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Y. Laizet edited this page May 28, 2018 · 5 revisions

CLINICAL

Patient

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Patient Id Patient_Id Patient Id Id du patient String mandatory Identifiant du patient dans le centre transmetteur de l'information C1 SHIVA_01-001
Patient Gender Patient_Gender Gender Sexe du patient v3 Code System AdministrativeGender String mandatory Sexe du patient C2
Patient Ethnicity Patient_Ethnicity Ethnicity Ethnicité HL7 v3 Code System Race String optional Origine ethnique du patient C3
Patient BirthDate Patient_BirthDate Birth Date Date de naissance Date mandatory Date de naissance du patient C4 YYYY-MM-DD
Patient DeathDate Patient_DeathDate Death Date Date de décès Date optional Date de décès du patient C5 YYYY-MM-DD
Patient ProviderCenterId Patient_ProviderCenterId Provider Center Id Id du Centre fournisseur de données String mandatory Identifiant du centre transmetteur de l'information (code FINESS) C6
Patient OriginCenterId Patient_OriginCenterId Origin Center Id Id du Centre d'origine du patient String mandatory Identifiant du centre d'origine du patient C71
Patient CauseOfDeath Patient_CauseOfDeath Cause of death Cause de décès UMLS:C0007465 String mandatory if DeathDate is set Descriptif de la cause de décès du patient C7
Patient LastNewsDate Patient_LastNewsDate Last News Date Date de dernières nouvelles Date mandatory Date de dernières nouvelles du patient (= date de dernière venue du patient si aucune autre information disponible) (le jour est fixé au 15) C8
Patient LastNewsStatus Patient_LastNewsStatus Last News Status Etat aux dernières nouvelles String mandatory Indicateur de l'état du patient aux dernières nouvelles (Vivant ou décédé) C9

Consent

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Consent Date Consent_Date Date Date de signature du consentement Date mandatory Date de signature du consentement Signed consent date C72
Consent GeneticAnalysisAuthorization Consent_GeneticAnalysisAuthorization Genetic Analysis Authorization Autorisation pour des analyses génétiques Boolean mandatory Autorisation pour des analyses génétiques C79

RelatedPathology

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
RelatedPathology PathologyCode RelatedPathology_PathologyCode Pathology Code Code ICD-10 String mandatory if ObjectClass is set Code international de la pathologie associée (hors autre cancer). 3 caractères C13 E11
RelatedPathology DiagnosisDate RelatedPathology_DiagnosisDate Diagnosis Date Date Date mandatory if ObjectClass is set Date du diagnostic de la pathologie associée C14 La date de diagnostic peut être inconnue, dans ce cas il est proposé de prendre la date du document de consultation dans lequel apparaît cette information
RelatedPathology PathologyEndDate RelatedPathology_PathologyEndDate Pathology End Date Date de fin Date optional Date de fin de la pathologie associée (si elle existe et est connue). C15

FamilyCancerHistory

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
FamilyCancerHistory TopographyCode FamilyCancerHistory_TopographyCode Topography Code Code Localisation CIM-O-3 Topo String mandatory if ObjectClass is set Code international de la localisation de l'antécédent carcinologique C17
FamilyCancerHistory Parentage FamilyCancerHistory_Parentage Parentage Parentage OSIRIS:FamilyCancerHistoryParentage String mandatory if ObjectClass is set Lien de parenté C77

