Ferlab.bio Example/cqdg-task-multi-omic - TTL Representation

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: Ferlab.bio Example/cqdg-task-multi-omic - 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 -------------------------------------------------------------------

<http://hl7.org/fhir/Task/CQDGTaskMultiOmicExample> a fhir:Task ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:Resource.id [ fhir:value "CQDGTaskMultiOmicExample"] ;
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "https://fhir.cqdg.ca/StructureDefinition/CQDGTask" ;
       fhir:index 0 ;
       fhir:link <https://fhir.cqdg.ca/StructureDefinition/CQDGTask>
     ]
  ] ;
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "extensions" ] ;
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Task CQDGTaskMultiOmicExample</b></p><a name=\"CQDGTaskMultiOmicExample\"> </a><a name=\"hcCQDGTaskMultiOmicExample\"> </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></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>experimentalStrategy: <a href=\"CodeSystem-experimental-strategy.html#experimental-strategy-RNAS\">Ferlab.bio CodeSystem/experimental-strategy: RNAS</a> (RNA-Seq)</li><li>platform: <a href=\"CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-Chromium\">Ferlab.bio CodeSystem/sequencing-experiment-platform: Chromium</a> (Chromium)</li><li>selection: <a href=\"CodeSystem-sequencing-experiment-selection.html#sequencing-experiment-selection-TN5\">Ferlab.bio CodeSystem/sequencing-experiment-selection: TN5</a> (Tn5)</li><li>source: <a href=\"CodeSystem-sequencing-experiment-source.html#sequencing-experiment-source-MUL\">Ferlab.bio CodeSystem/sequencing-experiment-source: MUL</a> (Multi-omic)</li><li>experimentalStrategy: <a href=\"CodeSystem-experimental-strategy.html#experimental-strategy-ATACS\">Ferlab.bio CodeSystem/experimental-strategy: ATACS</a> (ATAC-Seq)</li><li>profilingResolution: <a href=\"CodeSystem-profiling-resolution.html#profiling-resolution-Single-Nucleus\">Ferlab.bio CodeSystem/profiling-resolution: Single-Nucleus</a> (Single Nucleus)</li><li>profilingResolution: <a href=\"CodeSystem-profiling-resolution.html#profiling-resolution-Single-Nucleus\">Ferlab.bio CodeSystem/profiling-resolution: Single-Nucleus</a> (Single Nucleus)</li><li>platform: <a href=\"CodeSystem-sequencing-experiment-platform.html#sequencing-experiment-platform-Illumina\">Ferlab.bio CodeSystem/sequencing-experiment-platform: Illumina</a> (Illumina)</li><li>instrumentModel: Chromium X</li><li>instrumentModel: NovaSeq X</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sample</b></p><ul><li>ldmSampleId: LDM67890</li><li>labAliquotId: AliquotID3</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 MOA}\">Multi-omic 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 Filtered-Feature-Count-Matrix}\">Filtered Feature Count Matrix</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 Filtered-Peak-Barcode-Matrix}\">Filtered Peak Barcode Matrix</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>"
  ] ;
  fhir:DomainResource.extension [
     fhir:index 0 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "genomeBuild" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/genome-build" ] ;
         fhir:Coding.code [ fhir:value "GRCh38" ] ;
         fhir:Coding.display [ fhir:value "GRCh38" ]
       ]
     ] ;
     fhir:Extension.url [ fhir:value "https://fhir.cqdg.ca/StructureDefinition/workflowExtension" ]
  ], [
     fhir:index 1 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "experimentalStrategy" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/experimental-strategy" ] ;
         fhir:Coding.code [ fhir:value "RNAS" ] ;
         fhir:Coding.display [ fhir:value "RNA-Seq" ]
       ]
     ], [
       fhir:index 1 ;
       fhir:Extension.url [ fhir:value "platform" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform" ] ;
         fhir:Coding.code [ fhir:value "Chromium" ] ;
         fhir:Coding.display [ fhir:value "Chromium" ]
       ]
     ], [
       fhir:index 2 ;
       fhir:Extension.url [ fhir:value "selection" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-selection" ] ;
         fhir:Coding.code [ fhir:value "TN5" ] ;
         fhir:Coding.display [ fhir:value "Tn5" ]
       ]
     ], [
       fhir:index 3 ;
       fhir:Extension.url [ fhir:value "source" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-source" ] ;
         fhir:Coding.code [ fhir:value "MUL" ] ;
         fhir:Coding.display [ fhir:value "Multi-omic" ]
       ]
     ], [
       fhir:index 4 ;
       fhir:Extension.url [ fhir:value "experimentalStrategy" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/experimental-strategy" ] ;
         fhir:Coding.code [ fhir:value "ATACS" ] ;
