Genomic Study Data Format

• Official URL: http://hl7.org/fhir/genomicstudy-dataformat
• Version: 6.0.0
• Status: draft
• Name: GenomicStudyDataFormat
• Title: Genomic Study Data Format
• Publisher: HL7 (FHIR Project)
• Description: The data format relevant to genomics. These formats and relevant codes were pulled from Integrative Genomics Viewer Documentation by Broad Institute.
• Case Sensitive: true
• Content: complete

Concepts

CodeSystem XML

<?xml version="1.0" encoding="UTF-8"?>

<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-dataformat"/>
  <meta>
    <lastUpdated value="2021-01-05T10:01:24.148+11:00"/>

  </meta>
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
    <valueCode value="normative"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/>
  </extension>
  <url value="http://hl7.org/fhir/genomicstudy-dataformat"/>
  <identifier>
    <system value="urn:ietf:rfc:3986"/>
    <value value="urn:oid:2.16.840.1.113883.4.642.4.1978"/>
  </identifier>
  <version value="6.0.0"/>
  <name value="GenomicStudyDataFormat"/>
  <title value="Genomic Study Data Format"/>
  <status value="draft"/>
  <experimental value="true"/>
  <date value="2022-08-17T14:49:24-05:00"/>
  <publisher value="HL7 (FHIR Project)"/>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="http://hl7.org/fhir"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="fhir@lists.hl7.org"/>
    </telecom>
  </contact>
  <description value="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."/>
  <caseSensitive value="true"/>
  <valueSet value="http://hl7.org/fhir/ValueSet/genomicstudy-dataformat"/>
  <content value="complete"/>
  <concept>
    <code value="bam"/>
    <display value="BAM"/>
  </concept>
  <concept>
    <code value="bed"/>
    <display value="BED"/>
  </concept>
  <concept>
    <code value="bedpe"/>
    <display value="BEDPE"/>
  </concept>
  <concept>
    <code value="bedgraph"/>
    <display value="BedGraph"/>
  </concept>
  <concept>
    <code value="bigbed"/>
    <display value="bigBed"/>
  </concept>
  <concept>
    <code value="bigWig"/>
    <display value="bigWig"/>
  </concept>
  <concept>
    <code value="birdsuite-files"/>
    <display value="Birdsuite-Files"/>
  </concept>
  <concept>
    <code value="broadpeak"/>
    <display value="broadPeak"/>
  </concept>
  <concept>
    <code value="cbs"/>
    <display value="CBS"/>
  </concept>
  <concept>
    <code value="chemical-reactivity-probing-profiles"/>
    <display value="Chemical-Reactivity-Probing-Profiles"/>
  </concept>
  <concept>
    <code value="chrom-sizes"/>
    <display value="chrom-sizes"/>
  </concept>
  <concept>
    <code value="cn"/>
    <display value="CN"/>
  </concept>
  <concept>
    <code value="custom-file-formats"/>
    <display value="Custom-File-Formats"/>
  </concept>
  <concept>
    <code value="cytoband"/>
    <display value="Cytoband"/>
  </concept>
  <concept>
    <code value="fasta"/>
    <display value="FASTA"/>
  </concept>
  <concept>
    <code value="gct"/>
    <display value="GCT"/>
  </concept>
  <concept>
    <code value="cram"/>
    <display value="CRAM"/>
  </concept>
  <concept>
    <code value="genepred"/>
    <display value="genePred"/>
  </concept>
  <concept>
    <code value="gff-gtf"/>
    <display value="GFF/GTF"/>
  </concept>
  <concept>
    <code value="gistic"/>
    <display value="GISTIC"/>
  </concept>
  <concept>
    <code value="goby"/>
    <display value="Goby"/>
  </concept>
  <concept>
    <code value="gwas"/>
    <display value="GWAS"/>
  </concept>
  <concept>
    <code value="igv"/>
    <display value="IGV"/>
  </concept>
  <concept>
    <code value="loh"/>
    <display value="LOH"/>
  </concept>
  <concept>
    <code value="maf-multiple-alignment-format"/>
    <display value="MAF-Multiple Alignment Format"/>
  </concept>
  <concept>
    <code value="maf-mutation-annotation-format"/>
    <display value="MAF-Mutation-Annotation-Format"/>
  </concept>
  <concept>
    <code value="merged-bam-file"/>
    <display value="Merged BAM File"/>
  </concept>
  <concept>
    <code value="mut"/>
    <display value="MUT"/>
  </concept>
  <concept>
    <code value="narrowpeak"/>
    <display value="narrowPeak"/>
  </concept>
  <concept>
    <code value="psl"/>
    <display value="PSL"/>
  </concept>
  <concept>
    <code value="res"/>
    <display value="RES"/>
  </concept>
  <concept>
    <code value="rna-secondary-structure-formats"/>
    <display value="RNA-Secondary-Structure-Formats"/>
  </concept>
  <concept>
    <code value="sam"/>
    <display value="SAM"/>
  </concept>
  <concept>
    <code value="sample-info-attributes-file"/>
    <display value="Sample-Info-Attributes-file"/>
  </concept>
  <concept>
    <code value="seg"/>
    <display value="SEG"/>
  </concept>
  <concept>
    <code value="tdf"/>
    <display value="TDF"/>
  </concept>
  <concept>
    <code value="track-line"/>
    <display value="Track Line"/>
  </concept>
  <concept>
    <code value="type-line"/>
    <display value="Type Line"/>
  </concept>
  <concept>
    <code value="vcf"/>
    <display value="VCF"/>
  </concept>
  <concept>
    <code value="wig"/>
    <display value="WIG"/>
  </concept>
</CodeSystem>