TumorPathologyEvent

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
TumorPathologyEvent Type TumorPathologyEvent_Type Type Type d'événement OSIRIS:EventType String mandatory Le champ 'Type' permet de décrire à la fois l'événement 'Cancer' en tant que maladie globale que les différents événements constituant cette maladie (Tumeur initiale, Récidive locale, Récidive métastatique). C20
TumorPathologyEvent StartDate TumorPathologyEvent_StartDate Start Date Date de début de l'évènement Date mandatory Date de début de l'événement tumoral ou de la maladie C21 La date de début de l'événement = la date de diagnostic si elle n'existe pas de date de début de l'événement facilement identifiable. La date de début de l'événement pourrait être égale à la date de la première consultation
TumorPathologyEvent PerformanceStatus TumorPathologyEvent_PerformanceStatus Performance Status Echelle d'autonomie / Performance status OMS String optional Définition de l'échelle d'autonomie (échelle de Karnofsky ou OMS) C22
TumorPathologyEvent G8 TumorPathologyEvent_G8 G8 Outil de dépistage G8 G8 Integer optional outil d'évaluation de l'état général des patients âgés ayant un cancer C23
TumorPathologyEvent T TumorPathologyEvent_T T T OSIRIS:T_TNM String optional, mandatory if either N, M or TNMType is set Taille de la tumeur, propagation sur le site de la tumeur primitive C24
TumorPathologyEvent N TumorPathologyEvent_N N N OSIRIS:N_TNM String optional, mandatory if either T, M or TNMType is set Propagation au niveau ganglionnaire C25
TumorPathologyEvent M TumorPathologyEvent_M M M OSIRIS:M_TNM String optional, mandatory if either T, N or TNMType is set Propagation à distance, présence de métastases C26
TumorPathologyEvent TNMVersion TumorPathologyEvent_TNMVersion TNM Version Version du TNM OSIRIS:TNMVersion String optional Version de la classification TNM C27
TumorPathologyEvent TNMType TumorPathologyEvent_TNMType TNM Type Type de TNM OSIRIS:TNMType String optional, mandatory if either T, N or M is set c, p, r,... C28
TumorPathologyEvent HistologicalGradeType TumorPathologyEvent_HistologicalGradeType Histological Grade Type HistologicalGradeType String optional, mandatory if HistologicalGradeValue is set Liste des échelles de grading histologique C29
TumorPathologyEvent HistologicalGradeValue TumorPathologyEvent_HistologicalGradeValue Histological Grade Value HistologicalGradeValue String optional, mandatory if HistologicalGradeType is set Valeur du grade histologique C30
TumorPathologyEvent StadeType TumorPathologyEvent_StadeType Stade Type StadeType String optional, mandatory if StadeValue is set Liste des échelles de stade C31
TumorPathologyEvent StadeValue TumorPathologyEvent_StadeValue Stade Value StadeValue String optional, mandatory if StadeType is set Valeur du stade C32
TumorPathologyEvent DiagnosisDate TumorPathologyEvent_DiagnosisDate Diagnosis Date Date du diagnostic Date mandatory Date du diagnostic de l'événement tumoral C33
TumorPathologyEvent TopographyCode TumorPathologyEvent_TopographyCode Topography Code Code Localisation CIM-O-3 Topo String mandatory Code international de la localisation de l'événement tumoral C34
TumorPathologyEvent MorphologyCode TumorPathologyEvent_MorphologyCode Morphology Code Code Morphologie / Lésion CIM-O-3 Morpho String mandatory Code international de la lésion / type histologique / morphologie de l'événement tumoral C35
TumorPathologyEvent Laterality TumorPathologyEvent_Laterality Laterality Latéralité Laterality String optional Latéralité de la localisation (si elle existe) C36

Analysis

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Analysis Code Analysis_Code Code Code unique de l'analyse String optional Code de l'analyse C70
Analysis Type Analysis_Type Type Type d'analyse String mandatory if ObjectClass is set Type d'analyse C37
Analysis Date Analysis_Date Date Date d'analyse Date mandatory if ObjectClass is set Date d'analyse C38

ResponseEvaluation

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
ResponseEvaluation Date ResponseEvaluation_Date Date Date de l'évaluation de la réponse Date mandatory if ObjectClass is set Date de l'évaluation de la réponse au traitement C78
ResponseEvaluation Status ResponseEvaluation_Status Status Statut de l'évaluation de la réponse String mandatory if ObjectClass is set Evaluation de la réponse au traitement C73

Biomarker

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Biomarker Code Biomarker_Code Code Code du marqueur String mandatory if ObjectClass is set Nom du marqueur C39
Biomarker Value Biomarker_Value Value Valeur du marqueur String mandatory if ObjectClass is set Valeur du marqueur C40
Biomarker Unit Biomarker_Unit Unit Unité d'expression du marqueur String optional Unité d'expression du marqueur C81

