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OSIRIS Data Elements Concepts

Patient

Property	Definition EN
Id	Patient ID in the center providing the information
Gender	Gender of the patient
Ethnicity	Ethnicity of the patient
BirthDate	Date of birth of the patient
DeathDate	Date of death of the patient
ProviderCenterId	Center ID of the center providing the information
OriginCenterId	Center ID of the center of origin of the patient
CauseOfDeath	Description of the cause of death of the patient
LastNewsDate	Date of last news (= date of last patient visit if there is no other information available) (day is set to the 15th)
LastNewsStatus	Indicator of the patient's last known vital status (alive or deceased)

Consent

Property	Definition EN
Date	Date of consent signature
GeneticAnalysisAuthorization	Consent for genetic analysis

RelatedPathology

Property	Definition EN
PathologyCode	International code for the related disease (other than cancer). 3 characters.
DiagnosisDate	Date of diagnosis for the related disease.
PathologyEndDate	Date of the end of the related disease (if occuring and known)

FamilyCancerHistory

Property	Definition EN
TopographyCode	International code for the localization of the oncologic primary site
Parentage	Family relationship

TumorPathologyEvent

Property	Definition EN
Type	The field 'Type' allows to describe the 'Cancer' event as a global disease, as well as the various events constituting this disease (primary tumor, local relapse, metastatic relapse...)
StartDate	Date of start of cancer event or disease
EndDate	Date of end of cancer event or disease
PerformanceStatus	Definition of the autonomy scale (Karnofsky scale or OMS)
G8	Tool for the evaluation of the general condition of the patient
HistologicalGradeType	List of histological grading scales
HistologicalGradeValue	Value of histological grade
StadeType	List of stage scales
StadeValue	Stage value
DiagnosisDate	Date of diagnosis of the tumor event
TopographyCode	Localisation of the primary tumor
MorphologyCode	International code of lesion / histological type / tumor morphology of the tumoral event
Laterality	Laterality of location (if it exists)

TNM

Property	Definition EN
T	Size of the tumor, propagation the site of the primary tumor
N	Propagation at the ganglion level
M	Remote propagation, presence of metastases
Version	TNM classification version
Type	c, p, r,...

Analysis

Property	Definition EN
Code	Code of analysis
Type	Type of analysis
Date	Date of analysis

ResponseEvaluation

Property	Definition EN
Date	Date of assessment of treatment response
Status	Assessment of treatment response

Biomarker

Property	Definition EN
Code	Biomarker name
Value	Biomarker value
Unit	Biomarker unit

Treatment

Property	Definition EN
Type	Type of treatment
LineNumber	Line of treatment
ActivityCode	CCAM code of the medical act
StartDate	Date of treatment start
EndDate	Date of treatment end
ClinicalTrialContext	Treatment performed in a clinical study setting
ClinicalTrialName	Name of the clinical study
ClinicalTrialId	NCT identifier of the clinical study
SurgeryResectionQuality	Quality of resection (anapath)
SurgeryNature	Nature of the surgery

AdverseEvent

Property	Definition EN
Code	International code of the adverse event occurring during treatment (excluding other cancer), only the first 4 letters.
Date	Date of the diagnosis of the adverse event
EndDate	End date of the adverse event (if known)
Grade	Grade of the adverse event

Drug

Property	Definition EN
Code	Therapeutic classification code (5th level if possible)
Name	Name of the molecule

BiologicalSample

Property	Definition EN
ExternalAccession	Unique identifier of the sample
ParentExternalAccession	Unique identifier of the parent sample (if there is one, example histo#)
CollectDate	Date of sampling
TopographyCode	Code of tumor localization
Nature	Nature of the sample
Origin	Nature of the original sample (Healthy or Tumoral)
StorageTemperature	Mode of preservation
TumorCellularity	Percentage of tumor cells quantified in the sample

Technology

Property	Definition EN
TechnicalProtocol	Protocol used for the experiment
PlatformName	Technological platform name (provider followed by the platform name)
PlatformAccession	GEO Identifier of the platform
DateOfExperiment	Date when the experiment was performed

Panel

Property	Definition EN
Name	Name of the panel targeted by the experimental analysis (provider followed by the panel name)

