Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions 
@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 -------------------------------------------------------------------
a fhir:Bundle;
fhir:nodeRole fhir:treeRoot;
fhir:Resource.id [ fhir:value "bundle-pgxexample"];
fhir:Bundle.type [ fhir:value "transaction"];
fhir:Bundle.entry [
fhir:index 0;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/DiagnosticReport/pgx-report" ];
fhir:Bundle.entry.resource <http://example.org/fhir/DiagnosticReport/pgx-report>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "DiagnosticReport" ] ]
], [
fhir:index 1;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Patient/ExamplePatient" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Patient/ExamplePatient>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Patient" ] ]
], [
fhir:index 2;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Specimen/ExampleSpecimen" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Specimen/ExampleSpecimen>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Specimen" ] ]
], [
fhir:index 3;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Organization/ExampleLab" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Organization/ExampleLab>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Organization" ] ]
], [
fhir:index 4;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/ServiceRequest/pgx-request" ];
fhir:Bundle.entry.resource <http://example.org/fhir/ServiceRequest/pgx-request>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "ServiceRequest" ] ]
], [
fhir:index 5;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/med-impact-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/med-impact-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 6;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/genotype-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/genotype-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 7;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype-1-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype-1-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 8;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/haplotype-2-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/haplotype-2-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 9;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/variant-1-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/variant-1-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 10;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Observation/variant-2-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Observation/variant-2-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ]
], [
fhir:index 11;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "MolecularSequence" ] ]
], [
fhir:index 12;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "MolecularSequence" ] ]
], [
fhir:index 13;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/Task/med-usage-impact-task-pgx-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/Task/med-usage-impact-task-pgx-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "Task" ] ]
], [
fhir:index 14;
fhir:Bundle.entry.fullUrl [ fhir:value "http://example.org/fhir/MedicationStatement/current-med-example" ];
fhir:Bundle.entry.resource <http://example.org/fhir/MedicationStatement/current-med-example>;
fhir:Bundle.entry.request [
fhir:Bundle.entry.request.method [ fhir:value "POST" ];
fhir:Bundle.entry.request.url [ fhir:value "MedicationStatement" ] ]
].
<http://example.org/fhir/DiagnosticReport/pgx-report> a fhir:DiagnosticReport;
fhir:Resource.id [ fhir:value "pgx-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 "extensions" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"pgx-report\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomics-report.html\">Genomics Report</a></p></div><p><b>Recommended Action</b>: <a href=\"#Task_med-usage-impact-task-pgx-example\">See above (Task/med-usage-impact-task-pgx-example)</a></p><p><b>basedOn</b>: <a href=\"#ServiceRequest_pgx-request\">See above (ServiceRequest/pgx-request)</a></p><p><b>status</b>: final</p><p><b>category</b>: Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>result</b>: </p><ul><li><a href=\"#Observation_med-impact-pgx-example\">See above (Observation/med-impact-pgx-example: genetics impact for medication metabolism accessment)</a></li><li><a href=\"#Observation_genotype-pgx-example\">See above (Observation/genotype-pgx-example)</a></li><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</a></li><li><a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</a></li><li><a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</a></li></ul></div>"
];
fhir:DomainResource.extension [
fhir:index 0;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action" ];
fhir:Extension.valueReference [
fhir:Reference.reference [ fhir:value "Task/med-usage-impact-task-pgx-example" ] ]
];
fhir:DiagnosticReport.basedOn [
fhir:index 0;
fhir:Reference.reference [ fhir:value "ServiceRequest/pgx-request" ]
];
fhir:DiagnosticReport.status [ fhir:value "final"];
fhir:DiagnosticReport.category [
fhir:index 0;
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:Coding.display [ fhir:value "Genetics" ] ]
];
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/ExamplePatient" ]
];
fhir:DiagnosticReport.effectiveDateTime [ fhir:value "2016"^^xsd:gYear];
fhir:DiagnosticReport.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
fhir:DiagnosticReport.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:DiagnosticReport.result [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/med-impact-pgx-example" ];
fhir:Reference.display [ fhir:value "genetics impact for medication metabolism accessment" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/genotype-pgx-example" ]
], [
fhir:index 2;
fhir:Reference.reference [ fhir:value "Observation/haplotype-1-pgx-example" ]
], [
fhir:index 3;
fhir:Reference.reference [ fhir:value "Observation/haplotype-2-pgx-example" ]
], [
fhir:index 4;
fhir:Reference.reference [ fhir:value "Observation/variant-1-pgx-example" ]
], [
fhir:index 5;
fhir:Reference.reference [ fhir:value "Observation/variant-2-pgx-example" ]
].
