minimal Common Oncology Data Elements (mCODE) Implementation Guide
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minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/fhir-mCODE-ig/ and changes regularly. See the Directory of published versions

: gx-genomic-variant-somatic-polrmt - TTL Representation

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@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 "gx-genomic-variant-somatic-polrmt"] ; # 
  fhir:meta [
    ( fhir:profile [
fhir:v "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant>     ] )
  ] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation gx-genomic-variant-somatic-polrmt</b></p><a name=\"gx-genomic-variant-somatic-polrmt\"> </a><a name=\"hcgx-genomic-variant-somatic-polrmt\"> </a><a name=\"gx-genomic-variant-somatic-polrmt-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-gx-cancer-patient-adam-anyperson.html\">Adam Anyperson  Male, DoB: 1990-01-01 ( Medical Record Number: 123456789)</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Practitioner-us-core-practitioner-owen-oncologist.html\">Practitioner Owen Oncologist </a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes:{https://www.ncbi.nlm.nih.gov/gene 5442}\">POLRMT</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6684-0}\">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org/ SO:0001583}\">missense_variant</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_004656}\">NM_005035</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_005035.4:c.598G&gt;A}\">NM_005035.4:c.598G&gt;A</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_005026.3:p.(Gly200Arg)}\">NP_005026.3:p.(Gly200Arg)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81258-6}\">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 75.6 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  code% = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</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/gx-cancer-patient-adam-anyperson" ]
  ] ; # 
  fhir:effective [ fhir:v "2019-04-01"^^xsd:date] ; # 
  fhir:performer ( [
fhir:reference [ fhir:v "Practitioner/us-core-practitioner-owen-oncologist" ]
  ] ) ; # 
  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:display [ fhir:v "Present" ]     ] )
  ] ; # 
  fhir:method [
    ( fhir:coding [
a loinc:LA26398-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA26398-0" ] ;
fhir:display [ fhir:v "Sequencing" ]     ] )
  ] ; # 
  fhir:component ( [
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.ncbi.nlm.nih.gov/gene"^^xsd:anyURI ] ;
fhir:code [ fhir:v "5442" ] ;
fhir:display [ fhir:v "POLRMT" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
a loinc:48002-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "48002-0" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
a loinc:LA6684-0 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA6684-0" ] ;
fhir:display [ fhir:v "Somatic" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ;
fhir:code [ fhir:v "molecular-consequence" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:system [ fhir:v "http://www.sequenceontology.org/"^^xsd:anyURI ] ;
fhir:code [ fhir:v "SO:0001583" ] ;
fhir:display [ fhir:v "missense_variant" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
a loinc:51958-7 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "51958-7" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ;
fhir:code [ fhir:v "NM_004656" ] ;
fhir:display [ fhir:v "NM_005035" ]       ] )     ]
  ] [
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 "NM_005035.4:c.598G>A" ] ;
fhir:display [ fhir:v "NM_005035.4:c.598G>A" ]       ] )     ]
  ] [
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 "NP_005026.3:p.(Gly200Arg)" ] ;
fhir:display [ fhir:v "NP_005026.3:p.(Gly200Arg)" ]       ] )     ]
  ] [
fhir:code [
      ( fhir:coding [
a loinc:81258-6 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "81258-6" ]       ] )     ] ;
fhir:value [
a fhir:Quantity ;
fhir:value [ fhir:v "75.6"^^xsd:decimal ] ;
fhir:unit [ fhir:v "%" ] ;
fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "%" ]     ]
  ] [
fhir:code [
      ( fhir:coding [
a loinc:62374-4 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "62374-4" ]       ] )     ] ;
fhir:value [
a fhir:CodeableConcept ;
      ( fhir:coding [
a loinc:LA14029-5 ;
fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ;
fhir:code [ fhir:v "LA14029-5" ] ;
fhir:display [ fhir:v "GRCh37" ]       ] )     ]
  ] ) . #