Genomics Reporting Implementation Guide (STU1)

This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example - Genomics Reporting - TTL Representation

(back to narrative)

Raw ttl 

@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:Bundle;
  fhir:nodeRole fhir:treeRoot;
  fhir:Resource.id [ fhir:value "diagnosticreport-cgexample"];
  fhir:Bundle.type [ fhir:value "collection"];
  fhir:Bundle.entry [
     fhir:index 0;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/DiagnosticReport/report" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/DiagnosticReport/report>
  ], [
     fhir:index 1;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Patient/patient" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Patient/patient>
  ], [
     fhir:index 2;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Specimen/specimen" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Specimen/specimen>
  ], [
     fhir:index 3;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Organization/lab" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Organization/lab>
  ], [
     fhir:index 4;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/DiagnosticRequest/request" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/DiagnosticRequest/request>
  ], [
     fhir:index 5;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/overall-interp" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/overall-interp>
  ], [
     fhir:index 6;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/discrete-variant" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/discrete-variant>
  ], [
     fhir:index 7;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/dis-path" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/dis-path>
  ], [
     fhir:index 8;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-variant" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-variant>
  ], [
     fhir:index 9;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-dis-path" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-dis-path>
  ], [
     fhir:index 10;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-component-D" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-component-D>
  ], [
     fhir:index 11;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/complex-component-E" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/complex-component-E>
  ], [
     fhir:index 12;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/pharmPanel" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/pharmPanel>
  ], [
     fhir:index 13;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype>
  ], [
     fhir:index 14;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/genotype" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/genotype>
  ], [
     fhir:index 15;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/metab" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/metab>
  ], [
     fhir:index 16;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/efficacy" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/efficacy>
  ], [
     fhir:index 17;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/highrisk" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Observation/highrisk>
  ], [
     fhir:index 18;
     fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Task/usage" ];
     fhir:Bundle.entry.resource <http://example.org/fhir/Task/usage>
  ].

<http://example.org/fhir/DiagnosticReport/report> a fhir:DiagnosticReport;
  fhir:Resource.id [ fhir:value "report"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:DiagnosticReport.basedOn [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "DiagnosticRequest/request" ]
  ];
  fhir:DiagnosticReport.status [ fhir:value "final"];
  fhir:DiagnosticReport.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:81247-9;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "81247-9" ]     ]
  ];
  fhir:DiagnosticReport.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:DiagnosticReport.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:DiagnosticReport.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:DiagnosticReport.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:DiagnosticReport.result [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/overall-interp" ]
  ], [
     fhir:index 1;
     fhir:Reference.reference [ fhir:value "Observation/discrete-variant" ]
  ], [
     fhir:index 2;
     fhir:Reference.reference [ fhir:value "Observation/dis-path" ]
  ], [
     fhir:index 3;
     fhir:Reference.reference [ fhir:value "Observation/complex-variant" ]
  ], [
     fhir:index 4;
     fhir:Reference.reference [ fhir:value "Observation/complex-dis-path" ]
  ], [
     fhir:index 5;
     fhir:Reference.reference [ fhir:value "Observation/pharmPanel" ]
  ];
  fhir:DiagnosticReport.presentedForm [
     fhir:index 0;
     fhir:Attachment.contentType [ fhir:value "text/plain" ];
     fhir:Attachment.data [ fhir:value "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"^^xsd:base64Binary ]
  ].

<http://example.org/fhir/Patient/patient> a fhir:Patient;
  fhir:Resource.id [ fhir:value "patient"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "additional" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">This would contain patient identifiers, demographics, etc.</div>"
  ].

<http://example.org/fhir/Specimen/specimen> a fhir:Specimen;
  fhir:Resource.id [ fhir:value "specimen"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:Specimen.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ].

<http://example.org/fhir/Organization/lab> a fhir:Organization;
  fhir:Resource.id [ fhir:value "lab"];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:Organization.name [ fhir:value "Some lab"].

