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 |
@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "genomicstudy-dataformat"] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir: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>"^^rdf:XMLLiteral
] ; #
fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ] ;
fhir:value [
a fhir:code ;
fhir:v "informative" ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ] ;
fhir:value [
a fhir:integer ;
fhir:v 1 ]
] [
( fhir:extension [
fhir:url [ fhir:v "packageId"^^xsd:anyURI ] ;
fhir:value [
a fhir:id ;
fhir:v "hl7.fhir.uv.xver-r5.r4" ] ] [
fhir:url [ fhir:v "version"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "0.0.1-snapshot-2" ] ] ) ;
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/package-source"^^xsd:anyURI ]
] [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [
a fhir:code ;
fhir:v "cg" ]
] ) ; #
fhir:url [ fhir:v "http://hl7.org/fhir/genomicstudy-dataformat"^^xsd:anyURI] ; #
fhir:version [ fhir:v "5.0.0"] ; #
fhir:name [ fhir:v "GenomicStudyDataFormat"] ; #
fhir:title [ fhir:v "Genomic Study Data Format"] ; #
fhir:status [ fhir:v "active"] ; #
fhir:experimental [ fhir:v true] ; #
fhir:date [ fhir:v "2022-08-18T05:49:24+10:00"^^xsd:dateTime] ; #
fhir:publisher [ fhir:v "Clinical Genomics"] ; #
fhir:contact ( [
fhir:name [ fhir:v "Clinical Genomics" ] ;
( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] )
] ) ; #
fhir:description [ fhir:v "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."] ; #
fhir:jurisdiction ( [
( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ] ] )
] ) ; #
fhir:caseSensitive [ fhir:v true] ; #
fhir:valueSet [
fhir:v "http://hl7.org/fhir/ValueSet/genomicstudy-dataformat"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/ValueSet/genomicstudy-dataformat>
] ; #
fhir:content [ fhir:v "complete"] ; #
fhir:concept ( [
fhir:code [ fhir:v "bam" ] ;
fhir:display [ fhir:v "BAM" ]
] [
fhir:code [ fhir:v "bed" ] ;
fhir:display [ fhir:v "BED" ]
] [
fhir:code [ fhir:v "bedpe" ] ;
fhir:display [ fhir:v "BEDPE" ]
] [
fhir:code [ fhir:v "bedgraph" ] ;
fhir:display [ fhir:v "BedGraph" ]
] [
fhir:code [ fhir:v "bigbed" ] ;
fhir:display [ fhir:v "bigBed" ]
] [
fhir:code [ fhir:v "bigWig" ] ;
fhir:display [ fhir:v "bigWig" ]
] [
fhir:code [ fhir:v "birdsuite-files" ] ;
fhir:display [ fhir:v "Birdsuite-Files" ]
] [
fhir:code [ fhir:v "broadpeak" ] ;
fhir:display [ fhir:v "broadPeak" ]
] [
fhir:code [ fhir:v "cbs" ] ;
fhir:display [ fhir:v "CBS" ]
] [
fhir:code [ fhir:v "chemical-reactivity-probing-profiles" ] ;
fhir:display [ fhir:v "Chemical-Reactivity-Probing-Profiles" ]
] [
fhir:code [ fhir:v "chrom-sizes" ] ;
fhir:display [ fhir:v "chrom-sizes" ]
] [
fhir:code [ fhir:v "cn" ] ;
fhir:display [ fhir:v "CN" ]
] [
fhir:code [ fhir:v "custom-file-formats" ] ;
fhir:display [ fhir:v "Custom-File-Formats" ]
] [
fhir:code [ fhir:v "cytoband" ] ;
fhir:display [ fhir:v "Cytoband" ]
] [
fhir:code [ fhir:v "fasta" ] ;
fhir:display [ fhir:v "FASTA" ]
] [
fhir:code [ fhir:v "gct" ] ;
fhir:display [ fhir:v "GCT" ]
] [
fhir:code [ fhir:v "cram" ] ;
fhir:display [ fhir:v "CRAM" ]
] [
fhir:code [ fhir:v "genepred" ] ;
fhir:display [ fhir:v "genePred" ]
] [
fhir:code [ fhir:v "gff-gtf" ] ;
fhir:display [ fhir:v "GFF/GTF" ]
] [
fhir:code [ fhir:v "gistic" ] ;
fhir:display [ fhir:v "GISTIC" ]
] [
fhir:code [ fhir:v "goby" ] ;
fhir:display [ fhir:v "Goby" ]
] [
fhir:code [ fhir:v "gwas" ] ;
fhir:display [ fhir:v "GWAS" ]
] [
fhir:code [ fhir:v "igv" ] ;
fhir:display [ fhir:v "IGV" ]
] [
fhir:code [ fhir:v "loh" ] ;
fhir:display [ fhir:v "LOH" ]
] [
fhir:code [ fhir:v "maf-multiple-alignment-format" ] ;
fhir:display [ fhir:v "MAF-Multiple Alignment Format" ]
] [
fhir:code [ fhir:v "maf-mutation-annotation-format" ] ;
fhir:display [ fhir:v "MAF-Mutation-Annotation-Format" ]
] [
fhir:code [ fhir:v "merged-bam-file" ] ;
fhir:display [ fhir:v "Merged BAM File" ]
] [
fhir:code [ fhir:v "mut" ] ;
fhir:display [ fhir:v "MUT" ]
] [
fhir:code [ fhir:v "narrowpeak" ] ;
fhir:display [ fhir:v "narrowPeak" ]
] [
fhir:code [ fhir:v "psl" ] ;
fhir:display [ fhir:v "PSL" ]
] [
fhir:code [ fhir:v "res" ] ;
fhir:display [ fhir:v "RES" ]
] [
fhir:code [ fhir:v "rna-secondary-structure-formats" ] ;
fhir:display [ fhir:v "RNA-Secondary-Structure-Formats" ]
] [
fhir:code [ fhir:v "sam" ] ;
fhir:display [ fhir:v "SAM" ]
] [
fhir:code [ fhir:v "sample-info-attributes-file" ] ;
fhir:display [ fhir:v "Sample-Info-Attributes-file" ]
] [
fhir:code [ fhir:v "seg" ] ;
fhir:display [ fhir:v "SEG" ]
] [
fhir:code [ fhir:v "tdf" ] ;
fhir:display [ fhir:v "TDF" ]
] [
fhir:code [ fhir:v "track-line" ] ;
fhir:display [ fhir:v "Track Line" ]
] [
fhir:code [ fhir:v "type-line" ] ;
fhir:display [ fhir:v "Type Line" ]
] [
fhir:code [ fhir:v "vcf" ] ;
fhir:display [ fhir:v "VCF" ]
] [
fhir:code [ fhir:v "wig" ] ;
fhir:display [ fhir:v "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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