         fhir:Coding.display [ fhir:value "ATAC-Seq" ]
       ]
     ], [
       fhir:index 5 ;
       fhir:Extension.url [ fhir:value "profilingResolution" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/profiling-resolution" ] ;
         fhir:Coding.code [ fhir:value "Single-Nucleus" ] ;
         fhir:Coding.display [ fhir:value "Single Nucleus" ]
       ]
     ], [
       fhir:index 6 ;
       fhir:Extension.url [ fhir:value "profilingResolution" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/profiling-resolution" ] ;
         fhir:Coding.code [ fhir:value "Single-Nucleus" ] ;
         fhir:Coding.display [ fhir:value "Single Nucleus" ]
       ]
     ], [
       fhir:index 7 ;
       fhir:Extension.url [ fhir:value "platform" ] ;
       fhir:Extension.valueCoding [
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/sequencing-experiment-platform" ] ;
         fhir:Coding.code [ fhir:value "Illumina" ] ;
         fhir:Coding.display [ fhir:value "Illumina" ]
       ]
     ], [
       fhir:index 8 ;
       fhir:Extension.url [ fhir:value "instrumentModel" ] ;
       fhir:Extension.valueString [ fhir:value "Chromium X" ]
     ], [
       fhir:index 9 ;
       fhir:Extension.url [ fhir:value "instrumentModel" ] ;
       fhir:Extension.valueString [ fhir:value "NovaSeq X" ]
     ] ;
     fhir:Extension.url [ fhir:value "https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension" ]
  ], [
     fhir:index 2 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "ldmSampleId" ] ;
       fhir:Extension.valueString [ fhir:value "LDM67890" ]
     ], [
       fhir:index 1 ;
       fhir:Extension.url [ fhir:value "labAliquotId" ] ;
       fhir:Extension.valueString [ fhir:value "AliquotID3" ]
     ] ;
     fhir:Extension.url [ fhir:value "https://fhir.cqdg.ca/StructureDefinition/sampleExtension" ]
  ] ;
  fhir:Task.status [ fhir:value "completed"] ;
  fhir:Task.intent [ fhir:value "order"] ;
  fhir:Task.priority [ fhir:value "routine"] ;
  fhir:Task.code [
     fhir:CodeableConcept.coding [
       fhir:index 0 ;
       fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code" ] ;
       fhir:Coding.code [ fhir:value "MOA" ] ;
       fhir:Coding.display [ fhir:value "Multi-omic Analysis" ]
     ]
  ] ;
  fhir:Task.requester [
     fhir:link <http://hl7.org/fhir/Organization/OrganizationExample> ;
     fhir:Reference.reference [ fhir:value "Organization/OrganizationExample" ]
  ] ;
  fhir:Task.owner [
     fhir:link <http://hl7.org/fhir/Organization/OrganizationExample> ;
     fhir:Reference.reference [ fhir:value "Organization/OrganizationExample" ]
  ] ;
  fhir:Task.input [
     fhir:index 0 ;
     fhir:Task.input.type [
       fhir:CodeableConcept.text [ fhir:value "Analysed sample" ]
     ] ;
     fhir:Task.input.valueReference [
       fhir:link <http://hl7.org/fhir/Specimen/SpecimenExample> ;
       fhir:Reference.reference [ fhir:value "Specimen/SpecimenExample" ] ;
       fhir:Reference.display [ fhir:value "Submitter Sample ID: SpecimenExample" ]
     ]
  ] ;
  fhir:Task.output [
     fhir:index 0 ;
     fhir:Task.output.type [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/data-type" ] ;
         fhir:Coding.code [ fhir:value "Filtered-Feature-Count-Matrix" ] ;
         fhir:Coding.display [ fhir:value "Filtered Feature Count Matrix" ]
       ]
     ] ;
     fhir:Task.output.valueReference [
       fhir:link <http://hl7.org/fhir/DocumentReference/DocumentReferenceExample1> ;
       fhir:Reference.reference [ fhir:value "DocumentReference/DocumentReferenceExample1" ]
     ]
  ], [
     fhir:index 1 ;
     fhir:Task.output.type [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         fhir:Coding.system [ fhir:value "https://fhir.cqdg.ca/CodeSystem/data-type" ] ;
         fhir:Coding.code [ fhir:value "Filtered-Peak-Barcode-Matrix" ] ;
         fhir:Coding.display [ fhir:value "Filtered Peak Barcode Matrix" ]
       ]
     ] ;
     fhir:Task.output.valueReference [
       fhir:link <http://hl7.org/fhir/DocumentReference/DocumentReferenceExample2> ;
       fhir:Reference.reference [ fhir:value "DocumentReference/DocumentReferenceExample2" ]
     ]
  ] .

<http://hl7.org/fhir/Organization/OrganizationExample> a fhir:Organization .

<http://hl7.org/fhir/Specimen/SpecimenExample> a fhir:Specimen .

<http://hl7.org/fhir/DocumentReference/DocumentReferenceExample1> a fhir:DocumentReference .

<http://hl7.org/fhir/DocumentReference/DocumentReferenceExample2> a fhir:DocumentReference .

# - ontology header ------------------------------------------------------------

<http://hl7.org/fhir/Task/CQDGTaskMultiOmicExample.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/Task/CQDGTaskMultiOmicExample.ttl> .