<http://example.org/fhir/DiagnosticRequest/request> a fhir:ServiceRequest;
  fhir:Resource.id [ fhir:value "request"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/servicerequest>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:ServiceRequest.status [ fhir:value "active"];
  fhir:ServiceRequest.intent [ fhir:value "original-order"];
  fhir:ServiceRequest.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:81247-9;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "81247-9" ]     ]
  ];
  fhir:ServiceRequest.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:ServiceRequest.reasonCode [
     fhir:index 0;
     fhir:CodeableConcept.text [ fhir:value "Worried about family planning" ]
  ].

<http://example.org/fhir/Observation/overall-interp> a fhir:Observation;
  fhir:Resource.id [ fhir:value "overall-interp"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:51968-6;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "51968-6" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA6576-8;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA6576-8" ];
       fhir:Coding.display [ fhir:value "Positive" ]     ], [
       fhir:index 1;
       a sct:10828004;
       fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
       fhir:Coding.code [ fhir:value "10828004" ];
       fhir:Coding.display [ fhir:value "Positive" ]     ]
  ];
  fhir:Observation.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ].

<http://example.org/fhir/Observation/discrete-variant> a fhir:Observation;
  fhir:Resource.id [ fhir:value "discrete-variant"];
  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 "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  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.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81252-9;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81252-9" ];
         fhir:Coding.display [ fhir:value "Discrete genetic variant" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/clinvar" ];
         fhir:Coding.version [ fhir:value "???" ];
         fhir:Coding.code [ fhir:value "30880" ];
         fhir:Coding.display [ fhir:value "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)" ]       ], [
         fhir:index 1;
         fhir:Coding.system [ fhir:value "http://example.org/cigar" ];
         fhir:Coding.code [ fhir:value "tbd" ]       ]     ]
  ], [
     fhir:index 1;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/hgnc" ];
         fhir:Coding.code [ fhir:value "21497" ];
         fhir:Coding.display [ fhir:value "ACAD9" ]       ]     ]
  ], [
     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: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_014049.4" ]       ]     ]
  ], [
     fhir:index 3;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48013-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48013-7" ]       ]     ];
     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 "NG_017064.1" ]       ]     ]
  ], [
     fhir:index 4;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81290-9;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81290-9" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.g" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "NC_000003.11:g.128625063C>T" ]       ]     ]
  ], [
     fhir:index 5;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81255-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81255-2" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/dbsnp" ];
         fhir:Coding.version [ fhir:value "137" ];
         fhir:Coding.code [ fhir:value "rs368949613" ]       ]     ]
  ], [
     fhir:index 6;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.c" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "c.1249C>T" ]       ]     ]
  ], [
     fhir:index 7;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48005-3;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48005-3" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.p" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "p.Arg417Cys" ]       ]     ]
  ], [
     fhir:index 8;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48019-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48019-4" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6690-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6690-7" ];
         fhir:Coding.display [ fhir:value "Substitution" ]       ]     ]
  ], [
     fhir:index 9;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48006-1;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48006-1" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6698-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6698-0" ];
         fhir:Coding.display [ fhir:value "Missense" ]       ]     ]
  ], [
     fhir:index 10;
     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:Observation.component.valueString [ fhir:value "C" ]
  ], [
     fhir:index 11;
     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:Observation.component.valueRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "31731"^^xsd:decimal ]       ];
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "31731"^^xsd:decimal ]       ]     ]
  ], [
     fhir:index 12;
     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:Observation.component.valueString [ fhir:value "T" ]
  ], [
     fhir:index 13;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/Chrom-Loc" ];
         fhir:Coding.code [ fhir:value "3q21" ]       ]     ]
  ], [
     fhir:index 14;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48002-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48002-0" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6683-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6683-2" ];
         fhir:Coding.display [ fhir:value "Germline" ]       ]     ]
  ], [
     fhir:index 15;
     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: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:index 16;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81258-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81258-6" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "47"^^xsd:decimal ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "%" ]     ]
  ], [
     fhir:index 17;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:82121-5;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "82121-5" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "208"^^xsd:decimal ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "1" ]     ]
  ], [
     fhir:index 18;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:82155-3;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "82155-3" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "1"^^xsd:decimal ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "1" ]     ]
  ], [
     fhir:index 19;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81299-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81299-0" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "0.48"^^xsd:decimal ]     ]
  ], [
     fhir:index 20;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81300-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81300-6" ]       ]     ];
     fhir:Observation.component.valueQuantity [
       fhir:Quantity.value [ fhir:value "1396929"^^xsd:decimal ];
       fhir:Quantity.system [ fhir:value "http://unitsofmeasure.org" ];
       fhir:Quantity.code [ fhir:value "1" ]     ]
  ], [
     fhir:index 21;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81301-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81301-4" ]       ]     ];
     fhir:Observation.component.valueRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "13200589"^^xsd:decimal ]       ];
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "15592000"^^xsd:decimal ]       ]     ]
  ], [
     fhir:index 22;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81302-2;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81302-2" ]       ]     ];
     fhir:Observation.component.valueRange [
       fhir:Range.low [
         fhir:Quantity.value [ fhir:value "14184616"^^xsd:decimal ]       ];
       fhir:Range.high [
         fhir:Quantity.value [ fhir:value "15581544"^^xsd:decimal ]       ]     ]
  ].

