Ferlab.bio CodeSystem/data-type - TTL Representation - Cqgc Implementation Guide v0.1.0

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: Ferlab.bio CodeSystem/data-type - TTL Representation

Active as of 2025-08-25
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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 "data-type"] ; # 
  fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem data-type</b></p><a name=\"data-type\"> </a><a name=\"hcdata-type\"> </a><p>This case-sensitive code system <code>http://fhir.cqgc.ferlab.bio/CodeSystem/data-type</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>French (fr)</b></td></tr><tr><td style=\"white-space:nowrap\">ALIR<a name=\"data-type-ALIR\"> </a></td><td>Aligned Reads</td><td>Fragments alignés</td></tr><tr><td style=\"white-space:nowrap\">ALIRPG<a name=\"data-type-ALIRPG\"> </a></td><td>Aligned Reads from Variants Non-Repetitive Regions Report</td><td>Fragments alignés pour les variants annotés provenant de régions non répétées</td></tr><tr><td style=\"white-space:nowrap\">SNV<a name=\"data-type-SNV\"> </a></td><td>Germline SNV</td><td>SNV germinal</td></tr><tr><td style=\"white-space:nowrap\">SSNV<a name=\"data-type-SSNV\"> </a></td><td>Somatic SNV</td><td>SNV somatic</td></tr><tr><td style=\"white-space:nowrap\">SNVPG<a name=\"data-type-SNVPG\"> </a></td><td>Germline SNV from Variants Non-Repetitive Regions Report</td><td>Variants SNV germinales annotés provenant de régions non répétées</td></tr><tr><td style=\"white-space:nowrap\">GCNV<a name=\"data-type-GCNV\"> </a></td><td>Germline CNV</td><td>CNV germinal</td></tr><tr><td style=\"white-space:nowrap\">SCNV<a name=\"data-type-SCNV\"> </a></td><td>Somatic CNV</td><td>CNV somatic</td></tr><tr><td style=\"white-space:nowrap\">GSV<a name=\"data-type-GSV\"> </a></td><td>Germline SV</td><td>SV germinal</td></tr><tr><td style=\"white-space:nowrap\">SSV<a name=\"data-type-SSV\"> </a></td><td>Somatic SV</td><td>SV somatic</td></tr><tr><td style=\"white-space:nowrap\">SOMFU<a name=\"data-type-SOMFU\"> </a></td><td>Somatic Fusion Dragen VCF</td><td>VCF Dragen des fusions somatiques</td></tr><tr><td style=\"white-space:nowrap\">SSUP<a name=\"data-type-SSUP\"> </a></td><td>Sequencing Data Supplement</td><td>Données de séquençage supplémentaires</td></tr><tr><td style=\"white-space:nowrap\">IGV<a name=\"data-type-IGV\"> </a></td><td>IGV Track</td><td>Track IGV</td></tr><tr><td style=\"white-space:nowrap\">CNVVIS<a name=\"data-type-CNVVIS\"> </a></td><td>CNV Visualization</td><td>Visualization de CNVs</td></tr><tr><td style=\"white-space:nowrap\">EXP<a name=\"data-type-EXP\"> </a></td><td>Expression PNG</td><td>PNG des expressions</td></tr><tr><td style=\"white-space:nowrap\">COVGENE<a name=\"data-type-COVGENE\"> </a></td><td>Coverage by Gene Report</td><td>Rapport de couverture par gène</td></tr><tr><td style=\"white-space:nowrap\">QCRUN<a name=\"data-type-QCRUN\"> </a></td><td>Sequencing Run QC Report</td><td>Rapport de controle de qualité de la run de séquençage</td></tr><tr><td style=\"white-space:nowrap\">EXOMISER<a name=\"data-type-EXOMISER\"> </a></td><td>Exomiser SNV Report</td><td>Rapport SNV Exomiser</td></tr><tr><td style=\"white-space:nowrap\">EXOMISER_CNV<a name=\"data-type-EXOMISER_CNV\"> </a></td><td>Exomiser CNV Report</td><td>Rapport CNV Exomiser</td></tr><tr><td style=\"white-space:nowrap\">PFUSION<a name=\"data-type-PFUSION\"> </a></td><td>Preliminary Fusion TSV</td><td>TSV préliminaire des fusions</td></tr><tr><td style=\"white-space:nowrap\">RNASEQ<a name=\"data-type-RNASEQ\"> </a></td><td>RNA Sequences</td><td>Séquences d'ARN</td></tr><tr><td style=\"white-space:nowrap\">SRNASEQFCP<a name=\"data-type-SRNASEQFCP\"> </a></td><td>Somatic RNA Sequences Fusion Candidate Preliminary</td><td>Fichier