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Patient

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Patient	id	Id du patient	C1
Patient	Sexe	Sexe	C2
Patient	Date de naissance	Date de naissance	C3
Patient	Date de décès	Date de décès	C4
Patient	id	Id du Centre	C5
Patient	Cause du décès	Cause du décès	C6
Patient	Date de dernières nouvelles	Date de dernières nouvelles	C7
Patient	Etat aux dernières nouvelles	Etat aux dernières nouvelles	C8

Pathologie associée

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Pathologie associée	Code	Code	C9
Pathologie associée	Date	Date	C10
Pathologie associée	Date de fin	Date de fin	C11

Antécédent carcinologique personnel ou familial

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Antécédent carcinologique personnel ou familial	Date de diagnostic	Date de diagnostic	C12
Antécédent carcinologique personnel ou familial	Code Localisation	Code Localisation	C13
Antécédent carcinologique personnel ou familial	Code Morphologie / Lésion	Code Morphologie / Lésion	C14

Evénement tumoral

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Evénement tumoral	Type	Type	C15
Evénement tumoral	Date de début de l'évènement	Date de début de l'évènement	C16
Evénement tumoral	Echelle d'autonomie / Performance status	Echelle d'autonomie / Performance status	C17
Evénement tumoral	Outil de dépistage G8	Outil de dépistage G8	C18
Evénement tumoral	T	T	C19
Evénement tumoral	N	N	C20
Evénement tumoral	M	M	C21
Evénement tumoral	Version du TNM	Version du TNM	C22
Evénement tumoral	Type de TNM	Type de TNM	C23
Evénement tumoral	Date du diagnostic	Date du diagnostic	C24
Evénement tumoral	Code Localisation	Code Localisation	C25
Evénement tumoral	Code Morphologie / Lésion	Code Morphologie / Lésion	C26
Evénement tumoral	Latéralité	Latéralité	C27

Traitement

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Traitement	Acte	Acte	C28
Traitement	Type	Type	C29
Traitement	Date de début	Date de début	C30
Traitement	Date de fin	Date de fin	C31
Traitement	Clinical trial (Yes	No)	Clinical trial (Yes	No)	C32

Traitement (Chirurgie)

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Traitement (Chirurgie)	Qualité de la résection (anapath)	Qualité de la résection (anapath)	C33

Evénement indésirable

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Evénement indésirable	Date	Date	C34
Evénement indésirable	Date de fin	Date de fin	C35

Molécule Administrée

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Molécule Administrée	Code molécule	Code molécule	C36

Echantillon biologique

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Echantillon biologique	Id du prélèvement	Id du prélèvement	C37
Echantillon biologique	Id de l'échantillon	Id de l'échantillon	C38
Echantillon biologique	Date du prélèvement	Date du prélèvement	C39
Echantillon biologique	Code Localisation	Code Localisation	C40
Echantillon biologique	Nature de l'échantillon	Nature de l'échantillon	C41
Echantillon biologique	Type de dérivé (si dérivé)	Type de dérivé (si dérivé)	C42
Echantillon biologique	Mode de conservation	Mode de conservation	C43
Echantillon biologique	% de cellules tumorales	% de cellules tumorales	C44

Primary tumor

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Primary tumor	Date de début	Date de début (primary)
Primary tumor	Echelle d'autonomie / Performance status	Echelle d'autonomie / Performance status (primary)
Primary tumor	Outil de dépistage G8	Outil de dépistage G8 (primary)
Primary tumor	T	T (primary)
Primary tumor	N	N (primary)
Primary tumor	M	M (primary)
Primary tumor	Version du TNM	Version du TNM (primary)
Primary tumor	Type de TNM	Type de TNM (primary)
Primary tumor	Date du diagnostic	Date du diagnostic (primary)
Primary tumor	Code Localisation	Code Localisation (primary)
Primary tumor	Code Morphologie / Lésion	Code Morphologie / Lésion (primary)
Primary tumor	Latéralité	Latéralité (primary)

Local recurence

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Local recurence	Date de début	Date de début (local recurence)
Local recurence	Echelle d'autonomie / Performance status	Echelle d'autonomie / Performance status (local recurence)
Local recurence	Outil de dépistage G8	Outil de dépistage G8 (local recurence)
Local recurence	T	T (local recurence)
Local recurence	N	N (local recurence)
Local recurence	M	M (local recurence)
Local recurence	Version du TNM	Version du TNM (local recurence)
Local recurence	Type de TNM	Type de TNM (local recurence)
Local recurence	Date du diagnostic	Date du diagnostic (local recurence)
Local recurence	Code Localisation	Code Localisation (local recurence)
Local recurence	Code Morphologie / Lésion	Code Morphologie / Lésion (local recurence)
Local recurence	Latéralité	Latéralité (local recurence)

