NCPI FHIR Implementation Guide v2
0.2.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

: 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 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: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:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram>     ] )
  ] ; # 
  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: Observation gregor-example-metadata</b></p><a name=\"gregor-example-metadata\"> </a><a name=\"hcgregor-example-metadata\"> </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-ncpi-bamcram.html\">BAM or CRAM file profile</a></p></div><p><b>Part of Study</b>: <a href=\"ResearchStudy-research-study-gregor.html\">ResearchStudy: identifier = AnVIL_GREGoR_GSS_U08_GRU; status = completed</a></p><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: extension = -&gt;ResearchStudy: identifier = AnVIL_GREGoR_GSS_U08_GRU; status = completed; identifier = GSS123456-s1; type = </a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements AssayStrategy}\">Assay strategy</span></p><p><b>value</b>: <span title=\"Codes:{http://purl.obolibrary.org/obo/obi.owl 0002117}\">whole genome sequencing assay</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements PlatformInstrument}\">Platform instrument</span></p><p><b>value</b>: <span title=\"Codes:{http://purl.obolibrary.org/obo/obi.owl 0002001}\">Illumina HiSeq 2000</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements LibraryPrep}\">Library preparation</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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements LibrarySelection}\">Library selection</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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements TargetRegion}\">Target region</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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements Strandedness}\">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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements ReferenceGenome}\">Reference genome</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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements IsPairedEnd}\">Is paired end</span></p><p><b>value</b>: false</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements WorkflowTool}\">Workflow tool</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:{https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements WorkflowType}\">Workflow type</span></p><p><b>value</b>: <span title=\"Codes:\">alignment</span></p></blockquote></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:extension ( [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/part-of-study"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/part-of-study>     ] ;
fhir:value [
a fhir:Reference ;
fhir:l fhir:ResearchStudy/research-study-gregor ;
fhir:reference [ fhir:v "ResearchStudy/research-study-gregor" ]     ]
  ] ) ; # 
  fhir:status [ fhir:v "final"] ; # 
  fhir:code [
    ( fhir:coding [
fhir:system [
fhir:v "http://edamontology.org"^^xsd:anyURI ;
fhir:l <http://edamontology.org>       ] ;
fhir:code [ fhir:v "format_2572" ]     ] )
  ] ; # 
  fhir:focus ( [
fhir:l fhir:Patient/GSS123456 ;
fhir:reference [ fhir:v "Patient/GSS123456" ]
  ] ) ; # 
  fhir:specimen [
fhir:l fhir:Specimen/GSS123456-01-010 ;
fhir:reference [ fhir:v "Specimen/GSS123456-01-010" ]
  ] ; # 
  fhir:component ( [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "AssayStrategy" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:system [
fhir:v "http://purl.obolibrary.org/obo/obi.owl"^^xsd:anyURI ;
fhir:l <http://purl.obolibrary.org/obo/obi.owl>         ] ;
fhir:code [ fhir:v "0002117" ] ;
fhir:display [ fhir:v "whole genome sequencing assay" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "PlatformInstrument" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:system [
fhir:v "http://purl.obolibrary.org/obo/obi.owl"^^xsd:anyURI ;
fhir:l <http://purl.obolibrary.org/obo/obi.owl>         ] ;
fhir:code [ fhir:v "0002001" ] ;
fhir:display [ fhir:v "Illumina HiSeq 2000" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "LibraryPrep" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "polyA" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "LibrarySelection" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "PolyTEnrichment" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "TargetRegion" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
fhir:text [ fhir:v "Not Applicable" ]     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "Strandedness" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "stranded" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "ReferenceGenome" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "GRCh38" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "IsPairedEnd" ]       ] )     ] ;
fhir:value [
a fhir:Boolean ;
fhir:v false     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "WorkflowTool" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "bammem" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements>         ] ;
fhir:code [ fhir:v "WorkflowType" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:code [ fhir:v "alignment" ]       ] )     ]
  ] ) . #