Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
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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 -------------------------------------------------------------------
a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "genomic-study-type-cs"] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><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:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [ fhir:v "cg" ]
] ) ; #
fhir:url [ fhir:v "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-type-cs"^^xsd:anyURI] ; #
fhir:version [ fhir:v "3.0.1-SNAPSHOT"] ; #
fhir:name [ fhir:v "GenomicStudyTypeCS"] ; #
fhir:title [ fhir:v "Genomic Study Type CodeSystem"] ; #
fhir:status [ fhir:v "active"] ; #
fhir:experimental [ fhir:v "true"^^xsd:boolean] ; #
fhir:date [ fhir:v "2024-04-09T13:57:55+00:00"^^xsd:dateTime] ; #
fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; #
fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "cg@lists.HL7.org" ] ] )
] ) ; #
fhir:description [ fhir:v "Backport of http://hl7.org/fhir/genomicstudy-type"] ; #
fhir:jurisdiction ( [
( fhir:coding [
fhir:system [ fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ] ] )
] ) ; #
fhir:caseSensitive [ fhir:v "true"^^xsd:boolean] ; #
fhir:content [ fhir:v "complete"] ; #
fhir:count [ fhir:v "12"^^xsd:nonNegativeInteger] ; #
fhir:concept ( [
fhir:code [ fhir:v "alt-splc" ] ;
fhir:display [ fhir:v "Alternative splicing detection" ] ;
fhir:definition [ fhir:v "Identification of multiple different processed mRNA transcripts from the same DNA template" ]
] [
fhir:code [ fhir:v "chromatin" ] ;
fhir:display [ fhir:v "Chromatin conformation" ] ;
fhir:definition [ fhir:v "Analysis of the spacial organization of chromatin within a cell" ]
] [
fhir:code [ fhir:v "cnv" ] ;
fhir:display [ fhir:v "CNV detection" ] ;
fhir:definition [ fhir:v "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:code [ fhir:v "epi-alt-hist" ] ;
fhir:display [ fhir:v "Epigenetic Alterations - histone modifications" ] ;
fhir:definition [ fhir:v "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:code [ fhir:v "epi-alt-dna" ] ;
fhir:display [ fhir:v "Epigenetic Alterations -DNA methylation" ] ;
fhir:definition [ fhir:v "Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription" ]
] [
fhir:code [ fhir:v "fam-var-segr" ] ;
fhir:display [ fhir:v "Familial variant segregation" ] ;
fhir:definition [ fhir:v "Determining if a variant identified in an individual is present in other family members" ]
] [
fhir:code [ fhir:v "func-var" ] ;
fhir:display [ fhir:v "Functional variation detection" ] ;
fhir:definition [ fhir:v "Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence" ]
] [
fhir:code [ fhir:v "gene-expression" ] ;
fhir:display [ fhir:v "Gene expression profiling" ] ;
fhir:definition [ fhir:v "Measurement and characterization of activity from all gene products" ]
] [
fhir:code [ fhir:v "post-trans-mod" ] ;
fhir:display [ fhir:v "Post-translational Modification Identification" ] ;
fhir:definition [ fhir:v "Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein" ]
] [
fhir:code [ fhir:v "snp" ] ;
fhir:display [ fhir:v "SNP Detection" ] ;
fhir:definition [ fhir:v "Determination of which nucleotide is base present at a known variable location of the genomic sequence" ]
] [
fhir:code [ fhir:v "str" ] ;
fhir:display [ fhir:v "STR count" ] ;
fhir:definition [ fhir:v "Quantification of the number of sequential microsatellite units in a repetitive sequence region" ]
] [
fhir:code [ fhir:v "struc-var" ] ;
fhir:display [ fhir:v "Structural variation detection" ] ;
fhir:definition [ fhir:v "Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence" ]
] ) . #
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