Treatment

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Treatment Type Treatment_Type Type Type de traitement TreatmentType String mandatory if ObjectClass is set Type de traitement C41
Treatment LineNumber Treatment_LineNumber Line Number Numéro de ligne String optional Ligne de traitement C74
Treatment ActivityCode Treatment_ActivityCode Activity Code Codification de l'acte CCAM String optional Code CCAM de l'acte C42
Treatment StartDate Treatment_StartDate Start Date Date de début Date mandatory if ObjectClass is set Date de début du traitement C43
Treatment EndDate Treatment_EndDate End Date Date de fin Date mandatory if ObjectClass is set Date de fin du traitement C44
Treatment ClinicalTrialContext Treatment_ClinicalTrialContext Clinical Trial Context Clinical trial (Yes | No) Boolean optional Traitement effectué dans un contexte d'étude clinique C45
Treatment ClinicalTrialName Treatment_ClinicalTrialName Clinical Trial Name Nom de l'essai clinique String optional, mandatory if ClinicalTrialContext is 'Yes' Nome de l'étude clinique C75
Treatment ClinicalTrialId Treatment_ClinicalTrialId Clinical Trial Id Identifiant de l'essai clinique String optional, mandatory if ClinicalTrialContext is 'Yes' Identifiant NCT de l'étude clinique C76
Treatment SurgeryResectionQuality Treatment_SurgeryResectionQuality Surgery Resection Quality Qualité de la résection (anapath) SurgeryResection String optional Qualité de la résection (anapath) C46
Treatment SurgeryNature Treatment_SurgeryNature Surgery Nature Nature de la chirurgie String optional Nature de la chirurgie C47

AdverseEvent

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
AdverseEvent Code AdverseEvent_Code Code Code de l'événement indésirable String mandatory if ObjectClass is set Code international de l'événement indésirable survenu en cours de traitement (hors autre cancer), seulement les 4 premières lettres. C48
AdverseEvent Date AdverseEvent_Date Date Date de l'événement indésirable Date mandatory if ObjectClass is set Date du diagnostic de l'événement indésirable C49
AdverseEvent EndDate AdverseEvent_EndDate End Date Date de fin Date optional Date de fin de l'événement indésirable (si elle est connue) C50
AdverseEvent Grade AdverseEvent_Grade Grade Grade String mandatory if ObjectClass is set Grade de l'évenement indésirable C80

Drug

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Drug Code Drug_Code Code Code molécule ATC 5e niveau String mandatory if ObjectClass is set Code de la classification thérapeutique (5ème niveau si possible) C51
Drug Name Drug_Name Name Nom de la molécule String mandatory if ObjectClass is set Nom de la molécule C52

BiologicalSample

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
BiologicalSample SampleExternalAccession BiologicalSample_SampleExternalAccession Sample External Accession Id unique de l'échantillon MIABIS-39 String mandatory if ObjectClass is set Identifiant unique de l'échantillon C53
BiologicalSample ParentSampleExternalAccession BiologicalSample_ParentSampleExternalAccession Parent Sample External Accession Identifiant unique de l'échantillon parent MIABIS-40 String optional Identifiant unique de l'échantillon parent (s'il en existe un, exemple N°histo) C54
BiologicalSample CollectDate BiologicalSample_CollectDate Collect Date Date du prélèvement MIABIS-43 Date mandatory if ObjectClass is set Date du prélèvement C56
BiologicalSample TopographyCode BiologicalSample_TopographyCode Topography Code Code Localisation CIM-O-3 Topo String mandatory if ObjectClass is set Code de la localisation tumorale C57
BiologicalSample Nature BiologicalSample_Nature Nature Nature de l'échantillon MIABIS-41 String mandatory if ObjectClass is set La nature de l'échantillon C58
BiologicalSample Origin BiologicalSample_Origin Origin Nature du prélèvement (tumoral / sain) OSIRIS:SampleOrigin String mandatory if ObjectClass is set Nature du prélèvement d'origine (Sain ou Tumoral) C59
BiologicalSample StorageTemperature BiologicalSample_StorageTemperature Storage Temperature Mode de conservation MIABIS-42 String optional Le mode de conservation C60
BiologicalSample TumorCellularity BiologicalSample_TumorCellularity Tumor Cellularity % de cellules tumorales Integer optional Le pourcentage de cellules tumorales quantifié dans l'échantillon C61

