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 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/CodeSystem/genomic-study-data-format-cs> a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:Resource.id [ fhir:value "genomic-study-data-format-cs"] ;
fhir:DomainResource.text [
fhir:Narrative.status [ fhir:value "generated" ] ;
fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem genomic-study-data-format-cs</b></p><a name=\"genomic-study-data-format-cs\"> </a><a name=\"hcgenomic-study-data-format-cs\"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">bam<a name=\"genomic-study-data-format-cs-bam\"> </a></td><td>BAM</td><td>BAM</td></tr><tr><td style=\"white-space:nowrap\">bed<a name=\"genomic-study-data-format-cs-bed\"> </a></td><td>BED</td><td>BED</td></tr><tr><td style=\"white-space:nowrap\">bedpe<a name=\"genomic-study-data-format-cs-bedpe\"> </a></td><td>BEDPE</td><td>BEDPE</td></tr><tr><td style=\"white-space:nowrap\">bedgraph<a name=\"genomic-study-data-format-cs-bedgraph\"> </a></td><td>BedGraph</td><td>BedGraph</td></tr><tr><td style=\"white-space:nowrap\">bigbed<a name=\"genomic-study-data-format-cs-bigbed\"> </a></td><td>bigBed</td><td>bigBed</td></tr><tr><td style=\"white-space:nowrap\">bigWig<a name=\"genomic-study-data-format-cs-bigWig\"> </a></td><td>bigWig</td><td>bigWig</td></tr><tr><td style=\"white-space:nowrap\">birdsuite-files<a name=\"genomic-study-data-format-cs-birdsuite-files\"> </a></td><td>Birdsuite-Files</td><td>Birdsuite-Files</td></tr><tr><td style=\"white-space:nowrap\">broadpeak<a name=\"genomic-study-data-format-cs-broadpeak\"> </a></td><td>broadPeak</td><td>broadPeak</td></tr><tr><td style=\"white-space:nowrap\">cbs<a name=\"genomic-study-data-format-cs-cbs\"> </a></td><td>CBS</td><td>CBS</td></tr><tr><td style=\"white-space:nowrap\">chemical-reactivity-probing-profiles<a name=\"genomic-study-data-format-cs-chemical-reactivity-probing-profiles\"> </a></td><td>Chemical-Reactivity-Probing-Profiles</td><td>Chemical-Reactivity-Probing-Profiles</td></tr><tr><td style=\"white-space:nowrap\">chrom-sizes<a name=\"genomic-study-data-format-cs-chrom-sizes\"> </a></td><td>chrom-sizes</td><td>chrom-sizes</td></tr><tr><td style=\"white-space:nowrap\">cn<a name=\"genomic-study-data-format-cs-cn\"> </a></td><td>CN</td><td>CN</td></tr><tr><td style=\"white-space:nowrap\">custom-file-formats<a name=\"genomic-study-data-format-cs-custom-file-formats\"> </a></td><td>Custom-File-Formats</td><td>Custom-File-Formats</td></tr><tr><td style=\"white-space:nowrap\">cytoband<a name=\"genomic-study-data-format-cs-cytoband\"> </a></td><td>Cytoband</td><td>Cytoband</td></tr><tr><td style=\"white-space:nowrap\">fasta<a name=\"genomic-study-data-format-cs-fasta\"> </a></td><td>FASTA</td><td>FASTA</td></tr><tr><td style=\"white-space:nowrap\">gct<a name=\"genomic-study-data-format-cs-gct\"> </a></td><td>GCT</td><td>GCT</td></tr><tr><td style=\"white-space:nowrap\">cram<a name=\"genomic-study-data-format-cs-cram\"> </a></td><td>CRAM</td><td>CRAM</td></tr><tr><td style=\"white-space:nowrap\">genepred<a name=\"genomic-study-data-format-cs-genepred\"> </a></td><td>genePred</td><td>genePred</td></tr><tr><td style=\"white-space:nowrap\">gff-gtf<a name=\"genomic-study-data-format-cs-gff-gtf\"> </a></td><td>GFF/GTF</td><td>GFF/GTF</td></tr><tr><td style=\"white-space:nowrap\">gistic<a name=\"genomic-study-data-format-cs-gistic\"> </a></td><td>GISTIC</td><td>GISTIC</td></tr><tr><td