préliminaire des candidats de fusion de séquences d'ARN somatique</td></tr><tr><td style=\"white-space:nowrap\">SRNASEQFCF<a name=\"data-type-SRNASEQFCF\"> </a></td><td>Somatic RNA Sequences Fusion Candidate Final</td><td>Fichier final des candidats de fusion de séquences d'ARN somatique</td></tr><tr><td style=\"white-space:nowrap\">SGENEXPSF<a name=\"data-type-SGENEXPSF\"> </a></td><td>Somatic Gene Expression SF</td><td>Expression génique somatique SF</td></tr><tr><td style=\"white-space:nowrap\">FFUSION<a name=\"data-type-FFUSION\"> </a></td><td>Final Fusion</td><td>Final des fusions</td></tr><tr><td style=\"white-space:nowrap\">MDALL<a name=\"data-type-MDALL\"> </a></td><td>Leukemia Classification by the MD-ALL Algorithm</td><td>Classification de la leucémie par l'algorithme MD-ALL</td></tr><tr><td style=\"white-space:nowrap\">KMBCOR<a name=\"data-type-KMBCOR\"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style=\"white-space:nowrap\">KMFLT3<a name=\"data-type-KMFLT3\"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style=\"white-space:nowrap\">KMUBTF<a name=\"data-type-KMUBTF\"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style=\"white-space:nowrap\">KMNPM1<a name=\"data-type-KMNPM1\"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style=\"white-space:nowrap\">INDX<a name=\"data-type-INDX\"> </a></td><td>Sequencing Data Index</td><td>Index de données de séquençage</td></tr><tr><td style=\"white-space:nowrap\">OTHER<a name=\"data-type-OTHER\"> </a></td><td>Undefined Data Type</td><td>Type de données indéfini</td></tr><tr><td style=\"white-space:nowrap\">FUSG<a name=\"data-type-FUSG\"> </a></td><td>Gene fusion</td><td>Fusion de gènes</td></tr><tr><td style=\"white-space:nowrap\">HLA<a name=\"data-type-HLA\"> </a></td><td>HLA Caller Results</td><td>Résultats de l'appel des allèles HLA</td></tr><tr><td style=\"white-space:nowrap\">PAC<a name=\"data-type-PAC\"> </a></td><td>Paralog Calling</td><td>Appel de variants dans les gènes paralogues</td></tr><tr><td style=\"white-space:nowrap\">PEC<a name=\"data-type-PEC\"> </a></td><td>Ploidy Estimation per Chromosome</td><td>Estimation de la ploïdie par chromosome</td></tr><tr><td style=\"white-space:nowrap\">ROH<a name=\"data-type-ROH\"> </a></td><td>Runs of Homozygosity</td><td>Segments d’homozygotie</td></tr><tr><td style=\"white-space:nowrap\">STR<a name=\"data-type-STR\"> </a></td><td>Tandem Repeat Calls</td><td>Appel de répétions en tandem</td></tr><tr><td style=\"white-space:nowrap\">NORM_VEPPG<a name=\"data-type-NORM_VEPPG\"> </a></td><td>Annotated Variants from Non-Repetitive Regions (Legacy Batch) VCF File</td><td>Fichier VCF des variants annotés provenant de régions non répétées (ancien traitement par lot)</td></tr><tr><td style=\"white-space:nowrap\">NRRV<a name=\"data-type-NRRV\"> </a></td><td>Annotated Variants from Non-Repetitive Regions Report</td><td>Rapport de variants annotés provenant de régions non répétées</td></tr><tr><td style=\"white-space:nowrap\">PHENOVAR<a name=\"data-type-PHENOVAR\"> </a></td><td>Phenovar Detailed Results</td><td>Résultats détaillés de Phenovar</td></tr></table></div>"^^rdf:XMLLiteral
  ] ; # 
  fhir:url [ fhir:v "http://fhir.cqgc.ferlab.bio/CodeSystem/data-type"^^xsd:anyURI] ; # 
  fhir:version [ fhir:v "0.1.0"] ; # 
  fhir:name [ fhir:v "data-type"] ; # 
  fhir:title [ fhir:v "Data types"] ; # 
  fhir:status [ fhir:v "active"] ; # 
  fhir:experimental [ fhir:v false] ; # 
  fhir:date [ fhir:v "2025-08-25T15:12:45+00:00"^^xsd:dateTime] ; # 
  fhir:publisher [ fhir:v "Ferlab.bio"] ; # 
  fhir:contact ( [
fhir:name [ fhir:v "Cqgc" ] ;
    ( fhir:telecom [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "mailto:support@ferlab.bio" ]     ] )
  ] ) ; # 
  fhir:description [ fhir:v "Data types"] ; # 
  fhir:caseSensitive [ fhir:v true] ; # 