Metastasis

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Metastasis	Date de début	Date de début (metastasis)
Metastasis	Echelle d'autonomie / Performance status	Echelle d'autonomie / Performance status (metastasis)
Metastasis	Outil de dépistage G8	Outil de dépistage G8 (metastasis)
Metastasis	T	T (metastasis)
Metastasis	N	N (metastasis)
Metastasis	M	M (metastasis)
Metastasis	Version du TNM	Version du TNM (metastasis)
Metastasis	Type de TNM	Type de TNM (metastasis)
Metastasis	Date du diagnostic	Date du diagnostic (metastasis)
Metastasis	Code Localisation	Code Localisation (metastasis)
Metastasis	Code Morphologie / Lésion	Code Morphologie / Lésion (metastasis)
Metastasis	Latéralité	Latéralité (metastasis)

Specimen

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Specimen	SpecimenId	SpecimenId	O3		Genetic sample or derived product identifier

Technology

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Technology	TechnicalProtocol	TechnicalProtocol	O6		Protocol used for the experiment
Technology	PlatformName	PlatformName	O7		Technological platform name (provider followed by the platform name)
Technology	PlatformAccession	PlatformAccession	O8		GEO Identifier of the platform
Technology	DateOfExperiment	DateOfExperiment	O9		Date when the experiment was performed

Panel

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Panel	PanelName	PanelName	O10		Name of the panel targeted by the experimental analysis (provider + name)

Analysis

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Analysis	AnalyticPipelineCode	AnalyticPipelineCode	O11		Identifier of the pipeline used into the analysis (unique in the center)

Experiment on specimen

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Experiment on specimen	AlgorithmicCellularity	AlgorithmicCellularity	O12		Calculated percentage of tumor cells in sample
Experiment on specimen	AlgorithmicPloïdy	AlgorithmicPloïdy	O13		Calculated number of sets of chromosomes in a cell of the sample

Experiment on specimen/CpyNb Quality filter

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Experiment on specimen/CpyNb Quality filter	NumberOfBreakPoints	NumberOfBreakPoints	O14		Calculated number of break points in genomic profile

Alteration in specimen

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Alteration in specimen	AlterationType	AlterationType	O15		General type of the detected genetic alteration (high level type)

Validation

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Validation	ValidationType	ValidationType	O16		Type of validation of the detected alteration
Validation	ValidationMethod	ValidationMethod	O17		Validation method depending on the type of validation
Validation	ValidationStatus	ValidationStatus	O18		Validation status of the detected alteration

Alteration

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Alteration	Chromosome	Chromosome	O19		Chromosome containing the genetic finding
Alteration	GenomicStart	GenomicStart	O20		Nucleotide location for start of genomic finding on the positive (+) genomics strand, 1-based
Alteration	GenomicStop	GenomicStop	O21		Nucleotide location for end of genomic finding on the positive (+) genomic strand, 1-based
Alteration	GenomeBuild	GenomeBuild	O22		Genome Build used for reference
Alteration	Cytoband	Cytoband	O23		Cytogenetic location

Genome entity

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Genome entity	GenomeEntityType	GenomeEntityType	O24		Type of the genome entity. For eg: gene, mRNA, ncRNA...
Genome entity	GenomeEntityDatabase	GenomeEntityDatabase	O25		Database of the genome entity
Genome entity	GenomeEntityId	GenomeEntityId	O26		Identifier of the genome entity in the genome entity database
Genome entity	GeneSymbol	GeneSymbol	O27		Hugo gene symbol

Fusion

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Fusion	FusionType	FusionType	O28		Type of the fusion event. For eg: translocation, readthrough
Fusion	FusionTranscript	FusionTranscript	O29		Have been found from a fusion transcript ?
Fusion	FusionTranscriptReference	FusionTranscriptReference	O30		Accession number of observed fusion
Fusion	GeneSymbol	FusionGeneSymbol5prime	O31		Gene symbol (HUGO) of the gene involved in the fusion on 5 prime end
Fusion	FusionRegionName5prime	FusionRegionName5prime	O32		Human readable name for the region of interest from the 5 prime fusion partner. For eg : Exon, Intron
Fusion	TranscriptReferenceSequenceId	FusionTranscriptReferenceSequenceId5prime	O33		Reference identifier for cDNA transcript of the 5 prime fusion partner, with version, from NCBI's RefSeq or ENSEMBL.
Fusion	FusionStrand5prime	FusionStrand5prime	O34		Strand of the 5 prime fusion partner
Fusion	FusionPoint5prime	FusionPoint5prime	O35		Position of the fusion point on the 5 prime partner
Fusion	GeneSymbol	FusionGeneSymbol3prime	O36		Gene symbol (HUGO) of the gene involved in the fusion on 3 prime end
Fusion	FusionRegionName3prime	FusionRegionName3prime	O37		Human readable name for the region of interest from the 3 prime fusion partner. For eg : Exon, Intron
Fusion	TranscriptReferenceSequenceId	FusionTranscriptReferenceSequenceId3prime	O38		Reference identifier for cDNA transcript of the 3 prime fusion partner, with version, from NCBI's RefSeq or ENSEMBL.
Fusion	FusionStrand3prime	FusionStrand3prime	O39		Strand of the 3 prime fusion partner
Fusion	FusionPoint3prime	FusionPoint3prime	O40		Position of the fusion point on the 3 prime partner
Fusion	FusionInFrame	FusionInFrame	O41		Specify whether the fusion is in frame

