Genomics Reporting Implementation Guide
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Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot 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 - 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 rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

 a fhir:GenomicStudy ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "lungMass"] ; # 
  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: GenomicStudy lungMass</b></p><a name=\"lungMass\"> </a><a name=\"hclungMass\"> </a><p><b>status</b>: Available</p><p><b>type</b>: <span title=\"Codes:\">Solid tumor whole exome sequencing panel</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>startDate</b>: 2019-03-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-genomicServiceRequest.html\">ServiceRequest Molecular genetic test (procedure)</a></p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://snomed.info/sct 309529002}\">Lung mass (finding)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable.</p>\n</div></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-methodtype sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001483}\">SNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span>, <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>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 --&gt; (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://example.org/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>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote><p><b>regionsStudied</b>: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/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></p><p><b>regionsCalled</b>: <a href=\"DocumentReference-SimpleVariantAnalysis-called.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_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></p><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicVCFfile-simple.html\">DocumentReference: identifier = http://example.org/identifiers/files#11119; status = current; docStatus = preliminary; description = genomicVCFfile_simple: 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></td><td><span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-triodenovo-software.html\">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>methodType</b>: <span title=\"Codes:{http://hl7.org/fhir/genomicstudy-methodtype deletion-duplication-analysis}\">Deletion/duplication analysis</span></p><p><b>changeType</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0001019}\">CNV</span></p><p><b>genomeBuild</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>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 --&gt; (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-genomicSpecimen.html\">Specimen: identifier = http://example.org/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>date</b>: 2019-03-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote><p><b>regionsStudied</b>: <a href=\"DocumentReference-WES-FullSequencedRegion-GRCh38.html\">DocumentReference: identifier = http://example.org/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></p><p><b>regionsCalled</b>: <a href=\"DocumentReference-CNVAnalysis-called.html\">DocumentReference: identifier = http://example.org/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></p><h3>Outputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicVCFfile-cnv.html\">DocumentReference: identifier = http://example.org/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></td><td><span title=\"Codes:{http://hl7.org/fhir/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table></blockquote></div>"^^rdf:XMLLiteral
  ] ; # 
  fhir:status [ fhir:v "available"] ; # 
  fhir:type ( [
fhir:text [ fhir:v "Solid tumor whole exome sequencing panel" ]
  ] ) ; # 
  fhir:subject [
fhir:reference [ fhir:v "Patient/genomicPatient" ]
  ] ; # 
  fhir:startDate [ fhir:v "2019-03-01"^^xsd:date] ; # 
  fhir:basedOn ( [
fhir:reference [ fhir:v "ServiceRequest/genomicServiceRequest" ]
  ] ) ; # 
  fhir:interpreter ( [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]
  ] ) ; # 
  fhir:reason ( [
fhir:concept [
      ( fhir:coding [
a sct:309529002 ;
fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ;
fhir:code [ fhir:v "309529002" ] ;
fhir:display [ fhir:v "Lung mass (finding)" ]       ] )     ]
  ] ) ; # 
  fhir:note ( [
fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable." ]
  ] ) ; # 
  fhir:analysis ( [
    ( fhir:methodType [
      ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-methodtype"^^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:changeType [
      ( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001483" ] ;
fhir:display [ fhir:v "SNV" ]       ] )     ] [
      ( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0002007" ] ;
fhir:display [ fhir:v "MNV" ]       ] )     ] [
      ( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:1000032" ] ;
fhir:display [ fhir:v "delins" ]       ] )     ] ) ;
fhir:genomeBuild [
      ( 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:instantiatesUri [ fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI ] ;
    ( fhir:focus [
fhir:reference [ fhir:v "Patient/genomicPatient" ]     ] ) ;
    ( fhir:specimen [
fhir:reference [ fhir:v "Specimen/genomicSpecimen" ]     ] ) ;
fhir:date [ fhir:v "2019-03-01T01:01:10-06:00"^^xsd:dateTime ] ;
    ( fhir:note [
fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable using this method." ]     ] ) ;
    ( fhir:regionsStudied [
fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ]     ] ) ;
    ( fhir:regionsCalled [
fhir:reference [ fhir:v "DocumentReference/SimpleVariantAnalysis-called" ]     ] ) ;
    ( fhir:output [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicVCFfile-simple" ]       ] ;
fhir:type [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]         ] )       ]     ] ) ;
    ( fhir:performer [
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]       ] ;
fhir:role [
        ( 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:device [
fhir:device [
fhir:reference [ fhir:v "Device/triodenovo-software" ]       ]     ] )
  ] [
    ( fhir:methodType [
      ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-methodtype"^^xsd:anyURI ] ;
fhir:code [ fhir:v "deletion-duplication-analysis" ] ;
fhir:display [ fhir:v "Deletion/duplication analysis" ]       ] )     ] ) ;
    ( fhir:changeType [
      ( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001019" ] ;
fhir:display [ fhir:v "CNV" ]       ] )     ] ) ;
fhir:genomeBuild [
      ( 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:instantiatesUri [ fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI ] ;
    ( fhir:focus [
fhir:reference [ fhir:v "Patient/genomicPatient" ]     ] ) ;
    ( fhir:specimen [
fhir:reference [ fhir:v "Specimen/genomicSpecimen" ]     ] ) ;
fhir:date [ fhir:v "2019-03-01T01:01:10-06:00"^^xsd:dateTime ] ;
    ( fhir:note [
fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable using this method." ]     ] ) ;
    ( fhir:regionsStudied [
fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ]     ] ) ;
    ( fhir:regionsCalled [
fhir:reference [ fhir:v "DocumentReference/CNVAnalysis-called" ]     ] ) ;
    ( fhir:output [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicVCFfile-cnv" ]       ] ;
fhir:type [
        ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]         ] )       ]     ] ) ;
    ( fhir:performer [
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]       ] ;
fhir:role [
        ( 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" ]         ] )       ]     ] )
  ] ) . #