FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide
2.1.0 - ci-build
FHIR Osiris Implementation Guide - Local Development build (v2.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
@prefix fhir: <http://hl7.org/fhir/> .
@prefix loinc: <https://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:id [ fhir:v "fhir-osiris-annotation-1"] ; #
fhir:meta [
( fhir:profile [
fhir:v "https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/variant-annotation"^^xsd:anyURI ;
fhir:link <https://build.fhir.org/ig/arkhn/arkhn-ig-osiris/StructureDefinition/variant-annotation> ] )
] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"fhir-osiris-annotation-1\"> </a><a name=\"hcfhir-osiris-annotation-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 "fhir-osiris-annotation-1" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant-annotation.html\">Variant Annotation</a></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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic var assess <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"Patient-L304.html\">Patient/L304</a></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>hasMember</b>: </p><ul><li><a href=\"MolecularSequence-fhir-osiris-genome-entity-1.html\">MolecularSequence/fhir-osiris-genome-entity-1</a></li><li><a href=\"MolecularSequence-fhir-osiris-annotation-reference-1.html\">MolecularSequence/fhir-osiris-annotation-reference-1</a></li></ul><p><b>derivedFrom</b>: <a href=\"Observation-fhir-osiris-example-snp-1.html\">Observation/fhir-osiris-example-snp-1</a></p><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: O15-4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (OSIRIS#O15-4)</span></p></blockquote><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>: PI3K <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (#PI3K)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Prediction software <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LP91038-7)</span></p><p><b>value</b>: SIFT <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (OSIRIS#SIFT)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Prediction of the variation effect over the protein <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LP70194-3)</span></p><p><b>value</b>: 0.35</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Confidence score <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#93044-6)</span></p><p><b>value</b>: Deleterious</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cyto loc ID <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>: exon 2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: p.E542K <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#p.E542K)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48006-1)</span></p><p><b>value</b>: Missense <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6698-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Struct var HGVS name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: C0439673 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-umls.html\">Unified Medical Language System</a>#C0439673)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change <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.1624G>A <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#c.1624G>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Incidence on the transcript <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LP232001-0)</span></p><p><b>value</b>: C0439673 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-umls.html\">Unified Medical Language System</a>#C0439673)</span></p></blockquote></div>"
] ; #
fhir:status [ fhir:v "final"] ; #
fhir:category ( [
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ;
fhir:code [ fhir:v "laboratory" ] ] )
] ) ; #
fhir:code [
( fhir:coding [
a loinc:69548-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "69548-6" ] ] )
] ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/L304" ]
] ; #
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA9633-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA9633-4" ] ] )
] ; #
fhir:hasMember ( [
fhir:reference [ fhir:v "MolecularSequence/fhir-osiris-genome-entity-1" ]
] [
fhir:reference [ fhir:v "MolecularSequence/fhir-osiris-annotation-reference-1" ]
] ) ; #
fhir:derivedFrom ( [
fhir:reference [ fhir:v "Observation/fhir-osiris-example-snp-1" ]
] ) ; #
fhir:component ( [
fhir:code [
( fhir:coding [
a loinc:48019-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48019-4" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "https://github.com/siric-osiris/OSIRIS"^^xsd:anyURI ] ;
fhir:code [ fhir:v "O15-4" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48018-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48018-6" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "https://www.genenames.org/"^^xsd:anyURI ] ;
fhir:code [ fhir:v "PI3K" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:LP91038-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LP91038-7" ] ] ) ;
fhir:text [ fhir:v "Prediction software" ] ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "https://github.com/siric-osiris/OSIRIS"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SIFT" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:LP70194-3 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LP70194-3" ] ] ) ;
fhir:text [ fhir:v "Prediction of the variation effect over the protein" ] ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "0.35"^^xsd:decimal ] ]
] [
fhir:code [
( fhir:coding [
a loinc:93044-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "93044-6" ] ] ) ;
fhir:text [ fhir:v "Confidence score" ] ] ;
fhir:value [ fhir:v "Deleterious" ]
] [
fhir:code [
( fhir:coding [
a loinc:48001-2 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48001-2" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
fhir:text [ fhir:v "exon 2" ] ]
] [
fhir:code [
( fhir:coding [
a loinc:48005-3 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48005-3" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "p.E542K" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48006-1 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48006-1" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
a loinc:LA6698-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6698-0" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:81290-9 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81290-9" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/umls"^^xsd:anyURI ] ;
fhir:code [ fhir:v "C0439673" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:48004-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48004-6" ] ] ) ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "c.1624G>A" ] ] ) ]
] [
fhir:code [
( fhir:coding [
a loinc:LP232001-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LP232001-0" ] ] ) ;
fhir:text [ fhir:v "Incidence on the transcript" ] ] ;
fhir:value [
a fhir:CodeableConcept ;
( fhir:coding [
fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/umls"^^xsd:anyURI ] ;
fhir:code [ fhir:v "C0439673" ] ] ) ]
] ) . #
IG © 2020+ Arkhn. Package arkhn.fhir.uv.osiris#2.1.0 based on FHIR 4.0.1. Generated 2024-03-21
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