Fusion Analysis

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Fusion Analysis	FusionAnnotationReferentiel	FusionAnnotationReferentiel	O42		Reference database to annotate the fusion
Fusion Analysis	FusionAnnotationValue	FusionAnnotationValue	O43		Annotation of the fusion

Fusion/QualityFilter

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Fusion/QualityFilter	FusionNbSpanningPair	FusionNbSpanningPair	O44		Number of reads pairs spanning the fusion
Fusion/QualityFilter	FusionNbSplitReads	FusionNbSplitReads	O46		Number of split reads

Segment copy number

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Segment copy number	SegmentIntensity	SegmentIntensity	O47		Intensity of the measured signal
Segment copy number	SegmentGenomicStatus	SegmentGenomicStatus	O49		Copy number status
Segment copy number	CopyNumber	CopyNumber	O50		Estimated DNA copy number

Segment LOH

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Segment LOH	LossOfHeterozygosity	LossOfHeterozygosity	O51		Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information

Reference variant

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Reference variant	ReferenceAllele	ReferenceAllele	O53		Plus strand reference allele at this position. Include the sequence deleted for a deletion, or "-" for an insertion.
Reference variant	AlternativeAllele	AlternativeAllele	O54		Plus strand observed alternative allele at this position. Include the sequence inserted for a insertion, or "-" for a deletion.
Reference variant	DNASequenceVariationType	DNASequenceVariationType	O55		Codified type of the DNA sequence variation
Reference variant	VariationDatabase	VariationDatabase	O56		Name of the variation database
Reference variant	VariationId	VariationId	O57		Identifier for variant in the variation database
Reference variant	PfamDomain	PfamDomain	O58		Pfams domains related to alteration position
Reference variant	PfamId	PfamId	O59		Identifier of Pfams domains related to alteration position
Reference variant	MutationPredictionAlgorithm	MutationPredictionAlgorithm	O63		Algorithm to predict the variation effect over the protein
Reference variant	MutationPredictionValue	MutationPredictionValue	O64		Prediction of the variation effect over the protein
Reference variant	MutationPredictionScore	MutationPredictionScore	O65		Level of confidence of the prediction of the variation effect over the protein
Reference variant	DNARegionName	DNARegionName	O66		Human readable name for the region of interest related to the transcript (eg: exon1, intron1, UTR3')

Protein

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Protein	ProteinReferenceDatabase	ProteinReferenceDatabase	O67		Name of the protein reference database
Protein	ProteinReferenceSequenceId	ProteinReferenceSequenceId	O68		Reference identifier of the protein transcript

Exonic variant

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Exonic variant	TranscriptReferenceDatabase	TranscriptReferenceDatabase	O69		Name of the sequence reference database
Exonic variant	TranscriptReferenceSequenceId	TranscriptReferenceSequenceId	O70		Reference identifier of the transcript
Exonic variant	DNASequenceVariation	DNASequenceVariation	O71		HGVS nomenclature on the chosen transcript
Exonic variant	AminoAcidChange	AminoAcidChange	O72		HGVS nomenclature on the chosen protein transcript
Exonic variant	GenomicSequenceVariation	GenomicSequenceVariation	O73		HGVS nomenclature on the given GenomeReferenceSequenceId.
Exonic variant	RNASequenceVariation	RNASequenceVariation	O74		HGVS nomenclature on the given TranscriptReferenceSequenceId and experimentely observed on RNA.
Exonic variant	AminoAcidChangeType	AminoAcidChangeType	O75		HGVS nomenclature of changes at protein-level

Variant in specimen

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Variant in specimen	PositionCoverage	PositionCoverage	O76		Total coverage at the variant position observed in the specimen
Variant in specimen	VariantCoverage	VariantCoverage	O77		Coverage of the alternative allele at the variant position observed in the specimen
Variant in specimen	StrandBias	StrandBias	O78		Indication of the existence of strand bias at the variant position
Variant in specimen	GenomicSourceClass	GenomicSourceClass	O79		Genomic class of the variant (eg: germline, somatic, and prenatal)
Variant in specimen	AllelicState	AllelicState	O80		Level of allelic occurrence of a DNA Sequence Variation
Variant in specimen	MolecularTumorBoardConclusion	MolecularTumorBoardConclusion	O81		Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
Variant in specimen	ClinicalTumorBoardConclusion	ClinicalTumorBoardConclusion	O82		Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
Variant in specimen	ProposedForOrientation	ProposedForOrientation	O83		Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?

Gene expression

ObjectClass	ObjectProperty	DataElementConcept	IdDataElementConcept	DataElementConceptDefFR	DataElementConceptDefEN
Gene expression	ExpressionDataType	ExpressionDataType	O84		Type of the expression value corresponding to the level of data processing
Gene expression	ExpressionValue	ExpressionValue	O85		Numerical value for expression
Gene expression	ExpressionPvalue	ExpressionPvalue	O86		p-value of the dataset comparison through a statistical method
Gene expression	ExpressionPvalueAdjustmentMethod	ExpressionPvalueAdjustmentMethod	O87		Method used to adjust the nominal value of the p-value when multiple tests are performed in parallel