Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, 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 sct: <http://snomed.info/id/> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- a fhir:Bundle ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "bundle-cgexample"] ; # fhir:type [ fhir:v "collection"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "http://example.org/fhir/DiagnosticReport/report"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/DiagnosticReport/report> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Patient/ExamplePatient"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Patient/ExamplePatient> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Specimen/ExampleSpecimen"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Specimen/ExampleSpecimen> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Organization/ExampleLab"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Organization/ExampleLab> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/ServiceRequest/ExampleServiceRequest"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/ServiceRequest/ExampleServiceRequest> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/overall-interp"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/overall-interp> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/discrete-variant"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/discrete-variant> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/dis-path"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/dis-path> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-variant"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-variant> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-dis-path"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-dis-path> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-component-D"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-component-D> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/complex-component-E"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/complex-component-E> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/haplotype"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/haplotype> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/genotype"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/genotype> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/metab"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/metab> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/efficacy"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/efficacy> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Observation/highrisk"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Observation/highrisk> ) ] [ fhir:fullUrl [ fhir:v "http://example.org/fhir/Task/usage"^^xsd:anyURI ] ; ( fhir:resource <http://example.org/fhir/Task/usage> ) ] ) . # <http://example.org/fhir/DiagnosticReport/report> a fhir:DiagnosticReport ; fhir:id [ fhir:v "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\"><p><b>Generated Narrative: DiagnosticReport</b><a name=\"report\"> </a></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 DiagnosticReport "report" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-report.html\">Genomic Report</a></p></div><p><b>basedOn</b>: <a href=\"#ServiceRequest_ExampleServiceRequest\">See above (ServiceRequest/ExampleServiceRequest)</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/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</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>: Sep 6, 2016, 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_overall-interp\">See above (Observation/overall-interp)</a></li><li><a href=\"#Observation_discrete-variant\">See above (Observation/discrete-variant)</a></li><li><a href=\"#Observation_dis-path\">See above (Observation/dis-path)</a></li><li><a href=\"#Observation_complex-variant\">See above (Observation/complex-variant)</a></li><li><a href=\"#Observation_complex-dis-path\">See above (Observation/complex-dis-path)</a></li><li><a href=\"#Observation_haplotype\">See above (Observation/haplotype)</a></li><li><a href=\"#Observation_genotype\">See above (Observation/genotype)</a></li><li><a href=\"#Observation_metab\">See above (Observation/metab)</a></li><li><a href=\"#Observation_efficacy\">See above (Observation/efficacy)</a></li></ul><h3>PresentedForms</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>ContentType</b></td><td><b>Data</b></td></tr><tr><td style=\"display: none\">*</td><td>text/plain</td><td>(base64 data - 39 bytes)</td></tr></table></div>" ] ; # fhir:basedOn ( [ fhir:reference [ fhir:v "ServiceRequest/ExampleServiceRequest" ] ] ) ; # 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 "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "Observation/overall-interp" ] ] [ fhir:reference [ fhir:v "Observation/discrete-variant" ] ] [ fhir:reference [ fhir:v "Observation/dis-path" ] ] [ fhir:reference [ fhir:v "Observation/complex-variant" ] ] [ fhir:reference [ fhir:v "Observation/complex-dis-path" ] ] [ fhir:reference [ fhir:v "Observation/haplotype" ] ] [ fhir:reference [ fhir:v "Observation/genotype" ] ] [ fhir:reference [ fhir:v "Observation/metab" ] ] [ fhir:reference [ fhir:v "Observation/efficacy" ] ] ) ; # fhir:presentedForm ( [ fhir:contentType [ fhir:v "text/plain" ] ; fhir:data [ fhir:v "UHV0IHRoZSByZXBvcnQgdGV4dCBoZXJlIC0gbWltZS1lbmNvZGVk"^^xsd:base64Binary ] ] ) . # <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\"><p><b>Generated Narrative: Specimen</b><a name=\"ExampleSpecimen\"> </a></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 Specimen "ExampleSpecimen" </p></div><p><b>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</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\"><p><b>Generated Narrative: Organization</b><a name=\"ExampleLab\"> </a></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 Organization "ExampleLab" </p></div><p><b>name</b>: Some lab</p></div>" ] ; # fhir:name [ fhir:v "Some lab"] . # <http://example.org/fhir/ServiceRequest/ExampleServiceRequest> a fhir:ServiceRequest ; fhir:id [ fhir:v "ExampleServiceRequest"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: ServiceRequest</b><a name=\"ExampleServiceRequest\"> </a></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 ServiceRequest "ExampleServiceRequest" </p></div><p><b>status</b>: active</p><p><b>intent</b>: original-order</p><p><b>code</b>: Genetic analysis report <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51969-4)</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: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:display [ fhir:v "Genetic analysis report" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:reasonCode ( [ fhir:text [ fhir:v "Worried about family planning" ] ] ) . # <http://example.org/fhir/Observation/overall-interp> a fhir:Observation ; fhir:id [ fhir:v "overall-interp"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/overall-interpretation> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"overall-interp\"> </a></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 Observation "overall-interp" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-overall-interpretation.html\">Overall Interpretation</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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Discrete variation analysis overall interpretation <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51968-6)</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>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: Positive <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6576-8; <a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#10828004)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p></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:51968-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51968-6" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6576-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6576-8" ] ; fhir:display [ fhir:v "Positive" ] ] [ a sct:10828004 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ; fhir:code [ fhir:v "10828004" ] ; fhir:display [ fhir:v "Positive" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] . # <http://example.org/fhir/Observation/discrete-variant> a fhir:Observation ; fhir:id [ fhir:v "discrete-variant"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"discrete-variant\"> </a></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 Observation "discrete-variant" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></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><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>: NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-ClinVarV.html\">ClinVar Variant ID</a>#30880)</span></p></blockquote><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>: ACAD9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:21497)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_014049.