<http://example.org/fhir/Observation/dis-path> a fhir:Observation;
  fhir:Resource.id [ fhir:value "dis-path"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:53037-8;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "53037-8" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA6668-3;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA6668-3" ];
       fhir:Coding.display [ fhir:value "Pathogenic" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/discrete-variant" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81259-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81259-4" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/MedGen-Dis" ];
         fhir:Coding.code [ fhir:value "C1970173" ];
         fhir:Coding.display [ fhir:value "Acyl-CoA dehydrogenase family, member 9, deficiency of" ]       ]     ]
  ].

<http://example.org/fhir/Observation/complex-variant> a fhir:Observation;
  fhir:Resource.id [ fhir:value "complex-variant"];
  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 "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  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.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.hasMember [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/complex-component-D" ]
  ], [
     fhir:index 1;
     fhir:Reference.reference [ fhir:value "Observation/complex-component-E" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81263-6;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81263-6" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA26218-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA26218-0" ];
         fhir:Coding.display [ fhir:value "Haplotype" ]       ]     ]
  ].

<http://example.org/fhir/Observation/complex-dis-path> a fhir:Observation;
  fhir:Resource.id [ fhir:value "complex-dis-path"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:53037-8;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "53037-8" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA6668-3;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA6668-3" ];
       fhir:Coding.display [ fhir:value "Pathogenic" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/complex-variant" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81259-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81259-4" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a sct:293498008;
         fhir:Coding.system [ fhir:value "http://snomed.info/sct" ];
         fhir:Coding.code [ fhir:value "293498008" ];
         fhir:Coding.display [ fhir:value "Debrisoquine adverse reaction (disorder)" ]       ]     ]
  ].

<http://example.org/fhir/Observation/complex-component-D> a fhir:Observation;
  fhir:Resource.id [ fhir:value "complex-component-D"];
  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 "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  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.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81252-9;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81252-9" ];
         fhir:Coding.display [ fhir:value "Discrete genetic variant" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/clinvar" ];
         fhir:Coding.version [ fhir:value "???" ];
         fhir:Coding.code [ fhir:value "31934" ];
         fhir:Coding.display [ fhir:value "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)" ]       ]     ]
  ], [
     fhir:index 1;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/RefSeq-T" ];
         fhir:Coding.code [ fhir:value "NM_000106.5" ]       ]     ]
  ], [
     fhir:index 2;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.c" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "c.886C>T" ]       ]     ]
  ], [
     fhir:index 3;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48005-3;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48005-3" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.p" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "p.Arg296Cys" ]       ]     ]
  ], [
     fhir:index 4;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48019-4;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48019-4" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6690-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6690-7" ];
         fhir:Coding.display [ fhir:value "Substitution" ]       ]     ]
  ], [
     fhir:index 5;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:48006-1;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "48006-1" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:LA6698-0;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "LA6698-0" ];
         fhir:Coding.display [ fhir:value "Missense" ]       ]     ]
  ].