<http://example.org/fhir/Patient/ExamplePatient> a fhir:Patient;
fhir:Resource.id [ fhir:value "ExamplePatient"];
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/ExampleSpecimen> a fhir:Specimen;
fhir:Resource.id [ fhir:value "ExampleSpecimen"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"ExampleSpecimen\" </p></div><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p></div>"
];
fhir:Specimen.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
].
<http://example.org/fhir/Organization/ExampleLab> a fhir:Organization;
fhir:Resource.id [ fhir:value "ExampleLab"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"ExampleLab\" </p></div><p><b>name</b>: Some lab</p></div>"
];
fhir:Organization.name [ fhir:value "Some lab"].
<http://example.org/fhir/ServiceRequest/pgx-request> a fhir:ServiceRequest;
fhir:Resource.id [ fhir:value "pgx-request"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"pgx-request\" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81247-9)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>reasonCode</b>: Worried about family planning <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></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/ExamplePatient" ]
];
fhir:ServiceRequest.reasonCode [
fhir:index 0;
fhir:CodeableConcept.text [ fhir:value "Worried about family planning" ]
].
<http://example.org/fhir/Observation/med-impact-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "med-impact-pgx-example"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"med-impact-pgx-example\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-therapeutic-implication.html\">Therapeutic Implication</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#therapeutic-implication)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_genotype-pgx-example\">See above (Observation/genotype-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Predicted Therapeutic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#predicted-therapeutic-implication)</span></p><p><b>value</b>: Rapid metabolizer <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA25390-8)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51963-7)</span></p><p><b>value</b>: mercaptopurine <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#103)</span></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:Observation.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 "therapeutic-implication" ];
fhir:Coding.display [ fhir:value "Therapeutic Implication" ] ]
];
fhir:Observation.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.performer [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Organization/ExampleLab" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/genotype-pgx-example" ]
];
fhir:Observation.component [
fhir:index 0;
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 "predicted-therapeutic-implication" ] ] ];
fhir:Observation.component.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:index 1;
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:Coding.display [ fhir:value "Medication assessed" ] ] ];
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 "103" ];
fhir:Coding.display [ fhir:value "mercaptopurine" ] ] ]
].
<http://example.org/fhir/Observation/genotype-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "genotype-pgx-example"];
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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"genotype-pgx-example\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genotype.html\">Genotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: genotype display name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84413-4)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *4/*35B <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *4/*35B)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"#Observation_haplotype-1-pgx-example\">See above (Observation/haplotype-1-pgx-example)</a></li><li><a href=\"#Observation_haplotype-2-pgx-example\">See above (Observation/haplotype-2-pgx-example)</a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></td></tr></table></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:Coding.display [ fhir:value "genotype display name" ] ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.pharmvar.org" ];
fhir:Coding.code [ fhir:value "CYP2C9 *4/*35B" ];
fhir:Coding.display [ fhir:value "CYP2C9 *4/*35B" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/haplotype-1-pgx-example" ]
], [
fhir:index 1;
fhir:Reference.reference [ fhir:value "Observation/haplotype-2-pgx-example" ]
];
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/geneId" ];
fhir:Coding.code [ fhir:value "2623" ];
fhir:Coding.display [ fhir:value "CYP2C9" ] ] ]
].
<http://example.org/fhir/Observation/haplotype-1-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "haplotype-1-pgx-example"];
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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"haplotype-1-pgx-example\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-haplotype.html\">Haplotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Haplotype Name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84414-2)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *35B <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *35B)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-1-pgx-example\">See above (Observation/variant-1-pgx-example)</a></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></td></tr></table></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:Coding.display [ fhir:value "Haplotype Name" ] ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.pharmvar.org" ];
fhir:Coding.code [ fhir:value "CYP2C9 *35B" ];
fhir:Coding.display [ fhir:value "CYP2C9 *35B" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/variant-1-pgx-example" ]
];
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/geneId" ];
fhir:Coding.code [ fhir:value "2623" ];
fhir:Coding.display [ fhir:value "CYP2C9" ] ] ]
].