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_014049.4)</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_017064.1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NG_017064.1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000003.11:g.128625063C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NC_000003.11:g.128625063C>T)</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>: rs368949613 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (Genetic Sequence polymorphism database[137]#rs368949613)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_014049.4:c.1249C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_014049.4:c.1249C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_054768.2:p.Arg417Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NP_054768.2:p.Arg417Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: Substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <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>: C</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>: 31731-31731</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic alt allele [ID] <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>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48001-2)</span></p><p><b>value</b>: 3q21 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> ()</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Germline <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6683-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53034-5)</span></p><p><b>value</b>: Heterozygous <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 47 %<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code % = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 208 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic structural variant copy number <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82155-3)</span></p><p><b>value</b>: 1 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant reported arrCGH [Ratio] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81299-0)</span></p><p><b>value</b>: 0.48</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant [Length] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81300-6)</span></p><p><b>value</b>: 1396929 1<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant outer start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81301-4)</span></p><p><b>value</b>: 13200589-15592000</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Structural variant inner start and end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81302-2)</span></p><p><b>value</b>: 14184616-15581544</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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^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:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:code [ fhir:v "30880" ] ; fhir:display [ fhir:v "NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:21497" ] ; fhir:display [ fhir:v "ACAD9" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_014049.4" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48013-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48013-7" ] ] ) ] ; 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_017064.1" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81290-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81290-9" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NC_000003.11:g.128625063C>T" ] ] ) ] ] [ 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:version [ fhir:v "137" ] ; fhir:code [ fhir:v "rs368949613" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_014049.4:c.1249C>T" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_054768.2:p.Arg417Cys" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48019-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48019-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6690-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6690-7" ] ; fhir:display [ fhir:v "Substitution" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:69547-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69547-8" ] ] ) ] ; fhir:value [ fhir:v "C" ] ] [ 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 "31731"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "31731"^^xsd:decimal ] ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:69551-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "69551-0" ] ] ) ] ; fhir:value [ fhir:v "T" ] ] [ fhir:code [ ( fhir:coding [ a loinc:48001-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48001-2" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; fhir:text [ fhir:v "3q21" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:48002-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48002-0" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:53034-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53034-5" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6706-1 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6706-1" ] ; fhir:display [ fhir:v "Heterozygous" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81258-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81258-6" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "47"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "%" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:82121-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "82121-5" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "208"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:82155-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "82155-3" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "1"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81299-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81299-0" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "0.48"^^xsd:decimal ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81300-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81300-6" ] ] ) ] ; fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "1396929"^^xsd:decimal ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1" ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81301-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81301-4" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "13200589"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "15592000"^^xsd:decimal ] ] ] ] [ fhir:code [ ( fhir:coding [ a loinc:81302-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81302-2" ] ] ) ] ; fhir:value [ a fhir:Range ; fhir:low [ fhir:value [ fhir:v "14184616"^^xsd:decimal ] ] ; fhir:high [ fhir:value [ fhir:v "15581544"^^xsd:decimal ] ] ] ] ) . # <http://example.org/fhir/Observation/dis-path> a fhir:Observation ; fhir:id [ fhir:v "dis-path"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"dis-path\"> </a></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 