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| Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative | Compartments: Patient |
Raw Turtle (+ also see Turtle/RDF Format Specification)
GenomicStudy - Trio study - De novo mutation 2
@prefix fhir: <http://hl7.org/fhir/> .
@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:GenomicStudy ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "example-trio2"] ; # from Resource: id, meta, implicitRules, and language
fhir:identifier ( [
fhir:use [ fhir:v "temp" ] ;
fhir:system [ fhir:v "http://www.somesystemabc.net/identifiers/genomicstudies"^^xsd:anyURI ] ;
fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1113" ]
] ) ; # from DomainResource: text, contained, extension, and modifierExtension
fhir:status [ fhir:v "available"] ; #
fhir:type ( [
fhir:coding ( [
fhir:code [ fhir:v "trio" ] ;
fhir:display [ fhir:v "Trio-analysis" ]
] )
] ) ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/proband" ]
] ; #
fhir:encounter [
fhir:reference [ fhir:v "Encounter/denovoEncounter" ]
] ; #
fhir:startDate [ fhir:v "2022-05-01"^^xsd:date] ; #
fhir:basedOn ( [
fhir:reference [ fhir:v "ServiceRequest/genomicSRProband" ]
] [
fhir:reference [ fhir:v "ServiceRequest/genomicSRMother" ]
] [
fhir:reference [ fhir:v "ServiceRequest/genomicSRFather" ]
] ) ; #
fhir:referrer [
fhir:reference [ fhir:v "Practitioner/practitioner01" ]
] ; #
fhir:interpreter ( [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]
] ) ; #
fhir:reason ( [
fhir:concept [
fhir:coding ( [
a sct:67799006 ;
fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ] ;
fhir:code [ fhir:v "67799006" ] ;
fhir:display [ fhir:v "Cystic fibrosis, prenatal detection (procedure)" ]
] )
]
] ) ; #
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. The Prenatal Trio Whole Exome Sequencing (Prenatal Trio WES) test is ordered by a physician and must be accompanied with a consent form and detailed clinical information. In general, the test is used when prenatal imaging detects an anomaly that strongly suggests that there is an underlying genetic etiology. Prenatal Trio WES is often considered only after fetal chromosome microarray analysis has been non-diagnostic."] ; #
fhir:analysis ( [
fhir:identifier ( [
fhir:use [ fhir:v "temp" ] ;
fhir:system [ fhir:v "http://www.somesystemabc.net/identifiers/genomicAnalyses"^^xsd:anyURI ] ;
fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1112" ]
] ) ; # 0..* Genomic Analysis Event of mother
fhir:instantiatesUri [ fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI ] ; # <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:reference [ fhir:v "Patient/mother" ]
] ) ; # 0..1 Name of the analysis event (human friendly)
fhir:specimen ( [
fhir:reference [ fhir:v "Specimen/specimenMother" ]
] ) ;
fhir:date [ fhir:v "2022-07-01T01:01:10-06:00"^^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:performer ( [
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]
] ; # 0..* Performer for the analysis event
fhir:role [
fhir:coding ( [
fhir:system [ fhir:v "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"^^xsd:anyURI ] ;
fhir:code [ fhir:v "PRF" ] ;
fhir:display [ fhir:v "Performer" ]
] )
]
] ) ; # <input>\n <file>\n <reference value=\"DocumentReference\/genomicFile2\"\/>\n <\/file>\n <type>\n <coding>\n <code value=\"vcf\"\/>\n <display value=\"VCF\"\/>\n <\/coding>\n <\/type>\n <\/input>
fhir:device ( [
fhir: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://www.somesystemabc.net/identifiers/genomicAnalyses"^^xsd:anyURI ] ;
fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1113" ]
] ) ; # 0..* Genomic Analysis Event of father
fhir:instantiatesUri [ fhir:v "https://pubmed.ncbi.nlm.nih.gov/33927380/"^^xsd:anyURI ] ; # <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:reference [ fhir:v "Patient/father" ]
] ) ;
fhir:specimen ( [
fhir:reference [ fhir:v "Specimen/specimenFather" ]
] ) ;
fhir:date [ fhir:v "2022-07-01T01:01:10-06:00"^^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:performer ( [
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]
] ; # 0..* Performer for the analysis event
fhir:role [
fhir:coding ( [
fhir:system [ fhir:v "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"^^xsd:anyURI ] ;
fhir:code [ fhir:v "PRF" ] ;
fhir:display [ fhir:v "Performer" ]
] )
]
] ) ; # <input>\n <file>\n <reference value=\"DocumentReference\/genomicFile3\"\/>\n <\/file>\n <type>\n <coding>\n <code value=\"vcf\"\/>\n <display value=\"VCF\"\/>\n <\/coding>\n <\/type>\n <\/input>
fhir:device ( [
fhir: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://www.somesystemabc.net/identifiers/genomicAnalyses"^^xsd:anyURI ] ;
fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1114" ]
] ) ; # 0..* De Novo Mutation Analysis
fhir:instantiatesUri [ fhir:v "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885382/"^^xsd:anyURI ] ; # <instantiatesCanonical>0..1 canonical(PlanDefinition) The defined protocol that describes the analysis<\/instantiatesCanonical>
fhir:title [ fhir:v "De Novo Mutation Detection and Interpretation" ] ;
fhir:focus ( [
fhir:reference [ fhir:v "Patient/denovoChild" ]
] [
fhir:reference [ fhir:v "RelatedPerson/relatedPersonDenovoFather" ]
] [
fhir:reference [ fhir:v "RelatedPerson/relatedPersonDenovoMother" ]
] ) ;
fhir:date [ fhir:v "2022-07-01T03:01:10-06:00"^^xsd:dateTime ] ; # 0..1<specimen> 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:reference [ fhir:v "DocumentReference/genomicFileProband" ]
] ; # 0..* Inputs for the analysis event, a combined vcf file
fhir:type [
fhir:coding ( [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "bam" ] ;
fhir:display [ fhir:v "BAM" ]
] )
]
] [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicFileMother" ]
] ; # 0..* Inputs for the analysis event, a combined vcf file
fhir:type [
fhir:coding ( [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "bam" ] ;
fhir:display [ fhir:v "BAM" ]
] )
]
] [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicFileFather" ]
] ; # 0..* Inputs for the analysis event, a combined vcf file
fhir:type [
fhir:coding ( [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "bam" ] ;
fhir:display [ fhir:v "BAM" ]
] )
]
] ) ; # <generatedBy[x]>0..1 Identifier|Reference(GenomicStudy) The analysis event or other GenomicStudy that generated this input file<\/generatedBy[x]>
fhir:output ( [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicFileGroupAsSubject" ]
] ; # 0..* Outputs for the analysis event
fhir:type [
fhir:coding ( [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI ] ;
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]
] )
]
] ) ;
fhir:performer ( [
fhir:actor [
fhir:reference [ fhir:v "Practitioner/practitioner02" ]
] ; # 0..* Performer for the analysis event
fhir:role [
fhir:coding ( [
fhir:system [ fhir:v "http://terminology.hl7.org/3.1.0/CodeSystem-v3-ParticipationType.html"^^xsd:anyURI ] ;
fhir:code [ fhir:v "PRF" ] ;
fhir:display [ fhir:v "Performer" ]
] )
]
] ) ;
fhir:device ( [
fhir:device [
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>
] )] . #
# -------------------------------------------------------------------------------------
Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.
FHIR ®© HL7.org 2011+. FHIR R6 hl7.fhir.core#6.0.0-ballot2 generated on Thu, Nov 14, 2024 10:11+0000.
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