Genomics Reporting Implementation Guide
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Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

: Genomic Study Type CodeSystem - TTL Representation

Page standards status: Informative

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

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

<http://hl7.org/fhir/CodeSystem/genomic-study-type-cs> a fhir:CodeSystem ;
  fhir:nodeRole fhir:treeRoot ;
  fhir:Resource.id [ fhir:value "genomic-study-type-cs"] ;
  fhir:DomainResource.text [
     fhir:Narrative.status [ fhir:value "generated" ] ;
     fhir:Narrative.div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem genomic-study-type-cs</b></p><a name=\"genomic-study-type-cs\"> </a><a name=\"hcgenomic-study-type-cs\"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs</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\">alt-splc<a name=\"genomic-study-type-cs-alt-splc\"> </a></td><td>Alternative splicing detection</td><td>Identification of multiple different processed mRNA transcripts from the same DNA template</td></tr><tr><td style=\"white-space:nowrap\">chromatin<a name=\"genomic-study-type-cs-chromatin\"> </a></td><td>Chromatin conformation</td><td>Analysis of the spacial organization of chromatin within a cell</td></tr><tr><td style=\"white-space:nowrap\">cnv<a name=\"genomic-study-type-cs-cnv\"> </a></td><td>CNV detection</td><td>Detection of a change in the number of copies of a defined region of genomic DNA sequence resulting in structural variation when compared to the reference sequence</td></tr><tr><td style=\"white-space:nowrap\">epi-alt-hist<a name=\"genomic-study-type-cs-epi-alt-hist\"> </a></td><td>Epigenetic Alterations - histone modifications</td><td>Detection of biochemical modifications covalently bound to the N-terminal tail of a histone protein. These modifications may alter chromatin compaction and gene expression</td></tr><tr><td style=\"white-space:nowrap\">epi-alt-dna<a name=\"genomic-study-type-cs-epi-alt-dna\"> </a></td><td>Epigenetic Alterations -DNA methylation</td><td>Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription</td></tr><tr><td style=\"white-space:nowrap\">fam-var-segr<a name=\"genomic-study-type-cs-fam-var-segr\"> </a></td><td>Familial variant segregation</td><td>Determining if a variant identified in an individual is present in other family members</td></tr><tr><td style=\"white-space:nowrap\">func-var<a name=\"genomic-study-type-cs-func-var\"> </a></td><td>Functional variation detection</td><td>Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence</td></tr><tr><td style=\"white-space:nowrap\">gene-expression<a name=\"genomic-study-type-cs-gene-expression\"> </a></td><td>Gene expression profiling</td><td>Measurement and characterization of activity from all gene products</td></tr><tr><td style=\"white-space:nowrap\">post-trans-mod<a name=\"genomic-study-type-cs-post-trans-mod\"> </a></td><td>Post-translational Modification Identification</td><td>Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein</td></tr><tr><td style=\"white-space:nowrap\">snp<a name=\"genomic-study-type-cs-snp\"> </a></td><td>SNP Detection</td><td>Determination of which nucleotide is base present at a known variable location of the genomic sequence</td></tr><tr><td style=\"white-space:nowrap\">str<a name=\"genomic-study-type-cs-str\"> </a></td><td>STR count</td><td>Quantification of the number of sequential microsatellite units in a repetitive sequence region</td></tr><tr><td style=\"white-space:nowrap\">struc-var<a name=\"genomic-study-type-cs-struc-var\"> </a></td><td>Structural variation detection</td><td>Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence</td></tr></table></div>"
  ] ;
  fhir:DomainResource.extension [
     fhir:index 0 ;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg" ] ;
     fhir:Extension.valueCode [ fhir:value "cg" ]
  ], [
     fhir:index 1 ;
     fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status" ] ;
     fhir:Extension.valueCode [
       fhir:value "informative" ;
       fhir:Element.extension [
         fhir:index 0 ;
         fhir:Extension.url [ fhir:value "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom" ] ;
         fhir:Extension.valueCanonical [
           fhir:value "http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting" ;
           fhir:link <http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting>
         ]
       ]
     ]
  ] ;
  fhir:CodeSystem.url [ fhir:value "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs"] ;
  fhir:CodeSystem.version [ fhir:value "4.0.0-cibuild"] ;
  fhir:CodeSystem.name [ fhir:value "GenomicStudyTypeCS"] ;
  fhir:CodeSystem.title [ fhir:value "Genomic Study Type CodeSystem"] ;
  fhir:CodeSystem.status [ fhir:value "active"] ;
  fhir:CodeSystem.experimental [ fhir:value "true"^^xsd:boolean] ;