  fhir:content [ fhir:v "complete"] ; # 
  fhir:count [ fhir:v "5"^^xsd:nonNegativeInteger] ; # 
  fhir:concept ( [
fhir:code [ fhir:v "ALIR" ] ;
fhir:display [ fhir:v "Aligned Reads" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fragments alignés" ]     ] )
  ] [
fhir:code [ fhir:v "ALIRPG" ] ;
fhir:display [ fhir:v "Aligned Reads from Variants Non-Repetitive Regions Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fragments alignés pour les variants annotés provenant de régions non répétées" ]     ] )
  ] [
fhir:code [ fhir:v "SNV" ] ;
fhir:display [ fhir:v "Germline SNV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "SNV germinal" ]     ] )
  ] [
fhir:code [ fhir:v "SSNV" ] ;
fhir:display [ fhir:v "Somatic SNV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "SNV somatic" ]     ] )
  ] [
fhir:code [ fhir:v "SNVPG" ] ;
fhir:display [ fhir:v "Germline SNV from Variants Non-Repetitive Regions Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Variants SNV germinales annotés provenant de régions non répétées" ]     ] )
  ] [
fhir:code [ fhir:v "GCNV" ] ;
fhir:display [ fhir:v "Germline CNV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "CNV germinal" ]     ] )
  ] [
fhir:code [ fhir:v "SCNV" ] ;
fhir:display [ fhir:v "Somatic CNV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "CNV somatic" ]     ] )
  ] [
fhir:code [ fhir:v "GSV" ] ;
fhir:display [ fhir:v "Germline SV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "SV germinal" ]     ] )
  ] [
fhir:code [ fhir:v "SSV" ] ;
fhir:display [ fhir:v "Somatic SV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "SV somatic" ]     ] )
  ] [
fhir:code [ fhir:v "SOMFU" ] ;
fhir:display [ fhir:v "Somatic Fusion Dragen VCF" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "VCF Dragen des fusions somatiques" ]     ] )
  ] [
fhir:code [ fhir:v "SSUP" ] ;
fhir:display [ fhir:v "Sequencing Data Supplement" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Données de séquençage supplémentaires" ]     ] )
  ] [
fhir:code [ fhir:v "IGV" ] ;
fhir:display [ fhir:v "IGV Track" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Track IGV" ]     ] )
  ] [
fhir:code [ fhir:v "CNVVIS" ] ;
fhir:display [ fhir:v "CNV Visualization" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Visualization de CNVs" ]     ] )
  ] [
fhir:code [ fhir:v "EXP" ] ;
fhir:display [ fhir:v "Expression PNG" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "PNG des expressions" ]     ] )
  ] [
fhir:code [ fhir:v "COVGENE" ] ;
fhir:display [ fhir:v "Coverage by Gene Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Rapport de couverture par gène" ]     ] )
  ] [
fhir:code [ fhir:v "QCRUN" ] ;
fhir:display [ fhir:v "Sequencing Run QC Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Rapport de controle de qualité de la run de séquençage" ]     ] )
  ] [
fhir:code [ fhir:v "EXOMISER" ] ;
fhir:display [ fhir:v "Exomiser SNV Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Rapport SNV Exomiser" ]     ] )
  ] [
fhir:code [ fhir:v "EXOMISER_CNV" ] ;
fhir:display [ fhir:v "Exomiser CNV Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Rapport CNV Exomiser" ]     ] )
  ] [
fhir:code [ fhir:v "PFUSION" ] ;
fhir:display [ fhir:v "Preliminary Fusion TSV" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "TSV préliminaire des fusions" ]     ] )
  ] [
fhir:code [ fhir:v "RNASEQ" ] ;
fhir:display [ fhir:v "RNA Sequences" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Séquences d'ARN" ]     ] )
  ] [
fhir:code [ fhir:v "SRNASEQFCP" ] ;
fhir:display [ fhir:v "Somatic RNA Sequences Fusion Candidate Preliminary" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fichier préliminaire des candidats de fusion de séquences d'ARN somatique" ]     ] )
  ] [
fhir:code [ fhir:v "SRNASEQFCF" ] ;
