@prefix fhir: . @prefix loinc: . @prefix owl: . @prefix rdf: . @prefix rdfs: . @prefix sct: . @prefix xsd: . # - 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-lungMass"] ; # from Resource: id, meta, implicitRules, and language , from DomainResource: text, contained, extension, and modifierExtension fhir:language [ fhir:v "en"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div [ fhir:v "

Generated Narrative: GenomicStudy example-lungMass

Language: en

identifier: http://example.org/identifiers/genomicstudies/urn:uuid:1111-1111-1111-1112 (use: temp, )

status: Registered

type: Sequencing of entire coding region of gene (procedure)

subject: John Junior Doe (official) Unknown, DoB: 2001-01-01 ( Medical record number: 11117 (use: temp, period: 2021-01-01 --> (ongoing)))

encounter: Encounter: status = in-progress; class = inpatient encounter

startDate: 2019-03-01

basedOn: ServiceRequest Carrier detection, molecular genetics (procedure)

referrer: Practitioner John Doel

interpreter: Practitioner Jane Doel

Reasons

-Concept
*Lung mass (finding)

note:

For technical reasons, PIK3CA was deemed uncallable.

\n

description:

Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable.

\n

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1112 (use: official, )

methodType: Nucleic acid sequencing (procedure)

changeType: SNV, MNV, delins

genomeBuild: GRCh38

genomicSourceClass: Somatic

title: Simple variant analysis

specimen: Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

date: 2019-03-01 01:01:10-0600

note:

For technical reasons, PIK3CA was deemed uncallable using this method.

\n

Metrics

-ReadDepthSequencingCoverageDescription
*120 x (Details: UCUM code1 = '1')98 % (Details: UCUM code% = '%')120x average read depth with 98% coverage of target regions.

genomicRegion

type: Studied

Locus

-Reference
*DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

genomicRegion

type: Called

Locus

-Reference
*DocumentReference: identifier = http://example.org/identifiers/files#11118; status = current; docStatus = preliminary; description = SimpleVariantAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

genomicRegion

type: Uncalled

Locus

-Concept
*PIK3CA

Outputs

-Type
*VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer

Devices

-DeviceFunction
*Device: identifier = http://example.org/identifiers/devices#11111; status = active; manufacturer = Illumina; type = Device (physical object)Sequencing

analysis

identifier: http://example.org/identifiers/genomicAnalyses/urn:uuid:1111-1111-1111-1115 (use: official, )

methodType: Nucleic acid sequencing (procedure)

changeType: CNV

genomeBuild: GRCh38

genomicSourceClass: Somatic

title: CNV analysis

specimen: Specimen: identifier = http://example.org/identifiers/specimens#4; status = available; type = Specimen from lung obtained by biopsy (specimen); receivedTime = 2019-03-01 01:01:01+0000

date: 2019-03-01 01:01:10-0600

genomicRegion

type: Studied

Locus

-Reference
*DocumentReference: identifier = http://example.org/identifiers/files#11117; status = current; docStatus = preliminary; description = WES_FullSequencedRegion_GRCh38: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

genomicRegion

type: Called

Locus

-Reference
*DocumentReference: identifier = http://example.org/identifiers/files#11120; status = current; docStatus = preliminary; description = CNVAnalysis_called: A sample Document Reference instance representing a BED file that may be used as input or output of a genomic analysis pipeline.

genomicRegion

type: Uncalled

Locus

-Concept
*PIK3CA

description: PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay.

