@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 xsd: <http://www.w3.org/2001/XMLSchema#> .

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

<http://hl7.org/fhir/uv/genomics-reporting/Procedure/lungMass-analysis1> 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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis>
     ] )
  ] ; # 
  fhir:text [
     fhir:status [ fhir:v "extensions" ] ;
     fhir:div [ fhir:v "<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><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-study-analysis.html\">Genomic Study Analysis</a></p></div><p><b>Genomic Study Analysis Method Type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs sequence-analysis-of-the-entire-coding-region}\">Sequence analysis of the entire coding region</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:0001483}\">SNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:0002007}\">MNV</span></p><p><b>Genomic Study Analysis Change Type</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:1000032}\">delins</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://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>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 --&gt; (ongoing)))</a></p><blockquote><p><b>Genomic Study Analysis Device</b></p><ul><li>device: <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></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Regions</b></p><ul><li>studied: <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></li><li>uncalled: <a href=\"DocumentReference-UncallableRegions.html\">DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = Representing a BED file that represents uncallable regions; securityLabel = Restricted</a></li><li>called: <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></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-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></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 --&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>: </p><blockquote><div><p>For technical reasons, PIK3CB was deemed uncallable using this method.</p>\n</div></blockquote></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:extension ( [
     fhir:url [
       fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type"^^xsd:anyURI ;
       fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type>
     ] ;
     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:l <http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-method-type-cs>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class>
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         a loinc:LA6684-0 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type>
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type>
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type>
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         fhir:system [
           fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ;
           fhir:l <http://www.sequenceontology.org>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build>
     ] ;
     fhir:value [
       a fhir:CodeableConcept ;
       fhir:coding ( [
         a loinc:LA26806-2 ;
         fhir:system [
           fhir:v "http://loinc.org"^^xsd:anyURI ;
           fhir:l <http://loinc.org>
         ] ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen>
     ] ;
     fhir:value [
       a fhir:Reference ;
       fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Specimen/genomicSpecimen> ;
       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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus>
     ] ;
     fhir:value [
       a fhir:Reference ;
       fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Patient/genomicPatient> ;
       fhir:reference [ fhir:v "Patient/genomicPatient" ]
     ]
  ] [
     fhir:extension ( [
       fhir:url [
         fhir:v "device"^^xsd:anyURI ;
         fhir:l fhir:device
       ] ;
       fhir:value [
         a fhir:Reference ;
         fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Device/triodenovo-software> ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device>
     ]
  ] [
     fhir:extension ( [
       fhir:url [
         fhir:v "studied"^^xsd:anyURI ;
         fhir:l fhir:studied
       ] ;
       fhir:value [
         a fhir:Reference ;
         fhir:l <http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/WES-FullSequencedRegion-GRCh38> ;
         fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ]
       ]
     ] [
       fhir:url [
         fhir:v "uncalled"^^xsd:anyURI ;
         fhir:l fhir:uncalled
       ] ;
       fhir:value [
         a fhir:Reference ;
         fhir:l <http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/UncallableRegions> ;
         fhir:reference [ fhir:v "DocumentReference/UncallableRegions" ]
       ]
     ] [
       fhir:url [
         fhir:v "called"^^xsd:anyURI ;
         fhir:l fhir:called
       ] ;
       fhir:value [
         a fhir:Reference ;
         fhir:l <http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/SimpleVariantAnalysis-called> ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions>
     ]
  ] [
     fhir:extension ( [
       fhir:url [
         fhir:v "type"^^xsd:anyURI ;
         fhir:l fhir:type
       ] ;
       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:l <http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs>
           ] ;
           fhir:code [ fhir:v "vcf" ] ;
           fhir:display [ fhir:v "VCF" ]
         ] )
       ]
     ] [
       fhir:url [
         fhir:v "file"^^xsd:anyURI ;
         fhir:l fhir:file
       ] ;
       fhir:value [
         a fhir:Reference ;
         fhir:l <http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/genomicVCFfile-simple> ;
         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:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output>
     ]
  ] ) ; # 
  fhir:instantiatesUri ( [
     fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI ;
     fhir:l <https://pubmed.ncbi.nlm.nih.gov/33927380/>
  ] ) ; # 
  fhir:status [ fhir:v "completed"] ; # 
  fhir:category [
     fhir:coding ( [
       fhir:system [
         fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ;
         fhir:l <http://terminology.hl7.org/CodeSystem/observation-category>
       ] ;
       fhir:code [ fhir:v "laboratory" ]
     ] )
  ] ; # 
  fhir:subject [
     fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Patient/genomicPatient> ;
     fhir:reference [ fhir:v "Patient/genomicPatient" ]
  ] ; # 
  fhir:performed [
     a fhir:DateTime ;
     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:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType>
         ] ;
         fhir:code [ fhir:v "PRF" ] ;
         fhir:display [ fhir:v "Performer" ]
       ] )
     ] ;
     fhir:actor [
       fhir:l <http://hl7.org/fhir/uv/genomics-reporting/Practitioner/practitioner02> ;
       fhir:reference [ fhir:v "Practitioner/practitioner02" ]
     ]
  ] ) ; # 
  fhir:note ( [
     fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable using this method." ]
  ] ) . # 

<http://hl7.org/fhir/uv/genomics-reporting/Specimen/genomicSpecimen> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/Patient/genomicPatient> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/Device/triodenovo-software> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/WES-FullSequencedRegion-GRCh38> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/UncallableRegions> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/SimpleVariantAnalysis-called> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/DocumentReference/genomicVCFfile-simple> a fhir:Uv .

<http://hl7.org/fhir/uv/genomics-reporting/Practitioner/practitioner02> a fhir:Uv .

# -------------------------------------------------------------------------------------