Release 5 Ballot

This page is part of the FHIR Specification (v5.0.0-ballot: R5 Ballot - see ballot notes). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

Example GenomicStudy/example-lungMass (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: InformativeCompartments: Patient

Raw Turtle (+ also see Turtle/RDF Format Specification)

GenomicStudy - Lung mass - sequencing analysis

@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 sct: <http://snomed.info/id/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

# - resource -------------------------------------------------------------------

[a fhir:GenomicStudy;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "example-lungMass"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "additional" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CB was deemed uncallable.</div>"
  ];
  fhir:GenomicStudy.identifier [
     fhir:index 0;
     fhir:Identifier.use [ fhir:value "temp" ];
     fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicstudies" ];
     fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1112" ]
  ];
  fhir:GenomicStudy.status [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://hl7.org/fhir/genomicstudy-status" ];
       fhir:Coding.code [ fhir:value "registered" ];
       fhir:Coding.display [ fhir:value "Registered" ]
     ]
  ];
  fhir:GenomicStudy.type [
     fhir:index 0;
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a sct:443968007;
       fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
       fhir:Coding.code [ fhir:value "443968007" ];
       fhir:Coding.display [ fhir:value "Whole Exome Sequencing - Sequencing of entire coding region of gene (procedure)" ]
     ]
  ];
  fhir:GenomicStudy.subject [
     fhir:Reference.reference [ fhir:value "Patient/genomicPatient" ]
  ];
  fhir:GenomicStudy.encounter [
     fhir:Reference.reference [ fhir:value "Encounter/genomicEncounter" ]
  ];
  fhir:GenomicStudy.startDate [ fhir:value "2019-03-01"^^xsd:date];
  fhir:GenomicStudy.basedOn [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "ServiceRequest/genomicServiceRequest2" ]
  ];
  fhir:GenomicStudy.referrer [
     fhir:Reference.reference [ fhir:value "Practitioner/practitioner01" ]
  ];
  fhir:GenomicStudy.interpreter [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
  ];
  fhir:GenomicStudy.reason [
     fhir:index 0;
     fhir:CodeableReference.concept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:309529002;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "309529002" ];
         fhir:Coding.display [ fhir:value "Lung mass (finding) " ]
       ]
     ]
  ];
  fhir:GenomicStudy.note [
     fhir:index 0;
     fhir:Annotation.text [ fhir:value "For technical reasons, PIK3CB was deemed uncallable." ]
  ];
  fhir:GenomicStudy.description [ fhir:value "Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CB was deemed uncallable."];
  fhir:GenomicStudy.analysis [
     fhir:index 0;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "official" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1112" ]
     ];
     fhir:GenomicStudy.analysis.methodType [
       fhir:index 0;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:117040002;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "117040002" ];
         fhir:Coding.display [ fhir:value "Nucleic acid sequencing (procedure)" ]
       ]
     ];
     fhir:GenomicStudy.analysis.changeType [
       fhir:index 0;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
         fhir:Coding.code [ fhir:value "SO:0001483" ];
         fhir:Coding.display [ fhir:value "SNV" ]
       ]
     ], [
       fhir:index 1;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
         fhir:Coding.code [ fhir:value "SO:0002007" ];
         fhir:Coding.display [ fhir:value "MNV" ]
       ]
     ], [
       fhir:index 2;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
         fhir:Coding.code [ fhir:value "SO:1000032" ];
         fhir:Coding.display [ fhir:value "delins" ]
       ]
     ];
     fhir:GenomicStudy.analysis.genomeBuild [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA26806-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA26806-2" ];
         fhir:Coding.display [ fhir:value "GRCh38" ]
       ]
     ];
     fhir:GenomicStudy.analysis.title [ fhir:value "Simple variant analysis" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/genomicPatient" ]
     ];
     fhir:GenomicStudy.analysis.specimen [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "Specimen/genomicSpecimen" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2019-03-01T01:01:10-06:00"^^xsd:dateTime ];
