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Source1

{
  "resourceType": "CodeSystem",
  "id": "genomicstudy-dataformat",
  "meta": {
    "lastUpdated": "2021-01-05T10:01:24.148+11:00",
    "profile": [
      "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "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."
    }
  ]
}