Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <https://loinc.org/rdf/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- a fhir:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "bundle-pgxexample"] ; # fhir:type [ fhir:v "transaction"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "http://example.org/fhir/DiagnosticReport/pgx-report"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/DiagnosticReport/pgx-report> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "DiagnosticReport"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Patient/ExamplePatient"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Patient/ExamplePatient> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Patient"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Specimen/ExampleSpecimen"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Specimen/ExampleSpecimen> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Specimen"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Organization/ExampleLab"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Organization/ExampleLab> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Organization"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/ServiceRequest/pgx-request"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/ServiceRequest/pgx-request> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "ServiceRequest"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/med-impact-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/med-impact-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/genotype-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/genotype-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/variant-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/variant-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/variant-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/variant-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MolecularSequence/sequence-1-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MolecularSequence"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MolecularSequence/sequence-2-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MolecularSequence"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Task/med-usage-impact-task-pgx-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Task"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/MedicationStatement/current-med-example"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/MedicationStatement/current-med-example> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "MedicationStatement"^^xsd:anyURI ] ] ] ) . # <http://example.org/fhir/DiagnosticReport/pgx-report> a fhir:DiagnosticReport ; fhir:id [ fhir:v "pgx-report"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_pgx-report\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport pgx-report</b></p><a name=\"pgx-report\"> </a><a name=\"hcpgx-report\"> </a><a name=\"pgx-report-en-US\"> </a><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>Subject</td><td>Anonymous Patient (no stated gender), DoB Unknown</td></tr><tr><td>When For</td><td>2016</td></tr><tr><td>Reported</td><td>2018-03-06 00:00:00-0500</td></tr><tr><td>Performer</td><td> <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></td></tr></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>" ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/recommended-action"^^xsd:anyURI ] ; fhir:value [ a fhir:Reference ; fhir:reference [ fhir:v "Task/med-usage-impact-task-pgx-example" ] ] ] ) ; # fhir:basedOn ( [ fhir:reference [ fhir:v "ServiceRequest/pgx-request" ] ] ) ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:51969-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51969-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "Observation/med-impact-pgx-example" ] ; fhir:display [ fhir:v "genetics impact for medication metabolism accessment" ] ] [ fhir:reference [ fhir:v "Observation/genotype-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-2-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/variant-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/variant-2-pgx-example" ] ] ) . # <http://example.org/fhir/Patient/ExamplePatient> a fhir:Patient ; fhir:id [ fhir:v "ExamplePatient"] ; # fhir:text [ fhir:status [ fhir:v "additional" ] ; fhir: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:id [ fhir:v "ExampleSpecimen"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Specimen_ExampleSpecimen\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen ExampleSpecimen</b></p><a name=\"ExampleSpecimen\"> </a><a name=\"hcExampleSpecimen\"> </a><a name=\"ExampleSpecimen-en-US\"> </a><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>" ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] . # <http://example.org/fhir/Organization/ExampleLab> a fhir:Organization ; fhir:id [ fhir:v "ExampleLab"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_ExampleLab\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ExampleLab</b></p><a name=\"ExampleLab\"> </a><a name=\"hcExampleLab\"> </a><a name=\"ExampleLab-en-US\"> </a><p><b>name</b>: Some lab</p></div>" ] ; # fhir:name [ fhir:v "Some lab"] . # <http://example.org/fhir/ServiceRequest/pgx-request> a fhir:ServiceRequest ; fhir:id [ fhir:v "pgx-request"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_pgx-request\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest pgx-request</b></p><a name=\"pgx-request\"> </a><a name=\"hcpgx-request\"> </a><a name=\"pgx-request-en-US\"> </a><p><b>status</b>: Active</p><p><b>intent</b>: Original Order</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonCode</b>: <span title=\"Codes:\">Worried about family planning</span></p></div>" ] ; # fhir:status [ fhir:v "active"] ; # fhir:intent [ fhir:v "original-order"] ; # fhir:code [ ( fhir:coding [ a loinc:51969-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51969-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonCode ( [ fhir:text [ fhir:v "Worried about family planning" ] ] ) . # <http://example.org/fhir/Observation/med-impact-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "med-impact-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/therapeutic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_med-impact-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation med-impact-pgx-example</b></p><a name=\"med-impact-pgx-example\"> </a><a name=\"hcmed-impact-pgx-example\"> </a><a name=\"med-impact-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_genotype-pgx-example\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs therapeutic-implication}\">Therapeutic Implication</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA25390-8}\">Rapid