NCPI FHIR Implementation Guide
0.2.0 - ci-build
NCPI FHIR Implementation Guide - Local Development build (v0.2.0). See the Directory of published versions
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <http://loinc.org/rdf#> .
@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 -------------------------------------------------------------------
a fhir:Observation;
fhir:nodeRole fhir:treeRoot;
fhir:Resource.id [ fhir:value "variant-example-1"]; #
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"variant-example-1\"> </a></p><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\">Resource Observation "variant-example-1" </p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.0.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26398-0)</span></p><p><b>specimen</b>: <a href=\"Specimen-specimen-example-1.html\">Specimen/specimen-example-1: Specimen</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: HGNC:6518 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (gene#LBR)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48001-2)</span></p><p><b>value</b>: Chr1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (loinc-answers#LA21254-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes.html\">ToBeDeterminedCodes ('TbdCodes')</a>#exact-start-end)</span></p><p><b>value</b>: 225592153-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic alt allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: Heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Human reference sequence assembly version <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA14029-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_002296.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.0.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_002296.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: c.1640A>G <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.0.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#c.1640A>G)</span></p></blockquote></div>"
]; #
fhir:Observation.status [ fhir:value "final"]; #
fhir:Observation.category [
fhir:index 0;
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ];
fhir:Coding.code [ fhir:value "laboratory" ] ]
]; #
fhir:Observation.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69548-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69548-6" ];
fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ]
]; #
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA9633-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA9633-4" ];
fhir:Coding.display [ fhir:value "Present" ] ]
]; #
fhir:Observation.method [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA26398-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA26398-0" ];
fhir:Coding.display [ fhir:value "Sequencing" ] ]
]; #
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/specimen-example-1" ];
fhir:Reference.display [ fhir:value "Specimen" ]
]; #
fhir:Observation.component [
fhir:index 0;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48018-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48018-6" ];
fhir:Coding.display [ fhir:value "Gene studied ID" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "https://www.ncbi.nlm.nih.gov/gene" ];
fhir:Coding.code [ fhir:value "LBR" ];
fhir:Coding.display [ fhir:value "HGNC:6518" ] ] ]
], [
fhir:index 1;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48001-2;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48001-2" ];
fhir:Coding.display [ fhir:value "Cytogenetic (chromosome) location" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://fhir.ncpi-project-forge.io/ValueSet/loinc-answers" ];
fhir:Coding.code [ fhir:value "LA21254-0" ];
fhir:Coding.display [ fhir:value "Chr1" ] ];
fhir:CodeableConcept.text [ fhir:value "Chr1" ] ]
], [
fhir:index 2;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ];
fhir:Coding.code [ fhir:value "exact-start-end" ];
fhir:Coding.display [ fhir:value "Variant exact start and end" ] ] ];
fhir:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "225592153"^^xsd:decimal ] ] ]
], [
fhir:index 3;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69547-8;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69547-8" ];
fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "T" ]
], [
fhir:index 4;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:69551-0;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "69551-0" ];
fhir:Coding.display [ fhir:value "Genomic alt allele [ID]" ] ] ];
fhir:Observation.component.valueString [ fhir:value "C" ]
], [
fhir:index 5;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:53034-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "53034-5" ];
fhir:Coding.display [ fhir:value "Allelic state" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA6706-1;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA6706-1" ];
fhir:Coding.display [ fhir:value "Heterozygous" ] ];
fhir:CodeableConcept.text [ fhir:value "Heterozygous" ] ]
], [
fhir:index 6;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:62374-4;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "62374-4" ];
fhir:Coding.display [ fhir:value "Human reference sequence assembly version" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:LA14029-5;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "LA14029-5" ];
fhir:Coding.display [ fhir:value "GRCh37" ] ];
fhir:CodeableConcept.text [ fhir:value "GRCh37" ] ]
], [
fhir:index 7;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:51958-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "51958-7" ];
fhir:Coding.display [ fhir:value "Transcript reference sequence [ID]" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ];
fhir:Coding.code [ fhir:value "NM_002296.3" ];
fhir:Coding.display [ fhir:value "NM_002296.3" ] ] ]
], [
fhir:index 8;
fhir:Observation.component.code [
fhir:CodeableConcept.coding [
fhir:index 0;
a loinc:48004-6;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48004-6" ];
fhir:Coding.display [ fhir:value "DNA change (c.HGVS)" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://varnomen.hgvs.org" ];
fhir:Coding.code [ fhir:value "c.1640A>G" ];
fhir:Coding.display [ fhir:value "c.1640A>G" ] ] ]
]. #
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2021+ NCPI FHIR Working Group. Package NCPI-FHIR-Implementation-Guide#0.2.0 based on FHIR 4.0.1. Generated 2022-12-09
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