Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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 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 -------------------------------------------------------------------

     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: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-analysis2</b></p><a name=\"lungMass-analysis2\"> </a><a name=\"hclungMass-analysis2\"> </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 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://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 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>called: <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></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://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></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 "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: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: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: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 fhir: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 fhir:Patient/genomicPatient ;
    fhir:reference [ fhir:v "Patient/genomicPatient" ]     ]
      ] [
        ( fhir:extension [
    fhir:url [
    fhir:v "studied"^^xsd:anyURI ;
    fhir:l fhir:studied       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/WES-FullSequencedRegion-GRCh38 ;
    fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ]       ]     ] [
    fhir:url [
    fhir:v "called"^^xsd:anyURI ;
    fhir:l fhir:called       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/CNVAnalysis-called ;
    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: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 fhir:DocumentReference/genomicVCFfile-cnv ;
    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: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 fhir: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 fhir:Practitioner/practitioner02 ;
    fhir:reference [ fhir:v "Practitioner/practitioner02" ]     ]
      ] ) ; #
      fhir:note ( [
    fhir:text [ fhir:v "For technical reasons, PIK3CB was deemed uncallable using this method." ]
      ] ) . #