Release 5 Ballot

This page is part of the FHIR Specification (v5.0.0-ballot: FHIR R5 Ballot Preview). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions

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

Clinical Genomics Work Group Maturity Level: 0Trial Use Use Context: Any

This is a code system defined by the FHIR project.

Summary

Defining URL:http://hl7.org/fhir/genomicstudy-dataformat
Version:5.0.0-ballot
Name:GenomicStudyDataFormat
Title:GenomicStudyDataFormat
Status:draft
Definition:

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

Committee:Clinical Genomics Work Group
OID:2.16.840.1.113883.4.642.4.1978 (for OID based terminology systems)
Flags:CaseSensitive, Complete
All codes ValueSet:GenomicStudyDataFormat

This Code system is used in the following value sets:

4.3.2.492.1 Content

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

CodeDisplayCopy
bam BAM 
bed BED 
bedpe BEDPE 
bedgraph BedGraph 
bigbed bigBed 
bigWig bigWig 
birdsuite-files Birdsuite-Files 
broadpeak broadPeak 
cbs CBS 
chemical-reactivity-probing-profiles Chemical-Reactivity-Probing-Profiles 
chrom-sizes chrom-sizes 
cn CN 
custom-file-formats Custom-File-Formats 
cytoband Cytoband 
fasta FASTA 
gct GCT 
cram CRAM 
genepred genePred 
gff-gtf GFF/GTF 
gistic GISTIC 
goby Goby 
gwas GWAS 
igv IGV 
loh LOH 
maf-multiple-alignment-format MAF-Multiple Alignment Format 
maf-mutation-annotation-format MAF-Mutation-Annotation-Format 
merged-bam-file Merged BAM File 
mut MUT 
narrowpeak narrowPeak 
psl PSL 
res RES 
rna-secondary-structure-formats RNA-Secondary-Structure-Formats 
sam SAM 
sample-info-attributes-file Sample-Info-Attributes-file 
seg SEG 
tdf TDF 
track-line Track Line 
type-line Type Line 
vcf VCF 
wig WIG 

 

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