OMIC

Technology

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Technology TechnicalProtocol Technology_TechnicalProtocol Technical Protocol Technical Protocol OSIRIS:TechnicalProtocol String mandatory Protocol used for the experiment O6
Technology PlatformName Technology_PlatformName Platform Name Platform Name OSIRIS:PlatformName String mandatory Technological platform name (provider followed by the platform name) O7 Agilent Human CGH 1x1M
Technology PlatformAccession Technology_PlatformAccession Platform Accession Platform Accession OSIRIS:PlatformAccession String optional GEO Identifier of the platform O8 GPL21026
Technology DateOfExperiment Technology_DateOfExperiment Date Of Experiment Date Of Experiment OSIRIS:DateOfExperiment Date cle primaire Date when the experiment was performed O9 2018-20-03

Panel

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Panel Name Panel_Name Name Name OSIRIS:PanelName String optional Name of the panel targeted by the experimental analysis (provider + name) O10 Ion AmpliSeq Cancer Hotspot Panel v2

AnalysisProcess

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
AnalysisProcess AnalyticPipelineCode AnalysisProcess_AnalyticPipelineCode Analytic Pipeline Code Analytic Pipeline Code OSIRIS:AnalyticPipelineCode String mandatory Identifier of the pipeline used into the analysis (unique in the center) O11 sbd54dsf57s

OmicAnalysis

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
OmicAnalysis AlgorithmicCellularity OmicAnalysis_AlgorithmicCellularity Algorithmic Cellularity Algorithmic Cellularity OSIRIS:AlgorithmicCellularity Integer optional Calculated percentage of tumor cells in sample O12 50
OmicAnalysis AlgorithmicPloidy OmicAnalysis_AlgorithmicPloidy Algorithmic Ploidy Algorithmic Ploidy OSIRIS:AlgorithmicPloïdy String optional Calculated number of sets of chromosomes in a cell of the sample O13 O13-2
OmicAnalysis NumberOfBreakPoints OmicAnalysis_NumberOfBreakPoints Number Of Break Points Number Of Break Points OSIRIS:NumberOfBreakPoints Integer optional Calculated number of break points in genomic profile O14 320

AlterationOnSample

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
AlterationOnSample AlterationType AlterationOnSample_AlterationType Alteration Type Alteration Type OSIRIS:AlterationType String mandatory General type of the detected genetic alteration (high level type) O15 Copy number variation
AlterationOnSample Pathogenicity AlterationOnSample_Pathogenicity Pathogenicity Pathogenicity ACMG String optional Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board O81
AlterationOnSample Actionability AlterationOnSample_Actionability Actionability Actionability OBI String optional Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board O82
AlterationOnSample ProposedForOrientation AlterationOnSample_ProposedForOrientation Proposed For Orientation Proposed For Orientation OBI Boolean optional Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? O83

Validation

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Validation Type Validation_Type Type Type OSIRIS:ValidationType String mandatory Type of validation of the detected alteration O16 Experimental
Validation Method Validation_Method Method Method OSIRIS:ValidationMethod String mandatory Validation method depending on the type of validation O17
Validation Status Validation_Status Status Status OSIRIS:ValidationStatus String mandatory Validation status of the detected alteration O18 Validated

Alteration

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Alteration Chromosome Alteration_Chromosome Chromosome Chromosome OSIRIS:Chromosome String mandatory Chromosome containing the genetic finding O19
Alteration GenomicStart Alteration_GenomicStart Genomic Start Genomic Start FHIR:extension-geneticsGenomicStart Integer mandatory Nucleotide location for start of genomic finding on the positive (+) genomics strand, 1-based O20
Alteration GenomicStop Alteration_GenomicStop Genomic Stop Genomic Stop FHIR:extension-geneticsGenomicStop Integer mandatory Nucleotide location for end of genomic finding on the positive (+) genomic strand, 1-based O21
Alteration GenomeBuild Alteration_GenomeBuild Genome Build Genome Build FHIR:extension-geneticsGenomeBuild String mandatory Genome Build used for reference O22
Alteration Cytoband Alteration_Cytoband Cytoband Cytoband OSIRIS:Cytoband String optional Cytogenetic location O23

