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
: lungMass-analysis2 - 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:Procedure ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "lungMass-analysis2"] ; #
fhir:meta [
( fhir:profile [
fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis> ] )
] ; #
fhir:text [
fhir:status [ fhir:v "extensions" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure lungMass-analysis2</b></p><a name=\"lungMass-analysis2\"> </a><a name=\"hclungMass-analysis2\"> </a><a name=\"lungMass-analysis2-en-US\"> </a><p><b>Genomic Study Analysis Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs deletion-duplication-analysis}\">Deletion/duplication analysis</span></p><p><b>Genomic Study Analysis Source Class</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">CNV</span></p><p><b>Genomic Study Analysis Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://www.somesystemabc.net/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-genomicPatient.html\">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>called: <a href=\"DocumentReference-CNVAnalysis-called.html\">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11120; status = current; docStatus = preliminary; description = CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></li><li>file: <a href=\"DocumentReference-genomicVCFfile-cnv.html\">DocumentReference: identifier = http://www.somesystemabc.net/identifiers/files#11121; status = current; docStatus = preliminary; description = genomicVCFfile_cnv: A sample Document Reference instance representing a VCF file that may be used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li></ul></blockquote><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>subject</b>: <a href=\"Patient-genomicPatient.html\">John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>performed</b>: 2019-03-01 01:01:10-0600</p><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Function</b></td><td><b>Actor</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td></tr></table><p><b>note</b>: For technical reasons, PIK3CB was deemed uncallable using this method.</p></div>"
] ; #
fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type"^^xsd:anyURI ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "deletion-duplication-analysis" ] ;
fhir:display [ fhir:v "Deletion/duplication analysis" ] ] ) ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class"^^xsd:anyURI ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA6684-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6684-0" ] ;
fhir:display [ fhir:v "Somatic" ] ] ) ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type"^^xsd:anyURI ] ;
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 "CNV" ] ] ) ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build"^^xsd:anyURI ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA26806-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA26806-2" ] ;
fhir:display [ fhir:v "GRCh38" ] ] ) ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Specimen/genomicSpecimen" ] ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Patient/genomicPatient" ] ]
] [
( fhir:extension [
fhir:url [ fhir:v "studied"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ] ] ] [
fhir:url [ fhir:v "called"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/CNVAnalysis-called" ] ] ] ) ;
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"^^xsd:anyURI ]
] [
( fhir:extension [
fhir:url [ fhir:v "type"^^xsd:anyURI ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ] ] ) ] ] [
fhir:url [ fhir:v "file"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/genomicVCFfile-cnv" ] ] ] ) ;
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output"^^xsd:anyURI ]
] ) ; #
fhir:instantiatesUri ( [ fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI] ) ; #
fhir:status [ fhir:v "completed"] ; #
fhir:category [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ] ] )
] ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/genomicPatient" ]
] ; #
fhir:performed [ fhir:v "2019-03-01T01:01:10-06:00"^^xsd:dateTime] ; #
fhir:performer ( [
fhir:function [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ] ;
fhir:code [ fhir:v "PRF" ] ;
fhir:display [ fhir:v "Performer" ] ] ) ] ;
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ] ]
] ) ; #
fhir:note ( [
fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable using this method." ]
] ) . #
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