Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
| Page standards status: Draft | Maturity Level: 1 |
{
"resourceType" : "CodeSystem",
"id" : "genomicstudy-dataformat",
"meta" : {
"lastUpdated" : "2021-01-05T10:01:24.148+11:00",
"profile" : [
🔗 "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
]
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"language" : "en",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem genomicstudy-dataformat</b></p><a name=\"genomicstudy-dataformat\"> </a><a name=\"hcgenomicstudy-dataformat\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Last updated: 2021-01-05 10:01:24+1100</p><p style=\"margin-bottom: 0px\">Profile: <a href=\"http://hl7.org/fhir/R5/shareablecodesystem.html\">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/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><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">bam<a name=\"genomicstudy-dataformat-bam\"> </a></td><td>BAM</td><td>Binary Alignment/Map format for storing read alignments against reference sequences.</td></tr><tr><td style=\"white-space:nowrap\">bed<a name=\"genomicstudy-dataformat-bed\"> </a></td><td>BED</td><td>Browser Extensible Data format for representing genomic regions and associated annotations.</td></tr><tr><td style=\"white-space:nowrap\">bedpe<a name=\"genomicstudy-dataformat-bedpe\"> </a></td><td>BEDPE</td><td>Paired-End BED format for representing pairwise genomic interactions.</td></tr><tr><td style=\"white-space:nowrap\">bedgraph<a name=\"genomicstudy-dataformat-bedgraph\"> </a></td><td>BedGraph</td><td>BED Graph format for representing genomic signals as continuous-valued data.</td></tr><tr><td style=\"white-space:nowrap\">bigbed<a name=\"genomicstudy-dataformat-bigbed\"> </a></td><td>bigBed</td><td>Binary indexed BED format for efficiently storing large amounts of genomic region data.</td></tr><tr><td style=\"white-space:nowrap\">bigWig<a name=\"genomicstudy-dataformat-bigWig\"> </a></td><td>bigWig</td><td>Binary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data.</td></tr><tr><td style=\"white-space:nowrap\">birdsuite-files<a name=\"genomicstudy-dataformat-birdsuite-files\"> </a></td><td>Birdsuite-Files</td><td>File format used by the Birdsuite suite of software for SNP genotyping and copy number analysis.</td></tr><tr><td style=\"white-space:nowrap\">broadpeak<a name=\"genomicstudy-dataformat-broadpeak\"> </a></td><td>broadPeak</td><td>BED format variant for representing broad peaks in ChIP-Seq data.</td></tr><tr><td style=\"white-space:nowrap\">cbs<a name=\"genomicstudy-dataformat-cbs\"> </a></td><td>CBS</td><td>Copy number data format output by Circular Binary Segmentation analysis.</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><td>Profiles of chemical reactivity for RNA structure analysis.</td></tr><tr><td style=\"white-space:nowrap\">chrom-sizes<a name=\"genomicstudy-dataformat-chrom-sizes\"> </a></td><td>chrom-sizes</td><td>File listing chromosome names and their sizes.</td></tr><tr><td style=\"white-space:nowrap\">cn<a name=\"genomicstudy-dataformat-cn\"> </a></td><td>CN</td><td>Copy number data format.</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><td>User-defined or proprietary file formats for genomic data.</td></tr><tr><td style=\"white-space:nowrap\">cytoband<a name=\"genomicstudy-dataformat-cytoband\"> </a></td><td>Cytoband</td><td>Chromosome cytogenetic band locations and characteristics.</td></tr><tr><td style=\"white-space:nowrap\">fasta<a name=\"genomicstudy-dataformat-fasta\"> </a></td><td>FASTA</td><td>Format for representing sequences of nucleic acids or proteins using single letter codes.</td></tr><tr><td style=\"white-space:nowrap\">gct<a name=\"genomicstudy-dataformat-gct\"> </a></td><td>GCT</td><td>Gene Cluster Text format for storing gene expression data.</td></tr><tr><td style=\"white-space:nowrap\">cram<a name=\"genomicstudy-dataformat-cram\"> </a></td><td>CRAM</td><td>Compressed Reference-Aligned Map format for storing read alignments more compactly than BAM.</td></tr><tr><td style=\"white-space:nowrap\">genepred<a name=\"genomicstudy-dataformat-genepred\"> </a></td><td>genePred</td><td>Format for storing gene predictions with exon and CDS information.</td></tr><tr><td style=\"white-space:nowrap\">gff-gtf<a name=\"genomicstudy-dataformat-gff-gtf\"> </a></td><td>GFF/GTF</td><td>General Feature Format / Gene Transfer Format for storing genomic features and annotations.</td></tr><tr><td style=\"white-space:nowrap\">gistic<a name=\"genomicstudy-dataformat-gistic\"> </a></td><td>GISTIC</td><td>Genomic Identification of Significant Targets in Cancer output format for copy number analysis.</td></tr><tr><td style=\"white-space:nowrap\">goby<a name=\"genomicstudy-dataformat-goby\"> </a></td><td>Goby</td><td>Compact file format for storing read alignments, variations, and base quality information.