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" : "gregor-example-metadata",
"meta" : {
"profile" : [
🔗 "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-bamcram"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation gregor-example-metadata</b></p><a name=\"gregor-example-metadata\"> </a><a name=\"hcgregor-example-metadata\"> </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-bamcram.html\">BAM or CRAM file profile</a></p></div><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>status</b>: Final</p><p><b>code</b>: <span title=\"Codes:{http://edamontology.org format_2572}\">format_2572</span></p><p><b>focus</b>: <a href=\"Patient-GSS123456.html\">Anonymous Patient (no stated gender), DoB Unknown ( https://anvil.terra.bio/#GSS123456)</a></p><p><b>specimen</b>: <a href=\"Specimen-GSS123456-01-010.html\">Specimen: extension = ->ResearchStudy: identifier = AnVIL_GREGoR_GSS_U08_GRU; status = completed; identifier = GSS123456-s1; 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 TargetRegion}\">Target region</span></p><p><b>value</b>: <span title=\"Codes:\">Not Applicable</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:\">stranded</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 ReferenceGenome}\">Reference genome</span></p><p><b>value</b>: <span title=\"Codes:\">GRCh38</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 WorkflowTool}\">Workflow tool</span></p><p><b>value</b>: <span title=\"Codes:\">bammem</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 WorkflowType}\">Workflow type</span></p><p><b>value</b>: <span title=\"Codes:\">alignment</span></p></blockquote></div>"
},
"extension" : [
{
"url" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/part-of-study",
"valueReference" : {
🔗 "reference" : "ResearchStudy/research-study-gregor"
}
}
],
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://edamontology.org",
"code" : "format_2572"
}
]
},
"focus" : [
{
🔗 "reference" : "Patient/GSS123456"
}
],
"specimen" : {
🔗 "reference" : "Specimen/GSS123456-01-010"
},
"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"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "polyA"
}
]
}
},
{
"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" : "TargetRegion"
}
]
},
"valueCodeableConcept" : {
"text" : "Not Applicable"
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "Strandedness"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "stranded"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "ReferenceGenome"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "GRCh38"
}
]
}
},
{
"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" : "WorkflowTool"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "bammem"
}
]
}
},
{
"code" : {
"coding" : [
{
"system" : "https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/metadata-elements",
"code" : "WorkflowType"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"code" : "alignment"
}
]
}
}
]
}