Genomics Reporting Implementation Guide
3.0.0 - release International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

: Genomic Study Data Format CodeSystem - TTL Representation

Active as of 2024-11-19

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@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 -------------------------------------------------------------------

 a fhir:CodeSystem ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:id [ fhir:v "genomic-study-data-format-cs"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir: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><a name=\"genomic-study-data-format-cs-en-US\"> </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></tr><tr><td style=\"white-space:nowrap\">bam<a name=\"genomic-study-data-format-cs-bam\"> </a></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></tr><tr><td style=\"white-space:nowrap\">bedpe<a name=\"genomic-study-data-format-cs-bedpe\"> </a></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></tr><tr><td style=\"white-space:nowrap\">bigbed<a name=\"genomic-study-data-format-cs-bigbed\"> </a></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></tr><tr><td style=\"white-space:nowrap\">birdsuite-files<a name=\"genomic-study-data-format-cs-birdsuite-files\"> </a></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></tr><tr><td style=\"white-space:nowrap\">cbs<a name=\"genomic-study-data-format-cs-cbs\"> </a></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></tr><tr><td style=\"white-space:nowrap\">chrom-sizes<a name=\"genomic-study-data-format-cs-chrom-sizes\"> </a></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></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></tr><tr><td style=\"white-space:nowrap\">cytoband<a name=\"genomic-study-data-format-cs-cytoband\"> </a></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></tr><tr><td style=\"white-space:nowrap\">gct<a name=\"genomic-study-data-format-cs-gct\"> </a></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></tr><tr><td style=\"white-space:nowrap\">genepred<a name=\"genomic-study-data-format-cs-genepred\"> </a></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></tr><tr><td style=\"white-space:nowrap\">gistic<a name=\"genomic-study-data-format-cs-gistic\"> </a></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></tr><tr><td style=\"white-space:nowrap\">gwas<a name=\"genomic-study-data-format-cs-gwas\"> </a></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></tr><tr><td style=\"white-space:nowrap\">loh<a name=\"genomic-study-data-format-cs-loh\"> </a></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></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></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></tr><tr><td style=\"white-space:nowrap\">mut<a name=\"genomic-study-data-format-cs-mut\"> </a></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></tr><tr><td style=\"white-space:nowrap\">psl<a name=\"genomic-study-data-format-cs-psl\"> </a></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></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></tr><tr><td style=\"white-space:nowrap\">sam<a name=\"genomic-study-data-format-cs-sam\"> </a></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></tr><tr><td style=\"white-space:nowrap\">seg<a name=\"genomic-study-data-format-cs-seg\"> </a></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></tr><tr><td style=\"white-space:nowrap\">track-line<a name=\"genomic-study-data-format-cs-track-line\"> </a></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></tr><tr><td style=\"white-space:nowrap\">vcf<a name=\"genomic-study-data-format-cs-vcf\"> </a></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></tr></table></div>"
  ] ; # 
  fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [ fhir:v "cg" ]
  ] ) ; # 
  fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "3.0.0"] ; # 
  fhir:name [ fhir:v "GenomicStudyDataFormatCS"] ; # 
