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
{
"resourceType" : "Task",
"id" : "CQDGTaskExample",
"meta" : {
"profile" : [
"https://fhir.cqdg.ca/StructureDefinition/cqgc-analysis-task"
]
},
"text" : {
"status" : "extensions",
"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><blockquote><p><b>Ferlab.bio StructureDefinition/workflow</b></p><ul><li>workflowName: Dragen</li><li>genomeBuild: <a href=\"CodeSystem-genome-build.html#genome-build-GRCh38\">Ferlab.bio CodeSystem/genome-build</a> GRCh38: GRCh38</li><li>workflowVersion: SW null</li></ul></blockquote><blockquote><p><b>Ferlab.bio StructureDefinition/sequencing-experiment</b></p><ul><li>runName: 1898</li><li>platform: Illumina NovaSeq 6000 S4 PE150</li><li>isPairedEnd: true</li><li>readLength: 151,8,8,151</li><li>experimentalStrategy: <a href=\"CodeSystem-experimental-strategy.html#experimental-strategy-WXS\">Ferlab.bio CodeSystem/experimental-strategy</a> WXS: Whole Exome Sequencing</li><li>runDate: 2020-11-06</li><li>labAliquotId: MPS12348274-B04</li><li>ldmSampleId: S03344</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>"
},
"extension" : [
{
"extension" : [
{
"url" : "workflowName",
"valueString" : "Dragen"
},
{
"url" : "genomeBuild",
"valueCoding" : {
"system" : "https://fhir.cqdg.ca/CodeSystem/genome-build",
"code" : "GRCh38",
"display" : "GRCh38"
}
},
{
"url" : "workflowVersion",
"valueString" : "SW null"
}
],
"url" : "https://fhir.cqdg.ca/StructureDefinition/workflowExtension"
},
{
"extension" : [
{
"url" : "runName",
"valueString" : "1898"
},
{
"url" : "platform",
"valueString" : "Illumina NovaSeq 6000 S4 PE150"
},
{
"url" : "isPairedEnd",
"valueBoolean" : true
},
{
"url" : "readLength",
"valueString" : "151,8,8,151"
},
{
"url" : "experimentalStrategy",
"valueCoding" : {
"system" : "https://fhir.cqdg.ca/CodeSystem/experimental-strategy",
"code" : "WXS",
"display" : "Whole Exome Sequencing"
}
},
{
"url" : "runDate",
"valueDateTime" : "2020-11-06"
},
{
"url" : "labAliquotId",
"valueString" : "MPS12348274-B04"
},
{
"url" : "ldmSampleId",
"valueString" : "S03344"
}
],
"url" : "https://fhir.cqdg.ca/StructureDefinition/sequencingExperimentExtension"
}
],
"status" : "completed",
"intent" : "order",
"priority" : "routine",
"code" : {
"coding" : [
{
"system" : "https://fhir.cqdg.ca/CodeSystem/bioinfo-analysis-code",
"code" : "RABA",
"display" : "Reads Alignement Bioinformatic Analysis"
}
]
},
"requester" : {
🔗 "reference" : "Organization/OrganizationExample"
},
"owner" : {
🔗 "reference" : "Organization/OrganizationExample"
},
"input" : [
{
"type" : {
"text" : "Analysed sample"
},
"valueReference" : {
🔗 "reference" : "Specimen/SpecimenExample",
"display" : "Submitter Sample ID: SpecimenExample"
}
}
],
"output" : [
{
"type" : {
"coding" : [
{
"system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
"code" : "Aligned-reads",
"display" : "Aligned Reads"
}
]
},
"valueReference" : {
🔗 "reference" : "DocumentReference/DocumentReferenceExample1"
}
},
{
"type" : {
"coding" : [
{
"system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
"code" : "SNV",
"display" : "SNV"
}
]
},
"valueReference" : {
🔗 "reference" : "DocumentReference/DocumentReferenceExample1"
}
},
{
"type" : {
"coding" : [
{
"system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
"code" : "Germline-CNV",
"display" : "Germline CNV"
}
]
},
"valueReference" : {
🔗 "reference" : "DocumentReference/DocumentReferenceExample2"
}
},
{
"type" : {
"coding" : [
{
"system" : "https://fhir.cqdg.ca/CodeSystem/data-type",
"code" : "Sequencing-data-supplement",
"display" : "Sequencing-data-supplement"
}
]
},
"valueReference" : {
🔗 "reference" : "DocumentReference/DocumentReferenceExample2"
}
}
]
}