Outputs

-Type
*VCF

Performers

-ActorRole
*Practitioner Jane Doel Performer
"^^rdf:XMLLiteral ] ] ; # fhir:identifier ( [ fhir:use [ fhir:v "temp" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicstudies"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1112" ] ] ) ; # from DomainResource: text, contained, extension, and modifierExtension fhir:status [ fhir:v "registered"] ; # fhir:type ( [ fhir:coding ( [ a sct:443968007 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "443968007" ] ; fhir:display [ fhir:v "Sequencing of entire coding region of gene (procedure)" ] ] ) ] ) ; # fhir:subject [ fhir:l ; fhir:reference [ fhir:v "Patient/genomicPatient" ] ] ; # fhir:encounter [ fhir:l ; fhir:reference [ fhir:v "Encounter/genomicEncounter" ] ] ; # fhir:startDate [ fhir:v "2019-03-01"^^xsd:date] ; # fhir:basedOn ( [ fhir:l ; fhir:reference [ fhir:v "ServiceRequest/genomicServiceRequest2" ] ] ) ; # fhir:referrer [ fhir:l ; fhir:reference [ fhir:v "Practitioner/practitioner01" ] ] ; # fhir:interpreter ( [ fhir:l ; fhir:reference [ fhir:v "Practitioner/practitioner02" ] ] ) ; # fhir:reason ( [ fhir:concept [ fhir:coding ( [ a sct:309529002 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "309529002" ] ; fhir:display [ fhir:v "Lung mass (finding)" ] ] ) ] ] ) ; # fhir:note ( [ fhir:text [ fhir:v "For technical reasons, PIK3CA was deemed uncallable." ] ] ) ; # fhir:description [ fhir:v "Whole exome sequencing of lung biopsy. 300 genes are examined for simple variants (SNV, MNV, InDel), and 170 genes are also examined for CNVs. For technical reasons, PIK3CA was deemed uncallable."] ; # fhir:analysis ( [ fhir:identifier ( [ fhir:use [ fhir:v "official" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1112" ] ] ) ; fhir:methodType ( [ fhir:coding ( [ a sct:117040002 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "117040002" ] ; fhir:display [ fhir:v "Nucleic acid sequencing (procedure)" ] ] ) ] ) ; fhir:changeType ( [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:0001483" ] ; fhir:display [ fhir:v "SNV" ] ] ) ] [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:0002007" ] ; fhir:display [ fhir:v "MNV" ] ] ) ] [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:1000032" ] ; fhir:display [ fhir:v "delins" ] ] ) ] ) ; fhir:genomeBuild [ fhir:coding ( [ a loinc:LA26806-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA26806-2" ] ; fhir:display [ fhir:v "GRCh38" ] ] ) ] ; fhir:genomicSourceClass [ fhir:coding ( [ a loinc:LA6684-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA6684-0" ] ; fhir:display [ fhir:v "Somatic" ] ] ) ] ; fhir:title [ fhir:v "Simple variant analysis" ] ; fhir:specimen ( [ fhir:l ; fhir:reference [ fhir:v "Specimen/genomicSpecimen" ] ] ) ; # 0..1 Name of the analysis event (human friendly) fhir:date [ fhir:v "2019-03-01T01:01:10-06:00"^^xsd:dateTime ] ; fhir:note ( [ fhir:text [ fhir:v "For technical reasons, PIK3CA was deemed uncallable using this method." ] ] ) ; # 0..1 The date of the analysis event fhir:metrics [ fhir:readDepth [ fhir:value [ fhir:v "120"^^xsd:decimal ] ; fhir:unit [ fhir:v "x" ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "1" ] ] ; fhir:sequencingCoverage [ fhir:value [ fhir:v "98"^^xsd:decimal ] ; fhir:unit [ fhir:v "%" ] ; fhir:system [ fhir:v "http://unitsofmeasure.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "%" ] ] ; fhir:description [ fhir:v "120x average read depth with 98% coverage of target regions." ] ] ; fhir:genomicRegion ( [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "studied" ] ; fhir:display [ fhir:v "Studied" ] ] ) ] ; fhir:locus ( [ fhir:reference [ fhir:l ; fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ] ] ] ) ] [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "called" ] ; fhir:display [ fhir:v "Called" ] ] ) ] ; fhir:locus ( [ fhir:reference [ fhir:l ; fhir:reference [ fhir:v "DocumentReference/SimpleVariantAnalysis-called" ] ] ] ) ] [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "uncalled" ] ; fhir:display [ fhir:v "Uncalled" ] ] ) ] ; fhir:locus ( [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:8975" ] ; fhir:display [ fhir:v "PIK3CA" ] ] ) ] ] ) ] ) ; # genomicRegion: studied scope = full exome BED file fhir:output ( [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] # 0..