Release 5

This page is part of the FHIR Specification (v5.0.0: R5 - STU). This is the current published version in it's permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Example CodeSystem/genomicstudy-dataformat (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: Informative

Raw Turtle (+ also see Turtle/RDF Format Specification)

Definition for Code SystemGenomicStudyDataFormat

@prefix fhir: <http://hl7.org/fhir/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

# - resource -------------------------------------------------------------------

[] a fhir:CodeSystem ;
  fhir:id [ fhir:v "genomicstudy-dataformat"] ;
  fhir:meta [
     fhir:lastUpdated [ fhir:v "2023-03-26T15:21:02.749+11:00" ] ;
     fhir:profile ( [ fhir:v "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ] )
  ] ;
  fhir:text [
     fhir:status [ fhir:v "generated" ]
  ] ;
  fhir:extension ( [
     fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ] ;
     fhir:value [ fhir:v "cg" ]
  ] [
     fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status" ] ;
     fhir:value [ fhir:v "trial-use" ]
  ] [
     fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm" ] ;
     fhir:value [ fhir:v "1" ]
  ] ) ;
  fhir:url [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"], [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"] ;
  fhir:identifier ( [
     fhir:system [ fhir:v "urn:ietf:rfc:3986" ] ;
     fhir:value [ fhir:v "urn:oid:2.16.840.1.113883.4.642.4.1978" ]
  ] [
     fhir:system [ fhir:v "urn:ietf:rfc:3986" ] ;
     fhir:value [ fhir:v "urn:oid:2.16.840.1.113883.4.642.4.1978" ]
  ] ) ;
  fhir:version [ fhir:v "5.0.0"], [ fhir:v "5.0.0"] ;
  fhir:name [ fhir:v "GenomicStudyDataFormat"], [ fhir:v "GenomicStudyDataFormat"] ;
  fhir:title [ fhir:v "Genomic Study Data Format"], [ fhir:v "Genomic Study Data Format"] ;
  fhir:status [ fhir:v "active"], [ fhir:v "active"] ;
  fhir:experimental [ fhir:v "true"], [ fhir:v "true"] ;
  fhir:date [ fhir:v "2022-08-17T14:49:24-05:00"], [ fhir:v "2022-08-17T14:49:24-05:00"] ;
  fhir:publisher [ fhir:v "HL7 (FHIR Project)"], [ fhir:v "HL7 (FHIR Project)"] ;
  fhir:contact ( [
     fhir:telecom ( [
       fhir:system [ fhir:v "url" ] ;
       fhir:value [ fhir:v "http://hl7.org/fhir" ]
     ] [
       fhir:system [ fhir:v "email" ] ;
       fhir:value [ fhir:v "fhir@lists.hl7.org" ]
     ] )
  ] [
     fhir:telecom ( [
       fhir:system [ fhir:v "url" ] ;
       fhir:value [ fhir:v "http://hl7.org/fhir" ]
     ] [
       fhir:system [ fhir:v "email" ] ;
       fhir:value [ fhir:v "fhir@lists.hl7.org" ]
     ] )
  ] ) ;
  fhir:description [ fhir:v "The data format relevant to genomics. These formats and relevant codes were pulled from [Integrative Genomics Viewer Documentation](https://software.broadinstitute.org/software/igv/FileFormats) by Broad Institute."], [ fhir:v "The data format relevant to genomics. These formats and relevant codes were pulled from [Integrative Genomics Viewer Documentation](https://software.broadinstitute.org/software/igv/FileFormats) by Broad Institute."] ;
  fhir:jurisdiction ( [
     fhir:coding ( [
       fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm" ] ;
       fhir:code [ fhir:v "001" ] ;
       fhir:display [ fhir:v "World" ]
     ] )
  ] [
     fhir:coding ( [
       fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm" ] ;
       fhir:code [ fhir:v "001" ] ;
       fhir:display [ fhir:v "World" ]
     ] )
  ] ) ;
  fhir:caseSensitive [ fhir:v "true"] ;
  fhir:valueSet [ fhir:v "http://hl7.org/fhir/ValueSet/genomicstudy-dataformat"] ;
  fhir:content [ fhir:v "complete"] ;
  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" ]
  ] ) .

# -------------------------------------------------------------------------------------

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.