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-oncology-diagnostic"] ; # fhir:type [ fhir:v "transaction"] ; # fhir:entry ( [ fhir:fullUrl [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Patient"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Practitioner"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Specimen"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "Observation"^^xsd:anyURI ] ] ] [ fhir:fullUrl [ fhir:v "urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5"^^xsd:anyURI ] ; ( fhir:resource <urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> ) ; fhir:request [ fhir:method [ fhir:v "POST" ] ; fhir:url [ fhir:v "DiagnosticReport"^^xsd:anyURI ] ] ] ) . # <urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d> a fhir:Patient ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-1"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Patient_Inline-Instance-for-oncology-diagnostic-1\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Patient Inline-Instance-for-oncology-diagnostic-1</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-1\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-1\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-1-en-US\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">Carrot John Mr Male, DoB: 1962-12-31 ( 1007)</p><hr/><table class=\"grid\"><tr><td style=\"background-color: #f3f5da\" title=\"Patient Links\">Links:</td><td colspan=\"3\"><ul><li>General Practitioner: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></li></ul></td></tr></table></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "1007" ] ] ) ; # fhir:name ( [ ( fhir:given [ fhir:v "Carrot" ] [ fhir:v "John" ] [ fhir:v "Mr" ] ) ] ) ; # fhir:gender [ fhir:v "male"] ; # fhir:birthDate [ fhir:v "1962-12-31"^^xsd:date] ; # fhir:generalPractitioner ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) . # <urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef> a fhir:Practitioner ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-2"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Practitioner_Inline-Instance-for-oncology-diagnostic-2\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Practitioner Inline-Instance-for-oncology-diagnostic-2</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-2\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-2\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-2-en-US\"> </a><p><b>identifier</b>: 4654765876</p><p><b>name</b>: Akerman Philip Prof </p><p><b>address</b>: Castro Valley CA </p></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "4654765876" ] ] ) ; # fhir:name ( [ ( fhir:given [ fhir:v "Akerman" ] [ fhir:v "Philip" ] [ fhir:v "Prof" ] ) ] ) ; # fhir:address ( [ fhir:city [ fhir:v "Castro Valley" ] ; fhir:state [ fhir:v "CA" ] ] ) . # <urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d> a fhir:Specimen ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-3"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Specimen_Inline-Instance-for-oncology-diagnostic-3\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Specimen Inline-Instance-for-oncology-diagnostic-3</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-3\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-3\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-3-en-US\"> </a><p><b>identifier</b>: 076e1948-2217-11e9-94d8-12e241dc1f66</p><p><b>status</b>: Available</p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><h3>Collections</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Collector</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></td></tr></table></div>" ] ; # fhir:identifier ( [ fhir:value [ fhir:v "076e1948-2217-11e9-94d8-12e241dc1f66" ] ] ) ; # fhir:status [ fhir:v "available"] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:collection [ fhir:collector [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ] . # <urn:uuid:40e85eda-4d31-4bd2-a5a0-c39d63f9824f> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-4"] ; # fhir:meta [ ( fhir:profile [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker"^^xsd:anyURI ; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-biomarker> ] ) ] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncology-diagnostic-4\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-4</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-4\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-4\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-4-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}\">A characterization of a given biomarker observation.</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 94076-7}\">Mutations/Megabase [# Ratio] in Tumor</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>value</b>: 25 Mutations/Megabase<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code1/1000000 = '1/1000000')</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs biomarker-category}\">A characterization of a given biomarker observation.</span></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs molgen}\">molecular sequence adjacent category</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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "biomarker-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:94076-7 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "94076-7" ] ; fhir:display [ fhir:v "Mutations/Megabase [# Ratio] in Tumor" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:value [ a fhir:Quantity ; fhir:value [ fhir:v "25"^^xsd:decimal ] ; fhir:unit [ fhir:v "Mutations/Megabase" ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "1/1000000" ] ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # 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 "biomarker-category" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/molecular-biomarker-ontology-cs"^^xsd:anyURI ] ; fhir:code [ fhir:v "molgen" ] ; fhir:display [ fhir:v "molecular sequence adjacent category" ] ] ) ] ] ) . # <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-5"] ; # 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_Inline-Instance-for-oncology-diagnostic-5\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-5</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-5\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-5\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-5-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=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 62374-4}\">Human reference sequence assembly version</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA14029-5}\">GRCh37</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81290-9}\">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NC_000007.13:g.140453136A>T}\">NC_000007.13:g.140453136A>T</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/clinvar 13961}\">Clinvar ID 