<http://example.org/fhir/Observation/haplotype-2-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "haplotype-2-pgx-example"];
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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"haplotype-2-pgx-example\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-haplotype.html\">Haplotype</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Haplotype Name <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#84414-2)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: CYP2C9 *4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_variant-2-pgx-example\">See above (Observation/variant-2-pgx-example)</a></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></td><td>CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></td></tr></table></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:Coding.display [ fhir:value "Haplotype Name" ] ]
];
fhir:Observation.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
fhir:Observation.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.pharmvar.org" ];
fhir:Coding.code [ fhir:value "CYP2C9 *4" ];
fhir:Coding.display [ fhir:value "CYP2C9 *4" ] ]
];
fhir:Observation.specimen [
fhir:Reference.reference [ fhir:value "Specimen/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "Observation/variant-2-pgx-example" ]
];
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/geneId" ];
fhir:Coding.code [ fhir:value "2623" ];
fhir:Coding.display [ fhir:value "CYP2C9" ] ] ]
].
<http://example.org/fhir/Observation/variant-1-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "variant-1-pgx-example"];
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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"variant-1-pgx-example\" </p><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>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-1-pgx-example\">See above (MolecularSequence/sequence-1-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs12345 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-dbSNP.html\">Genetic Sequence polymorphism database</a>#rs12345)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 55227976-55227977</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: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.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
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/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "MolecularSequence/sequence-1-pgx-example" ]
];
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/geneId" ];
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:81252-9;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "81252-9" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/projects/SNP" ];
fhir:Coding.code [ fhir:value "rs12345" ] ] ]
], [
fhir:index 2;
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:Coding.display [ fhir:value "Ref nucleotide" ] ] ];
fhir:Observation.component.valueString [ fhir:value "T" ]
], [
fhir:index 3;
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:Coding.display [ fhir:value "Alt allele" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
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:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "55227976"^^xsd:decimal ] ];
fhir:Range.high [
fhir:Quantity.value [ fhir:value "55227977"^^xsd:decimal ] ] ]
].
<http://example.org/fhir/Observation/variant-2-pgx-example> a fhir:Observation;
fhir:Resource.id [ fhir:value "variant-2-pgx-example"];
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\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"variant-2-pgx-example\" </p><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>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>effective</b>: 2018</p><p><b>issued</b>: Mar 6, 2018 5:00:00 AM</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#MolecularSequence_sequence-2-pgx-example\">See above (MolecularSequence/sequence-2-pgx-example)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: CYP2C9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (geneId#2623)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NG_007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NG_007726.3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81252-9)</span></p><p><b>value</b>: rs233455 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-dbSNP.html\">Genetic Sequence polymorphism database</a>#rs233455)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Ref nucleotide <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 55227978-55227979</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: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.effectiveDateTime [ fhir:value "2018"^^xsd:gYear];
fhir:Observation.issued [ fhir:value "2018-03-06T00:00:00-05:00"^^xsd:dateTime];
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/ExampleSpecimen" ]
];
fhir:Observation.derivedFrom [
fhir:index 0;
fhir:Reference.reference [ fhir:value "MolecularSequence/sequence-2-pgx-example" ]
];
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/geneId" ];
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:48013-7;
fhir:Coding.system [ fhir:value "http://loinc.org" ];
fhir:Coding.code [ fhir:value "48013-7" ];
fhir:Coding.display [ fhir:value "Genomic reference sequence ID" ] ] ];
fhir:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
fhir:Coding.code [ fhir:value "NG_007726.3" ] ] ]
], [
fhir:index 2;
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:Observation.component.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/projects/SNP" ];
fhir:Coding.code [ fhir:value "rs233455" ] ] ]
], [
fhir:index 3;
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:Coding.display [ fhir:value "Ref nucleotide" ] ] ];
fhir:Observation.component.valueString [ fhir:value "T" ]
], [
fhir:index 4;
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:Coding.display [ fhir:value "Alt allele" ] ] ];
fhir:Observation.component.valueString [ fhir:value "G" ]
], [
fhir:index 5;
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:Observation.component.valueRange [
fhir:Range.low [
fhir:Quantity.value [ fhir:value "55227978"^^xsd:decimal ] ];
fhir:Range.high [
fhir:Quantity.value [ fhir:value "55227979"^^xsd:decimal ] ] ]
].
