NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

• Narrative Content
• XML
• JSON
• TTL

: Example file metadata for a BAM-CRAM file from GREGoR - TTL Representation

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

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

 a fhir:Observation ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "gregor-example-metadata"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram"^^xsd:anyURI ;
fhir:link <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram>     ] )
  ] ; # 
  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: Observation gregor-example-metadata</b></p><a name=\"gregor-example-metadata\"> </a><a name=\"hcgregor-example-metadata\"> </a><a name=\"gregor-example-metadata-en-US\"> </a><p><b>status</b>: Final</p><p><b>code</b>: <span title=\"Codes:{http://edamontology.org format_2572}\">format_2572</span></p><p><b>focus</b>: <a href=\"Patient-GSS123456.html\">Anonymous Patient (no stated gender), DoB Unknown ( https://anvil.terra.bio/#GSS123456)</a></p><p><b>specimen</b>: <a href=\"Specimen-GSS123456-01-010.html\">Specimen: identifier = GSS123456-s1; type = </a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">AssayStrategy</span></p><p><b>value</b>: <span title=\"Codes:\">WGS</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">PlatformInstrument</span></p><p><b>value</b>: <span title=\"Codes:\">IlluminaHiSeq2000</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">LibraryPrep</span></p><p><b>value</b>: <span title=\"Codes:\">polyA</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">LibrarySelection</span></p><p><b>value</b>: <span title=\"Codes:\">PolyTEnrichment</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">TargetRegion</span></p><p><b>value</b>: <span title=\"Codes:\">Not Applicable</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">Strandedness</span></p><p><b>value</b>: <span title=\"Codes:\">stranded</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">ReferenceGenome</span></p><p><b>value</b>: <span title=\"Codes:\">GRCh38</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">IsPairedEnd</span></p><p><b>value</b>: false</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">WorkflowTool</span></p><p><b>value</b>: <span title=\"Codes:\">bammem</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:\">WorkflowType</span></p><p><b>value</b>: <span title=\"Codes:\">alignment</span></p></blockquote></div>"
  ] ; # 
  fhir:status [ fhir:v "final"] ; # 
  fhir:code [
    ( fhir:coding [
fhir:system [ fhir:v "http://edamontology.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "format_2572" ]     ] )
  ] ; # 
  fhir:focus ( [
fhir:reference [ fhir:v "Patient/GSS123456" ]
  ] ) ; # 
  fhir:specimen [
fhir:reference [ fhir:v "Specimen/GSS123456-01-010" ]
  ] ; # 
  fhir:component ( [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "AssayStrategy" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "WGS" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "PlatformInstrument" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "IlluminaHiSeq2000" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "LibraryPrep" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "polyA" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "LibrarySelection" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "PolyTEnrichment" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "TargetRegion" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
fhir:text [ fhir:v "Not Applicable" ]     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "Strandedness" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "stranded" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "ReferenceGenome" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "GRCh38" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "IsPairedEnd" ]       ] )     ] ;
fhir:value [ fhir:v "false"^^xsd:boolean ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "WorkflowTool" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "bammem" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:code [ fhir:v "WorkflowType" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "alignment" ]       ] )     ]
  ] ) . #