Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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-analysis1 - 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-analysis1"] ; # 
  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 "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure lungMass-analysis1</b></p><a name=\"lungMass-analysis1\"> </a><a name=\"hclungMass-analysis1\"> </a><a name=\"lungMass-analysis1-en-US\"> </a><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 --&gt; (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 "sequence-analysis-of-the-entire-coding-region" ] ;
fhir:display [ fhir:v "Sequence analysis of the entire coding region" ]       ] )     ]
  ] [
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://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001483" ] ;
fhir:display [ fhir:v "SNV" ]       ] )     ]
  ] [
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://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0002007" ] ;
fhir:display [ fhir:v "MNV" ]       ] )     ]
  ] [
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://sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:1000032" ] ;
fhir:display [ fhir:v "delins" ]       ] )     ]
  ] [
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 "device"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Device/triodenovo-software" ]       ]     ] ) ;
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device"^^xsd:anyURI ]
  ] [
    ( 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 "uncalled"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/UncallableRegions" ]       ]     ] [
fhir:url [ fhir:v "called"^^xsd:anyURI ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/SimpleVariantAnalysis-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-simple" ]       ]     ] ) ;
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." ]
  ] ) . #