Observation "dis-path" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic 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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</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>: Sep 6, 2016, 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_discrete-variant\">See above (Observation/discrete-variant)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: acyl-CoA dehydrogenase 9 deficiency <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-MONDO.html\">Mondo Disease Ontology</a>#MONDO:0012624)</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 "diagnostic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/discrete-variant" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:53037-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53037-8" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6668-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6668-3" ] ; fhir:display [ fhir:v "Pathogenic" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81259-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81259-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://purl.obolibrary.org/obo/mondo.owl"^^xsd:anyURI ] ; fhir:code [ fhir:v "MONDO:0012624" ] ; fhir:display [ fhir:v "acyl-CoA dehydrogenase 9 deficiency" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-variant> a fhir:Observation ; fhir:id [ fhir:v "complex-variant"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"complex-variant\"> </a></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 Observation "complex-variant" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></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>hasMember</b>: </p><ul><li><a href=\"#Observation_complex-component-D\">See above (Observation/complex-component-D)</a></li><li><a href=\"#Observation_complex-component-E\">See above (Observation/complex-component-E)</a></li></ul></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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^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:hasMember ( [ fhir:reference [ fhir:v "Observation/complex-component-D" ] ] [ fhir:reference [ fhir:v "Observation/complex-component-E" ] ] ) . # <http://example.org/fhir/Observation/complex-dis-path> a fhir:Observation ; fhir:id [ fhir:v "complex-dis-path"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnostic-implication> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"complex-dis-path\"> </a></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 Observation "complex-dis-path" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-diagnostic-implication.html\">Diagnostic 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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Diagnostic Implication <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"CodeSystem-tbd-codes-cs.html\">To Be Determined Codes</a>#diagnostic-implication)</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>: Sep 6, 2016, 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_complex-variant\">See above (Observation/complex-variant)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#53037-8)</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6668-3)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81259-4)</span></p><p><b>value</b>: Debrisoquine adverse reaction (disorder) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://browser.ihtsdotools.org/\">SNOMED CT</a>#293498008)</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 "diagnostic-implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/complex-variant" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:53037-8 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "53037-8" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6668-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6668-3" ] ; fhir:display [ fhir:v "Pathogenic" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81259-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81259-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a sct:293498008 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ; fhir:code [ fhir:v "293498008" ] ; fhir:display [ fhir:v "Debrisoquine adverse reaction (disorder)" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-component-D> a fhir:Observation ; fhir:id [ fhir:v "complex-component-D"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"complex-component-D\"> </a></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 Observation "complex-component-D" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></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><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>: NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-ClinVarV.html\">ClinVar Variant ID</a>#31934)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000106.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000106.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_000106.5:c.886C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_000106.5:c.886C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_000097.3:p.Arg296Cys <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NP_000097.3:p.Arg296Cys)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48019-4)</span></p><p><b>value</b>: Substitution <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6690-7)</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 [ 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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^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:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:code [ fhir:v "31934" ] ; fhir:display [ fhir:v "NM_000106.5(CYP2D6):c.886C>T (p.Arg296Cys)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5:c.886C>T" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_000097.3:p.Arg296Cys" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48019-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48019-4" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA6690-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6690-7" ] ; fhir:display [ fhir:v "Substitution" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/complex-component-E> a fhir:Observation ; fhir:id [ fhir:v "complex-component-E"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"complex-component-E\"> </a></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 Observation "complex-component-E" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></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><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>: NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (ClinVar Variant ID[???]#38486)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_000106.5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_000106.