context value="component" />
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<element value="code" />
<variable value="code" />
<transform value="cc" />
<parameter>
<valueString value="''" />
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<valueString value="''" />
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<parameter>
<valueString value="Strand bias ratio" />
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<target>
<context value="component" />
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<name value="Strandbiaspvalue" />
<source>
<context value="queried" />
<max value="1" />
<element value="Strand bias p-value" />
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<target>
<context value="target" />
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<valueString value="Strand bias p-value" />
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<target>
<context value="component" />
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<rule>
<name value="Allelicstate" />
<source>
<context value="queried" />
<max value="1" />
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<context value="target" />
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<valueString value="http://loinc.org" />
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<name value="Additionaldetails" />
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<context value="queried" />
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<context value="target" />
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<name value="GenotypeInformation" />
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<input>
<name value="source" />
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<name value="queried" />
<type value="KnowledgeBaseReference" />
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<input>
<name value="target" />
<type value="Genotype" />
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<name value="Diplotype" />
<source>
<context value="source" />
<max value="1" />
<element value="Diplotype" />
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<target>
<context value="target" />
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<name value="Overallactivityscore" />
<source>
<context value="source" />
<max value="1" />
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<context value="target" />
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<variable value="component" />
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<context value="component" />
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<element value="code" />
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<parameter>
<valueString value="''" />
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<parameter>
<valueString value="Overall activity score" />
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<target>
<context value="component" />
<contextType value="variable" />
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<rule>
<name value="Genomicregion" />
<source>
<context value="source" />
<element value="Genomic region" />
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</source>
<source>
<context value="source" />
<element value="Allele covered" />
<variable value="b" />
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<source>
<context value="queried" />
<element value="Knowledge base URI" />
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<source>
<context value="queried" />
<element value="Item name" />
<variable value="d" />
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<target>
<context value="target" />
<contextType value="variable" />
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<variable value="component" />
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<target>
<context value="component" />
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<element value="code" />
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<parameter>
<valueString value="http://loinc.org" />
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<parameter>
<valueString value="48018-6" />
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<target>
<context value="component" />
<contextType value="variable" />
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<valueId value="a" />
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<context value="component" />
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<valueId value="b" />
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<context value="component" />
<contextType value="variable" />
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<parameter>
<valueString value="Extension" />
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</target>
<target>
<context value="extension" />
<contextType value="variable" />
<element value="url" />
<transform value="copy" />
<parameter>
<valueString value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent" />
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<target>
<context value="extension" />
<contextType value="variable" />
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<valueId value="c" />
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<valueId value="d" />
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<name value="Genotype" />
<source>
<context value="queried" />
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<element value="Genotype" />
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<context value="target" />
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<element value="value" />
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<valueId value="a" />
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<name value="Genotypequality" />
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<context value="queried" />
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<context value="target" />
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<valueString value="''" />
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<valueString value="''" />
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<parameter>
<valueString value="Genotype quality" />
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<context value="component" />
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<rule>
<name value="Genotypeprobability" />
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<context value="queried" />
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<context value="target" />
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<context value="component" />
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<parameter>
<valueString value="''" />
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<parameter>
<valueString value="Genotype probability" />
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<target>
<context value="component" />
<contextType value="variable" />
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<rule>
<name value="Specimenidentifier" />
<source>
<context value="queried" />
<max value="1" />
<element value="Specimen identifier" />
<variable value="a" />
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<target>
<context value="target" />
<contextType value="variable" />
<element value="specimen" />
<transform value="pointer" />
<parameter>
<valueId value="a" />
</parameter>
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<group>
<name value="DiagnosticImplicationInformation" />
<typeMode value="types" />
<input>
<name value="source" />
<type value="PharmacogeneticTestResult" />
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<input>
<name value="queried" />
<type value="GenomicVariantResult" />
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<input>
<name value="target" />
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<rule>
<name value="Phenotype" />
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<context value="source" />
<element value="Phenotype" />
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<target>
<context value="target" />
<contextType value="variable" />
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<variable value="component" />
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<context value="component" />
<contextType value="variable" />
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<parameter>
<valueString value="http://loinc.org" />
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<parameter>
<valueString value="81259-4" />
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<target>
<context value="component" />
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<rule>
<name value="ACMGclassification" />
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<context value="source" />
<element value="ACMG classification" />
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<context value="target" />
<contextType value="variable" />
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<parameter>
<valueString value="http://loinc.org" />
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<parameter>
<valueId value="a" />
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<group>
<name value="HaplotypeInformation" />
<typeMode value="types" />
<input>
<name value="source" />
<type value="PharmacogeneticTestResult" />
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<type value="Haplotype" />
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<rule>
<name value="Allelehaplotype" />
<source>
<context value="source" />
<element value="Allele haplotype" />
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<target>
<context value="target" />
<contextType value="variable" />
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<rule>
<name value="Activityvalue" />
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<context value="target" />
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<rule>
<name value="Predictedimpactknowledgebase" />
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<context value="queried" />
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<context value="target" />
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<name value="score" />
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<target>
<context value="target" />
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<rule>
<name value="Qualitativeprediction" />
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<context value="queried" />
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<target>
<context value="target" />
<contextType value="variable" />
<element value="interpretation" />
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<rule>
<name value="Impact" />
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<context value="queried" />
<element value="Impact" />
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<source>
<context value="queried" />
<element value="Source" />
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<target>
<context value="target" />
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<target>
<context value="component" />
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<element value="code" />
<variable value="code" />
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<parameter>
<valueString value="functional-effect" />
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<target>
<context value="component" />
<contextType value="variable" />
<element value="value" />
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<parameter>
<valueString value="http://www.sequenceontology.org" />
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<parameter>
<valueId value="a" />
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<target>
<context value="component" />
<contextType value="variable" />
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<variable value="extension" />
<transform value="create" />
<parameter>
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</target>
<target>
<context value="extension" />
<contextType value="variable" />
<element value="url" />
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<parameter>
<valueString value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/workflow-relatedArtifactComponent" />
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</target>
<target>
<context value="extension" />
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<element value="value" />
<transform value="copy" />
<parameter>
<valueId value="b" />
</parameter>
</target>
</rule>
</group>
</StructureMap>

JSON View

{
"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",
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{
"context": "queried",
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"max": "1",
"element": "Reference genome",
"variable": "a"
}
],
"target": [
{
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"element": "component",
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},
{
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"variable": "code",
"transform": "cc",
"parameter": [
{
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},
{
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}
]
},
{
"context": "component",
"contextType": "variable",
"element": "value",
"transform": "copy"
}
]
},
{
"name": "Variantidentification",
"source": [
{
"context": "queried",
"element": "Variant identification",
"variable": "a"
}
],
"target": [
{
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"contextType": "variable",
"element": "component",
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},
{
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"transform": "cc",
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{
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},
{
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}
]
},
{
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