  fhir:CodeSystem.date [ fhir:value "2026-09-21T13:24:35+00:00"^^xsd:dateTime] ;
  fhir:CodeSystem.publisher [ fhir:value "HL7 International / Clinical Genomics"] ;
  fhir:CodeSystem.contact [
     fhir:index 0 ;
     fhir:ContactDetail.name [ fhir:value "HL7 International / Clinical Genomics" ] ;
     fhir:ContactDetail.telecom [
       fhir:index 0 ;
       fhir:ContactPoint.system [ fhir:value "url" ] ;
       fhir:ContactPoint.value [ fhir:value "http://www.hl7.org/Special/committees/clingenomics" ]
     ], [
       fhir:index 1 ;
       fhir:ContactPoint.system [ fhir:value "email" ] ;
       fhir:ContactPoint.value [ fhir:value "cg@lists.HL7.org" ]
     ]
  ] ;
  fhir:CodeSystem.description [ fhir:value "Backport of http://hl7.org/fhir/genomicstudy-type"] ;
  fhir:CodeSystem.jurisdiction [
     fhir:index 0 ;
     fhir:CodeableConcept.coding [
       fhir:index 0 ;
       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"^^xsd:boolean] ;
  fhir:CodeSystem.content [ fhir:value "complete"] ;
  fhir:CodeSystem.count [ fhir:value "12"^^xsd:nonNegativeInteger] ;
  fhir:CodeSystem.concept [
     fhir:index 0 ;
     fhir:CodeSystem.concept.code [ fhir:value "alt-splc" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Alternative splicing detection" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Identification of multiple different processed mRNA transcripts from the same DNA template" ]
  ], [
     fhir:index 1 ;
     fhir:CodeSystem.concept.code [ fhir:value "chromatin" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Chromatin conformation" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Analysis of the spacial organization of chromatin within a cell" ]
  ], [
     fhir:index 2 ;
     fhir:CodeSystem.concept.code [ fhir:value "cnv" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "CNV detection" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of a change in the number of copies of a defined region of genomic DNA sequence resulting in structural variation when compared to the reference sequence" ]
  ], [
     fhir:index 3 ;
     fhir:CodeSystem.concept.code [ fhir:value "epi-alt-hist" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Epigenetic Alterations - histone modifications" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of biochemical modifications covalently bound to the N-terminal tail of a histone protein. These modifications may alter chromatin compaction and gene expression" ]
  ], [
     fhir:index 4 ;
     fhir:CodeSystem.concept.code [ fhir:value "epi-alt-dna" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Epigenetic Alterations -DNA methylation" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription" ]
  ], [
     fhir:index 5 ;
     fhir:CodeSystem.concept.code [ fhir:value "fam-var-segr" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Familial variant segregation" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Determining if a variant identified in an individual is present in other family members" ]
  ], [
     fhir:index 6 ;
     fhir:CodeSystem.concept.code [ fhir:value "func-var" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Functional variation detection" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence" ]
  ], [
     fhir:index 7 ;
     fhir:CodeSystem.concept.code [ fhir:value "gene-expression" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Gene expression profiling" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Measurement and characterization of activity from all gene products" ]
  ], [
     fhir:index 8 ;
     fhir:CodeSystem.concept.code [ fhir:value "post-trans-mod" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Post-translational Modification Identification" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein" ]
  ], [
     fhir:index 9 ;
     fhir:CodeSystem.concept.code [ fhir:value "snp" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "SNP Detection" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Determination of which nucleotide is base present at a known variable location of the genomic sequence" ]
  ], [
     fhir:index 10 ;
     fhir:CodeSystem.concept.code [ fhir:value "str" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "STR count" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Quantification of the number of sequential microsatellite units in a repetitive sequence region" ]
  ], [
     fhir:index 11 ;
     fhir:CodeSystem.concept.code [ fhir:value "struc-var" ] ;
     fhir:CodeSystem.concept.display [ fhir:value "Structural variation detection" ] ;
     fhir:CodeSystem.concept.definition [ fhir:value "Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence" ]
  ] .

# - ontology header ------------------------------------------------------------

<http://hl7.org/fhir/CodeSystem/genomic-study-type-cs.ttl> a owl:Ontology ;
  owl:imports fhir:fhir.ttl ;
  owl:versionIRI <http://build.fhir.org/CodeSystem/genomic-study-type-cs.ttl> .