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 |
@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:meta [ fhir:lastUpdated [ fhir:v "2021-01-05T10:01:24.148+11:00"^^xsd:dateTime ] ; ( fhir:profile [ fhir:v "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/StructureDefinition/shareablecodesystem> ] ) ] ; # fhir:language [ fhir:v "en"] ; # fhir:text [ fhir:status [ fhir:v "generated" ] ; fhir:div [ fhir:v "<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>"^^rdf:XMLLiteral ] ] ; # fhir:extension ( [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-wg> ] ; fhir:value [ a fhir:Code ; fhir:v "cg" ] ] [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status> ] ; fhir:value [ a fhir:Code ; fhir:v "draft" ] ] [ fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm> ] ; fhir:value [ a fhir:Integer ; fhir:v 1 ] ] ) ; # fhir:url [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat> ] ; # fhir:identifier ( [ fhir:system [ fhir:v "urn:ietf:rfc:3986"^^xsd:anyURI ; fhir:l <urn:ietf:rfc:3986> ] ; fhir:value [ fhir:v "urn:oid:2.16.840.1.113883.4.642.4.1978" ] ] ) ; # fhir:version [ fhir:v "0.1.0-ci-build"] ; # fhir:name [ fhir:v "GenomicStudyDataFormat"] ; # fhir:title [ fhir:v "Genomic Study Data Format"] ; # fhir:status [ fhir:v "draft"] ; # fhir:experimental [ fhir:v true] ; # fhir:date [ fhir:v "2022-08-17T14:49:24-05:00"^^xsd:dateTime] ; # fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; # fhir:contact ( [ fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ; ( fhir:telecom [ fhir:system [ fhir:v "url" ] ; fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] [ fhir:system [ fhir:v "email" ] ; fhir:value [ fhir:v "clingenomics@lists.hl7.org" ] ] ) ] ) ; # 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:l <http://unstats.un.org/unsd/methods/m49/m49.htm> ] ; fhir:code [ fhir:v "001" ] ; fhir:display [ fhir:v "World" ] ] ) ] ) ; # fhir:caseSensitive [ fhir:v true] ; # fhir:valueSet [ fhir:v "http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"^^xsd:anyURI ; fhir:l <http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat> ] ; # fhir:content [ fhir:v "complete"] ; # fhir:concept ( [ fhir:code [ fhir:v "bam" ] ; fhir:display [ fhir:v "BAM" ] ; fhir:definition [ fhir:v "Binary Alignment/Map format for storing read alignments against reference sequences." ] ] [ fhir:code [ fhir:v "bed" ] ; fhir:display [ fhir:v "BED" ] ; fhir:definition [ fhir:v "Browser Extensible Data format for representing genomic regions and associated annotations." ] ] [ fhir:code [ fhir:v "bedpe" ] ; fhir:display [ fhir:v "BEDPE" ] ; fhir:definition [ fhir:v "Paired-End BED format for representing pairwise genomic interactions." ] ] [ fhir:code [ fhir:v "bedgraph" ] ; fhir:display [ fhir:v "BedGraph" ] ; fhir:definition [ fhir:v "BED Graph format for representing genomic signals as continuous-valued data." ] ] [ fhir:code [ fhir:v "bigbed" ] ; fhir:display [ fhir:v "bigBed" ] ; fhir:definition [ fhir:v "Binary indexed BED format for efficiently storing large amounts of genomic region data." ] ] [ fhir:code [ fhir:v "bigWig" ] ; fhir:display [ fhir:v "bigWig" ] ; fhir:definition [ fhir:v "Binary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data." ] ] [ fhir:code [ fhir:v "birdsuite-files" ] ; fhir:display [ fhir:v "Birdsuite-Files" ] ; fhir:definition [ fhir:v "File format used by the Birdsuite suite of software for SNP genotyping and copy number analysis." ] ] [ fhir:code [ fhir:v "broadpeak" ] ; fhir:display [ fhir:v "broadPeak" ] ; fhir:definition [ fhir:v "BED format variant for representing broad peaks in ChIP-Seq data." ] ] [ fhir:code [ fhir:v "cbs" ] ; fhir:display [ fhir:v "CBS" ] ; fhir:definition [ fhir:v "Copy number data format output by Circular Binary Segmentation analysis." ] ] [ fhir:code [ fhir:v "chemical-reactivity-probing-profiles" ] ; fhir:display [ fhir:v "Chemical-Reactivity-Probing-Profiles" ] ; fhir:definition [ fhir:v "Profiles of chemical reactivity for RNA structure analysis." ] ] [ fhir:code [ fhir:v "chrom-sizes" ] ; fhir:display [ fhir:v "chrom-sizes" ] ; fhir:definition [ fhir:v "File listing chromosome names and their sizes." ] ] [ fhir:code [ fhir:v "cn" ] ; fhir:display [ fhir:v "CN" ] ; fhir:definition [ fhir:v "Copy number data format." ] ] [ fhir:code [ fhir:v "custom-file-formats" ] ; fhir:display [ fhir:v "Custom-File-Formats" ] ; fhir:definition [ fhir:v "User-defined or proprietary file formats for genomic data." ] ] [ fhir:code [ fhir:v "cytoband" ] ; fhir:display [ fhir:v "Cytoband" ] ; fhir:definition [ fhir:v "Chromosome cytogenetic band locations and characteristics." ] ] [ fhir:code [ fhir:v "fasta" ] ; fhir:display [ fhir:v "FASTA" ] ; fhir:definition [ fhir:v "Format for representing sequences of nucleic acids or proteins using single letter codes." ] ] [ fhir:code [ fhir:v "gct" ] ; fhir:display [ fhir:v "GCT" ] ; fhir:definition [ fhir:v "Gene Cluster Text format for storing gene expression data." ] ] [ fhir:code [ fhir:v "cram" ] ; fhir:display [ fhir:v "CRAM" ] ; fhir:definition [ fhir:v "Compressed Reference-Aligned Map format for storing read alignments more compactly than BAM." ] ] [ fhir:code [ fhir:v "genepred" ] ; fhir:display [ fhir:v "genePred" ] ; fhir:definition [ fhir:v "Format for storing gene predictions with exon and CDS information." ] ] [ fhir:code [ fhir:v "gff-gtf" ] ; fhir:display [ fhir:v "GFF/GTF" ] ; fhir:definition [ fhir:v "General Feature Format / Gene Transfer Format for storing genomic features and annotations." ] ] [ fhir:code [ fhir:v "gistic" ] ; fhir:display [ fhir:v "GISTIC" ] ; fhir:definition [ fhir:v "Genomic Identification of Significant Targets in Cancer output format for copy number analysis." ] ] [ fhir:code [ fhir:v "goby" ] ; fhir:display [ fhir:v "Goby" ] ; fhir:definition [ fhir:v "Compact file format for storing read alignments, variations, and base quality information." ] ] [ fhir:code [ fhir:v "gwas" ] ; fhir:display [ fhir:v "GWAS" ] ; fhir:definition [ fhir:v "Genome-Wide Association Study format for storing association results." ] ] [ fhir:code [ fhir:v "igv" ] ; fhir:display [ fhir:v "IGV" ] ; fhir:definition [ fhir:v "Integrative Genomics Viewer session or display format." ] ] [ fhir:code [ fhir:v "loh" ] ; fhir:display [ fhir:v "LOH" ] ; fhir:definition [ fhir:v "Loss of Heterozygosity data format." ] ] [ fhir:code [ fhir:v "maf-multiple-alignment-format" ] ; fhir:display [ fhir:v "MAF-Multiple Alignment Format" ] ; fhir:definition [ fhir:v "Multiple Alignment Format for storing aligned sequences." ] ] [ fhir:code [ fhir:v "maf-mutation-annotation-format" ] ; fhir:display [ fhir:v "MAF-Mutation-Annotation-Format" ] ; fhir:definition [ fhir:v "Mutation Annotation Format for storing somatic mutation data." ] ] [ fhir:code [ fhir:v "merged-bam-file" ] ; fhir:display [ fhir:v "Merged BAM File" ] ; fhir:definition [ fhir:v "BAM file containing read alignments from multiple samples or lanes merged together." ] ] [ fhir:code [ fhir:v "mut" ] ; fhir:display [ fhir:v "MUT" ] ; fhir:definition [ fhir:v "Mutation data format." ] ] [ fhir:code [ fhir:v "narrowpeak" ] ; fhir:display [ fhir:v "narrowPeak" ] ; fhir:definition [ fhir:v "BED format variant for representing narrow peaks in ChIP-Seq data." ] ] [ fhir:code [ fhir:v "psl" ] ; fhir:display [ fhir:v "PSL" ] ; fhir:definition [ fhir:v "Pattern Space Layout format for storing sequence alignments." ] ] [ fhir:code [ fhir:v "res" ] ; fhir:display [ fhir:v "RES" ] ; fhir:definition [ fhir:v "Resolution data format." ] ] [ fhir:code [ fhir:v "rna-secondary-structure-formats" ] ; fhir:display [ fhir:v "RNA-Secondary-Structure-Formats" ] ; fhir:definition [ fhir:v "Formats for representing RNA secondary structure information." ] ] [ fhir:code [ fhir:v "sam" ] ; fhir:display [ fhir:v "SAM" ] ; fhir:definition [ fhir:v "Sequence Alignment/Map format for storing read alignments, the uncompressed version of BAM." ] ] [ fhir:code [ fhir:v "sample-info-attributes-file" ] ; fhir:display [ fhir:v "Sample-Info-Attributes-file" ] ; fhir:definition [ fhir:v "File containing sample information and attributes." ] ] [ fhir:code [ fhir:v "seg" ] ; fhir:display [ fhir:v "SEG" ] ; fhir:definition [ fhir:v "Segmented data format for storing copy number or other segmented genomic data." ] ] [ fhir:code [ fhir:v "tdf" ] ; fhir:display [ fhir:v "TDF" ] ; fhir:definition [ fhir:v "Tiled Data Format for efficient storage and display of large genomic datasets." ] ] [ fhir:code [ fhir:v "track-line" ] ; fhir:display [ fhir:v "Track Line" ] ; fhir:definition [ fhir:v "UCSC Genome Browser track line header defining display properties for genomic data." ] ] [ fhir:code [ fhir:v "type-line" ] ; fhir:display [ fhir:v "Type Line" ] ; fhir:definition [ fhir:v "Type line header for defining genomic data track properties." ] ] [ fhir:code [ fhir:v "vcf" ] ; fhir:display [ fhir:v "VCF" ] ; fhir:definition [ fhir:v "Variant Call Format for storing variant information including SNPs, indels, and structural variations." ] ] [ fhir:code [ fhir:v "wig" ] ; fhir:display [ fhir:v "WIG" ] ; fhir:definition [ fhir:v "Wiggle Track format for storing continuous-valued genomic data." ] ] ) . #
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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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