</td></tr><tr><td style=\"white-space:nowrap\">gwas<a name=\"genomicstudy-dataformat-gwas\"> </a></td><td>GWAS</td><td>Genome-Wide Association Study format for storing association results.</td></tr><tr><td style=\"white-space:nowrap\">igv<a name=\"genomicstudy-dataformat-igv\"> </a></td><td>IGV</td><td>Integrative Genomics Viewer session or display format.</td></tr><tr><td style=\"white-space:nowrap\">loh<a name=\"genomicstudy-dataformat-loh\"> </a></td><td>LOH</td><td>Loss of Heterozygosity data format.</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><td>Multiple Alignment Format for storing aligned sequences.</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><td>Mutation Annotation Format for storing somatic mutation data.</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><td>BAM file containing read alignments from multiple samples or lanes merged together.</td></tr><tr><td style=\"white-space:nowrap\">mut<a name=\"genomicstudy-dataformat-mut\"> </a></td><td>MUT</td><td>Mutation data format.</td></tr><tr><td style=\"white-space:nowrap\">narrowpeak<a name=\"genomicstudy-dataformat-narrowpeak\"> </a></td><td>narrowPeak</td><td>BED format variant for representing narrow peaks in ChIP-Seq data.</td></tr><tr><td style=\"white-space:nowrap\">psl<a name=\"genomicstudy-dataformat-psl\"> </a></td><td>PSL</td><td>Pattern Space Layout format for storing sequence alignments.</td></tr><tr><td style=\"white-space:nowrap\">res<a name=\"genomicstudy-dataformat-res\"> </a></td><td>RES</td><td>Resolution data format.</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><td>Formats for representing RNA secondary structure information.</td></tr><tr><td style=\"white-space:nowrap\">sam<a name=\"genomicstudy-dataformat-sam\"> </a></td><td>SAM</td><td>Sequence Alignment/Map format for storing read alignments, the uncompressed version of BAM.</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><td>File containing sample information and attributes.</td></tr><tr><td style=\"white-space:nowrap\">seg<a name=\"genomicstudy-dataformat-seg\"> </a></td><td>SEG</td><td>Segmented data format for storing copy number or other segmented genomic data.</td></tr><tr><td style=\"white-space:nowrap\">tdf<a name=\"genomicstudy-dataformat-tdf\"> </a></td><td>TDF</td><td>Tiled Data Format for efficient storage and display of large genomic datasets.</td></tr><tr><td style=\"white-space:nowrap\">track-line<a name=\"genomicstudy-dataformat-track-line\"> </a></td><td>Track Line</td><td>UCSC Genome Browser track line header defining display properties for genomic data.</td></tr><tr><td style=\"white-space:nowrap\">type-line<a name=\"genomicstudy-dataformat-type-line\"> </a></td><td>Type Line</td><td>Type line header for defining genomic data track properties.</td></tr><tr><td style=\"white-space:nowrap\">vcf<a name=\"genomicstudy-dataformat-vcf\"> </a></td><td>VCF</td><td>Variant Call Format for storing variant information including SNPs, indels, and structural variations.</td></tr><tr><td style=\"white-space:nowrap\">wig<a name=\"genomicstudy-dataformat-wig\"> </a></td><td>WIG</td><td>Wiggle Track format for storing continuous-valued genomic data.</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" : "draft"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger" : 1
}
],
"url" : "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat",
"identifier" : [
{
"system" : "urn:ietf:rfc:3986",
"value" : "urn:oid:2.16.840.1.113883.4.642.4.1978"
}
],
"version" : "0.1.0-ci-build",
"name" : "GenomicStudyDataFormat",
"title" : "Genomic Study Data Format",
"status" : "draft",
"experimental" : true,
"date" : "2022-08-17T14:49:24-05:00",
"publisher" : "HL7 International / Clinical Genomics",
"contact" : [
{
"name" : "HL7 International / Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "clingenomics@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/uv/cg-incubator/ValueSet/genomicstudy-dataformat",
"content" : "complete",
"concept" : [
{
"code" : "bam",
"display" : "BAM",
"definition" : "Binary Alignment/Map format for storing read alignments against reference sequences."
},
{
"code" : "bed",
"display" : "BED",
"definition" : "Browser Extensible Data format for representing genomic regions and associated annotations."
},
{
"code" : "bedpe",
"display" : "BEDPE",
"definition" : "Paired-End BED format for representing pairwise genomic interactions."
},
{
"code" : "bedgraph",
"display" : "BedGraph",
"definition" : "BED Graph format for representing genomic signals as continuous-valued data."
},
{
"code" : "bigbed",
"display" : "bigBed",
"definition" : "Binary indexed BED format for efficiently storing large amounts of genomic region data."
},
{
"code" : "bigWig",
"display" : "bigWig",
"definition" : "Binary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data."
