Release 5
TerminologyThis 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 
| Clinical Genomics Work Group | Maturity Level: N/A | Standards Status: Informative |
Raw JSON (canonical form + also see JSON Format Specification)
Definition for Code SystemGenomicStudyDataFormat
{
"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"
}]
}
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.
FHIR ®© HL7.org 2011+. FHIR R5 hl7.fhir.core#5.0.0 generated on Sun, Mar 26, 2023 15:22+1100.
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