GenomeEntity

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
GenomeEntity Type GenomeEntity_Type Type Type OSIRIS:GenomeEntityType String mandatory Type of the genome entity. For eg: gene, mRNA, ncRNA... O24
GenomeEntity Database GenomeEntity_Database Database Database OSIRIS:GenomeEntityDatabase String mandatory Database of the genome entity O25
GenomeEntity Id GenomeEntity_Id Id Id FHIR:extension-observation-geneticsGene String mandatory Identifier of the genome entity in the genome entity database O26
GenomeEntity Symbol GenomeEntity_Symbol Symbol Symbol LOINC:48018-6 String mandatory if gene Hugo gene symbol O27

Fusion

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Fusion Type Fusion_Type Type Type OSIRIS:FusionType String optional Type of the fusion event. For eg: translocation, readthrough O28
Fusion Point5prime Fusion_Point5prime Point 5 prime Point 5 prime OSIRIS:FusionPoint5prime String mandatory Position of the fusion point on the 5 prime partner O35
Fusion Point3prime Fusion_Point3prime Point 3 prime Point 3 prime OSIRIS:FusionPoint3prime Integer mandatory Position of the fusion point on the 3 prime partner O40
Fusion InFrame Fusion_InFrame In Frame In Frame OSIRIS:FusionInFrame Boolean optional Specify whether the fusion is in frame O41
Fusion NbSpanningPair Fusion_NbSpanningPair Nb Spanning Pair Nb Spanning Pair OSIRIS:FusionNbSpanningPair Integer mandatory Number of reads pairs spanning the fusion O44
Fusion NbSplitReads Fusion_NbSplitReads Nb Split Reads Nb Split Reads OSIRIS:FusionNbSplitReads Integer optional Number of reads containing the fusion point O46

CNV

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
CNV SegmentIntensity CNV_SegmentIntensity Segment Intensity Segment Intensity OSIRIS:SegmentIntensity Float mandatory Intensity of the measured signal O47
CNV SegmentGenomicStatus CNV_SegmentGenomicStatus Segment Genomic Status Segment Genomic Status OSIRIS:SegmentGenomicStatus String mandatory Copy number status O49
CNV CopyNumber CNV_CopyNumber Copy Number Copy Number OSIRIS:CopyNumber Integer optional Estimated DNA copy number O50
CNV LOH CNV_LOH LOH LOH OSIRIS:LossOfHeterozygosity Boolean optional Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information O51

Variant

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Variant ReferenceAllele Variant_ReferenceAllele Reference Allele Reference Allele FHIR:Sequence.referenceAllele String mandatory Plus strand reference allele at this position. Include the sequence deleted for a deletion, or '-' for an insertion. O53
Variant AlternativeAllele Variant_AlternativeAllele Alternative Allele Alternative Allele FHIR:Sequence.observedAllele String mandatory Plus strand observed alternative allele at this position. Include the sequence inserted for a insertion, or '-' for a deletion. O54
Variant DNASequenceVariationType Variant_DNASequenceVariationType DNA Sequence Variation Type DNA Sequence Variation Type LOINC:48019-4 String mandatory Codified type of the DNA sequence variation O55