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "For technical reasons, PIK3CB was deemed uncallable using this method." ]
     ];
     fhir:GenomicStudy.analysis.regionsStudied [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "DocumentReference/WES_FullSequencedRegion_GRCh38" ]
     ];
     fhir:GenomicStudy.analysis.regionsCalled [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "DocumentReference/SimpleVariantAnalysis_called" ]
     ];
     fhir:GenomicStudy.analysis.output [
       fhir:index 0;
       fhir:GenomicStudy.analysis.output.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicVCFfile_simple" ]
       ];
       fhir:GenomicStudy.analysis.output.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ];
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.device [
       fhir:index 0;
       fhir:GenomicStudy.analysis.device.device [
         fhir:Reference.reference [ fhir:value "Device/NGS-device" ]
       ];
       fhir:GenomicStudy.analysis.device.function [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.display [ fhir:value "Next Generation Sequencing" ]
         ]
       ]
     ]
  ], [
     fhir:index 1;
     fhir:GenomicStudy.analysis.identifier [
       fhir:index 0;
       fhir:Identifier.use [ fhir:value "official" ];
       fhir:Identifier.system [ fhir:value "http://www.somesystemabc.net/identifiers/genomicAnalyses" ];
       fhir:Identifier.value [ fhir:value "urn:uuid:1111-1111-1111-1115" ]
     ];
     fhir:GenomicStudy.analysis.methodType [
       fhir:index 0;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:117040002;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "117040002" ];
         fhir:Coding.display [ fhir:value "Nucleic acid sequencing (procedure)" ]
       ]
     ];
     fhir:GenomicStudy.analysis.changeType [
       fhir:index 0;
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://sequenceontology.org" ];
         fhir:Coding.code [ fhir:value "SO:0001019" ];
         fhir:Coding.display [ fhir:value "CNV" ]
       ]
     ];
     fhir:GenomicStudy.analysis.genomeBuild [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA26806-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA26806-2" ];
         fhir:Coding.display [ fhir:value "GRCh38" ]
       ]
     ];
     fhir:GenomicStudy.analysis.title [ fhir:value "CNV analysis" ];
     fhir:GenomicStudy.analysis.subject [
       fhir:Reference.reference [ fhir:value "Patient/genomicPatient" ]
     ];
     fhir:GenomicStudy.analysis.specimen [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "Specimen/genomicSpecimen" ]
     ];
     fhir:GenomicStudy.analysis.date [ fhir:value "2019-03-01T01:01:10-06:00"^^xsd:dateTime ];
     fhir:GenomicStudy.analysis.note [
       fhir:index 0;
       fhir:Annotation.text [ fhir:value "For technical reasons, PIK3CB was deemed uncallable using this method." ]
     ];
     fhir:GenomicStudy.analysis.regionsStudied [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "DocumentReference/WES_FullSequencedRegion_GRCh38" ]
     ];
     fhir:GenomicStudy.analysis.regionsCalled [
       fhir:index 0;
       fhir:Reference.reference [ fhir:value "DocumentReference/CNVAnalysis_called" ]
     ];
     fhir:GenomicStudy.analysis.output [
       fhir:index 0;
       fhir:GenomicStudy.analysis.output.file [
         fhir:Reference.reference [ fhir:value "DocumentReference/genomicVCFfile_cnv" ]
       ];
       fhir:GenomicStudy.analysis.output.type [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.code [ fhir:value "vcf" ];
           fhir:Coding.display [ fhir:value "VCF" ]
         ]
       ]
     ];
     fhir:GenomicStudy.analysis.performer [
       fhir:index 0;
       fhir:GenomicStudy.analysis.performer.actor [
         fhir:Reference.reference [ fhir:value "Practitioner/practitioner02" ]
       ];
       fhir:GenomicStudy.analysis.performer.role [
         fhir:CodeableConcept.coding [
           fhir:index 0;
           fhir:Coding.system [ fhir:value "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html" ];
           fhir:Coding.code [ fhir:value "PRF" ];
           fhir:Coding.display [ fhir:value "Performer" ]
         ]
       ]
     ]
  ]] .

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

[a owl:Ontology;
  owl:imports fhir:fhir.ttl] .

# -------------------------------------------------------------------------------------

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.