FHIR Cross-Version Extensions package for FHIR R4 from FHIR R5
0.0.1-snapshot-2 - informative International flag

FHIR Cross-Version Extensions package for FHIR R4 from FHIR R5 - Version 0.0.1-snapshot-2. See the Directory of published versions

: Genomic Study Type - TTL Representation

Page standards status: Informative Maturity Level: 1

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@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@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 "genomicstudy-type"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n            <p>This code system \n              <code>http://hl7.org/fhir/genomicstudy-type</code> defines the following codes:\n            </p>\n            <table class=\"codes\">\n              <tr>\n                <td style=\"white-space:nowrap\">\n                  <b>Code</b>\n                </td>\n                <td>\n                  <b>Display</b>\n                </td>\n                <td>\n                  <b>Definition</b>\n                </td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">alt-splc\n                  <a name=\"genomicstudy-type-alt-splc\"> </a>\n                </td>\n                <td>Alternative splicing detection</td>\n                <td>Identification of multiple different processed mRNA transcripts from the same DNA template</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">chromatin\n                  <a name=\"genomicstudy-type-chromatin\"> </a>\n                </td>\n                <td>Chromatin conformation</td>\n                <td>Analysis of the spacial organization of chromatin within a cell</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">cnv\n                  <a name=\"genomicstudy-type-cnv\"> </a>\n                </td>\n                <td>CNV detection</td>\n                <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>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">epi-alt-hist\n                  <a name=\"genomicstudy-type-epi-alt-hist\"> </a>\n                </td>\n                <td>Epigenetic Alterations - histone modifications</td>\n                <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>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">epi-alt-dna\n                  <a name=\"genomicstudy-type-epi-alt-dna\"> </a>\n                </td>\n                <td>Epigenetic Alterations -DNA methylation</td>\n                <td>Detection of the presence of an additional methyl group on a DNA nucleobase, which may alter gene transcription</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">fam-var-segr\n                  <a name=\"genomicstudy-type-fam-var-segr\"> </a>\n                </td>\n                <td>Familial variant segregation</td>\n                <td>Determining if a variant identified in an individual is present in other family members</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">func-var\n                  <a name=\"genomicstudy-type-func-var\"> </a>\n                </td>\n                <td>Functional variation detection</td>\n                <td>Detection of sequence variants which may alter gene expression or gene product function when compared to the reference sequence</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">gene-expression\n                  <a name=\"genomicstudy-type-gene-expression\"> </a>\n                </td>\n                <td>Gene expression profiling</td>\n                <td>Measurement and characterization of activity from all gene products</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">post-trans-mod\n                  <a name=\"genomicstudy-type-post-trans-mod\"> </a>\n                </td>\n                <td>Post-translational Modification Identification</td>\n                <td>Detection of biochemical modifications covalently bound to the amino acid monomers of a processed protein</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">snp\n                  <a name=\"genomicstudy-type-snp\"> </a>\n                </td>\n                <td>SNP Detection</td>\n                <td>Determination of which nucleotide is base present at a known variable location of the genomic sequence</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">str\n                  <a name=\"genomicstudy-type-str\"> </a>\n                </td>\n                <td>STR count</td>\n                <td>Quantification of the number of sequential microsatellite units in a repetitive sequence region</td>\n              </tr>\n              <tr>\n                <td style=\"white-space:nowrap\">struc-var\n                  <a name=\"genomicstudy-type-struc-var\"> </a>\n                </td>\n                <td>Structural variation detection</td>\n                <td>Detection of deletions, insertions, or rearrangements of DNA segments compared to the reference sequence</td>\n              </tr>\n            </table>\n          </div>"^^rdf:XMLLiteral
  ] ; # 
  fhir:extension ( [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ] ;
fhir:value [
a fhir:code ;
fhir:v "informative"     ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ] ;
fhir:value [
a fhir:integer ;
fhir:v 1     ]
  ] [
    ( fhir:extension [
fhir:url [ fhir:v "packageId"^^xsd:anyURI ] ;
fhir:value [
a fhir:id ;
fhir:v "hl7.fhir.uv.xver-r5.r4"       ]     ] [
fhir:url [ fhir:v "version"^^xsd:anyURI ] ;
fhir:value [
a fhir:string ;
fhir:v "0.0.1-snapshot-2"       ]     ] ) ;
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/package-source"^^xsd:anyURI ]
  ] [
fhir:url [ fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ] ;
fhir:value [
a fhir:code ;
fhir:v "cg"     ]
  ] ) ; # 
  fhir:url [ fhir:v "http://hl7.org/fhir/genomicstudy-type"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "5.0.0"] ; # 
  fhir:name [ fhir:v "GenomicStudyType"] ; # 
  fhir:title [ fhir:v "Genomic Study Type"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:experimental [ fhir:v true] ; # 
  fhir:date [ fhir:v "2022-08-18T07:19:24+10:00"^^xsd:dateTime] ; # 
  fhir:publisher [ fhir:v "Clinical Genomics"] ; # 
  fhir:contact ( [
fhir:name [ fhir:v "Clinical Genomics" ] ;
    ( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ]     ] )
  ] ) ; # 
  fhir:description [ fhir:v "The type relevant to GenomicStudy."] ; # 
  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] ; # 
  fhir:valueSet [
fhir:v "http://hl7.org/fhir/ValueSet/genomicstudy-type"^^xsd:anyURI ;
fhir:link <http://hl7.org/fhir/ValueSet/genomicstudy-type>
  ] ; # 
  fhir:content [ fhir:v "complete"] ; # 
  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" ]
  ] ) . #