Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
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@prefix fhir: <http://hl7.org/fhir/> . @prefix loinc: <https://loinc.org/rdf/> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @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:GenomicStudy ; fhir:resourceDefinition http://hl7.org/fhir/StructureDefinition/GenomicStudy|0.1.0-ci-build ; fhir:nodeRole fhir:treeRoot ; fhir:id [ fhir:v "example"] ; # from Resource: id, meta, implicitRules, and language fhir:language [ fhir:v "en"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><p class=\"res-header-id\"><b>Generated Narrative: GenomicStudy example</b></p><a name=\"example\"> </a><a name=\"hcexample\"> </a><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\">Language: en</p></div><p><b>identifier</b>: <code>http://example.org/identifiers/genomicstudies</code>/urn:uuid:1111-1111-1111-1111 (use: temp, )</p><p><b>status</b>: Unknown</p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type fam-var-segr}\">Familial variant segregation</span></p><p><b>subject</b>: <a href=\"Patient-denovoChild.html\">Child Junior Doe (official) Unknown, DoB: 2021-01-01 ( Medical record number: 11111 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>encounter</b>: <a href=\"Encounter-denovoEncounter.html\">Encounter: status = in-progress; class = inpatient encounter</a></p><p><b>startDate</b>: 2021-01-01</p><p><b>basedOn</b>: <a href=\"ServiceRequest-genomicServiceRequest.html\">ServiceRequest Carrier detection, molecular genetics (procedure)</a></p><p><b>referrer</b>: <a href=\"Practitioner-practitioner01.html\">Practitioner John Doel </a></p><p><b>interpreter</b>: <a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></p><h3>Reasons</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Concept</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://snomed.info/sct 267431006}\">Disorder of lipid metabolism (disorder)</span></td></tr></table><p><b>note</b>: </p><blockquote><div><p>This de novo mutation is urgent and important for establishing the treatment plan.</p>\n</div></blockquote><p><b>description</b>: </p><div><p>De novo mutation study of the patient.</p>\n</div><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1111 (use: temp, )</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Proband Sequence Variation Detection Using Next Generation Sequencing</p><p><b>specimen</b>: <a href=\"Specimen-denovo-1.html\">Specimen: identifier = http://example.org/identifiers/specimens#1; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a proband.</p>\n</div></blockquote><h3>Inputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicFile1.html\">DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td><td><b>Function</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td><td><span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1112 (use: temp, )</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Maternal Sequence Variation Detection Using Next Generation Sequencing</p><p><b>focus</b>: <a href=\"Patient-denovoMother.html\">Jane Mother Doe (official) Female, DoB: 2000-01-01 ( Medical record number: 11112 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-denovo-2.html\">Specimen: identifier = http://example.org/identifiers/specimens#2; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a mother of a proband.</p>\n</div></blockquote><h3>Inputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicFile2.html\">DocumentReference: identifier = http://example.org/identifiers/files#11112; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1113 (use: temp, )</p><p><b>genomicSourceClass</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p><p><b>title</b>: Paternal Sequence Variation Detection Using Next Generation Sequencing</p><p><b>focus</b>: <a href=\"Patient-denovoFather.html\">John Father Doe (official) Male, DoB: 2000-01-01 ( Medical record number: 11113 (use: temp, period: 2021-01-01 --> (ongoing)))</a></p><p><b>specimen</b>: <a href=\"Specimen-denovo-3.html\">Specimen: identifier = http://example.org/identifiers/specimens#3; status = available; type = Venous blood specimen; receivedTime = 2021-01-01 01:01:01+0000</a></p><p><b>date</b>: 2021-01-01 01:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of a father of a proband.</p>\n</div></blockquote><h3>Inputs</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>File</b></td><td><b>Type</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"DocumentReference-genomicFile3.html\">DocumentReference: identifier = http://example.org/identifiers/files#11113; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></td><td><span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></td></tr></table><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-NGS-device.html\">Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)</a></td></tr></table></blockquote><blockquote><p><b>analysis</b></p><p><b>identifier</b>: <code>http://example.org/identifiers/genomicAnalyses</code>/urn:uuid:1111-1111-1111-1114 (use: temp, )</p><p><b>title</b>: De Novo Mutation Detection and Interpretation</p><p><b>date</b>: 2021-01-01 03:01:10-0600</p><p><b>note</b>: </p><blockquote><div><p>This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences.</p>\n</div></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFile1.html\">DocumentReference: identifier = http://example.org/identifiers/files#11111; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFile2.html\">DocumentReference: identifier = http://example.org/identifiers/files#11112; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></p></blockquote><blockquote><p><b>input</b></p><p><b>file</b>: <a href=\"DocumentReference-genomicFile3.html\">DocumentReference: identifier = http://example.org/identifiers/files#11113; status = current; docStatus = preliminary; description = A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</a></p><p><b>type</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat vcf}\">VCF</span></p></blockquote><h3>Performers</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Actor</b></td><td><b>Role</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Practitioner-practitioner02.html\">Practitioner Jane Doel </a></td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v3-ParticipationType PRF}\">Performer</span></td></tr></table><h3>Devices</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Device</b></td></tr><tr><td style=\"display: none\">*</td><td><a href=\"Device-Triodenovo-SW.html\">Device: identifier = http://example.org/identifiers/devices#11112; status = active; manufacturer = Vanderbilt Genetics Institute; type = Software (physical object)</a></td></tr></table></blockquote></div>"^^rdf:XMLLiteral ] ] ; # fhir:identifier ( [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicstudies"^^xsd:anyURI ; fhir:l <http://example.org/identifiers/genomicstudies> ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1111" ] ] ) ; # from DomainResource: text, contained, extension, and modifierExtension fhir:status [ fhir:v "unknown"] ; # fhir:type ( [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-type> ] ; fhir:code [ fhir:v "fam-var-segr" ] ; fhir:display [ fhir:v "Familial variant segregation" ] ] ) ] ) ; # fhir:subject [ fhir:l fhir:Patient/denovoChild ; fhir:reference [ fhir:v "Patient/denovoChild" ] ] ; # fhir:encounter [ fhir:l fhir:Encounter/denovoEncounter ; fhir:reference [ fhir:v "Encounter/denovoEncounter" ] ] ; # fhir:startDate [ fhir:v "2021-01-01"^^xsd:date] ; # fhir:basedOn ( [ fhir:l fhir:ServiceRequest/genomicServiceRequest ; fhir:reference [ fhir:v "ServiceRequest/genomicServiceRequest" ] ] ) ; # fhir:referrer [ fhir:l fhir:Practitioner/practitioner01 ; fhir:reference [ fhir:v "Practitioner/practitioner01" ] ] ; # fhir:interpreter ( [ fhir:l fhir:Practitioner/practitioner02 ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ) ; # fhir:reason ( [ fhir:concept [ ( fhir:coding [ a sct:267431006 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l <http://snomed.info/sct> ] ; fhir:code [ fhir:v "267431006" ] ; fhir:display [ fhir:v "Disorder of lipid metabolism (disorder)" ] ] ) ] ] ) ; # fhir:note ( [ fhir:text [ fhir:v "This de novo mutation is urgent and important for establishing the treatment plan." ] ] ) ; # fhir:description [ fhir:v "De novo mutation study of the patient."] ; # fhir:analysis ( [ ( fhir:identifier [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l <http://example.org/identifiers/genomicAnalyses> ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1111" ] ] ) ; # 0..* Genomic Analysis Event of proband fhir:genomicSourceClass [ ( fhir:coding [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l <http://loinc.org> ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ; # <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical> fhir:title [ fhir:v "Proband Sequence Variation Detection Using Next Generation Sequencing" ] ; ( fhir:specimen [ fhir:l fhir:Specimen/denovo-1 ; fhir:reference [ fhir:v "Specimen/denovo-1" ] ] ) ; fhir:date [ fhir:v "2021-01-01T01:01:10-06:00"^^xsd:dateTime ] ; ( fhir:note [ fhir:text [ fhir:v "This is a next generation sequencing analysis of a proband." ] ] ) ; # 0..1 The date of the analysis event ( fhir:input [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile1 ; fhir:reference [ fhir:v "DocumentReference/genomicFile1" ] ] ; # 0..* Inputs for the analysis event of Child fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] ) ; # <protocolPerformed>0..1 Reference(Procedure|Task) The protocol that was performed for the analysis event<\/protocolPerformed> , <genomicRegion> 0..* Grouped genomic region sets by type (studied\/called\/uncalled)\n Each repetition: <type> required code, <locus> 0..* CodeableReference(DocumentReference), <description> 0..1 string\n <\/genomicRegion> , <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]> ( fhir:performer [ fhir:actor [ fhir:l fhir:Practitioner/practitioner02 ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ; # 0..* Performer for the analysis event fhir:role [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ; fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType> ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; ( fhir:device [ fhir:device [ fhir:l fhir:Device/NGS-device ; fhir:reference [ fhir:v "Device/NGS-device" ] ] ; # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters fhir:function [ ( fhir:coding [ a loinc:LA26398-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l <http://loinc.org> ] ; fhir:code [ fhir:v "LA26398-0" ] ; fhir:display [ fhir:v "Sequencing" ] ] ) ] ] ) ] [ ( fhir:identifier [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l <http://example.org/identifiers/genomicAnalyses> ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1112" ] ] ) ; # 0..