Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 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/TbdCodes" ];
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/TbdCodes" ];
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 © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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