style=\"white-space:nowrap\">goby<a name=\"genomic-study-data-format-cs-goby\"> </a></td><td>Goby</td><td>Goby</td></tr><tr><td style=\"white-space:nowrap\">gwas<a name=\"genomic-study-data-format-cs-gwas\"> </a></td><td>GWAS</td><td>GWAS</td></tr><tr><td style=\"white-space:nowrap\">igv<a name=\"genomic-study-data-format-cs-igv\"> </a></td><td>IGV</td><td>IGV</td></tr><tr><td style=\"white-space:nowrap\">loh<a name=\"genomic-study-data-format-cs-loh\"> </a></td><td>LOH</td><td>LOH</td></tr><tr><td style=\"white-space:nowrap\">maf-multiple-alignment-format<a name=\"genomic-study-data-format-cs-maf-multiple-alignment-format\"> </a></td><td>MAF-Multiple Alignment Format</td><td>MAF-Multiple Alignment Format</td></tr><tr><td style=\"white-space:nowrap\">maf-mutation-annotation-format<a name=\"genomic-study-data-format-cs-maf-mutation-annotation-format\"> </a></td><td>MAF-Mutation-Annotation-Format</td><td>MAF-Mutation-Annotation-Format</td></tr><tr><td style=\"white-space:nowrap\">merged-bam-file<a name=\"genomic-study-data-format-cs-merged-bam-file\"> </a></td><td>Merged BAM File</td><td>Merged BAM File</td></tr><tr><td style=\"white-space:nowrap\">mut<a name=\"genomic-study-data-format-cs-mut\"> </a></td><td>MUT</td><td>MUT</td></tr><tr><td style=\"white-space:nowrap\">narrowpeak<a name=\"genomic-study-data-format-cs-narrowpeak\"> </a></td><td>narrowPeak</td><td>narrowPeak</td></tr><tr><td style=\"white-space:nowrap\">psl<a name=\"genomic-study-data-format-cs-psl\"> </a></td><td>PSL</td><td>PSL</td></tr><tr><td style=\"white-space:nowrap\">res<a name=\"genomic-study-data-format-cs-res\"> </a></td><td>RES</td><td>RES</td></tr><tr><td style=\"white-space:nowrap\">rna-secondary-structure-formats<a name=\"genomic-study-data-format-cs-rna-secondary-structure-formats\"> </a></td><td>RNA-Secondary-Structure-Formats</td><td>RNA-Secondary-Structure-Formats</td></tr><tr><td style=\"white-space:nowrap\">sam<a name=\"genomic-study-data-format-cs-sam\"> </a></td><td>SAM</td><td>SAM</td></tr><tr><td style=\"white-space:nowrap\">sample-info-attributes-file<a name=\"genomic-study-data-format-cs-sample-info-attributes-file\"> </a></td><td>Sample-Info-Attributes-file</td><td>Sample-Info-Attributes-file</td></tr><tr><td style=\"white-space:nowrap\">seg<a name=\"genomic-study-data-format-cs-seg\"> </a></td><td>SEG</td><td>SEG</td></tr><tr><td style=\"white-space:nowrap\">tdf<a name=\"genomic-study-data-format-cs-tdf\"> </a></td><td>TDF</td><td>TDF</td></tr><tr><td style=\"white-space:nowrap\">track-line<a name=\"genomic-study-data-format-cs-track-line\"> </a></td><td>Track Line</td><td>Track Line</td></tr><tr><td style=\"white-space:nowrap\">type-line<a name=\"genomic-study-data-format-cs-type-line\"> </a></td><td>Type Line</td><td>Type Line</td></tr><tr><td style=\"white-space:nowrap\">vcf<a name=\"genomic-study-data-format-cs-vcf\"> </a></td><td>VCF</td><td>VCF</td></tr><tr><td style=\"white-space:nowrap\">wig<a name=\"genomic-study-data-format-cs-wig\"> </a></td><td>WIG</td><td>WIG</td></tr></table></div>"
] ;
fhir:DomainResource.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ] ;
fhir:Extension.valueCode [ fhir:value "cg" ]
], [
fhir:index 1 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status" ] ;
fhir:Extension.valueCode [
fhir:value "informative" ;
fhir:Element.extension [
fhir:index 0 ;
fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom" ] ;
fhir:Extension.valueCanonical [
fhir:value "http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting" ;
fhir:link <http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting>
]
]
]
] ;
fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"] ;
fhir:CodeSystem.version [ fhir:value "4.0.0-cibuild"] ;
fhir:CodeSystem.name [ fhir:value "GenomicStudyDataFormatCS"] ;
fhir:CodeSystem.title [ fhir:value "Genomic Study Data Format CodeSystem"] ;
fhir:CodeSystem.status [ fhir:value "active"] ;
fhir:CodeSystem.experimental [ fhir:value "true"^^xsd:boolean] ;
fhir:CodeSystem.date [ fhir:value "2026-09-21T13:24:35+00:00"^^xsd:dateTime] ;
fhir:CodeSystem.publisher [ fhir:value "HL7 International / Clinical Genomics"] ;
fhir:CodeSystem.contact [
fhir:index 0 ;
fhir:ContactDetail.name [ fhir:value "HL7 International / Clinical Genomics" ] ;
fhir:ContactDetail.telecom [
fhir:index 0 ;
fhir:ContactPoint.system [ fhir:value "url" ] ;
fhir:ContactPoint.value [ fhir:value "http://www.hl7.org/Special/committees/clingenomics" ]
], [
fhir:index 1 ;
fhir:ContactPoint.system [ fhir:value "email" ] ;
fhir:ContactPoint.value [ fhir:value "cg@lists.HL7.org" ]
]
] ;
fhir:CodeSystem.description [ fhir:value "Backport of http://hl7.org/fhir/genomicstudy-dataformat"] ;
fhir:CodeSystem.jurisdiction [
fhir:index 0 ;
fhir:CodeableConcept.coding [
fhir:index 0 ;
fhir:Coding.system [ fhir:value "http://unstats.un.org/unsd/methods/m49/m49.htm" ] ;
fhir:Coding.code [ fhir:value "001" ] ;
fhir:Coding.display [ fhir:value "World" ]
]
] ;
fhir:CodeSystem.caseSensitive [ fhir:value "true"^^xsd:boolean] ;
fhir:CodeSystem.content [ fhir:value "complete"] ;
fhir:CodeSystem.count [ fhir:value "40"^^xsd:nonNegativeInteger] ;
fhir:CodeSystem.concept [
fhir:index 0 ;
fhir:CodeSystem.concept.code [ fhir:value "bam" ] ;
fhir:CodeSystem.concept.display [ fhir:value "BAM" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "BAM" ]
], [
fhir:index 1 ;
fhir:CodeSystem.concept.code [ fhir:value "bed" ] ;
fhir:CodeSystem.concept.display [ fhir:value "BED" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "BED" ]
], [
fhir:index 2 ;
fhir:CodeSystem.concept.code [ fhir:value "bedpe" ] ;
fhir:CodeSystem.concept.display [ fhir:value "BEDPE" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "BEDPE" ]
], [
fhir:index 3 ;
fhir:CodeSystem.concept.code [ fhir:value "bedgraph" ] ;
fhir:CodeSystem.concept.display [ fhir:value "BedGraph" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "BedGraph" ]
], [
fhir:index 4 ;
fhir:CodeSystem.concept.code [ fhir:value "bigbed" ] ;
fhir:CodeSystem.concept.display [ fhir:value "bigBed" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "bigBed" ]
], [
fhir:index 5 ;
fhir:CodeSystem.concept.code [ fhir:value "bigWig" ] ;
fhir:CodeSystem.concept.display [ fhir:value "bigWig" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "bigWig" ]
], [
fhir:index 6 ;
fhir:CodeSystem.concept.code [ fhir:value "birdsuite-files" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Birdsuite-Files" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Birdsuite-Files" ]
], [
fhir:index 7 ;
fhir:CodeSystem.concept.code [ fhir:value "broadpeak" ] ;
fhir:CodeSystem.concept.display [ fhir:value "broadPeak" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "broadPeak" ]
], [
fhir:index 8 ;
fhir:CodeSystem.concept.code [ fhir:value "cbs" ] ;
