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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 1
@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"] ; # from Resource: id, meta, implicitRules, and language
fhir:text [
fhir:status [ fhir:v "additional" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">This is a genomic study that involves a de novo mutation analysis of a proband, mother, and father. The analysis involves the use use of NGS device and a specilized analysis platform.</div>"
] ; # from DomainResource: text, contained, extension, and modifierExtension
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:1111-1111-1111-1111" ]
] ) ; #
fhir:status [ fhir:v "unknown"] ; #
fhir:type ( [
fhir:coding ( [
fhir:system [ fhir:v "http://hl7.org/fhir/genomicstudy-type"^^xsd:anyURI ] ;
fhir:code [ fhir:v "fam-var-segr" ] ;
fhir:display [ fhir:v "Familial variant segregation" ]
] )
] ) ; #
fhir:subject [
fhir:reference [ fhir:v "Patient/denovoChild" ]
] ; #
fhir:encounter [
fhir:reference [ fhir:v "Encounter/denovoEncounter" ]
] ; #
fhir:startDate [ fhir:v "2021-01-01"^^xsd:date] ; #
fhir:basedOn ( [
fhir:reference [ fhir:v "ServiceRequest/genomicServiceRequest" ]
] ) ; #
fhir:referrer [
fhir:reference [ fhir:v "Practitioner/practitioner01" ]
] ; #
fhir:interpreter ( [
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: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://www.somesystemabc.net/identifiers/genomicAnalyses"^^xsd:anyURI ] ;
fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1111" ]
] ) ; # 0..* Genomic Analysis Event of proband
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 "Proband Sequence Variation Detection Using Next Generation Sequencing" ] ;
fhir:specimen ( [
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:reference [ fhir:v "DocumentReference/genomicFile1" ]
] ; # 0..* Inputs for the analysis event of Child
fhir:type [
fhir:coding ( [
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> , <regionsCalled>0..1 Reference(DocumentReference) Genomic regions actually called in the analysis event (BED file)<\/regionsCalled> , <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: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/NGS-device" ]
] ; # 0..* Devices used for the analysis (e.g., instruments, software), with settings and parameters
fhir:function [
fhir:coding ( [
fhir:display [ fhir:v "Next Generation Sequencing" ]
] )
]
] )
] [
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/denovoMother" ]
] ) ; # 0..1 Name of the analysis event (human friendly)
fhir:specimen ( [
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:reference [ fhir:v "DocumentReference/genomicFile2" ]
] ; # 0..* Inputs for the analysis event of Mother
fhir:type [
fhir:coding ( [
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: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/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/denovoFather" ]
] ) ;
fhir:specimen ( [
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:reference [ fhir:v "DocumentReference/genomicFile3" ]
] ; # 0..* Inputs for the analysis event
fhir:type [
fhir:coding ( [
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: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/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: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:reference [ fhir:v "DocumentReference/genomicFile1" ]
] ; # 0..* Inputs for the analysis event of Child
fhir:type [
fhir:coding ( [
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]
] )
]
] [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicFile2" ]
] ; # 0..* Inputs for the analysis event of Mother
fhir:type [
fhir:coding ( [
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]
] )
]
] [
fhir:file [
fhir:reference [ fhir:v "DocumentReference/genomicFile3" ]
] ; # 0..* Inputs for the analysis event of Father
fhir:type [
fhir:coding ( [
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: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-cibuild generated on Thu, Apr 25, 2024 12:45+0000.
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