Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: MultipleRepeatExpansions - TTL Representation

Page standards status: Informative

Raw ttl | Download


@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 -------------------------------------------------------------------

<http://hl7.org/fhir/Observation/MultipleRepeatExpansions> a fhir:Observation ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:Resource.id [ fhir:value "MultipleRepeatExpansions"] ;
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant" ;
       fhir:index 0 ;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant>
     ]
  ] ;
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "extensions" ] ;
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation MultipleRepeatExpansions</b></p><a name=\"MultipleRepeatExpansions\"> </a><a name=\"hcMultipleRepeatExpansions\"> </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-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</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-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</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:{http://www.genenames.org HGNC:3775}\">FMR1</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48001-2}\">Cytogenetic (chromosome) location</span></p><p><b>value</b>: <span title=\"Codes:\">chrx</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_002024.5}\">NM_002024.5</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_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]}\">NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 10</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 2</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 3</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 9</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGA</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 4</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 1</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-motif}\">Repeat Expansion Motif</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 5</p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs repeat-number}\">Number of Repeat Expansions</span></p><p><b>value</b>: 10</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:index 1 ;
     fhir:CodeableConcept.coding [
       fhir:index 0 ;
       fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/v2-0074" ] ;
       fhir:Coding.code [ fhir:value "GE" ]
     ]
  ] ;
  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.subject [
     fhir:link <http://hl7.org/fhir/Patient/ExamplePatient> ;
     fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
  ] ;
  fhir:Observation.effectiveDateTime [ fhir:value "2023-06-01"^^xsd:date] ;
  fhir:Observation.performer [
     fhir:index 0 ;
     fhir:link <http://hl7.org/fhir/Organization/ExampleLab> ;
     fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
  ] ;
  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.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 "http://www.genenames.org" ] ;
         fhir:Coding.code [ fhir:value "HGNC:3775" ] ;
         fhir:Coding.display [ fhir:value "FMR1" ]
       ]
     ]
  ], [
     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.text [ fhir:value "chrx" ]
     ]
  ], [
     fhir:index 2 ;
     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_002024.5" ] ;
         fhir:Coding.display [ fhir:value "NM_002024.5" ]
       ]
     ]
  ], [
     fhir:index 3 ;
     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 "NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]" ] ;
         fhir:Coding.display [ fhir:value "NM_002024.5:c.-128_-69GGC[10]GGA[1]GGC[9]GGA[1]GGC[10]" ]
       ]
     ]
  ], [
     fhir:index 4 ;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0 ;
         a loinc:81254-5 ;
         fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
         fhir:Coding.code [ fhir:value "81254-5" ] ;
         fhir:Coding.display [ fhir:value "Genomic allele start-end" ]
       ]
     ] ;
     fhir:Observation.component.valueRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "3"^^xsd:decimal ]
       ]
     ]
  ], [
     fhir:index 5 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "1"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-motif" ] ;
         fhir:Coding.display [ fhir:value "Repeat Expansion Motif" ]
       ]
     ] ;
     fhir:Observation.component.valueString [ fhir:value "GGC" ]
  ], [
     fhir:index 6 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "1"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-number" ] ;
         fhir:Coding.display [ fhir:value "Number of Repeat Expansions" ]
       ]
     ] ;
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "10"^^xsd:decimal ]
     ]
  ], [
     fhir:index 7 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "2"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-motif" ] ;
         fhir:Coding.display [ fhir:value "Repeat Expansion Motif" ]
       ]
     ] ;
     fhir:Observation.component.valueString [ fhir:value "GGA" ]
  ], [
     fhir:index 8 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "2"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-number" ] ;
         fhir:Coding.display [ fhir:value "Number of Repeat Expansions" ]
       ]
     ] ;
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ]
     ]
  ], [
     fhir:index 9 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "3"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-motif" ] ;
         fhir:Coding.display [ fhir:value "Repeat Expansion Motif" ]
       ]
     ] ;
     fhir:Observation.component.valueString [ fhir:value "GGC" ]
  ], [
     fhir:index 10 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "3"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-number" ] ;
         fhir:Coding.display [ fhir:value "Number of Repeat Expansions" ]
       ]
     ] ;
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "9"^^xsd:decimal ]
     ]
  ], [
     fhir:index 11 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "4"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-motif" ] ;
         fhir:Coding.display [ fhir:value "Repeat Expansion Motif" ]
       ]
     ] ;
     fhir:Observation.component.valueString [ fhir:value "GGA" ]
  ], [
     fhir:index 12 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "4"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-number" ] ;
         fhir:Coding.display [ fhir:value "Number of Repeat Expansions" ]
       ]
     ] ;
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ]
     ]
  ], [
     fhir:index 13 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "5"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-motif" ] ;
         fhir:Coding.display [ fhir:value "Repeat Expansion Motif" ]
       ]
     ] ;
     fhir:Observation.component.valueString [ fhir:value "GGC" ]
  ], [
     fhir:index 14 ;
     fhir:Element.extension [
       fhir:index 0 ;
       fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order" ] ;
       fhir:Extension.valuePositiveInt [ fhir:value "5"^^xsd:positiveInteger ]
     ] ;
     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-cs" ] ;
         fhir:Coding.code [ fhir:value "repeat-number" ] ;
         fhir:Coding.display [ fhir:value "Number of Repeat Expansions" ]
       ]
     ] ;
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "10"^^xsd:decimal ]
     ]
  ] .

<http://hl7.org/fhir/Patient/ExamplePatient> a fhir:Patient .

<http://hl7.org/fhir/Organization/ExampleLab> a fhir:Organization .

# - ontology header ------------------------------------------------------------

<http://hl7.org/fhir/Observation/MultipleRepeatExpansions.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/Observation/MultipleRepeatExpansions.ttl> .