13961</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48005-3}\">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NP_004324.2:p.Val600Glu}\">NP_004324.2:p.Val600Glu</span></p></blockquote><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:1097}\">BRAF</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 "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # 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:method [ ( fhir:coding [ a loinc:LA26398-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26398-0" ] ; fhir:display [ fhir:v "Sequencing" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # fhir:component ( [ fhir:code [ ( fhir:coding [ a loinc:62374-4 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "62374-4" ] ; fhir:display [ fhir:v "Human reference sequence assembly version" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA14029-5 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA14029-5" ] ; fhir:display [ fhir:v "GRCh37" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:81290-9 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "81290-9" ] ; fhir:display [ fhir:v "Genomic DNA change (gHGVS)" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NC_000007.13:g.140453136A>T" ] ; fhir:display [ fhir:v "NC_000007.13:g.140453136A>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: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 "13961" ] ; fhir:display [ fhir:v "Clinvar ID 13961" ] ] ) ] ] [ fhir:code [ ( fhir:coding [ a loinc:48005-3 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "48005-3" ] ; fhir:display [ fhir:v "Amino acid change (pHGVS)" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ fhir:system [ fhir:v "http://varnomen.hgvs.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "NP_004324.2:p.Val600Glu" ] ; fhir:display [ fhir:v "NP_004324.2:p.Val600Glu" ] ] ) ] ] [ 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:1097" ] ; fhir:display [ fhir:v "BRAF" ] ] ) ] ] ) . # <urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524> a fhir:Observation ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-6"] ; # 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 "extensions" ] ; fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Observation_Inline-Instance-for-oncology-diagnostic-6\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Observation Inline-Instance-for-oncology-diagnostic-6</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-6\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-6\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-6-en-US\"> </a><p><b>Related artifact</b>: No display for RelatedArtifact (type: justification; display: https://pmkb.weill.cornell.edu/therapies/103)</p><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 diagnostic-implication}\">Diagnostic Implication</span></p><p><b>subject</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-d0b4affa-91d6-46d1-af01-b30d9f16ef6d\">Bundle: type = transaction</a></p><p><b>effective</b>: 2019-03-05</p><p><b>performer</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</a></p><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26811-2}\">Computational analysis</span></p><p><b>specimen</b>: <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a5d6a6a9-4859-480e-85b2-56974fef3b9d\">Bundle: type = transaction</a></p><p><b>derivedFrom</b>: <a href=\"Bundle-bundle-complexVariant-nonHGVS.html#urn-uuid-16fdd5fc-e665-48af-99e4-48d603f3e12d\">Bundle: type = transaction</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53037-8}\">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6668-3}\">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 93044-6}\">Level of Evidence</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30200-2}\">Very strong evidence pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81259-4}\">Associated phenotype</span></p><p><b>value</b>: <span title=\"Codes:\">melanoma</span></p></blockquote></div>" ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/workflow-relatedArtifact"^^xsd:anyURI ] ; fhir:value [ a fhir:RelatedArtifact ; fhir:type [ fhir:v "justification" ] ; fhir:display [ fhir:v "https://pmkb.weill.cornell.edu/therapies/103" ] ] ] ) ; # 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:display [ fhir:v "Diagnostic Implication" ] ] ) ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:method [ ( fhir:coding [ a loinc:LA26811-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA26811-2" ] ; fhir:display [ fhir:v "Computational analysis" ] ] ) ] ; # fhir:specimen [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ; # fhir:derivedFrom ( [ fhir:reference [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ] ] ) ; # 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:display [ fhir:v "Genetic variation clinical significance [Imp]" ] ] ) ] ; 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:93044-6 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "93044-6" ] ; fhir:display [ fhir:v "Level of Evidence" ] ] ) ] ; fhir:value [ a fhir:CodeableConcept ; ( fhir:coding [ a loinc:LA30200-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ] ; fhir:code [ fhir:v "LA30200-2" ] ; fhir:display [ fhir:v "Very strong evidence 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:text [ fhir:v "melanoma" ] ] ] ) . # <urn:uuid:ad7a499b-a43b-4cc8-bf46-cac62d9ecae5> a fhir:DiagnosticReport ; fhir:id [ fhir:v "Inline-Instance-for-oncology-diagnostic-7"] ; # 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_Inline-Instance-for-oncology-diagnostic-7\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport Inline-Instance-for-oncology-diagnostic-7</b></p><a name=\"Inline-Instance-for-oncology-diagnostic-7\"> </a><a name=\"hcInline-Instance-for-oncology-diagnostic-7\"> </a><a name=\"Inline-Instance-for-oncology-diagnostic-7-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>Not done yet</td></tr><tr><td>When For</td><td>2019-03-05</td></tr><tr><td>Performer</td><td> <a href=\"Bundle-bundle-oncology-diagnostic.html#urn-uuid-a48256f8-db37-44e0-a0f6-d7af16c7c9ef\">Bundle: type = transaction</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></table></div>" ] ; # 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:text [ fhir:v "Genetic analysis report" ] ] ; # fhir:subject [ fhir:reference [ fhir:v "urn:uuid:d0b4affa-91d6-46d1-af01-b30d9f16ef6d" ] ] ; # fhir:effective [ fhir:v "2019-03-05"^^xsd:date] ; # fhir:performer ( [ fhir:reference [ fhir:v "urn:uuid:a48256f8-db37-44e0-a0f6-d7af16c7c9ef" ] ] ) ; # fhir:specimen ( [ fhir:reference [ fhir:v "urn:uuid:a5d6a6a9-4859-480e-85b2-56974fef3b9d" ] ] ) ; # fhir:result ( [ fhir:reference [ fhir:v "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ] ; fhir:display [ fhir:v "BRAF V600E mutation observed" ] ] [ fhir:reference [ fhir:v "urn:uuid:1bf9642d-fd1c-4819-8c5d-44fae4bad524" ] ; fhir:display [ fhir:v "melanoma implicated" ] ] ) . #
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-24
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