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_000106.5:c.1457G>C <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_000106.5:c.1457G>C)</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 [ 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 "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^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:component ( [ fhir:code [ ( fhir:coding [ a loinc:81252-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81252-9" ] ; fhir:display [ fhir:v "Discrete genetic variant" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/clinvar"^^xsd:anyURI ] ; fhir:version [ fhir:v "???" ] ; fhir:code [ fhir:v "38486" ] ; fhir:display [ fhir:v "NM_000106.5(CYP2D6):c.1457G>C (p.Ser486Thr)" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51958-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51958-7" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ncbi.nlm.nih.gov/refseq"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48004-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48004-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NM_000106.5:c.1457G>C" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/haplotype> a fhir:Observation ; fhir:id [ fhir:v "haplotype"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"haplotype\"> </a></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 Observation "haplotype" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: *2 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (hla#*2)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_discrete-variant\">See above (Observation/discrete-variant)</a></p></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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.ebi.ac.uk/ipd/imgt/hla"^^xsd:anyURI ] ; fhir:code [ fhir:v "*2" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/discrete-variant" ] ] ) . # <http://example.org/fhir/Observation/genotype> a fhir:Observation ; fhir:id [ fhir:v "genotype"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"genotype\"> </a></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 Observation "genotype" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>subject</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>effective</b>: 2016</p><p><b>issued</b>: Sep 6, 2016, 5:00:00 AM</p><p><b>performer</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>value</b>: CYP2C9 *2/*5 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (www.pharmvar.org#CYP2C9 *2/*5)</span></p><p><b>specimen</b>: <a href=\"#Specimen_ExampleSpecimen\">See above (Specimen/ExampleSpecimen)</a></p><p><b>derivedFrom</b>: <a href=\"#Observation_haplotype\">See above (Observation/haplotype)</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\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:2623)</span></p></blockquote><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>: VKORC1 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:23663)</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 [ a loinc:84413-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "84413-4" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^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 *2/*5" ] ; fhir:display [ fhir:v "CYP2C9 *2/*5" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "Specimen/ExampleSpecimen" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/haplotype" ] ] ) ; # 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: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:48018-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48018-6" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "HGNC:23663" ] ; fhir:display [ fhir:v "VKORC1" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/metab> a fhir:Observation ; fhir:id [ fhir:v "metab"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"metab\"> </a></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 Observation "metab" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2016</p><p><b>issued</b>: Sep 6, 2016, 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\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <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>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</span></p></blockquote><blockquote><p><b>component</b></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>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></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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype" ] ] ) ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; 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 "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] [ 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" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/efficacy> a fhir:Observation ; fhir:id [ fhir:v "efficacy"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"efficacy\"> </a></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 Observation "efficacy" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2016</p><p><b>issued</b>: Sep 6, 2016, 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\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></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>value</b>: Resistant <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6676-6)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <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>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype" ] ] ) ; # 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:LA6676-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA6676-6" ] ; fhir:display [ fhir:v "Resistant" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; 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 "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] ) . # <http://example.org/fhir/Observation/highrisk> a fhir:Observation ; fhir:id [ fhir:v "highrisk"] ; # 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\"><p><b>Generated Narrative: Observation</b><a name=\"highrisk\"> </a></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 Observation "highrisk" </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/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</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>: 2016</p><p><b>issued</b>: Sep 6, 2016, 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\">See above (Observation/genotype)</a></p><blockquote><p><b>component</b></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>value</b>: Low risk <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA19542-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Medication assessed [ID] <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>: Warfarin <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-rxNorm.html\">RxNorm</a>#11289)</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:subject [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:effective [ fhir:v "2016"^^xsd:gYear] ; # fhir:issued [ fhir:v "2016-09-06T00:00:00-05:00"^^xsd:dateTime] ; # fhir:performer ( [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ) ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "Observation/genotype" ] ] ) ; # 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:LA19542-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA19542-2" ] ; fhir:display [ fhir:v "Low risk" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:51963-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "51963-7" ] ] ) ] ; 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 "11289" ] ; fhir:display [ fhir:v "Warfarin" ] ] ) ] ] ) . # <http://example.org/fhir/Task/usage> a fhir:Task ; fhir:id [ fhir:v "usage"] ; # 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\"><p><b>Generated Narrative: Task</b><a name=\"usage\"> </a></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 Task "usage" </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>: May need higher dosage than usual. <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>focus</b>: <a href=\"MedicationStatement-MedicationStatementWarfarin.html\">MedicationStatement/MedicationStatementWarfarin</a></p><p><b>for</b>: <a href=\"#Patient_ExamplePatient\">See above (Patient/ExamplePatient)</a></p><p><b>requester</b>: <a href=\"#Organization_ExampleLab\">See above (Organization/ExampleLab)</a></p><p><b>reasonReference</b>: <a href=\"#Observation_metab\">See above (Observation/metab)</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 "May need higher dosage than usual." ] ] ; # fhir:focus [ fhir:reference [ fhir:v "MedicationStatement/MedicationStatementWarfarin" ] ] ; # fhir:for [ fhir:reference [ fhir:v "Patient/ExamplePatient" ] ] ; # fhir:requester [ fhir:reference [ fhir:v "Organization/ExampleLab" ] ] ; # fhir:reasonReference [ fhir:reference [ fhir:v "Observation/metab" ] ] . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
Links: Table of Contents |
QA Report
| Version History |
|
Propose a change