metabolizer</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51963-7}\">Medication assessed</span></p><p><b>value</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ; fhir:display [ fhir:v "Therapeutic Implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "therapeutic-implication" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA25390-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA25390-8" ] ; fhir:display [ fhir:v "Rapid metabolizer" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ; fhir:display [ fhir:v "Medication assessed" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "103" ] ; fhir:display [ fhir:v "mercaptopurine" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/genotype-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "genotype-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_genotype-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation genotype-pgx-example</b></p><a name=\"genotype-pgx-example\"> </a><a name=\"hcgenotype-pgx-example\"> </a><a name=\"genotype-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84413-4}\">genotype display name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *4/*35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: </p><ul><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-1-pgx-example\">Bundle: type = transaction</a></li><li><a href=\"Bundle-bundle-pgxexample.html#Observation_haplotype-2-pgx-example\">Bundle: type = transaction</a></li></ul><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84413-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84413-4" ] ; fhir:display [ fhir:v "genotype display name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *4/*35B" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/haplotype-1-pgx-example" ] ] [ fhir:reference [ fhir:v "Observation/haplotype-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/haplotype-1-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "haplotype-1-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_haplotype-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-1-pgx-example</b></p><a name=\"haplotype-1-pgx-example\"> </a><a name=\"hchaplotype-1-pgx-example\"> </a><a name=\"haplotype-1-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *35B</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-1-pgx-example\">Bundle: type = transaction</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84414-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84414-2" ] ; fhir:display [ fhir:v "Haplotype Name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *35B" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/variant-1-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/haplotype-2-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "haplotype-2-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_haplotype-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation haplotype-2-pgx-example</b></p><a name=\"haplotype-2-pgx-example\"> </a><a name=\"hchaplotype-2-pgx-example\"> </a><a name=\"haplotype-2-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 84414-2}\">Haplotype Name</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://www.pharmvar.org "CYP2C9}\">CYP2C9 *4</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_variant-2-pgx-example\">Bundle: type = transaction</a></p><h3>Components</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></td><td><span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></td></tr></table></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:84414-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84414-2" ] ; fhir:display [ fhir:v "Haplotype Name" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.pharmvar.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "\"CYP2C9" ] ; fhir:display [ fhir:v "CYP2C9 *4" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/variant-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/variant-1-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "variant-1-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_variant-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-1-pgx-example</b></p><a name=\"variant-1-pgx-example\"> </a><a name=\"hcvariant-1-pgx-example\"> </a><a name=\"variant-1-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-1-pgx-example\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs12345}\">rs12345</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227976-55227977</p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:69548-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69548-6" ] ; fhir:display [ fhir:v "Genetic variant assessment" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA9633-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA9633-4" ] ; fhir:display [ fhir:v "Present" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "MolecularSequence/sequence-1-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/projects/SNP"^^xsd:anyURI ] ; fhir:code [ fhir:v "rs12345" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ; fhir:display [ fhir:v "Ref nucleotide" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ; fhir:display [ fhir:v "Alt allele" ] ] ) ] ; fhir:value [ fhir:v "G" ] ] [ fhir:code [ ( fhir:coding [ a loinc:81254-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81254-5" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "55227976"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "55227977"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/Observation/variant-2-pgx-example> a fhir:Observation ; fhir:id [ fhir:v "variant-2-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_variant-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation variant-2-pgx-example</b></p><a name=\"variant-2-pgx-example\"> </a><a name=\"hcvariant-2-pgx-example\"> </a><a name=\"variant-2-pgx-example-en-US\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>effective</b>: 2018</p><p><b>issued</b>: 2018-03-06 00:00:00-0500</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>specimen</b>: <a href=\"Specimen-ExampleSpecimen.html\">Specimen</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-pgxexample.html#MolecularSequence_sequence-2-pgx-example\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence ID</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG_007726.3}\">NG_007726.3</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81252-9}\">Discrete genetic variant</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/projects/SNP rs233455}\">rs233455</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Ref nucleotide</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Alt allele</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 55227978-55227979</p></blockquote></div>" ] ; # fhir:status [ fhir:v "final"] ; # fhir:category ( [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/observation-category"^^xsd:anyURI ] ; fhir:code [ fhir:v "laboratory" ] ] ) ] [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v2-0074"^^xsd:anyURI ] ; fhir:code [ fhir:v "GE" ] ] ) ] ) ; # fhir:code [ ( fhir:coding [ a loinc:69548-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69548-6" ] ; fhir:display [ fhir:v "Genetic variant assessment" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2018"^^xsd:gYear] ; # fhir:issued [ fhir:v "2018-03-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA9633-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA9633-4" ] ; fhir:display [ fhir:v "Present" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "MolecularSequence/sequence-2-pgx-example" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ; fhir:display [ fhir:v "Gene studied ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:2623" ] ; fhir:display [ fhir:v "CYP2C9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48013-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48013-7" ] ; fhir:display [ fhir:v "Genomic reference sequence ID" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG_007726.3" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/projects/SNP"^^xsd:anyURI ] ; fhir:code [ fhir:v "rs233455" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ; fhir:display [ fhir:v "Ref nucleotide" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ; fhir:display [ fhir:v "Alt allele" ] ] ) ] ; fhir:value [ fhir:v "G" ] ] [ fhir:code [ ( fhir:coding [ a loinc:81254-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81254-5" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "55227978"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "55227979"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/MolecularSequence/sequence-1-pgx-example> a fhir:MolecularSequence ; fhir:id [ fhir:v "sequence-1-pgx-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-1-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-1-pgx-example</b></p><a name=\"sequence-1-pgx-example\"> </a><a name=\"hcsequence-1-pgx-example\"> </a><a name=\"sequence-1-pgx-example-en-US\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; # fhir:type [ fhir:v "dna"] ; # fhir:coordinateSystem [ fhir:v "0"^^xsd:integer] ; # fhir:referenceSeq [ fhir:orientation [ fhir:v "sense" ] ; fhir:referenceSeqId [ ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG-007726.3" ] ] ) ] ; fhir:windowStart [ fhir:v "55227970"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "55227980"^^xsd:integer ] ] . # <http://example.org/fhir/MolecularSequence/sequence-2-pgx-example> a fhir:MolecularSequence ; fhir:id [ fhir:v "sequence-2-pgx-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MolecularSequence_sequence-2-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MolecularSequence sequence-2-pgx-example</b></p><a name=\"sequence-2-pgx-example\"> </a><a name=\"hcsequence-2-pgx-example\"> </a><a name=\"sequence-2-pgx-example-en-US\"> </a><p><b>type</b>: DNA Sequence</p><p><b>coordinateSystem</b>: 0</p><h3>ReferenceSeqs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Orientation</b></td><td><b>ReferenceSeqId</b></td><td><b>WindowStart</b></td><td><b>WindowEnd</b></td></tr><tr><td style=\"display: none\">*</td><td>Sense orientation of referenceSeq</td><td><span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NG-007726.3}\">NG-007726.3</span></td><td>55227970</td><td>55227980</td></tr></table></div>" ] ; # fhir:type [ fhir:v "dna"] ; # fhir:coordinateSystem [ fhir:v "0"^^xsd:integer] ; # fhir:referenceSeq [ fhir:orientation [ fhir:v "sense" ] ; fhir:referenceSeqId [ ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NG-007726.3" ] ] ) ] ; fhir:windowStart [ fhir:v "55227970"^^xsd:integer ] ; fhir:windowEnd [ fhir:v "55227980"^^xsd:integer ] ] . # <http://example.org/fhir/Task/med-usage-impact-task-pgx-example> a fhir:Task ; fhir:id [ fhir:v "med-usage-impact-task-pgx-example"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/medication-recommendation> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Task_med-usage-impact-task-pgx-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Task med-usage-impact-task-pgx-example</b></p><a name=\"med-usage-impact-task-pgx-example\"> </a><a name=\"hcmed-usage-impact-task-pgx-example\"> </a><a name=\"med-usage-impact-task-pgx-example-en-US\"> </a><p><b>status</b>: Requested</p><p><b>intent</b>: proposal</p><p><b>code</b>: <span title=\"Codes:{http://loinc.org LA26423-6}\">Any Increase does Recommendation Text from the provider</span></p><p><b>description</b>: Any Increase does Recommendation Text from the provider</p><p><b>focus</b>: <a href=\"Bundle-bundle-pgxexample.html#MedicationStatement_current-med-example\">Bundle: type = transaction</a></p><p><b>for</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p><p><b>reasonReference</b>: <a href=\"Bundle-bundle-pgxexample.html#Observation_med-impact-pgx-example\">Bundle: type = transaction</a></p></div>" ] ; # fhir:status [ fhir:v "requested"] ; # fhir:intent [ fhir:v "proposal"] ; # fhir:code [ ( fhir:coding [ a loinc:LA26423-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26423-6" ] ; fhir:display [ fhir:v "Increase dose" ] ] ) ; fhir:text [ fhir:v "Any Increase does Recommendation Text from the provider" ] ] ; # fhir:description [ fhir:v "Any Increase does Recommendation Text from the provider"] ; # fhir:focus [ fhir:reference [ fhir:v "MedicationStatement/current-med-example" ] ] ; # fhir:for [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonReference [ fhir:reference [ fhir:v "Observation/med-impact-pgx-example" ] ] . # <http://example.org/fhir/MedicationStatement/current-med-example> a fhir:MedicationStatement ; fhir:id [ fhir:v "current-med-example"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"MedicationStatement_current-med-example\"> </a><p class=\"res-header-id\"><b>Generated Narrative: MedicationStatement current-med-example</b></p><a name=\"current-med-example\"> </a><a name=\"hccurrent-med-example\"> </a><a name=\"current-med-example-en-US\"> </a><p><b>status</b>: Unknown</p><p><b>medication</b>: <span title=\"Codes:{http://www.nlm.nih.gov/research/umls/rxnorm 103}\">mercaptopurine</span></p><p><b>subject</b>: <a href=\"Patient-ExamplePatient.html\">Anonymous Patient (no stated gender), DoB Unknown</a></p></div>" ] ; # fhir:status [ fhir:v "unknown"] ; # fhir:medication [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.nlm.nih.gov/research/umls/rxnorm"^^xsd:anyURI ] ; fhir:code [ fhir:v "103" ] ; fhir:display [ fhir:v "mercaptopurine" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change