fhir:CodeSystem.concept.display [ fhir:value "CBS" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "CBS" ]
], [
fhir:index 9 ;
fhir:CodeSystem.concept.code [ fhir:value "chemical-reactivity-probing-profiles" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Chemical-Reactivity-Probing-Profiles" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Chemical-Reactivity-Probing-Profiles" ]
], [
fhir:index 10 ;
fhir:CodeSystem.concept.code [ fhir:value "chrom-sizes" ] ;
fhir:CodeSystem.concept.display [ fhir:value "chrom-sizes" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "chrom-sizes" ]
], [
fhir:index 11 ;
fhir:CodeSystem.concept.code [ fhir:value "cn" ] ;
fhir:CodeSystem.concept.display [ fhir:value "CN" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "CN" ]
], [
fhir:index 12 ;
fhir:CodeSystem.concept.code [ fhir:value "custom-file-formats" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Custom-File-Formats" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Custom-File-Formats" ]
], [
fhir:index 13 ;
fhir:CodeSystem.concept.code [ fhir:value "cytoband" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Cytoband" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Cytoband" ]
], [
fhir:index 14 ;
fhir:CodeSystem.concept.code [ fhir:value "fasta" ] ;
fhir:CodeSystem.concept.display [ fhir:value "FASTA" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "FASTA" ]
], [
fhir:index 15 ;
fhir:CodeSystem.concept.code [ fhir:value "gct" ] ;
fhir:CodeSystem.concept.display [ fhir:value "GCT" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "GCT" ]
], [
fhir:index 16 ;
fhir:CodeSystem.concept.code [ fhir:value "cram" ] ;
fhir:CodeSystem.concept.display [ fhir:value "CRAM" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "CRAM" ]
], [
fhir:index 17 ;
fhir:CodeSystem.concept.code [ fhir:value "genepred" ] ;
fhir:CodeSystem.concept.display [ fhir:value "genePred" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "genePred" ]
], [
fhir:index 18 ;
fhir:CodeSystem.concept.code [ fhir:value "gff-gtf" ] ;
fhir:CodeSystem.concept.display [ fhir:value "GFF/GTF" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "GFF/GTF" ]
], [
fhir:index 19 ;
fhir:CodeSystem.concept.code [ fhir:value "gistic" ] ;
fhir:CodeSystem.concept.display [ fhir:value "GISTIC" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "GISTIC" ]
], [
fhir:index 20 ;
fhir:CodeSystem.concept.code [ fhir:value "goby" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Goby" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Goby" ]
], [
fhir:index 21 ;
fhir:CodeSystem.concept.code [ fhir:value "gwas" ] ;
fhir:CodeSystem.concept.display [ fhir:value "GWAS" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "GWAS" ]
], [
fhir:index 22 ;
fhir:CodeSystem.concept.code [ fhir:value "igv" ] ;
fhir:CodeSystem.concept.display [ fhir:value "IGV" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "IGV" ]
], [
fhir:index 23 ;
fhir:CodeSystem.concept.code [ fhir:value "loh" ] ;
fhir:CodeSystem.concept.display [ fhir:value "LOH" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "LOH" ]
], [
fhir:index 24 ;
fhir:CodeSystem.concept.code [ fhir:value "maf-multiple-alignment-format" ] ;
fhir:CodeSystem.concept.display [ fhir:value "MAF-Multiple Alignment Format" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "MAF-Multiple Alignment Format" ]
], [
fhir:index 25 ;
fhir:CodeSystem.concept.code [ fhir:value "maf-mutation-annotation-format" ] ;
