Definition for Code SystemGenomicStudyDataFormat

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

<CodeSystem xmlns="http://hl7.org/fhir">
  <id value="genomicstudy-dataformat"/> 
  <meta> 
    <lastUpdated value="2023-12-18T15:12:07.602+11:00"/> 
    <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/> 
  </meta> 
  <text> 
    <status value="generated"/> 
    <div xmlns="http://www.w3.org/1999/xhtml">
      <p> This case-sensitive code system 
        <code> http://hl7.org/fhir/genomicstudy-dataformat</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="genomicstudy-dataformat-bam"> </a> 
          </td> 
          <td> BAM</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">bed
            <a name="genomicstudy-dataformat-bed"> </a> 
          </td> 
          <td> BED</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">bedpe
            <a name="genomicstudy-dataformat-bedpe"> </a> 
          </td> 
          <td> BEDPE</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">bedgraph
            <a name="genomicstudy-dataformat-bedgraph"> </a> 
          </td> 
          <td> BedGraph</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">bigbed
            <a name="genomicstudy-dataformat-bigbed"> </a> 
          </td> 
          <td> bigBed</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">bigWig
            <a name="genomicstudy-dataformat-bigWig"> </a> 
          </td> 
          <td> bigWig</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">birdsuite-files
            <a name="genomicstudy-dataformat-birdsuite-files"> </a> 
          </td> 
          <td> Birdsuite-Files</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">broadpeak
            <a name="genomicstudy-dataformat-broadpeak"> </a> 
          </td> 
          <td> broadPeak</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">cbs
            <a name="genomicstudy-dataformat-cbs"> </a> 
          </td> 
          <td> CBS</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">chemical-reactivity-probing-profiles
            <a name="genomicstudy-dataformat-chemical-reactivity-probing-profiles"> </a> 
          </td> 
          <td> Chemical-Reactivity-Probing-Profiles</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">chrom-sizes
            <a name="genomicstudy-dataformat-chrom-sizes"> </a> 
          </td> 
          <td> chrom-sizes</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">cn
            <a name="genomicstudy-dataformat-cn"> </a> 
          </td> 
          <td> CN</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">custom-file-formats
            <a name="genomicstudy-dataformat-custom-file-formats"> </a> 
          </td> 
          <td> Custom-File-Formats</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">cytoband
            <a name="genomicstudy-dataformat-cytoband"> </a> 
          </td> 
          <td> Cytoband</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">fasta
            <a name="genomicstudy-dataformat-fasta"> </a> 
          </td> 
          <td> FASTA</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">gct
            <a name="genomicstudy-dataformat-gct"> </a> 
          </td> 
          <td> GCT</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">cram
            <a name="genomicstudy-dataformat-cram"> </a> 
          </td> 
          <td> CRAM</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">genepred
            <a name="genomicstudy-dataformat-genepred"> </a> 
          </td> 
          <td> genePred</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">gff-gtf
            <a name="genomicstudy-dataformat-gff-gtf"> </a> 
          </td> 
          <td> GFF/GTF</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">gistic
            <a name="genomicstudy-dataformat-gistic"> </a> 
          </td> 
          <td> GISTIC</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">goby
            <a name="genomicstudy-dataformat-goby"> </a> 
          </td> 
          <td> Goby</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">gwas
            <a name="genomicstudy-dataformat-gwas"> </a> 
          </td> 
          <td> GWAS</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">igv
            <a name="genomicstudy-dataformat-igv"> </a> 
          </td> 
          <td> IGV</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">loh
            <a name="genomicstudy-dataformat-loh"> </a> 
          </td> 
          <td> LOH</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">maf-multiple-alignment-format
            <a name="genomicstudy-dataformat-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="genomicstudy-dataformat-maf-mutation-annotation-format"> </a> 
          </td> 
          <td> MAF-Mutation-Annotation-Format</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">merged-bam-file
            <a name="genomicstudy-dataformat-merged-bam-file"> </a> 
          </td> 
          <td> Merged BAM File</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">mut
            <a name="genomicstudy-dataformat-mut"> </a> 
          </td> 
          <td> MUT</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">narrowpeak
            <a name="genomicstudy-dataformat-narrowpeak"> </a> 
          </td> 
          <td> narrowPeak</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">psl
            <a name="genomicstudy-dataformat-psl"> </a> 
          </td> 
          <td> PSL</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">res
            <a name="genomicstudy-dataformat-res"> </a> 
          </td> 
          <td> RES</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">rna-secondary-structure-formats
            <a name="genomicstudy-dataformat-rna-secondary-structure-formats"> </a> 
          </td> 
          <td> RNA-Secondary-Structure-Formats</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">sam
            <a name="genomicstudy-dataformat-sam"> </a> 
          </td> 
          <td> SAM</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">sample-info-attributes-file
            <a name="genomicstudy-dataformat-sample-info-attributes-file"> </a> 
          </td> 
          <td> Sample-Info-Attributes-file</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">seg
            <a name="genomicstudy-dataformat-seg"> </a> 
          </td> 
          <td> SEG</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">tdf
            <a name="genomicstudy-dataformat-tdf"> </a> 
          </td> 
          <td> TDF</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">track-line
            <a name="genomicstudy-dataformat-track-line"> </a> 
          </td> 
          <td> Track Line</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">type-line
            <a name="genomicstudy-dataformat-type-line"> </a> 
          </td> 
          <td> Type Line</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">vcf
            <a name="genomicstudy-dataformat-vcf"> </a> 
          </td> 
          <td> VCF</td> 
        </tr> 
        <tr> 
          <td style="white-space:nowrap">wig
            <a name="genomicstudy-dataformat-wig"> </a> 
          </td> 
          <td> WIG</td> 
        </tr> 
      </table> 
    </div> 
  </text> 
  <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="trial-use"/> 
  </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-ballot1"/> 
  <name value="GenomicStudyDataFormat"/> 
  <title value="Genomic Study Data Format"/> 
  <status value="active"/> 
  <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."/> 
  <jurisdiction> 
    <coding> 
      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/> 
      <code value="001"/> 
      <display value="World"/> 
    </coding> 
  </jurisdiction> 
  <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>