AnalysisProcess

Property	Definition EN
AnalyticPipelineCode	Identifier of the pipeline used into the analysis (unique in the center)

OmicAnalysis

Property	Definition EN
AlgorithmicCellularity	Calculated percentage of tumor cells in sample
AlgorithmicPloidy	Calculated number of sets of chromosomes in a cell of the sample
NumberOfBreakPoints	Calculated number of break points in genomic profile

AlterationOnSample

Property	Definition EN
AlterationType	General type of the detected genetic alteration (high level type)
Pathogenicity	Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board
Actionability	Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board
ProposedForOrientation	Is the ClinicalTumorBoardConclusion used to orient the treatment decision ?

Validation

Property	Definition EN
Type	Type of validation of the detected alteration
Method	Validation method depending on the type of validation
Status	Validation status of the detected alteration

Alteration

Property	Definition EN
Chromosome	Chromosome containing the genetic finding
GenomicStart	Nucleotide location for start of genomic finding on the positive (+) genomics strand, 1-based
GenomicStop	Nucleotide location for end of genomic finding on the positive (+) genomic strand, 1-based
GenomeBuild	Genome Build used for reference
Cytoband	Cytogenetic location

GenomeEntity

Property	Definition EN
Type	Type of the genome entity. For eg: gene, mRNA, ncRNA...
Database	Database of the genome entity
Id	Identifier of the genome entity in the genome entity database
Symbol	Hugo gene symbol

Fusion

Property	Definition EN
Type	Type of the fusion event. For eg: translocation, readthrough
Point5prime	Position of the fusion point on the 5 prime partner
Chromosome5prime
Point3prime	Position of the fusion point on the 3 prime partner
Chromosome3prime
InFrame	Specify whether the fusion is in frame
NbSpanningPair	Number of reads pairs spanning the fusion
NbSplitReads	Number of reads containing the fusion point

CNV

Property	Definition EN
SegmentIntensity	Intensity of the measured signal
SegmentGenomicStatus	Copy number status
CopyNumber	Estimated DNA copy number
LOH	Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information
SegmentSize

Variant

Property	Definition EN
ReferenceAllele	Plus strand reference allele at this position. Include the sequence deleted for a deletion, or '-' for an insertion.
AlternativeAllele	Plus strand observed alternative allele at this position. Include the sequence inserted for a insertion, or '-' for a deletion.
DNASequenceVariationType	Codified type of the DNA sequence variation

Annotation

Property	Definition EN
ReferenceType
ReferenceDatabase
ReferenceValue
MutationPredictionAlgorithm	Algorithm to predict the variation effect over the protein
MutationPredictionValue	Prediction of the variation effect over the protein
MutationPredictionScore	Level of confidence of the prediction of the variation effect over the protein
PfamDomain	Pfams domains related to alteration position
PfamId	Identifier of Pfams domains related to alteration position
DNARegionName	Human readable name for the region of interest related to the transcript (eg: exon1, intron1, UTR3')
DNASequenceVariation	HGVS nomenclature on the chosen transcript
AminoAcidChange	HGVS nomenclature on the chosen protein transcript
GenomicSequenceVariation	HGVS nomenclature on the given GenomeReferenceSequenceId.
RNASequenceVariation	HGVS nomenclature on the given TranscriptReferenceSequenceId and experimentely observed on RNA.
AminoAcidChangeType	nomenclature of changes at protein-level
FusionPrimeEnd	Prime end of the fusion partner
Strand	Strand
OnSplicingSite	Indicate wether the variant is on a splicing site

VariantInSample

Property	Definition EN
PositionReadDepth	Total sequencing depth at the variant position observed in the specimen
VariantReadDepth	Sequencing depth of the alternative allele at the variant position observed in the specimen
StrandBias	Indication of the existence of strand bias at the variant position
GenomicSourceClass	Genomic class of the variant (eg: germline, somatic, and prenatal)
AllelicState	Level of allelic occurrence of a DNA Sequence Variation

GeneExpression

Property	Definition EN
DataType	Type of the expression value corresponding to the level of data processing
Value	Numerical value for expression