fhir:CodeSystem.concept.display [ fhir:value "MAF-Mutation-Annotation-Format" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "MAF-Mutation-Annotation-Format" ]
], [
fhir:index 26 ;
fhir:CodeSystem.concept.code [ fhir:value "merged-bam-file" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Merged BAM File" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Merged BAM File" ]
], [
fhir:index 27 ;
fhir:CodeSystem.concept.code [ fhir:value "mut" ] ;
fhir:CodeSystem.concept.display [ fhir:value "MUT" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "MUT" ]
], [
fhir:index 28 ;
fhir:CodeSystem.concept.code [ fhir:value "narrowpeak" ] ;
fhir:CodeSystem.concept.display [ fhir:value "narrowPeak" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "narrowPeak" ]
], [
fhir:index 29 ;
fhir:CodeSystem.concept.code [ fhir:value "psl" ] ;
fhir:CodeSystem.concept.display [ fhir:value "PSL" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "PSL" ]
], [
fhir:index 30 ;
fhir:CodeSystem.concept.code [ fhir:value "res" ] ;
fhir:CodeSystem.concept.display [ fhir:value "RES" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "RES" ]
], [
fhir:index 31 ;
fhir:CodeSystem.concept.code [ fhir:value "rna-secondary-structure-formats" ] ;
fhir:CodeSystem.concept.display [ fhir:value "RNA-Secondary-Structure-Formats" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "RNA-Secondary-Structure-Formats" ]
], [
fhir:index 32 ;
fhir:CodeSystem.concept.code [ fhir:value "sam" ] ;
fhir:CodeSystem.concept.display [ fhir:value "SAM" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "SAM" ]
], [
fhir:index 33 ;
fhir:CodeSystem.concept.code [ fhir:value "sample-info-attributes-file" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Sample-Info-Attributes-file" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Sample-Info-Attributes-file" ]
], [
fhir:index 34 ;
fhir:CodeSystem.concept.code [ fhir:value "seg" ] ;
fhir:CodeSystem.concept.display [ fhir:value "SEG" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "SEG" ]
], [
fhir:index 35 ;
fhir:CodeSystem.concept.code [ fhir:value "tdf" ] ;
fhir:CodeSystem.concept.display [ fhir:value "TDF" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "TDF" ]
], [
fhir:index 36 ;
fhir:CodeSystem.concept.code [ fhir:value "track-line" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Track Line" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Track Line" ]
], [
fhir:index 37 ;
fhir:CodeSystem.concept.code [ fhir:value "type-line" ] ;
fhir:CodeSystem.concept.display [ fhir:value "Type Line" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "Type Line" ]
], [
fhir:index 38 ;
fhir:CodeSystem.concept.code [ fhir:value "vcf" ] ;
fhir:CodeSystem.concept.display [ fhir:value "VCF" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "VCF" ]
], [
fhir:index 39 ;
fhir:CodeSystem.concept.code [ fhir:value "wig" ] ;
fhir:CodeSystem.concept.display [ fhir:value "WIG" ] ;
fhir:CodeSystem.concept.definition [ fhir:value "WIG" ]
] .
# - ontology header ------------------------------------------------------------
<http://hl7.org/fhir/CodeSystem/genomic-study-data-format-cs.ttl> a owl:Ontology ;
owl:imports fhir:fhir.ttl ;
owl:versionIRI <http://build.fhir.org/CodeSystem/genomic-study-data-format-cs.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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