Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
: ExampleGermlineCNV - TTL Representation
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@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://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:id [ fhir:v "ExampleGermlineCNV"] ; #
fhir:meta [
( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] )
] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation ExampleGermlineCNV</b></p><a name=\"ExampleGermlineCNV\"> </a><a name=\"hcExampleGermlineCNV\"> </a><a name=\"ExampleGermlineCNV-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</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\">Adam B. Everyman Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Organization-ExampleOrg.html\">Organization some lab</a></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 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">copy_number_variation</span></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>: T</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 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000022.10}\">NC_000022.10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82155-3}\">Genomic structural variant copy number</span></p><p><b>value</b>: 3 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1 = '1')</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://loinc.org 81302-2}\">Structural variant inner start and end</span></p><p><b>value</b>: 42523949-42533891</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 94186-4}\">Origin of germline genetic variant [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA26320-4}\">Maternal</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82309-6}\">Basis for allelic phase [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA26426-9}\">Directly measured</span></p></blockquote></div>"
] ; #
fhir:status [ fhir:v "final"] ; #
fhir:category ( [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ] ] )
] [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GE" ] ] )
] ) ; #
fhir:code [
( fhir:coding [
a loinc:69548-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69548-6" ] ] )
] ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/CGPatientExample01" ]
] ; #
fhir:effective [ fhir:v "2019-04-01"^^xsd:date] ; #
fhir:performer ( [
fhir:reference [ fhir:v "Organization/ExampleOrg" ]
] ) ; #
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA9633-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA9633-4" ] ;
fhir:display [ fhir:v "Present" ] ] )
] ; #
fhir:method [
( fhir:coding [
a loinc:LA26398-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA26398-0" ] ;
fhir:display [ fhir:v "Sequencing" ] ] )
] ; #
fhir:component ( [
fhir:code [
( fhir:coding [
a loinc:48019-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48019-4" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001019" ] ;
fhir:display [ fhir:v "copy_number_variation" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:69547-8 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69547-8" ] ] ) ] ;
fhir:value [ fhir:v "T" ]
] [
fhir:code [
( fhir:coding [
a loinc:48002-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48002-0" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA6683-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6683-2" ] ;
fhir:display [ fhir:v "Germline" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48013-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48013-7" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NC_000022.10" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:82155-3 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "82155-3" ] ] ) ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "3"^^xsd:decimal ] ;
fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "1" ] ]
] [
fhir:code [
( fhir:coding [
a loinc:92822-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "92822-6" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA30102-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA30102-0" ] ;
fhir:display [ fhir:v "1-based character counting" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:81302-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81302-2" ] ] ) ] ;
fhir:value [
a fhir:Range ;
fhir:low [
fhir:value [ fhir:v "42523949"^^xsd:decimal ] ] ;
fhir:high [
fhir:value [ fhir:v "42533891"^^xsd:decimal ] ] ]
] [
fhir:code [
( fhir:coding [
a loinc:94186-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "94186-4" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA26320-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA26320-4" ] ;
fhir:display [ fhir:v "Maternal" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:82309-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "82309-6" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA26426-9 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA26426-9" ] ;
fhir:display [ fhir:v "Directly measured" ] ] ) ]
] ) . #
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