fhir:display [ fhir:v "Somatic RNA Sequences Fusion Candidate Final" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fichier final des candidats de fusion de séquences d'ARN somatique" ]     ] )
  ] [
fhir:code [ fhir:v "SGENEXPSF" ] ;
fhir:display [ fhir:v "Somatic Gene Expression SF" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Expression génique somatique SF" ]     ] )
  ] [
fhir:code [ fhir:v "FFUSION" ] ;
fhir:display [ fhir:v "Final Fusion" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Final des fusions" ]     ] )
  ] [
fhir:code [ fhir:v "MDALL" ] ;
fhir:display [ fhir:v "Leukemia Classification by the MD-ALL Algorithm" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Classification de la leucémie par l'algorithme MD-ALL" ]     ] )
  ] [
fhir:code [ fhir:v "KMBCOR" ] ;
fhir:display [ fhir:v "Somatic Targeted Analysis by the KM Algorithm" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Analyse ciblée somatique par l'algorithme KM" ]     ] )
  ] [
fhir:code [ fhir:v "KMFLT3" ] ;
fhir:display [ fhir:v "Somatic Targeted Analysis by the KM Algorithm" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Analyse ciblée somatique par l'algorithme KM" ]     ] )
  ] [
fhir:code [ fhir:v "KMUBTF" ] ;
fhir:display [ fhir:v "Somatic Targeted Analysis by the KM Algorithm" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Analyse ciblée somatique par l'algorithme KM" ]     ] )
  ] [
fhir:code [ fhir:v "KMNPM1" ] ;
fhir:display [ fhir:v "Somatic Targeted Analysis by the KM Algorithm" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Analyse ciblée somatique par l'algorithme KM" ]     ] )
  ] [
fhir:code [ fhir:v "INDX" ] ;
fhir:display [ fhir:v "Sequencing Data Index" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Index de données de séquençage" ]     ] )
  ] [
fhir:code [ fhir:v "OTHER" ] ;
fhir:display [ fhir:v "Undefined Data Type" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Type de données indéfini" ]     ] )
  ] [
fhir:code [ fhir:v "FUSG" ] ;
fhir:display [ fhir:v "Gene fusion" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fusion de gènes" ]     ] )
  ] [
fhir:code [ fhir:v "HLA" ] ;
fhir:display [ fhir:v "HLA Caller Results" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Résultats de l'appel des allèles HLA" ]     ] )
  ] [
fhir:code [ fhir:v "PAC" ] ;
fhir:display [ fhir:v "Paralog Calling" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Appel de variants dans les gènes paralogues" ]     ] )
  ] [
fhir:code [ fhir:v "PEC" ] ;
fhir:display [ fhir:v "Ploidy Estimation per Chromosome" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Estimation de la ploïdie par chromosome" ]     ] )
  ] [
fhir:code [ fhir:v "ROH" ] ;
fhir:display [ fhir:v "Runs of Homozygosity" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Segments d’homozygotie" ]     ] )
  ] [
fhir:code [ fhir:v "STR" ] ;
fhir:display [ fhir:v "Tandem Repeat Calls" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Appel de répétions en tandem" ]     ] )
  ] [
fhir:code [ fhir:v "NORM_VEPPG" ] ;
fhir:display [ fhir:v "Annotated Variants from Non-Repetitive Regions (Legacy Batch) VCF File" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Fichier VCF des variants annotés provenant de régions non répétées (ancien traitement par lot)" ]     ] )
  ] [
fhir:code [ fhir:v "NRRV" ] ;
fhir:display [ fhir:v "Annotated Variants from Non-Repetitive Regions Report" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Rapport de variants annotés provenant de régions non répétées" ]     ] )
  ] [
fhir:code [ fhir:v "PHENOVAR" ] ;
fhir:display [ fhir:v "Phenovar Detailed Results" ] ;
    ( fhir:designation [
fhir:language [ fhir:v "fr" ] ;
fhir:value [ fhir:v "Résultats détaillés de Phenovar" ]     ] )
  ] ) . #