  fhir:title [ fhir:v "Genomic Study Data Format CodeSystem"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:experimental [ fhir:v "true"^^xsd:boolean] ; # 
  fhir:date [ fhir:v "2024-11-19T22:01:39+00:00"^^xsd:dateTime] ; # 
  fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; # 
  fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
    ( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ]     ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "cg@lists.HL7.org" ]     ] )
  ] ) ; # 
  fhir:description [ fhir:v "Backport of http://hl7.org/fhir/genomicstudy-dataformat"] ; # 
  fhir:jurisdiction ( [
    ( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ]     ] )
  ] ) ; # 
  fhir:caseSensitive [ fhir:v "true"^^xsd:boolean] ; # 
  fhir:content [ fhir:v "complete"] ; # 
  fhir:count [ fhir:v "40"^^xsd:nonNegativeInteger] ; # 
  fhir:concept ( [
fhir:code [ fhir:v "bam" ] ;
fhir:display [ fhir:v "BAM" ]
  ] [
fhir:code [ fhir:v "bed" ] ;
fhir:display [ fhir:v "BED" ]
  ] [
fhir:code [ fhir:v "bedpe" ] ;
fhir:display [ fhir:v "BEDPE" ]
  ] [
fhir:code [ fhir:v "bedgraph" ] ;
fhir:display [ fhir:v "BedGraph" ]
  ] [
fhir:code [ fhir:v "bigbed" ] ;
fhir:display [ fhir:v "bigBed" ]
  ] [
fhir:code [ fhir:v "bigWig" ] ;
fhir:display [ fhir:v "bigWig" ]
  ] [
fhir:code [ fhir:v "birdsuite-files" ] ;
fhir:display [ fhir:v "Birdsuite-Files" ]
  ] [
fhir:code [ fhir:v "broadpeak" ] ;
fhir:display [ fhir:v "broadPeak" ]
  ] [
fhir:code [ fhir:v "cbs" ] ;
fhir:display [ fhir:v "CBS" ]
  ] [
fhir:code [ fhir:v "chemical-reactivity-probing-profiles" ] ;
fhir:display [ fhir:v "Chemical-Reactivity-Probing-Profiles" ]
  ] [
fhir:code [ fhir:v "chrom-sizes" ] ;
fhir:display [ fhir:v "chrom-sizes" ]
  ] [
fhir:code [ fhir:v "cn" ] ;
fhir:display [ fhir:v "CN" ]
  ] [
fhir:code [ fhir:v "custom-file-formats" ] ;
fhir:display [ fhir:v "Custom-File-Formats" ]
  ] [
fhir:code [ fhir:v "cytoband" ] ;
fhir:display [ fhir:v "Cytoband" ]
  ] [
fhir:code [ fhir:v "fasta" ] ;
fhir:display [ fhir:v "FASTA" ]
  ] [
fhir:code [ fhir:v "gct" ] ;
fhir:display [ fhir:v "GCT" ]
  ] [
fhir:code [ fhir:v "cram" ] ;
fhir:display [ fhir:v "CRAM" ]
  ] [
fhir:code [ fhir:v "genepred" ] ;
fhir:display [ fhir:v "genePred" ]
  ] [
fhir:code [ fhir:v "gff-gtf" ] ;
fhir:display [ fhir:v "GFF/GTF" ]
  ] [
fhir:code [ fhir:v "gistic" ] ;
fhir:display [ fhir:v "GISTIC" ]
  ] [
fhir:code [ fhir:v "goby" ] ;
fhir:display [ fhir:v "Goby" ]
  ] [
fhir:code [ fhir:v "gwas" ] ;
fhir:display [ fhir:v "GWAS" ]
  ] [
fhir:code [ fhir:v "igv" ] ;
fhir:display [ fhir:v "IGV" ]
  ] [
fhir:code [ fhir:v "loh" ] ;
fhir:display [ fhir:v "LOH" ]
  ] [
fhir:code [ fhir:v "maf-multiple-alignment-format" ] ;
fhir:display [ fhir:v "MAF-Multiple Alignment Format" ]
  ] [
fhir:code [ fhir:v "maf-mutation-annotation-format" ] ;
fhir:display [ fhir:v "MAF-Mutation-Annotation-Format" ]
  ] [
fhir:code [ fhir:v "merged-bam-file" ] ;
fhir:display [ fhir:v "Merged BAM File" ]
  ] [
fhir:code [ fhir:v "mut" ] ;
fhir:display [ fhir:v "MUT" ]
  ] [
fhir:code [ fhir:v "narrowpeak" ] ;
fhir:display [ fhir:v "narrowPeak" ]
  ] [
fhir:code [ fhir:v "psl" ] ;
fhir:display [ fhir:v "PSL" ]
  ] [
fhir:code [ fhir:v "res" ] ;
fhir:display [ fhir:v "RES" ]
  ] [
fhir:code [ fhir:v "rna-secondary-structure-formats" ] ;
fhir:display [ fhir:v "RNA-Secondary-Structure-Formats" ]
  ] [
fhir:code [ fhir:v "sam" ] ;
fhir:display [ fhir:v "SAM" ]
  ] [
fhir:code [ fhir:v "sample-info-attributes-file" ] ;
fhir:display [ fhir:v "Sample-Info-Attributes-file" ]
  ] [
fhir:code [ fhir:v "seg" ] ;
fhir:display [ fhir:v "SEG" ]
  ] [
fhir:code [ fhir:v "tdf" ] ;
fhir:display [ fhir:v "TDF" ]
  ] [
fhir:code [ fhir:v "track-line" ] ;
fhir:display [ fhir:v "Track Line" ]
  ] [
fhir:code [ fhir:v "type-line" ] ;
fhir:display [ fhir:v "Type Line" ]
  ] [
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]
  ] [
fhir:code [ fhir:v "wig" ] ;
fhir:display [ fhir:v "WIG" ]
  ] ) . #