Snapshot 3: Connectathon 32 Base

This is Snapshot #3 for FHIR R5, released to support Connectathon 32. For a full list of available versions, see the Directory of published versions.

Example CodeSystem/genomicstudy-dataformat (Turtle)

Clinical Genomics Work GroupMaturity Level: N/AStandards Status: Informative

Raw Turtle (+ also see Turtle/RDF Format Specification)

Definition for Code SystemGenomicStudyDataFormat

@prefix fhir: <http://hl7.org/fhir/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .

# - resource -------------------------------------------------------------------

[] a fhir:CodeSystem;
  fhir:Resource.id [ fhir:value "genomicstudy-dataformat"];
  fhir:Resource.meta [
     fhir:Meta.lastUpdated [ fhir:value "2022-12-14T07:12:54.019+11:00" ];
     fhir:Meta.profile [ fhir:value "http://hl7.org/fhir/StructureDefinition/shareablecodesystem" ]
  ];
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ]
  ];
  fhir:DomainResource.extension [
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ];
     fhir:Extension.value [ fhir:value "cg" ]
  ], [
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status" ];
     fhir:Extension.value [ fhir:value "trial-use" ]
  ], [
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm" ];
     fhir:Extension.value [ fhir:value "0" ]
  ];
  fhir:CanonicalResource.url [ fhir:value "http://hl7.org/fhir/genomicstudy-dataformat"];
  fhir:CanonicalResource.identifier [
     fhir:Identifier.system [ fhir:value "urn:ietf:rfc:3986" ];
     fhir:Identifier.value [ fhir:value "urn:oid:2.16.840.1.113883.4.642.4.1978" ]
  ];
  fhir:CanonicalResource.version [ fhir:value "5.0.0-snapshot3"];
  fhir:CanonicalResource.name [ fhir:value "GenomicStudyDataFormat"];
  fhir:CanonicalResource.title [ fhir:value "GenomicStudyDataFormat"];
  fhir:CanonicalResource.status [ fhir:value "active"];
  fhir:CanonicalResource.experimental [ fhir:value "true"];
  fhir:CanonicalResource.date [ fhir:value "2022-08-17T14:49:24-05:00"];
  fhir:CanonicalResource.publisher [ fhir:value "HL7 (FHIR Project)"];
  fhir:CanonicalResource.contact [
     fhir:ContactDetail.telecom [
       fhir:ContactPoint.system [ fhir:value "url" ];
       fhir:ContactPoint.value [ fhir:value "http://hl7.org/fhir" ]
     ], [
       fhir:ContactPoint.system [ fhir:value "email" ];
       fhir:ContactPoint.value [ fhir:value "fhir@lists.hl7.org" ]
     ]
  ];
  fhir:CanonicalResource.description [ fhir:value "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:CanonicalResource.jurisdiction [
     fhir:CodeableConcept.coding [
       fhir:Coding.system [ fhir:value "http://unstats.un.org/unsd/methods/m49/m49.htm" ];
       fhir:Coding.code [ fhir:value "001" ];
       fhir:Coding.display [ fhir:value "World" ]
     ]
  ];
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/genomicstudy-dataformat"];
  fhir:CodeSystem.identifier [
     fhir:Identifier.system [ fhir:value "urn:ietf:rfc:3986" ];
     fhir:Identifier.value [ fhir:value "urn:oid:2.16.840.1.113883.4.642.4.1978" ]
  ];
  fhir:CodeSystem.version [ fhir:value "5.0.0-snapshot3"];
  fhir:CodeSystem.name [ fhir:value "GenomicStudyDataFormat"];
  fhir:CodeSystem.title [ fhir:value "GenomicStudyDataFormat"];
  fhir:CodeSystem.status [ fhir:value "active"];
  fhir:CodeSystem.experimental [ fhir:value "true"];
  fhir:CodeSystem.date [ fhir:value "2022-08-17T14:49:24-05:00"];
  fhir:CodeSystem.publisher [ fhir:value "HL7 (FHIR Project)"];
  fhir:CodeSystem.contact [
     fhir:ContactDetail.telecom [
       fhir:ContactPoint.system [ fhir:value "url" ];
       fhir:ContactPoint.value [ fhir:value "http://hl7.org/fhir" ]
     ], [
       fhir:ContactPoint.system [ fhir:value "email" ];
       fhir:ContactPoint.value [ fhir:value "fhir@lists.hl7.org" ]
     ]
  ];
  fhir:CodeSystem.description [ fhir:value "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:CodeSystem.jurisdiction [
     fhir:CodeableConcept.coding [
       fhir:Coding.system [ fhir:value "http://unstats.un.org/unsd/methods/m49/m49.htm" ];
       fhir:Coding.code [ fhir:value "001" ];
       fhir:Coding.display [ fhir:value "World" ]
     ]
  ];
  fhir:CodeSystem.caseSensitive [ fhir:value "true"];
  fhir:CodeSystem.valueSet [ fhir:value "http://hl7.org/fhir/ValueSet/genomicstudy-dataformat"];
  fhir:CodeSystem.content [ fhir:value "complete"];
  fhir:CodeSystem.concept [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bam" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "BAM" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bed" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "BED" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bedpe" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "BEDPE" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bedgraph" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "BedGraph" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bigbed" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "bigBed" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "bigWig" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "bigWig" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "birdsuite-files" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Birdsuite-Files" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "broadpeak" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "broadPeak" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "cbs" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "CBS" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "chemical-reactivity-probing-profiles" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Chemical-Reactivity-Probing-Profiles" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "chrom-sizes" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "chrom-sizes" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "cn" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "CN" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "custom-file-formats" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Custom-File-Formats" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "cytoband" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Cytoband" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "fasta" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "FASTA" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "gct" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "GCT" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "cram" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "CRAM" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "genepred" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "genePred" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "gff-gtf" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "GFF/GTF" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "gistic" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "GISTIC" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "goby" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Goby" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "gwas" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "GWAS" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "igv" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "IGV" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "loh" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "LOH" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "maf-multiple-alignment-format" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "MAF-Multiple Alignment Format" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "maf-mutation-annotation-format" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "MAF-Mutation-Annotation-Format" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "merged-bam-file" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Merged BAM File" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "mut" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "MUT" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "narrowpeak" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "narrowPeak" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "psl" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "PSL" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "res" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "RES" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "rna-secondary-structure-formats" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "RNA-Secondary-Structure-Formats" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "sam" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "SAM" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "sample-info-attributes-file" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Sample-Info-Attributes-file" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "seg" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "SEG" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "tdf" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "TDF" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "track-line" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Track Line" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "type-line" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "Type Line" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "vcf" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "VCF" ]
  ], [
     fhir:ConceptDefinitionComponent.code [ fhir:value "wig" ];
     fhir:ConceptDefinitionComponent.display [ fhir:value "WIG" ]
  ] .

# -------------------------------------------------------------------------------------

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.