<http://example.org/fhir/Observation/complex-component-E> a fhir:Observation;
  fhir:Resource.id [ fhir:value "complex-component-E"];
  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 "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  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.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:81252-9;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "81252-9" ];
         fhir:Coding.display [ fhir:value "Discrete genetic variant" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/clinvar" ];
         fhir:Coding.version [ fhir:value "???" ];
         fhir:Coding.code [ fhir:value "38486" ];
         fhir:Coding.display [ fhir:value "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)" ]       ]     ]
  ], [
     fhir:index 1;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/RefSeq-T" ];
         fhir:Coding.code [ fhir:value "NM_000106.5" ]       ]     ]
  ], [
     fhir:index 2;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/HGVS.c" ];
         fhir:Coding.version [ fhir:value "15.11" ];
         fhir:Coding.code [ fhir:value "c.1457G>C" ]       ]     ]
  ].

<http://example.org/fhir/Observation/pharmPanel> a fhir:Observation;
  fhir:Resource.id [ fhir:value "pharmPanel"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/grouper";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/grouper>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:DomainResource.extension [
     fhir:index 0;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction" ];
     fhir:Extension.valueReference [
       fhir:Reference.reference [ fhir:value "Task/usage" ]     ]
  ];
  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;
       fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ];
       fhir:Coding.code [ fhir:value "grouper" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.hasMember [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/haplotype" ]
  ], [
     fhir:index 1;
     fhir:Reference.reference [ fhir:value "Observation/genotype" ]
  ], [
     fhir:index 2;
     fhir:Reference.reference [ fhir:value "Observation/metab" ]
  ], [
     fhir:index 3;
     fhir:Reference.reference [ fhir:value "Observation/efficacy" ]
  ].

<http://example.org/fhir/Observation/haplotype> a fhir:Observation;
  fhir:Resource.id [ fhir:value "haplotype"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:84414-2;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "84414-2" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://example.org/???" ];
       fhir:Coding.code [ fhir:value "*2" ]     ]
  ];
  fhir:Observation.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/discrete-variant" ]
  ].

<http://example.org/fhir/Observation/genotype> a fhir:Observation;
  fhir:Resource.id [ fhir:value "genotype"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:84413-4;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "84413-4" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       fhir:Coding.system [ fhir:value "http://www.pharmvar.org" ];
       fhir:Coding.code [ fhir:value "CYP2C9 *2/*5" ];
       fhir:Coding.display [ fhir:value "CYP2C9 *2/*5" ]     ]
  ];
  fhir:Observation.specimen [
     fhir:Reference.reference [ fhir:value "Specimen/specimen" ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/haplotype" ]
  ];
  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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/hgnc" ];
         fhir:Coding.code [ fhir:value "2623" ];
         fhir:Coding.display [ fhir:value "CYP2C9" ]       ]     ]
  ], [
     fhir:index 1;
     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:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://example.org/hgnc" ];
         fhir:Coding.code [ fhir:value "23663" ];
         fhir:Coding.display [ fhir:value "VKORC1" ]       ]     ]
  ].

<http://example.org/fhir/Observation/metab> a fhir:Observation;
  fhir:Resource.id [ fhir:value "metab"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-metabolism";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-metabolism>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:53040-2;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "53040-2" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA25390-8;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA25390-8" ];
       fhir:Coding.display [ fhir:value "Rapid metabolizer" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/genotype" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:51963-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "51963-7" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
         fhir:Coding.code [ fhir:value "11289" ];
         fhir:Coding.display [ fhir:value "Warfarin" ]       ]     ]
  ].

