Genomic Study Data Format
activeContentcompleteURL
http://hl7.org/fhir/genomicstudy-dataformatCopied!
Version5.0.0Copied!
Date2022-08-17T14:49:24-05:00PublisherHL7 (FHIR Project)DescriptionThe 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.
Concepts
Select a concept to view details
This code system
http://hl7.org/fhir/genomicstudy-dataformat defines the following codes:
{
"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.",
"date" : "2022-08-17T14:49:24-05:00",
"meta" : {
"lastUpdated" : "2023-03-26T15:21:02.749+11:00",
"profile" : [ "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ]
},
"publisher" : "HL7 (FHIR Project)",
"jurisdiction" : [ {
"coding" : [ {
"system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
} ]
} ],
"content" : "complete",
"property" : null,
"name" : "GenomicStudyDataFormat",
"experimental" : true,
"resourceType" : "CodeSystem",
"title" : "Genomic Study Data Format",
"extension" : [ {
"valueCode" : "cg",
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"
}, {
"valueCode" : "trial-use",
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"
}, {
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
"valueInteger" : 1
}, {
"extension" : [ {
"valueString" : "concept",
"url" : "path"
}, {
"url" : "count",
"valueInteger" : 40
} ],
"url" : "http://health-samurai.io/extensions/excised-data"
}, {
"url" : "http://health-samurai.io/extensions/source",
"valueCode" : "db"
} ],
"status" : "active",
"id" : "genomicstudy-dataformat",
"valueSet" : "http://hl7.org/fhir/ValueSet/genomicstudy-dataformat",
"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"
} ],
"caseSensitive" : true,
"version" : "5.0.0",
"contact" : [ {
"telecom" : [ {
"system" : "url",
"value" : "http://hl7.org/fhir"
}, {
"system" : "email",
"value" : "fhir@lists.hl7.org"
} ]
} ],
"text" : {
"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>",
"status" : "generated"
}
}