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

## : genomicstudyanalysis-trio2 - 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 "genomicstudyanalysis-trio2"] ; #
      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 genomicstudyanalysis-trio2</b></p><a name=\"genomicstudyanalysis-trio2\"> </a><a name=\"hcgenomicstudyanalysis-trio2\"> </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 Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoFather.html\">Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoMother.html\">Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Title</b>: Parental Sequence Variation Detection Using Next Generation Sequencing</p><p><b>Genomic Study Analysis Protocol Performed</b>: <a href=\"Procedure-SequencingProcedure.html\">Procedure Sequencing of entire coding region of gene (procedure)</a></p><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileMotherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11125; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileFatherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11132; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandVCF.html\">DocumentReference: identifier = http://example.org/identifiers/files#11150; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></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-denovoChild.html\">Child Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 1234-11111 (use: temp, ))</a></p><p><b>performed</b>: 2023-10-01</p></div>"^^rdf:XMLLiteral ]
      ] ; #
      fhir:extension ( [
    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-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/denovoFather ;
    fhir:reference [ fhir:v "Patient/denovoFather" ]     ]
      ] [
    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/denovoMother ;
    fhir:reference [ fhir:v "Patient/denovoMother" ]     ]
      ] [
    fhir:url [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title>     ] ;
    fhir:value [
    a fhir:String ;
    fhir:v "Parental Sequence Variation Detection Using Next Generation Sequencing"     ]
      ] [
    fhir:url [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed>     ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:Procedure/SequencingProcedure ;
    fhir:reference [ fhir:v "Procedure/SequencingProcedure" ]     ]
      ] [
        ( fhir:extension [
    fhir:url [
    fhir:v "file"^^xsd:anyURI ;
    fhir:l fhir:file       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/genomicFileProbandBAM ;
    fhir:reference [ fhir:v "DocumentReference/genomicFileProbandBAM" ]       ]     ] [
    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 "bam" ] ;
    fhir:display [ fhir:v "BAM" ]         ] )       ]     ] ) ;
    fhir:url [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input>     ]
      ] [
        ( fhir:extension [
    fhir:url [
    fhir:v "file"^^xsd:anyURI ;
    fhir:l fhir:file       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/genomicFileMotherBAM ;
    fhir:reference [ fhir:v "DocumentReference/genomicFileMotherBAM" ]       ]     ] [
    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 "bam" ] ;
    fhir:display [ fhir:v "BAM" ]         ] )       ]     ] ) ;
    fhir:url [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input>     ]
      ] [
        ( fhir:extension [
    fhir:url [
    fhir:v "file"^^xsd:anyURI ;
    fhir:l fhir:file       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/genomicFileFatherBAM ;
    fhir:reference [ fhir:v "DocumentReference/genomicFileFatherBAM" ]       ]     ] [
    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 "bam" ] ;
    fhir:display [ fhir:v "BAM" ]         ] )       ]     ] ) ;
    fhir:url [
    fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input"^^xsd:anyURI ;
    fhir:l <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input>     ]
      ] [
        ( fhir:extension [
    fhir:url [
    fhir:v "file"^^xsd:anyURI ;
    fhir:l fhir:file       ] ;
    fhir:value [
    a fhir:Reference ;
    fhir:l fhir:DocumentReference/genomicFileProbandVCF ;
    fhir:reference [ fhir:v "DocumentReference/genomicFileProbandVCF" ]       ]     ] [
    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 "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/denovoChild ;
    fhir:reference [ fhir:v "Patient/denovoChild" ]
      ] ; #
      fhir:performed [
    a fhir:DateTime ;
    fhir:v "2023-10-01"^^xsd:date
      ] . #