Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: Genomic Study Data Format CodeSystem - XML Representation

Active as of 2023-12-18

Raw xml | Download



<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomic-study-data-format-cs"/>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><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>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
  <version value="3.0.0-ballot"/>
  <name value="GenomicStudyDataFormatCS"/>
  <title value="Genomic Study Data Format CodeSystem"/>
  <status value="active"/>
  <experimental value="true"/>
  <date value="2023-12-18T22:45:59+00:00"/>
  <publisher value="HL7 International / Clinical Genomics"/>
  <contact>
    <name value="HL7 International / Clinical Genomics"/>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics"/>
    </telecom>
    <telecom>
      <system value="email"/>
      <value value="cg@lists.HL7.org"/>
    </telecom>
  </contact>
  <description
               value="Backport of http://hl7.org/fhir/genomicstudy-dataformat"/>
  <jurisdiction>
    <coding>
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
      <code value="001"/>
      <display value="World"/>
    </coding>
  </jurisdiction>
  <caseSensitive value="true"/>
  <content value="complete"/>
  <count value="40"/>
  <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>