* outputs for the analysis event , \n \n <\/file> ] ) ; fhir:performer ( [ fhir:actor [ fhir:l ; 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 ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ; fhir:device ( [ fhir:device [ fhir:l ; 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 ] ; fhir:code [ fhir:v "LA26398-0" ] ; fhir:display [ fhir:v "Sequencing" ] ] ) ] ] ) ] [ fhir:identifier ( [ fhir:use [ fhir:v "official" ] ; fhir:system [ fhir:v "http://example.org/identifiers/genomicAnalyses"^^xsd:anyURI ; fhir:l ] ; fhir:value [ fhir:v "urn:uuid:1111-1111-1111-1115" ] ] ) ; fhir:methodType ( [ fhir:coding ( [ a sct:117040002 ; fhir:system [ fhir:v "http://snomed.info/sct"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "117040002" ] ; fhir:display [ fhir:v "Nucleic acid sequencing (procedure)" ] ] ) ] ) ; fhir:changeType ( [ fhir:coding ( [ fhir:system [ fhir:v "http://www.sequenceontology.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "SO:0001019" ] ; fhir:display [ fhir:v "CNV" ] ] ) ] ) ; fhir:genomeBuild [ fhir:coding ( [ a loinc:LA26806-2 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA26806-2" ] ; fhir:display [ fhir:v "GRCh38" ] ] ) ] ; fhir:genomicSourceClass [ fhir:coding ( [ a loinc:LA6684-0 ; fhir:system [ fhir:v "http://loinc.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "LA6684-0" ] ; fhir:display [ fhir:v "Somatic" ] ] ) ] ; fhir:title [ fhir:v "CNV analysis" ] ; fhir:specimen ( [ fhir:l ; fhir:reference [ fhir:v "Specimen/genomicSpecimen" ] ] ) ; # 0..1 Name of the analysis event (human friendly) fhir:date [ fhir:v "2019-03-01T01:01:10-06:00"^^xsd:dateTime ] ; fhir:genomicRegion ( [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "studied" ] ; fhir:display [ fhir:v "Studied" ] ] ) ] ; fhir:locus ( [ fhir:reference [ fhir:l ; fhir:reference [ fhir:v "DocumentReference/WES-FullSequencedRegion-GRCh38" ] ] ] ) ] [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "called" ] ; fhir:display [ fhir:v "Called" ] ] ) ] ; fhir:locus ( [ fhir:reference [ fhir:l ; fhir:reference [ fhir:v "DocumentReference/CNVAnalysis-called" ] ] ] ) ] [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-regiontype"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "uncalled" ] ; fhir:display [ fhir:v "Uncalled" ] ] ) ] ; fhir:locus ( [ fhir:concept [ fhir:coding ( [ fhir:system [ fhir:v "http://www.genenames.org"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "HGNC:8975" ] ; fhir:display [ fhir:v "PIK3CA" ] ] ) ] ] ) ; fhir:description [ fhir:v "PIK3CA was deemed uncallable using this CNV method due to technical limitations of the assay." ] ] ) ; # 0..1 The date of the analysis event , genomicRegion: studied scope = full exome BED file fhir:output ( [ fhir:type [ fhir:coding ( [ fhir:system [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l ] ; fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ] ) ] # 0..* Inputs for the analysis event , \n \n <\/file> ] ) ; fhir:performer ( [ fhir:actor [ fhir:l ; 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 ] ; fhir:code [ fhir:v "PRF" ] ; fhir:display [ fhir:v "Performer" ] ] ) ] ] ) ] ) . # 0..1 Description of the genomic study a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . a fhir:Uv . # -------------------------------------------------------------------------------------