Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <http://loinc.org/rdf#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . # - resource ------------------------------------------------------------------- a fhir:Bundle; fhir:nodeRole fhir:treeRoot; fhir:Resource.id [ fhir:value "complexVariant-nonHGVS"]; fhir:Bundle.type [ fhir:value "transaction"]; fhir:Bundle.entry [ fhir:index 0; fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ]; fhir:Bundle.entry.resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d>; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ]; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 1; fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e" ]; fhir:Bundle.entry.resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e>; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ]; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ], [ fhir:index 2; fhir:Bundle.entry.fullUrl [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a" ]; fhir:Bundle.entry.resource <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a>; fhir:Bundle.entry.request [ fhir:Bundle.entry.request.method [ fhir:value "POST" ]; fhir:Bundle.entry.request.url [ fhir:value "Observation" ] ] ]. <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d> a fhir:Observation; fhir:Resource.meta [ fhir:Meta.profile [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"; fhir:index 0; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ]; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ]; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.769G>A <span style=\"background: LightGoldenRodYellow\">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.769G>A'})</span></td></tr></table></div>" ]; fhir:Observation.status [ fhir:value "final"]; fhir:Observation.category [ fhir:index 0; fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ]; fhir:Coding.code [ fhir:value "laboratory" ] ] ]; fhir:Observation.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69548-6; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69548-6" ]; fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ] ]; fhir:Observation.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:LA9633-4; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "LA9633-4" ]; fhir:Coding.display [ fhir:value "Present" ] ] ]; fhir:Observation.component [ fhir:index 0; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:51958-7; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "51958-7" ]; fhir:Coding.display [ fhir:value "Transcript ref sequence ID" ] ] ]; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ]; fhir:Coding.code [ fhir:value "NM_022787.3" ]; fhir:Coding.display [ fhir:value "NM_022787.3" ] ] ] ], [ fhir:index 1; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ]; fhir:Coding.code [ fhir:value "exact-start-end" ]; fhir:Coding.display [ fhir:value "Variant exact start and end" ] ] ]; fhir:Observation.component.valueRange [ fhir:Range.low [ fhir:Quantity.value [ fhir:value "769"^^xsd:decimal ] ]; fhir:Range.high [ fhir:Quantity.value [ fhir:value "769"^^xsd:decimal ] ] ] ], [ fhir:index 2; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69547-8; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69547-8" ]; fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ]; fhir:Observation.component.valueString [ fhir:value "G" ] ], [ fhir:index 3; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69551-0; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69551-0" ]; fhir:Coding.display [ fhir:value "Genomic alt allele [ID]" ] ] ]; fhir:Observation.component.valueString [ fhir:value "A" ] ]. <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e> a fhir:Observation; fhir:Resource.meta [ fhir:Meta.profile [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"; fhir:index 0; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ]; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ]; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.53A>G <span style=\"background: LightGoldenRodYellow\">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.53A>G'})</span></td></tr></table></div>" ]; fhir:Observation.status [ fhir:value "final"]; fhir:Observation.category [ fhir:index 0; fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ]; fhir:Coding.code [ fhir:value "laboratory" ] ] ]; fhir:Observation.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69548-6; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69548-6" ]; fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ] ]; fhir:Observation.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:LA9633-4; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "LA9633-4" ]; fhir:Coding.display [ fhir:value "Present" ] ] ]; fhir:Observation.component [ fhir:index 0; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:51958-7; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "51958-7" ]; fhir:Coding.display [ fhir:value "Transcript ref sequence ID" ] ] ]; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://www.ncbi.nlm.nih.gov/refseq" ]; fhir:Coding.code [ fhir:value "NM_022787.3" ]; fhir:Coding.display [ fhir:value "NM_022787.3" ] ] ] ], [ fhir:index 1; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes" ]; fhir:Coding.code [ fhir:value "exact-start-end" ]; fhir:Coding.display [ fhir:value "Variant exact start and end" ] ] ]; fhir:Observation.component.valueRange [ fhir:Range.low [ fhir:Quantity.value [ fhir:value "53"^^xsd:decimal ] ]; fhir:Range.high [ fhir:Quantity.value [ fhir:value "53"^^xsd:decimal ] ] ] ], [ fhir:index 2; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69547-8; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69547-8" ]; fhir:Coding.display [ fhir:value "Genomic ref allele [ID]" ] ] ]; fhir:Observation.component.valueString [ fhir:value "A" ] ], [ fhir:index 3; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69551-0; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69551-0" ]; fhir:Coding.display [ fhir:value "Genomic alt allele [ID]" ] ] ]; fhir:Observation.component.valueString [ fhir:value "G" ] ]. <urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a> a fhir:Observation; fhir:Resource.meta [ fhir:Meta.profile [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"; fhir:index 0; fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant> ] ]; fhir:DomainResource.text [ fhir:Narrative.status [ fhir:value "generated" ]; fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>hasMember</b>: </p><ul><li>NM_022787.3:c.53A>G</li><li/></ul><h3>Components</h3><table class=\"grid\"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Complex Variant Type <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81263-6' = 'Complex variant type', given as 'Complex Variant Type'})</span></td><td>Compound heterozygous <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA26217-2' = 'Compound heterozygous', given as 'Compound heterozygous'})</span></td></tr></table></div>" ]; fhir:Observation.status [ fhir:value "final"]; fhir:Observation.category [ fhir:index 0; fhir:CodeableConcept.coding [ fhir:index 0; fhir:Coding.system [ fhir:value "http://terminology.hl7.org/CodeSystem/observation-category" ]; fhir:Coding.code [ fhir:value "laboratory" ] ] ]; fhir:Observation.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:69548-6; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "69548-6" ]; fhir:Coding.display [ fhir:value "Genetic variant assessment" ] ] ]; fhir:Observation.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:LA9633-4; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "LA9633-4" ]; fhir:Coding.display [ fhir:value "Present" ] ] ]; fhir:Observation.hasMember [ fhir:index 0; fhir:Reference.reference [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e" ]; fhir:Reference.display [ fhir:value "unpacked representation of NM_022787.3:c.53A>G" ] ], [ fhir:index 1; fhir:Reference.reference [ fhir:value "urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d" ]; fhir:Reference.display [ fhir:value "unpacked representation of NM_022787.3:c.769G>A" ] ]; fhir:Observation.component [ fhir:index 0; fhir:Observation.component.code [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:81263-6; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "81263-6" ]; fhir:Coding.display [ fhir:value "Complex Variant Type" ] ] ]; fhir:Observation.component.valueCodeableConcept [ fhir:CodeableConcept.coding [ fhir:index 0; a loinc:LA26217-2; fhir:Coding.system [ fhir:value "http://loinc.org" ]; fhir:Coding.code [ fhir:value "LA26217-2" ]; fhir:Coding.display [ fhir:value "Compound heterozygous" ] ] ] ]. # - ontology header ------------------------------------------------------------ a owl:Ontology; owl:imports fhir:fhir.ttl.
IG © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
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