<http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> a fhir:MolecularSequence;
fhir:Resource.id [ fhir:value "sequence-1-pgx-example"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"sequence-1-pgx-example\" </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NG-007726.3)</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
];
fhir:MolecularSequence.type [ fhir:value "dna"];
fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
fhir:MolecularSequence.referenceSeq [
fhir:MolecularSequence.referenceSeq.orientation [ fhir:value "sense" ];
fhir:MolecularSequence.referenceSeq.referenceSeqId [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
fhir:Coding.code [ fhir:value "NG-007726.3" ] ] ];
fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ];
fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ]
].
<http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> a fhir:MolecularSequence;
fhir:Resource.id [ fhir:value "sequence-2-pgx-example"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"sequence-2-pgx-example\" </p></div><p><b>type</b>: dna</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td>-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td>*</td><td>sense</td><td>NG-007726.3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (nuccore#NG-007726.3)</span></td><td>55227970</td><td>55227980</td></tr></table></div>"
];
fhir:MolecularSequence.type [ fhir:value "dna"];
fhir:MolecularSequence.coordinateSystem [ fhir:value "0"^^xsd:integer];
fhir:MolecularSequence.referenceSeq [
fhir:MolecularSequence.referenceSeq.orientation [ fhir:value "sense" ];
fhir:MolecularSequence.referenceSeq.referenceSeqId [
fhir:CodeableConcept.coding [
fhir:index 0;
fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/nuccore" ];
fhir:Coding.code [ fhir:value "NG-007726.3" ] ] ];
fhir:MolecularSequence.referenceSeq.windowStart [ fhir:value "55227970"^^xsd:integer ];
fhir:MolecularSequence.referenceSeq.windowEnd [ fhir:value "55227980"^^xsd:integer ]
].
<http://example.org/fhir/Task/med-usage-impact-task-pgx-example> a fhir:Task;
fhir:Resource.id [ fhir:value "med-usage-impact-task-pgx-example"];
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation";
fhir:index 0;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation> ]
];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"med-usage-impact-task-pgx-example\" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-medication-recommendation.html\">Medication Recommendation</a></p></div><p><b>status</b>: requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: Any Increase does Recommendation Text from the provider <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26423-6 \"Increase dose\")</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"#MedicationStatement_current-med-example\">See above (MedicationStatement/current-med-example)</a></p><p><b>for</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_med-impact-pgx-example\">See above (Observation/med-impact-pgx-example)</a></p></div>"
];
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 "Any Increase does Recommendation Text from the provider" ]
];
fhir:Task.description [ fhir:value "Any Increase does Recommendation Text from the provider"];
fhir:Task.focus [
fhir:Reference.reference [ fhir:value "MedicationStatement/current-med-example" ]
];
fhir:Task.for [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
];
fhir:Task.reasonReference [
fhir:Reference.reference [ fhir:value "Observation/med-impact-pgx-example" ]
].
<http://example.org/fhir/MedicationStatement/current-med-example> a fhir:MedicationStatement;
fhir:Resource.id [ fhir:value "current-med-example"];
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ];
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative</b></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource \"current-med-example\" </p></div><p><b>status</b>: unknown</p><p><b>medication</b>: mercaptopurine <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#103)</span></p><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p></div>"
];
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 "103" ];
fhir:Coding.display [ fhir:value "mercaptopurine" ] ]
];
fhir:MedicationStatement.subject [
fhir:Reference.reference [ fhir:value "Patient/ExamplePatient" ]
].
# - ontology header ------------------------------------------------------------
a owl:Ontology;
owl:imports fhir:fhir.ttl.
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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