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 based on 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:DocumentReference ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "GSS123456-01-010-SG-2"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file>     ] )
  ] ; # 
  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: DocumentReference GSS123456-01-010-SG-2</b></p><a name=\"GSS123456-01-010-SG-2\"> </a><a name=\"hcGSS123456-01-010-SG-2\"> </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-file.html\">NCPI File</a></p></div><p><b>Version of the contents of the file</b>: V1</p><p><b>The file format used</b>: <span title=\"Codes:{http://edamontology.org format_2572}\">BAM</span></p><p><b>The size of the file, e.g., in bytes.</b>: 1044770380 bytes</p><blockquote><p><b>Provides a list of hashes for confirming file transfers</b></p><ul><li>https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value: 9c2460c4647fdc57261f040042863fa0</li><li>https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type: md5</li></ul></blockquote><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>identifier</b>: GSS123456-01-010-SG-2</p><p><b>status</b>: Current</p><p><b>type</b>: <span title=\"Codes:{http://edamontology.org operation_3198}\">Read mapping</span></p><p><b>subject</b>: <a href=\"Patient-GSS123456.html\">Anonymous Patient (no stated gender), DoB Unknown ( https://anvil.terra.bio/#GSS123456)</a></p><p><b>description</b>: Aligned DNA short read</p><blockquote><p><b>content</b></p><p><b>If present, only those under the specific Access Policy can access the file in this location.</b>: <a href=\"Consent-kf-gru-dac-consent.html\">Consent: extension = Use of the data is limited only by the terms of the model Data Use Certification.,https://airtable.com/apperYvVD82ti3021/pagdArwI0TxJQpiVW/form,Controlled; status = draft; scope = Research; category = Research Information Access; policyRule = Common Rule Informed Consent</a></p><h3>Attachments</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Url</b></td></tr><tr><td style=\"display: none\">*</td><td>gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam</td></tr></table></blockquote></div>"^^rdf:XMLLiteral ]
  ] ; # 
  fhir:extension ( [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/content-version>     ] ;
fhir:value [
a fhir:String ;
fhir:v "V1"     ]
  ] [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-format>     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:system [
fhir:v "http://edamontology.org"^^xsd:anyURI ;
fhir:l <http://edamontology.org>         ] ;
fhir:code [ fhir:v "format_2572" ] ;
fhir:display [ fhir:v "BAM" ]       ] )     ]
  ] [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/file-size>     ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "1044770380"^^xsd:decimal ] ;
fhir:unit [ fhir:v "bytes" ]     ]
  ] [
    ( fhir:extension [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-value>       ] ;
fhir:value [
a fhir:String ;
fhir:v "9c2460c4647fdc57261f040042863fa0"       ]     ] [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-type>       ] ;
fhir:value [
a fhir:Code ;
fhir:v "md5"       ]     ] ) ;
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-extension"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/hash-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:identifier ( [
fhir:value [ fhir:v "GSS123456-01-010-SG-2" ]
  ] ) ; # 
  fhir:status [ fhir:v "current"] ; # 
  fhir:type [
    ( fhir:coding [
fhir:system [
fhir:v "http://edamontology.org"^^xsd:anyURI ;
fhir:l <http://edamontology.org>       ] ;
fhir:code [ fhir:v "operation_3198" ] ;
fhir:display [ fhir:v "Read mapping" ]     ] )
  ] ; # 
  fhir:subject [
fhir:l fhir:Patient/GSS123456 ;
fhir:reference [ fhir:v "Patient/GSS123456" ]
  ] ; # 
  fhir:description [ fhir:v "Aligned DNA short read"] ; # 
  fhir:content ( [
    ( fhir:extension [
fhir:url [
fhir:v "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access"^^xsd:anyURI ;
fhir:l <https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/location-access>       ] ;
fhir:value [
a fhir:Reference ;
fhir:l fhir:Consent/kf-gru-dac-consent ;
fhir:reference [ fhir:v "Consent/kf-gru-dac-consent" ]       ]     ] ) ;
fhir:attachment [
fhir:url [
fhir:v "gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam"^^xsd:anyURI ;
fhir:l fhir:gs://fc-secure-a1f0e28d-c9d9-43bb-b4ba-5e0h81784fb1/GSS123456/SR_GS/GSS123456.bam       ]     ]
  ] ) . #