0.1.0 - ci-build

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

: Ferlab.bio Example/cqdg-task - 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:Task ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "CQDGTaskExample"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "https://fhir.cqdg.ca/StructureDefinition/CQDGTask"^^xsd:anyURI ;
fhir:link <https://fhir.cqdg.ca/StructureDefinition/CQDGTask>     ] )
  ] ; # 
  fhir:text [
fhir:status [ fhir:v "extensions" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Task CQDGTaskExample</b></p><a name=\"CQDGTaskExample\"> </a><a name=\"hcCQDGTaskExample\"> </a><a name=\"CQDGTaskExample-en-US\"> </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=\"https://simplifier.net/resolve?scope=hl7.fhir.ca.baseline@1.0.2&amp;canonical=https://fhir.cqdg.ca/StructureDefinition/CQDGTask\">https://fhir.cqdg.ca/StructureDefinition/CQDGTask</a></p></div><blockquote><p><b>Ferlab.bio StructureDefinition/workflow</b></p><ul><li>genomeBuild: <a href=\"CodeSystem-genome-build.html#genome-build-GRCh38\">Ferlab.bio CodeSystem/genome-build GRCh38</a>: GRCh38</li><li>pipeline: Some Pipeline</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>experimentalStrategy: <a href=\"CodeSystem-experimental-strategy.html#experimental-strategy-WXS\">Ferlab.bio CodeSystem/experimental-strategy WXS</a>: Whole Exome Sequencing</li><li>isPairedEnd: true</li><li>platform: NovaSeq S4 PE150</li><li>readLength: 151,8,8,151</li><li>selection: <a href=\"CodeSystem-sequencing-experiment-selection.html#sequencing-experiment-selection-CHIP\">Ferlab.bio CodeSystem/sequencing-experiment-selection CHIP</a>: ChIP</li><li>source: <a href=\"CodeSystem-sequencing-experiment-source.html#sequencing-experiment-source-GEN\">Ferlab.bio CodeSystem/sequencing-experiment-source GEN</a>: Genomic</li><li>protocol: protocol2</li><li>targetCaptureKit: targetCaptureKit2</li><li>targetLoci: targetedLoci2</li><li>runIds: RunID12345</li><li>runIds: RunID67890</li><li>runDates: 2023-01-01</li><li>runDates: 2023-01-02</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sample</b></p><ul><li>ldmSampleId: LDM12345</li><li>labAliquotId: AliquotID1</li><li>labAliquotId: AliquotID2</li></ul></blockquote><p><b>status</b>: Completed</p><p><b>intent</b>: order</p><p><b>priority</b>: Routine</p><p><b>code</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code RABA}\">Reads Alignement Bioinformatic Analysis</span></p><p><b>requester</b>: <a href=\"Organization-OrganizationExample.html\">Organization CQDG</a></p><p><b>owner</b>: <a href=\"Organization-OrganizationExample.html\">Organization CQDG</a></p><h3>Inputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Type</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:\">Analysed sample</span></td><td><a href=\"Specimen-SpecimenExample.html\">Submitter Sample ID: SpecimenExample</a></td></tr></table><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Aligned-reads}\">Aligned Reads</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample1.html\">DocumentReference: status = current; type = Sequencing Data Supplement; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type SNV}\">SNV</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample1.html\">DocumentReference: status = current; type = Sequencing Data Supplement; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Germline-CNV}\">Germline CNV</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample2.html\">DocumentReference: status = current; type = Aligned Reads; category = Genomics; securityLabel = test</a></p></blockquote><blockquote><p><b>output</b></p><p><b>type</b>: <span title=\"Codes:{https://fhir.cqdg.ca/CodeSystem/data-type Sequencing-data-supplement}\">Sequencing-data-supplement</span></p><p><b>value</b>: <a href=\"DocumentReference-DocumentReferenceExample2.html\">DocumentReference: status = current; type = Aligned Reads; category = Genomics; securityLabel = test</a></p></blockquote></div>"^^rdf:XMLLiteral
  ] ; # 
  fhir:extension ( [
    ( fhir:extension [
fhir:url [ fhir:v "genomeBuild"^^xsd:anyURI ] ;
fhir:value [
a fhir:Coding ;
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/genome-build"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GRCh38" ] ;
fhir:display [ fhir:v "GRCh38" ]       ]     ] [
fhir:url [ fhir:v "pipeline"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "Some Pipeline"       ]     ] ) ;
fhir:url [ fhir:v "https://fhir.cqdg.ca/StructureDefinition/workflowExtension"^^xsd:anyURI ]
