FHIR Cross-Version Extensions package for FHIR R4 from FHIR R5
0.0.1-snapshot-2 - informative
FHIR Cross-Version Extensions package for FHIR R4 from FHIR R5
0.0.1-snapshot-2 - informative
FHIR Cross-Version Extensions package for FHIR R4 from FHIR R5 - Version 0.0.1-snapshot-2. See the Directory of published versions
| Page standards status: Informative | Maturity Level: 1 |
{
"resourceType" : "CodeSystem",
"id" : "genomicstudy-dataformat",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n <p>This code system \n <code>http://hl7.org/fhir/genomicstudy-dataformat</code> defines the following codes:\n </p>\n <table class=\"codes\">\n <tr>\n <td style=\"white-space:nowrap\">\n <b>Code</b>\n </td>\n <td>\n <b>Display</b>\n </td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bam\n <a name=\"genomicstudy-dataformat-bam\"> </a>\n </td>\n <td>BAM</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bed\n <a name=\"genomicstudy-dataformat-bed\"> </a>\n </td>\n <td>BED</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bedpe\n <a name=\"genomicstudy-dataformat-bedpe\"> </a>\n </td>\n <td>BEDPE</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bedgraph\n <a name=\"genomicstudy-dataformat-bedgraph\"> </a>\n </td>\n <td>BedGraph</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bigbed\n <a name=\"genomicstudy-dataformat-bigbed\"> </a>\n </td>\n <td>bigBed</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">bigWig\n <a name=\"genomicstudy-dataformat-bigWig\"> </a>\n </td>\n <td>bigWig</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">birdsuite-files\n <a name=\"genomicstudy-dataformat-birdsuite-files\"> </a>\n </td>\n <td>Birdsuite-Files</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">broadpeak\n <a name=\"genomicstudy-dataformat-broadpeak\"> </a>\n </td>\n <td>broadPeak</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">cbs\n <a name=\"genomicstudy-dataformat-cbs\"> </a>\n </td>\n <td>CBS</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">chemical-reactivity-probing-profiles\n <a name=\"genomicstudy-dataformat-chemical-reactivity-probing-profiles\"> </a>\n </td>\n <td>Chemical-Reactivity-Probing-Profiles</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">chrom-sizes\n <a name=\"genomicstudy-dataformat-chrom-sizes\"> </a>\n </td>\n <td>chrom-sizes</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">cn\n <a name=\"genomicstudy-dataformat-cn\"> </a>\n </td>\n <td>CN</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">custom-file-formats\n <a name=\"genomicstudy-dataformat-custom-file-formats\"> </a>\n </td>\n <td>Custom-File-Formats</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">cytoband\n <a name=\"genomicstudy-dataformat-cytoband\"> </a>\n </td>\n <td>Cytoband</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">fasta\n <a name=\"genomicstudy-dataformat-fasta\"> </a>\n </td>\n <td>FASTA</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">gct\n <a name=\"genomicstudy-dataformat-gct\"> </a>\n </td>\n <td>GCT</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">cram\n <a name=\"genomicstudy-dataformat-cram\"> </a>\n </td>\n <td>CRAM</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">genepred\n <a name=\"genomicstudy-dataformat-genepred\"> </a>\n </td>\n <td>genePred</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">gff-gtf\n <a name=\"genomicstudy-dataformat-gff-gtf\"> </a>\n </td>\n <td>GFF/GTF</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">gistic\n <a name=\"genomicstudy-dataformat-gistic\"> </a>\n </td>\n <td>GISTIC</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">goby\n <a name=\"genomicstudy-dataformat-goby\"> </a>\n </td>\n <td>Goby</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">gwas\n <a name=\"genomicstudy-dataformat-gwas\"> </a>\n </td>\n <td>GWAS</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">igv\n <a name=\"genomicstudy-dataformat-igv\"> </a>\n </td>\n <td>IGV</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">loh\n <a name=\"genomicstudy-dataformat-loh\"> </a>\n </td>\n <td>LOH</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">maf-multiple-alignment-format\n <a name=\"genomicstudy-dataformat-maf-multiple-alignment-format\"> </a>\n </td>\n <td>MAF-Multiple Alignment Format</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">maf-mutation-annotation-format\n <a name=\"genomicstudy-dataformat-maf-mutation-annotation-format\"> </a>\n </td>\n <td>MAF-Mutation-Annotation-Format</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">merged-bam-file\n <a name=\"genomicstudy-dataformat-merged-bam-file\"> </a>\n </td>\n <td>Merged BAM File</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">mut\n <a name=\"genomicstudy-dataformat-mut\"> </a>\n </td>\n <td>MUT</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">narrowpeak\n <a name=\"genomicstudy-dataformat-narrowpeak\"> </a>\n </td>\n <td>narrowPeak</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">psl\n <a name=\"genomicstudy-dataformat-psl\"> </a>\n </td>\n <td>PSL</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">res\n <a name=\"genomicstudy-dataformat-res\"> </a>\n </td>\n <td>RES</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">rna-secondary-structure-formats\n <a name=\"genomicstudy-dataformat-rna-secondary-structure-formats\"> </a>\n </td>\n <td>RNA-Secondary-Structure-Formats</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">sam\n <a name=\"genomicstudy-dataformat-sam\"> </a>\n </td>\n <td>SAM</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">sample-info-attributes-file\n <a name=\"genomicstudy-dataformat-sample-info-attributes-file\"> </a>\n </td>\n <td>Sample-Info-Attributes-file</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">seg\n <a name=\"genomicstudy-dataformat-seg\"> </a>\n </td>\n <td>SEG</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">tdf\n <a name=\"genomicstudy-dataformat-tdf\"> </a>\n </td>\n <td>TDF</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">track-line\n <a name=\"genomicstudy-dataformat-track-line\"> </a>\n </td>\n <td>Track Line</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">type-line\n <a name=\"genomicstudy-dataformat-type-line\"> </a>\n </td>\n <td>Type Line</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">vcf\n <a name=\"genomicstudy-dataformat-vcf\"> </a>\n </td>\n <td>VCF</td>\n </tr>\n <tr>\n <td style=\"white-space:nowrap\">wig\n <a name=\"genomicstudy-dataformat-wig\"> </a>\n </td>\n <td>WIG</td>\n </tr>\n </table>\n </div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
"valueCode" : "informative"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger" : 1
},
{
"extension" : [
{
"url" : "packageId",
"valueId" : "hl7.fhir.uv.xver-r5.r4"
},
{
"url" : "version",
"valueString" : "0.0.1-snapshot-2"
}
],
"url" : "http://hl7.org/fhir/StructureDefinition/package-source"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/genomicstudy-dataformat",
"version" : "5.0.0",
"name" : "GenomicStudyDataFormat",
"title" : "Genomic Study Data Format",
"status" : "active",
"experimental" : true,
"date" : "2022-08-18T05:49:24+10:00",
"publisher" : "Clinical Genomics",
"contact" : [
{
"name" : "Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
}
]
}
],
"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"
}
]
}
IG © 2025+ FHIR Infrastructure. Package hl7.fhir.uv.xver-r5.r4#0.0.1-snapshot-2 based on FHIR 4.0.1. Generated 2025-09-13
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