Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
| Page standards status: Informative |
@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 -------------------------------------------------------------------
<http://hl7.org/fhir/Procedure/genomicstudyanalysis-trio2> a fhir:Procedure ;
fhir:nodeRole fhir:treeRoot ;
fhir:Resource.id [ fhir:value "genomicstudyanalysis-trio2"] ;
fhir:Resource.meta [
fhir:Meta.profile [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis" ;
fhir:index 0 ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis>
]
] ;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "extensions" ] ;
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Procedure genomicstudyanalysis-trio2</b></p><a name=\"genomicstudyanalysis-trio2\"> </a><a name=\"hcgenomicstudyanalysis-trio2\"> </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\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-genomic-study-analysis.html\">Genomic Study Analysis</a></p></div><p><b>Genomic Study Analysis Genome Build</b>: <span title=\"Codes:{http://loinc.org LA26806-2}\">GRCh38</span></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoFather.html\">Father Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 6789-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Focus</b>: <a href=\"Patient-denovoMother.html\">Mother Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 0987-11111 (use: temp, ))</a></p><p><b>Genomic Study Analysis Title</b>: Parental Sequence Variation Detection Using Next Generation Sequencing</p><p><b>Genomic Study Analysis Protocol Performed</b>: <a href=\"Procedure-SequencingProcedure.html\">Procedure Sequencing of entire coding region of gene (procedure)</a></p><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11118; 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.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileMotherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11125; 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.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Input</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileFatherBAM.html\">DocumentReference: identifier = http://example.org/identifiers/files#11132; 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.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs bam}\">BAM</span></li></ul></blockquote><blockquote><p><b>Genomic Study Analysis Output</b></p><ul><li>file: <a href=\"DocumentReference-genomicFileProbandVCF.html\">DocumentReference: identifier = http://example.org/identifiers/files#11150; 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.; securityLabel = Restricted</a></li><li>type: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs vcf}\">VCF</span></li></ul></blockquote><p><b>instantiatesUri</b>: <a href=\"https://pubmed.ncbi.nlm.nih.gov/33927380/\">https://pubmed.ncbi.nlm.nih.gov/33927380/</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>subject</b>: <a href=\"Patient-denovoChild.html\">Child Denovo (official) (no stated gender), DoB Unknown ( Medical record number: 1234-11111 (use: temp, ))</a></p><p><b>performed</b>: 2023-10-01</p></div>"
] ;
fhir:DomainResource.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
a loinc:LA26806-2 ;
fhir:Coding.system [ fhir:value "http://loinc.org" ] ;
fhir:Coding.code [ fhir:value "LA26806-2" ] ;
fhir:Coding.display [ fhir:value "GRCh38" ]
]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Patient/denovoFather> ;
fhir:Reference.reference [ fhir:value "Patient/denovoFather" ]
]
], [
fhir:index 2 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Patient/denovoMother> ;
fhir:Reference.reference [ fhir:value "Patient/denovoMother" ]
]
], [
fhir:index 3 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title" ] ;
fhir:Extension.valueString [ fhir:value "Parental Sequence Variation Detection Using Next Generation Sequencing" ]
], [
fhir:index 4 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/Procedure/SequencingProcedure> ;
fhir:Reference.reference [ fhir:value "Procedure/SequencingProcedure" ]
]
], [
fhir:index 5 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "file" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/genomicFileProbandBAM> ;
fhir:Reference.reference [ fhir:value "DocumentReference/genomicFileProbandBAM" ]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs" ] ;
fhir:Coding.code [ fhir:value "bam" ] ;
fhir:Coding.display [ fhir:value "BAM" ]
]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input" ]
], [
fhir:index 6 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "file" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/genomicFileMotherBAM> ;
fhir:Reference.reference [ fhir:value "DocumentReference/genomicFileMotherBAM" ]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs" ] ;
fhir:Coding.code [ fhir:value "bam" ] ;
fhir:Coding.display [ fhir:value "BAM" ]
]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input" ]
], [
fhir:index 7 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "file" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/genomicFileFatherBAM> ;
fhir:Reference.reference [ fhir:value "DocumentReference/genomicFileFatherBAM" ]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs" ] ;
fhir:Coding.code [ fhir:value "bam" ] ;
fhir:Coding.display [ fhir:value "BAM" ]
]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input" ]
], [
fhir:index 8 ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "file" ] ;
fhir:Extension.valueReference [
fhir:link <http://hl7.org/fhir/DocumentReference/genomicFileProbandVCF> ;
fhir:Reference.reference [ fhir:value "DocumentReference/genomicFileProbandVCF" ]
]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "type" ] ;
fhir:Extension.valueCodeableConcept [
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs" ] ;
fhir:Coding.code [ fhir:value "vcf" ] ;
fhir:Coding.display [ fhir:value "VCF" ]
]
]
] ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output" ]
] ;
fhir:Procedure.instantiatesUri [
fhir:value "https://pubmed.ncbi.nlm.nih.gov/33927380/" ;
fhir:index 0
] ;
fhir:Procedure.status [ fhir:value "completed"] ;
fhir:Procedure.category [
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:Procedure.subject [
fhir:link <http://hl7.org/fhir/Patient/denovoChild> ;
fhir:Reference.reference [ fhir:value "Patient/denovoChild" ]
] ;
fhir:Procedure.performedDateTime [ fhir:value "2023-10-01"^^xsd:date] .
<http://hl7.org/fhir/Patient/denovoFather> a fhir:Patient .
<http://hl7.org/fhir/Patient/denovoMother> a fhir:Patient .
<http://hl7.org/fhir/Procedure/SequencingProcedure> a fhir:Procedure .
<http://hl7.org/fhir/DocumentReference/genomicFileProbandBAM> a fhir:DocumentReference .
<http://hl7.org/fhir/DocumentReference/genomicFileMotherBAM> a fhir:DocumentReference .
<http://hl7.org/fhir/DocumentReference/genomicFileFatherBAM> a fhir:DocumentReference .
<http://hl7.org/fhir/DocumentReference/genomicFileProbandVCF> a fhir:DocumentReference .
<http://hl7.org/fhir/Patient/denovoChild> a fhir:Patient .
# - ontology header ------------------------------------------------------------
<http://hl7.org/fhir/Procedure/genomicstudyanalysis-trio2.ttl> a owl:Ontology ;
owl:imports fhir:fhir.ttl ;
owl:versionIRI <http://build.fhir.org/Procedure/genomicstudyanalysis-trio2.ttl> .
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-09-21
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