  ] [
    ( fhir:extension [
fhir:url [ fhir:v "experimentalStrategy"^^xsd:anyURI ] ;
fhir:value [
a fhir:Coding ;
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/experimental-strategy"^^xsd:anyURI ] ;
fhir:code [ fhir:v "WXS" ] ;
fhir:display [ fhir:v "Whole Exome Sequencing" ]       ]     ] [
fhir:url [ fhir:v "isPairedEnd"^^xsd:anyURI ] ;
fhir:value [
a fhir:boolean ;
fhir:v true       ]     ] [
fhir:url [ fhir:v "platform"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "NovaSeq S4 PE150"       ]     ] [
fhir:url [ fhir:v "readLength"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "151,8,8,151"       ]     ] [
fhir:url [ fhir:v "selection"^^xsd:anyURI ] ;
fhir:value [
a fhir:Coding ;
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-selection"^^xsd:anyURI ] ;
fhir:code [ fhir:v "CHIP" ] ;
fhir:display [ fhir:v "ChIP" ]       ]     ] [
fhir:url [ fhir:v "source"^^xsd:anyURI ] ;
fhir:value [
a fhir:Coding ;
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-source"^^xsd:anyURI ] ;
fhir:code [ fhir:v "GEN" ] ;
fhir:display [ fhir:v "Genomic" ]       ]     ] [
fhir:url [ fhir:v "protocol"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "protocol2"       ]     ] [
fhir:url [ fhir:v "targetCaptureKit"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "targetCaptureKit2"       ]     ] [
fhir:url [ fhir:v "targetLoci"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "targetedLoci2"       ]     ] [
fhir:url [ fhir:v "runIds"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "RunID12345"       ]     ] [
fhir:url [ fhir:v "runIds"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "RunID67890"       ]     ] [
fhir:url [ fhir:v "runDates"^^xsd:anyURI ] ;
fhir:value [
a fhir:date ;
fhir:v "2023-01-01"^^xsd:date       ]     ] [
fhir:url [ fhir:v "runDates"^^xsd:anyURI ] ;
fhir:value [
a fhir:date ;
fhir:v "2023-01-02"^^xsd:date       ]     ] ) ;
fhir:url [ fhir:v "https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension"^^xsd:anyURI ]
  ] [
    ( fhir:extension [
fhir:url [ fhir:v "ldmSampleId"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "LDM12345"       ]     ] [
fhir:url [ fhir:v "labAliquotId"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "AliquotID1"       ]     ] [
fhir:url [ fhir:v "labAliquotId"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "AliquotID2"       ]     ] ) ;
fhir:url [ fhir:v "https://fhir.cqdg.ca/StructureDefinition/sampleExtension"^^xsd:anyURI ]
  ] ) ; # 
  fhir:status [ fhir:v "completed"] ; # 
  fhir:intent [ fhir:v "order"] ; # 
  fhir:priority [ fhir:v "routine"] ; # 
  fhir:code [
    ( fhir:coding [
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code"^^xsd:anyURI ] ;
fhir:code [ fhir:v "RABA" ] ;
fhir:display [ fhir:v "Reads Alignement Bioinformatic Analysis" ]     ] )
  ] ; # 
  fhir:requester [
fhir:reference [ fhir:v "Organization/OrganizationExample" ]
  ] ; # 
  fhir:owner [
fhir:reference [ fhir:v "Organization/OrganizationExample" ]
  ] ; # 
  fhir:input ( [
fhir:type [
fhir:text [ fhir:v "Analysed sample" ]     ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "Specimen/SpecimenExample" ] ;
fhir:display [ fhir:v "Submitter Sample ID: SpecimenExample" ]     ]
  ] ) ; # 
  fhir:output ( [
fhir:type [
      ( fhir:coding [
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/data-type"^^xsd:anyURI ] ;
fhir:code [ fhir:v "Aligned-reads" ] ;
fhir:display [ fhir:v "Aligned Reads" ]       ] )     ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/DocumentReferenceExample1" ]     ]
  ] [
fhir:type [
      ( fhir:coding [
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/data-type"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SNV" ] ;
fhir:display [ fhir:v "SNV" ]       ] )     ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/DocumentReferenceExample1" ]     ]
  ] [
fhir:type [
      ( fhir:coding [
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/data-type"^^xsd:anyURI ] ;
fhir:code [ fhir:v "Germline-CNV" ] ;
fhir:display [ fhir:v "Germline CNV" ]       ] )     ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/DocumentReferenceExample2" ]     ]
  ] [
fhir:type [
      ( fhir:coding [
fhir:system [ fhir:v "https://fhir.cqdg.ca/CodeSystem/data-type"^^xsd:anyURI ] ;
fhir:code [ fhir:v "Sequencing-data-supplement" ] ;
fhir:display [ fhir:v "Sequencing-data-supplement" ]       ] )     ] ;
fhir:value [
a fhir:Reference ;
fhir:reference [ fhir:v "DocumentReference/DocumentReferenceExample2" ]     ]
  ] ) . #