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-var-1016"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ]
];
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 69548-6}\">Genetic variant assessment</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://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes: {https://www.ncbi.nlm.nih.gov/nuccore NC_000010.10}\">b37 Chr10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 92822-6}\">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA30102-0}\">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes exact-start-end}\">Variant exact start and end</span></p><p><b>value</b>: 96541616-96541616</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 69551-0}\">Genomic alt allele [ID]</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes: {http://loinc.org LA6705-3}\">homozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes: {http://www.genenames.org/geneId HGNC:2621}\">CYP2C19</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 48019-4}\">DNA Change Type</span></p><p><b>value</b>: <span title=\"Codes: {http://sequenceontology.org SO:1000002}\">wild type</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes: {http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: >20</p></blockquote></div>"
];
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fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
];
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fhir:index 0;
a loinc:69548-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69548-6" ] ]
];
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;
a loinc:LA9633-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA9633-4" ];
fhir:Coding.display [ fhir:value "Present" ] ]
];
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fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26398-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26398-0" ];
fhir:Coding.display [ fhir:value "Sequencing" ] ]
];
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48013-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48013-7" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "https://www.ncbi.nlm.nih.gov/nuccore" ];
fhir:Coding.code [ fhir:value "NC_000010.10" ];
fhir:Coding.display [ fhir:value "b37 Chr10" ] ] ]
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fhir:index 1;
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fhir:index 0;
a loinc:92822-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "92822-6" ] ] ];
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fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA30102-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA30102-0" ];
fhir:Coding.display [ fhir:value "1-based character counting" ] ] ]
], [
fhir:index 2;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes" ];
fhir:Coding.code [ fhir:value "exact-start-end" ] ] ];
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "96541616"^^xsd:decimal ] ];
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fhir:Quantity.value [ fhir:value "96541616"^^xsd:decimal ] ] ]
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fhir:index 0;
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fhir:Observation.component.valueString [ fhir:value "G" ]
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fhir:index 0;
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fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69551-0" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
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fhir:index 0;
a loinc:48002-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48002-0" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6683-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6683-2" ];
fhir:Coding.display [ fhir:value "Germline" ] ] ]
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fhir:index 6;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53034-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53034-5" ] ] ];
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fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6705-3;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6705-3" ];
fhir:Coding.display [ fhir:value "homozygous" ] ] ]
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fhir:index 7;
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fhir:index 0;
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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" ] ] ]
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fhir:index 8;
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fhir:index 0;
a loinc:48019-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48019-4" ] ] ];
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fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
fhir:Coding.code [ fhir:value "SO:1000002" ];
fhir:Coding.display [ fhir:value "wild type" ] ] ]
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fhir:index 9;
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fhir:index 0;
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fhir:Coding.code [ fhir:value "82121-5" ] ] ];
fhir:Observation.component.valueQuantity [
fhir:Quantity.value [ fhir:value "20"^^xsd:decimal ];
fhir:Quantity.comparator [ fhir:value ">" ] ]
].
# - 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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