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
{
"resourceType" : "Observation",
"id" : "FASTQ-example",
"meta" : {
"profile" : [
🔗 "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-fastq"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation FASTQ-example</b></p><a name=\"FASTQ-example\"> </a><a name=\"hcFASTQ-example\"> </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-fastq.html\">NCPI FASTQ File</a></p></div><p><b>Part of Study</b>: <a href=\"ResearchStudy-kf-research-study-cbtn.html\">ResearchStudy Children's Brain Tumor Network (CBTN)</a></p><p><b>status</b>: Final</p><p><b>code</b>: <span title=\"Codes:{http://edamontology.org format_1930}\">format_1930</span></p><p><b>focus</b>: <a href=\"DocumentReference-GF-6BAD9S7D.html\">DocumentReference: extension = V1,VCF,1044770380 bytes,,->ResearchStudy Children's Brain Tumor Network (CBTN); identifier = GF-6BAD9S7D; status = current; type = Variant calling; description = Annotated Variant Call</a></p><p><b>specimen</b>: <a href=\"Specimen-SA-000.html\">Specimen: extension = ->ResearchStudy Children's Brain Tumor Network (CBTN); identifier = SA_RV52EY7S; 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 Strandedness}\">Strandedness</span></p><p><b>value</b>: <span title=\"Codes:\">unstranded</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 AdaptorTrimmed}\">Adaptor trimmed</span></p><p><b>value</b>: true</p></blockquote></div>"
},
"extension" : [
{
"url" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/part-of-study",
"valueReference" : {
🔗 "reference" : "ResearchStudy/kf-research-study-cbtn"
}
}
],
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://edamontology.org",
"code" : "format_1930"
}
]
},
"focus" : [
{
🔗 "reference" : "DocumentReference/GF-6BAD9S7D"
}
],
"specimen" : {
🔗 "reference" : "Specimen/SA-000"
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "AssayStrategy"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://purl.obolibrary.org/obo/obi.owl",
"code" : "0002117",
"display" : "whole genome sequencing assay"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "PlatformInstrument"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://purl.obolibrary.org/obo/obi.owl",
"code" : "0002001",
"display" : "Illumina HiSeq 2000"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "LibraryPrep"
}
]
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"valueCodeableConcept" : {
"coding" : [
{
"code" : "polyA"
}
]
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},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "LibrarySelection"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "PolyTEnrichment"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "Strandedness"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "unstranded"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "IsPairedEnd"
}
]
},
"valueBoolean" : false
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "AdaptorTrimmed"
}
]
},
"valueBoolean" : true
}
]
}