PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example Genomic Test - TTL Representation

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@prefix fhir: <http://hl7.org/fhir/> .
@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:Basic ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "genomic-test-example-1"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test>     ] )
  ] ; # 
  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: Basic genomic-test-example-1</b></p><a name=\"genomic-test-example-1\"> </a><a name=\"hcgenomic-test-example-1\"> </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-test.html\">Genomic Test</a></p></div><p><b>Reference Genome ID relationship</b>: <a href=\"Basic-reference-genome-grch38.html\">Basic GRCh38</a></p><p><b>Genomic Test Name</b>: ExomeSeq v1</p><p><b>Genomic Test Version</b>: 1.2.3</p><p><b>Sequencing device</b>: Illumina NovaSeq 6000</p><p><b>Target capture</b>: Exome capture kit XYZ v5</p><p><b>Read type</b>: Paired-end</p><p><b>Read length</b>: 150</p><p><b>Mean target coverage</b>: 120.5</p><p><b>Per target base cover x100</b>: 95.3</p><p><b>Alignment tools</b>: BWA-MEM 0.7.17</p><p><b>Variant calling tools</b>: GATK HaplotypeCaller 4.2.0</p><p><b>Chromosome coordinate</b>: GRCh38 (1-based, inclusive)</p><p><b>Annotation tools</b>: VEP 104</p><p><b>Annotation databases</b>: gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3</p><p><b>identifier</b>: <code>https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id</code>/GT0001</p><p><b>code</b>: <span title=\"Codes:{https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type exome}\">Exome sequencing</span></p></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:extension ( [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-reference-genome"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-reference-genome>     ] ;
fhir:value [
a fhir:Reference ;
fhir:l fhir:Basic/reference-genome-grch38 ;
fhir:reference [ fhir:v "Basic/reference-genome-grch38" ]     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-name"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-name>     ] ;
fhir:value [
a fhir:String ;
fhir:v "ExomeSeq v1"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-version"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-version>     ] ;
fhir:value [
a fhir:String ;
fhir:v "1.2.3"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-sequencing-device"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-sequencing-device>     ] ;
fhir:value [
a fhir:String ;
fhir:v "Illumina NovaSeq 6000"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-target-capture"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-target-capture>     ] ;
fhir:value [
a fhir:String ;
fhir:v "Exome capture kit XYZ v5"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-type"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-type>     ] ;
fhir:value [
a fhir:String ;
fhir:v "Paired-end"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-length"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-read-length>     ] ;
fhir:value [
a fhir:Integer ;
fhir:v 150     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-mean-target-coverage"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-mean-target-coverage>     ] ;
fhir:value [
a fhir:Decimal ;
fhir:v 120.5     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-per-target-base-cover-100x"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-per-target-base-cover-100x>     ] ;
fhir:value [
a fhir:Decimal ;
fhir:v 95.3     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-alignment-tools"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-alignment-tools>     ] ;
fhir:value [
a fhir:String ;
fhir:v "BWA-MEM 0.7.17"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-variant-calling-tools"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-variant-calling-tools>     ] ;
fhir:value [
a fhir:String ;
fhir:v "GATK HaplotypeCaller 4.2.0"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-chromosome-corrdinate"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-chromosome-corrdinate>     ] ;
fhir:value [
a fhir:String ;
fhir:v "GRCh38 (1-based, inclusive)"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-tools"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-tools>     ] ;
fhir:value [
a fhir:String ;
fhir:v "VEP 104"     ]
  ] [
fhir:url [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-databases"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/genomic-test-annotation-databases>     ] ;
fhir:value [
a fhir:String ;
fhir:v "gnomAD v3.1, ClinVar 2025-01, dbNSFP 4.3"     ]
  ] ) ; # 
  fhir:identifier ( [
fhir:system [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/genomic-test-id>     ] ;
fhir:value [ fhir:v "GT0001" ]
  ] ) ; # 
  fhir:code [
    ( fhir:coding [
fhir:system [
fhir:v "https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type"^^xsd:anyURI ;
fhir:l <https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/CodeSystem/genomic-test-type>       ] ;
fhir:code [ fhir:v "exome" ] ;
fhir:display [ fhir:v "Exome sequencing" ]     ] )
  ] . #