Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:Observation;
fhir:nodeRole fhir:treeRoot;
fhir:Resource.id [ fhir:value "Pgx-geno-1001"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><p></p><p><b>category</b>: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 84413-4}\">Genotype display name</span></p><p><b>subject</b>: <a href=\"Patient-CGPatientExample01.html\">Generated Summary: Medical Record Number: m123 (USUAL); Adam B. Everyman ; gender: male; birthDate: 1951-01-20</a></p><p><b>effective</b>: 2020-01-01</p><p><b>value</b>: <span title=\"Codes: {http://www.ncbi.nlm.nih.gov/clinvar 638797}\">CYP2C19*2/*2</span></p><p><b>specimen</b>: <a href=\"Specimen-GenomicSpecimenExample01.html\">Generated Summary: status: available; <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/v2-0487 TISS}\">Tissue</span></a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Observation-Pgx-var-1011.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1012.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1013.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1014.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1015.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1016.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1017.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li><li><a href=\"Observation-Pgx-var-1018.html\">Generated Summary: <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; effective: 2020-01-01; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td><span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied [ID]</span></td><td><span title=\"Codes: {http://www.genenames.org/geneId HGNC:2621}\">CYP2C19</span></td></tr></table></div>"
];
fhir:Observation.status [ fhir:value "final"];
fhir:Observation.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
];
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:84413-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "84413-4" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/CGPatientExample01" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2020-01-01"^^xsd:date];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/clinvar" ];
fhir:Coding.code [ fhir:value "638797" ];
fhir:Coding.display [ fhir:value "CYP2C19*2/*2" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/GenomicSpecimenExample01" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1011" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1012" ]
], [
fhir:index 2;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1013" ]
], [
fhir:index 3;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1014" ]
], [
fhir:index 4;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1015" ]
], [
fhir:index 5;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1016" ]
], [
fhir:index 6;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1017" ]
], [
fhir:index 7;
fhir:Reference.reference [ fhir:value "Observation/Pgx-var-1018" ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48018-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48018-6" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.genenames.org/geneId" ];
fhir:Coding.code [ fhir:value "HGNC:2621" ];
fhir:Coding.display [ fhir:value "CYP2C19" ] ] ]
].
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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