* Genomic Analysis Event of mother fhir:genomicSourceClass [ ( fhir:coding [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l <http://loinc.org> ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ; # <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical> fhir:title [ fhir:v "Maternal Sequence Variation Detection Using Next Generation Sequencing" ] ; ( fhir:focus [ fhir:l fhir:Patient/denovoMother ; fhir:reference [ fhir:v "Patient/denovoMother" ] ] ) ; # 0..1 Name of the analysis event (human friendly) ( fhir:specimen [ fhir:l fhir:Specimen/denovo-2 ; fhir:reference [ fhir:v "Specimen/denovo-2" ] ] ) ; fhir:date [ fhir:v "2021-01-01T01:01:10-06:00"^^xsd:dateTime ] ; ( fhir:note [ fhir:text [ fhir:v "This is a next generation sequencing analysis of a mother of a proband." ] ] ) ; # 0..1 The date of the analysis event ( fhir:input [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile2 ; fhir:reference [ fhir:v "DocumentReference/genomicFile2" ] ] ; # 0..* Inputs for the analysis event of Mother fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] ) ; # <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]> ( fhir:performer [ fhir:actor [ fhir:l fhir:Practitioner/practitioner02 ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ; # 0..* Performer for the analysis event fhir:role [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ; fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType> ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; ( fhir:device [ fhir:device [ fhir:l fhir:Device/NGS-device ; fhir:reference [ fhir:v "Device/NGS-device" ] ] # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters ] ) # <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function> ] [ ( fhir:identifier [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l <http://example.org/identifiers/genomicAnalyses> ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1113" ] ] ) ; # 0..* Genomic Analysis Event of father fhir:genomicSourceClass [ ( fhir:coding [ a loinc:LA6683-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l <http://loinc.org> ] ; fhir:code [ fhir:v "LA6683-2" ] ; fhir:display [ fhir:v "Germline" ] ] ) ] ; # <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical> fhir:title [ fhir:v "Paternal Sequence Variation Detection Using Next Generation Sequencing" ] ; ( fhir:focus [ fhir:l fhir:Patient/denovoFather ; fhir:reference [ fhir:v "Patient/denovoFather" ] ] ) ; ( fhir:specimen [ fhir:l fhir:Specimen/denovo-3 ; fhir:reference [ fhir:v "Specimen/denovo-3" ] ] ) ; fhir:date [ fhir:v "2021-01-01T01:01:10-06:00"^^xsd:dateTime ] ; ( fhir:note [ fhir:text [ fhir:v "This is a next generation sequencing analysis of a father of a proband." ] ] ) ; # 0..1 The date of the analysis event ( fhir:input [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile3 ; fhir:reference [ fhir:v "DocumentReference/genomicFile3" ] ] ; # 0..* Inputs for the analysis event fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] ) ; # <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]> ( fhir:performer [ fhir:actor [ fhir:l fhir:Practitioner/practitioner02 ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ; # 0..* Performer for the analysis event fhir:role [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ; fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType> ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; ( fhir:device [ fhir:device [ fhir:l fhir:Device/NGS-device ; fhir:reference [ fhir:v "Device/NGS-device" ] ] # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters ] ) # <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function> ] [ ( fhir:identifier [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l <http://example.org/identifiers/genomicAnalyses> ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1114" ] ] ) ; # 0..* De Novo Mutation Analysis fhir:title [ fhir:v "De Novo Mutation Detection and Interpretation" ] ; # <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical> fhir:date [ fhir:v "2021-01-01T03:01:10-06:00"^^xsd:dateTime ] ; # <specimen> 0..1 Reference(Specimen) The specimen used in the analysis event<\/specimen> ( fhir:note [ fhir:text [ fhir:v "This is a next generation sequencing analysis of the comparison analysis of proband and parents sequences." ] ] ) ; # 0..1 The date of the analysis event ( fhir:input [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile1 ; fhir:reference [ fhir:v "DocumentReference/genomicFile1" ] ] ; # 0..* Inputs for the analysis event of Child fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile2 ; fhir:reference [ fhir:v "DocumentReference/genomicFile2" ] ] ; # 0..* Inputs for the analysis event of Mother fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] [ fhir:file [ fhir:l fhir:DocumentReference/genomicFile3 ; fhir:reference [ fhir:v "DocumentReference/genomicFile3" ] ] ; # 0..* Inputs for the analysis event of Father fhir:type [ ( fhir:coding [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] ] ) ; # <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]> ( fhir:performer [ fhir:actor [ fhir:l fhir:Practitioner/practitioner02 ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ; # 0..* Performer for the analysis event fhir:role [ ( fhir:coding [ fhir:system [ fhir:v "http://terminology.hl7.org/CodeSystem/v3-ParticipationType"^^xsd:anyURI ; fhir:l <http://terminology.hl7.org/CodeSystem/v3-ParticipationType> ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; ( fhir:device [ fhir:device [ fhir:l fhir:Device/Triodenovo-SW ; fhir:reference [ fhir:v "Device/Triodenovo-SW" ] ] # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters ] ) # <function>0..1 CodeableConcept Specific function for the device used for the analysis<\/function> ] ) . #
IG © 2026+ HL7 International / Clinical Genomics.
Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3.
Generated
2026-03-24
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