Annotation

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
Annotation ReferenceType Annotation_ReferenceType Reference Type Reference Type OSIRIS:Annotation_ReferenceType String optional O90
Annotation ReferenceDatabase Annotation_ReferenceDatabase Reference Database Reference Database OSIRIS:Annotation_ReferenceDatabase String optional O91
Annotation ReferenceId Annotation_ReferenceId Reference Id Reference Id OSIRIS:Annotation_ReferenceId String optional O92
Annotation PfamDomain Annotation_PfamDomain Pfam Domain Pfam Domain OSIRIS:PfamDomain String optional Pfams domains related to alteration position O58
Annotation PfamId Annotation_PfamId Pfam Id Pfam Id OSIRIS:PfamId String optional Identifier of Pfams domains related to alteration position O59
Annotation MutationPredictionAlgorithm Annotation_MutationPredictionAlgorithm Mutation Prediction Algorithm Mutation Prediction Algorithm OSIRIS:MutationPredictionAlgorithm String optional Algorithm to predict the variation effect over the protein O63
Annotation MutationPredictionValue Annotation_MutationPredictionValue Mutation Prediction Value Mutation Prediction Value OSIRIS:MutationPredictionValue String optional Prediction of the variation effect over the protein O64
Annotation MutationPredictionScore Annotation_MutationPredictionScore Mutation Prediction Score Mutation Prediction Score OSIRIS:MutationPredictionScore Float optional Level of confidence of the prediction of the variation effect over the protein O65
Annotation DNARegionName Annotation_DNARegionName DNA Region Name DNA Region Name FHIR:extension-observation-geneticsDNARegionName String optional Human readable name for the region of interest related to the transcript (eg: exon1, intron1, UTR3') O66
Annotation DNASequenceVariation Annotation_DNASequenceVariation DNA Sequence Variation DNA Sequence Variation FHIR:extension-observation-geneticsDNASequenceVariation String mandatory HGVS nomenclature on the chosen transcript O71 c.6964C>T
Annotation AminoAcidChange Annotation_AminoAcidChange Amino Acid Change Amino Acid Change FHIR:extension-observation-geneticsAminoAcidChange String optional HGVS nomenclature on the chosen protein transcript O72 p.Arg2322Cys
Annotation GenomicSequenceVariation Annotation_GenomicSequenceVariation Genomic Sequence Variation Genomic Sequence Variation OSIRIS:GenomicSequenceVariation String optional HGVS nomenclature on the given GenomeReferenceSequenceId. O73 g.1567234_1567235insTG
Annotation RNASequenceVariation Annotation_RNASequenceVariation RNA Sequence Variation RNA Sequence Variation OSIRIS:RNASequenceVariation String optional HGVS nomenclature on the given TranscriptReferenceSequenceId and experimentely observed on RNA. O74 r.67g>u
Annotation AminoAcidChangeType Annotation_AminoAcidChangeType Amino Acid Change Type Amino Acid Change Type OSIRIS:AminoAcidChangeType String optional HGVS nomenclature of changes at protein-level O75
Annotation FusionPrimeEnd Annotation_FusionPrimeEnd Fusion Prime End Fusion Prime End OSIRIS:Annotation_FusionPrimeEnd String optional Prime end of the fusion partner O93 5prime
Annotation Strand Annotation_Strand Strand Strand OSIRIS:Annotation_Strand String optional Strand O94 +
Annotation Symbol Annotation_Symbol Symbol Symbol LOINC:48018-6 String mandatory Gene symbol (HUGO) of the gene O95 TP53

VariantInSample

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
VariantInSample PositionReadDepth VariantInSample_PositionReadDepth Position Read Depth Position Read Depth OSIRIS:PositionReadDepth Integer mandatory Total sequencing depth at the variant position observed in the specimen O76
VariantInSample VariantReadDepth VariantInSample_VariantReadDepth Variant Read Depth Variant Read Depth OSIRIS:VariantReadDepth Integer mandatory Sequencing depth of the alternative allele at the variant position observed in the specimen O77
VariantInSample StrandBias VariantInSample_StrandBias Strand Bias Strand Bias OSIRIS:StrandBias Boolean optional Indication of the existence of strand bias at the variant position O78
VariantInSample GenomicSourceClass VariantInSample_GenomicSourceClass Genomic Source Class Genomic Source Class LOINC:LL378-1 String mandatory Genomic class of the variant (eg: germline, somatic, and prenatal) O79 Somatic
VariantInSample AllelicState VariantInSample_AllelicState Allelic State Allelic State LOINC:LL381-5 String optional Level of allelic occurrence of a DNA Sequence Variation O80

GeneExpression

ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples Convention d'alimentation de la donnée
GeneExpression DataType GeneExpression_DataType Data Type Data Type OSIRIS:ExpressionDataType String mandatory Type of the expression value corresponding to the level of data processing O84
GeneExpression Value GeneExpression_Value Value Value OSIRIS:ExpressionValue Float mandatory Numerical value for expression O85

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