},
{
"code" : "birdsuite-files",
"display" : "Birdsuite-Files",
"definition" : "File format used by the Birdsuite suite of software for SNP genotyping and copy number analysis."
},
{
"code" : "broadpeak",
"display" : "broadPeak",
"definition" : "BED format variant for representing broad peaks in ChIP-Seq data."
},
{
"code" : "cbs",
"display" : "CBS",
"definition" : "Copy number data format output by Circular Binary Segmentation analysis."
},
{
"code" : "chemical-reactivity-probing-profiles",
"display" : "Chemical-Reactivity-Probing-Profiles",
"definition" : "Profiles of chemical reactivity for RNA structure analysis."
},
{
"code" : "chrom-sizes",
"display" : "chrom-sizes",
"definition" : "File listing chromosome names and their sizes."
},
{
"code" : "cn",
"display" : "CN",
"definition" : "Copy number data format."
},
{
"code" : "custom-file-formats",
"display" : "Custom-File-Formats",
"definition" : "User-defined or proprietary file formats for genomic data."
},
{
"code" : "cytoband",
"display" : "Cytoband",
"definition" : "Chromosome cytogenetic band locations and characteristics."
},
{
"code" : "fasta",
"display" : "FASTA",
"definition" : "Format for representing sequences of nucleic acids or proteins using single letter codes."
},
{
"code" : "gct",
"display" : "GCT",
"definition" : "Gene Cluster Text format for storing gene expression data."
},
{
"code" : "cram",
"display" : "CRAM",
"definition" : "Compressed Reference-Aligned Map format for storing read alignments more compactly than BAM."
},
{
"code" : "genepred",
"display" : "genePred",
"definition" : "Format for storing gene predictions with exon and CDS information."
},
{
"code" : "gff-gtf",
"display" : "GFF/GTF",
"definition" : "General Feature Format / Gene Transfer Format for storing genomic features and annotations."
},
{
"code" : "gistic",
"display" : "GISTIC",
"definition" : "Genomic Identification of Significant Targets in Cancer output format for copy number analysis."
},
{
"code" : "goby",
"display" : "Goby",
"definition" : "Compact file format for storing read alignments, variations, and base quality information."
},
{
"code" : "gwas",
"display" : "GWAS",
"definition" : "Genome-Wide Association Study format for storing association results."
},
{
"code" : "igv",
"display" : "IGV",
"definition" : "Integrative Genomics Viewer session or display format."
},
{
"code" : "loh",
"display" : "LOH",
"definition" : "Loss of Heterozygosity data format."
},
{
"code" : "maf-multiple-alignment-format",
"display" : "MAF-Multiple Alignment Format",
"definition" : "Multiple Alignment Format for storing aligned sequences."
},
{
"code" : "maf-mutation-annotation-format",
"display" : "MAF-Mutation-Annotation-Format",
"definition" : "Mutation Annotation Format for storing somatic mutation data."
},
{
"code" : "merged-bam-file",
"display" : "Merged BAM File",
"definition" : "BAM file containing read alignments from multiple samples or lanes merged together."
},
{
"code" : "mut",
"display" : "MUT",
"definition" : "Mutation data format."
},
{
"code" : "narrowpeak",
"display" : "narrowPeak",
"definition" : "BED format variant for representing narrow peaks in ChIP-Seq data."
},
{
"code" : "psl",
"display" : "PSL",
"definition" : "Pattern Space Layout format for storing sequence alignments."
},
{
"code" : "res",
"display" : "RES",
"definition" : "Resolution data format."
},
{
"code" : "rna-secondary-structure-formats",
"display" : "RNA-Secondary-Structure-Formats",
"definition" : "Formats for representing RNA secondary structure information."
},
{
"code" : "sam",
"display" : "SAM",
"definition" : "Sequence Alignment/Map format for storing read alignments, the uncompressed version of BAM."
},
{
"code" : "sample-info-attributes-file",
"display" : "Sample-Info-Attributes-file",
"definition" : "File containing sample information and attributes."
},
{
"code" : "seg",
"display" : "SEG",
"definition" : "Segmented data format for storing copy number or other segmented genomic data."
},
{
"code" : "tdf",
"display" : "TDF",
"definition" : "Tiled Data Format for efficient storage and display of large genomic datasets."
},
{
"code" : "track-line",
"display" : "Track Line",
"definition" : "UCSC Genome Browser track line header defining display properties for genomic data."
},
{
"code" : "type-line",
"display" : "Type Line",
"definition" : "Type line header for defining genomic data track properties."
},
{
"code" : "vcf",
"display" : "VCF",
"definition" : "Variant Call Format for storing variant information including SNPs, indels, and structural variations."
},
{
"code" : "wig",
"display" : "WIG",
"definition" : "Wiggle Track format for storing continuous-valued genomic data."
}
]
}
IG © 2026+ HL7 International / Clinical Genomics.
Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3.
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2026-03-24
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