{
  "resourceType": "CodeSystem",
  "id": "genomicstudy-dataformat",
  "meta": {
    "lastUpdated": "2023-03-26T15:21:02.749+11:00",
    "profile": [
      "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This 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>"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode": "cg"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode": "trial-use"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger": 1
    }
  ],
  "url": "http://hl7.org/fhir/genomicstudy-dataformat",
  "identifier": [
    {
      "system": "urn:ietf:rfc:3986",
      "value": "urn:oid:2.16.840.1.113883.4.642.4.1978"
    }
  ],
  "version": "5.0.0",
  "name": "GenomicStudyDataFormat",
  "title": "Genomic Study Data Format",
  "status": "active",
  "experimental": true,
  "date": "2022-08-17T14:49:24-05:00",
  "publisher": "HL7 (FHIR Project)",
  "contact": [
    {
      "telecom": [
        {
          "system": "url",
          "value": "http://hl7.org/fhir"
        },
        {
          "system": "email",
          "value": "fhir@lists.hl7.org"
        }
      ]
    }
  ],
  "description": "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": "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code": "001",
          "display": "World"
        }
      ]
    }
  ],
  "caseSensitive": true,
  "valueSet": "http://hl7.org/fhir/ValueSet/genomicstudy-dataformat",
  "content": "complete",
  "concept": [
    {
      "code": "bam",
      "display": "BAM"
    },
    {
      "code": "bed",
      "display": "BED"
    },
    {
      "code": "bedpe",
      "display": "BEDPE"
    },
    {
      "code": "bedgraph",
      "display": "BedGraph"
    },
    {
      "code": "bigbed",
      "display": "bigBed"
    },
    {
      "code": "bigWig",
      "display": "bigWig"
    },
    {
      "code": "birdsuite-files",
      "display": "Birdsuite-Files"
    },
    {
      "code": "broadpeak",
      "display": "broadPeak"
    },
    {
      "code": "cbs",
      "display": "CBS"
    },
    {
      "code": "chemical-reactivity-probing-profiles",
      "display": "Chemical-Reactivity-Probing-Profiles"
    },
    {
      "code": "chrom-sizes",
      "display": "chrom-sizes"
    },
    {
      "code": "cn",
      "display": "CN"
    },
    {
      "code": "custom-file-formats",
      "display": "Custom-File-Formats"
    },
    {
      "code": "cytoband",
      "display": "Cytoband"
    },
    {
      "code": "fasta",
      "display": "FASTA"
    },
    {
      "code": "gct",
      "display": "GCT"
    },
    {
      "code": "cram",
      "display": "CRAM"
    },
    {
      "code": "genepred",
      "display": "genePred"
    },
    {
      "code": "gff-gtf",
      "display": "GFF/GTF"
    },
    {
      "code": "gistic",
      "display": "GISTIC"
    },
    {
      "code": "goby",
      "display": "Goby"
    },
    {
      "code": "gwas",
      "display": "GWAS"
    },
    {
      "code": "igv",
      "display": "IGV"
    },
    {
      "code": "loh",
      "display": "LOH"
    },
    {
      "code": "maf-multiple-alignment-format",
      "display": "MAF-Multiple Alignment Format"
    },
    {
      "code": "maf-mutation-annotation-format",
      "display": "MAF-Mutation-Annotation-Format"
    },
    {
      "code": "merged-bam-file",
      "display": "Merged BAM File"
    },
    {
      "code": "mut",
      "display": "MUT"
    },
    {
      "code": "narrowpeak",
      "display": "narrowPeak"
    },
    {
      "code": "psl",
      "display": "PSL"
    },
    {
      "code": "res",
      "display": "RES"
    },
    {
      "code": "rna-secondary-structure-formats",
      "display": "RNA-Secondary-Structure-Formats"
    },
    {
      "code": "sam",
      "display": "SAM"
    },
    {
      "code": "sample-info-attributes-file",
      "display": "Sample-Info-Attributes-file"
    },
    {
      "code": "seg",
      "display": "SEG"
    },
    {
      "code": "tdf",
      "display": "TDF"
    },
    {
      "code": "track-line",
      "display": "Track Line"
    },
    {
      "code": "type-line",
      "display": "Type Line"
    },
    {
      "code": "vcf",
      "display": "VCF"
    },
    {
      "code": "wig",
      "display": "WIG"
    }
  ]
}