<http://example.org/fhir/Observation/efficacy> a fhir:Observation;
  fhir:Resource.id [ fhir:value "efficacy"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-efficacy";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-efficacy>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:51961-1;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "51961-1" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA6676-6;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA6676-6" ];
       fhir:Coding.display [ fhir:value "Resistant" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/genotype" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:51963-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "51963-7" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
         fhir:Coding.code [ fhir:value "11289" ];
         fhir:Coding.display [ fhir:value "Warfarin" ]       ]     ]
  ].

<http://example.org/fhir/Observation/highrisk> a fhir:Observation;
  fhir:Resource.id [ fhir:value "highrisk"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-high-risk";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-high-risk>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</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:83009-1;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "83009-1" ]     ]
  ];
  fhir:Observation.subject [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Observation.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
  fhir:Observation.issued [ fhir:value "2016-09-06T00:00:00-05:00"^^xsd:dateTime];
  fhir:Observation.performer [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Observation.valueCodeableConcept [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA19542-2;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA19542-2" ];
       fhir:Coding.display [ fhir:value "Low risk" ]     ]
  ];
  fhir:Observation.derivedFrom [
     fhir:index 0;
     fhir:Reference.reference [ fhir:value "Observation/genotype" ]
  ];
  fhir:Observation.component [
     fhir:index 0;
     fhir:Observation.component.code [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         a loinc:51963-7;
         fhir:Coding.system [ fhir:value "http://loinc.org" ];
         fhir:Coding.code [ fhir:value "51963-7" ]       ]     ];
     fhir:Observation.component.valueCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
         fhir:Coding.code [ fhir:value "11289" ];
         fhir:Coding.display [ fhir:value "Warfarin" ]       ]     ]
  ].

<http://example.org/fhir/Task/usage> a fhir:Task;
  fhir:Resource.id [ fhir:value "usage"];
  fhir:Resource.meta [
     fhir:Meta.profile [
       fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg";
       fhir:index 0;
       fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/task-med-chg>     ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ];
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\">TODO</div>"
  ];
  fhir:DomainResource.contained [
     a fhir:MedicationStatement;
     fhir:index 0;
     fhir:Resource.id [ fhir:value "med" ];
     fhir:MedicationStatement.status [ fhir:value "unknown" ];
     fhir:MedicationStatement.medicationCodeableConcept [
       fhir:CodeableConcept.coding [
         fhir:index 0;
         fhir:Coding.system [ fhir:value "http://www.nlm.nih.gov/research/umls/rxnorm" ];
         fhir:Coding.code [ fhir:value "11289" ];
         fhir:Coding.display [ fhir:value "Warfarin" ]       ]     ];
     fhir:MedicationStatement.subject [
       fhir:Reference.reference [ fhir:value "Patient/patient" ]     ]
  ];
  fhir:Task.status [ fhir:value "requested"];
  fhir:Task.intent [ fhir:value "proposal"];
  fhir:Task.code [
     fhir:CodeableConcept.coding [
       fhir:index 0;
       a loinc:LA26423-6;
       fhir:Coding.system [ fhir:value "http://loinc.org" ];
       fhir:Coding.code [ fhir:value "LA26423-6" ];
       fhir:Coding.display [ fhir:value "Increase dose" ]     ];
     fhir:CodeableConcept.text [ fhir:value "May need higher dosage than usual." ]
  ];
  fhir:Task.focus [
     fhir:Reference.reference [ fhir:value "#med" ]
  ];
  fhir:Task.for [
     fhir:Reference.reference [ fhir:value "Patient/patient" ]
  ];
  fhir:Task.requester [
     fhir:Reference.reference [ fhir:value "Organization/lab" ]
  ];
  fhir:Task.reasonReference [
     fhir:Reference.reference [ fhir:value "Observation/metab" ]
  ].

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

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