Snapshot 3: Connectathon 32 Base

This page is part of the FHIR Specification (v5.0.0-snapshot3: R5 Snapshot #3, to support Connectathon 32). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

4.3.2.454 CodeSystem http://hl7.org/fhir/genomicstudy-dataformat

Clinical Genomics icon Work Group Maturity Level: 0Trial Use Use Context: Country: World, Not yet ready for Production use, Not yet ready for Production use
Official URL: http://hl7.org/fhir/genomicstudy-dataformat Version: 5.0.0-snapshot3
active as of 2022-08-18 Computable Name: GenomicStudyDataFormat
Flags: Experimental, CaseSensitive, Complete. All codes ValueSet: GenomicStudyDataFormat OID: 2.16.840.1.113883.4.642.4.1978

This Code system is used in the following value sets:

4.3.2.454.1 Definition

The data format relevant to genomics. These formats and relevant codes were pulled from Integrative Genomics Viewer Documentation icon by Broad Institute.

4.3.2.454.2 Content

This code system http://hl7.org/fhir/genomicstudy-dataformat defines the following codes:

CodeDisplayCopy
bam BAMbtn btn
bed BEDbtn btn
bedpe BEDPEbtn btn
bedgraph BedGraphbtn btn
bigbed bigBedbtn btn
bigWig bigWigbtn btn
birdsuite-files Birdsuite-Filesbtn btn
broadpeak broadPeakbtn btn
cbs CBSbtn btn
chemical-reactivity-probing-profiles Chemical-Reactivity-Probing-Profilesbtn btn
chrom-sizes chrom-sizesbtn btn
cn CNbtn btn
custom-file-formats Custom-File-Formatsbtn btn
cytoband Cytobandbtn btn
fasta FASTAbtn btn
gct GCTbtn btn
cram CRAMbtn btn
genepred genePredbtn btn
gff-gtf GFF/GTFbtn btn
gistic GISTICbtn btn
goby Gobybtn btn
gwas GWASbtn btn
igv IGVbtn btn
loh LOHbtn btn
maf-multiple-alignment-format MAF-Multiple Alignment Formatbtn btn
maf-mutation-annotation-format MAF-Mutation-Annotation-Formatbtn btn
merged-bam-file Merged BAM Filebtn btn
mut MUTbtn btn
narrowpeak narrowPeakbtn btn
psl PSLbtn btn
res RESbtn btn
rna-secondary-structure-formats RNA-Secondary-Structure-Formatsbtn btn
sam SAMbtn btn
sample-info-attributes-file Sample-Info-Attributes-filebtn btn
seg SEGbtn btn
tdf TDFbtn btn
track-line Track Linebtn btn
type-line Type Linebtn btn
vcf VCFbtn btn
wig WIGbtn btn

 

See the full registry of code systems defined as part of FHIR.

Explanation of the columns that may appear on this page:

LevelA few code lists that FHIR defines are hierarchical - each code is assigned a level. See Code System for further information.
SourceThe source of the definition of the code (when the value set draws in codes defined elsewhere)
CodeThe code (used as the code in the resource instance). If the code is in italics, this indicates that the code is not selectable ('Abstract')
DisplayThe display (used in the display element of a Coding). If there is no display, implementers should not simply display the code, but map the concept into their application
DefinitionAn explanation of the meaning of the concept
CommentsAdditional notes about how to use the code