Update pivot files

pivot/OSIRIS_pivot_AdverseEvent.csv

@@ -1,2 +1,4 @@
-patient_id,instance_id,adverseevent_treatment_instance,adverseevent_code,adverseevent_date,adverseevent_enddate
-L304,1,2,"Mal à la tete",2007-06-13,2007-07-10
+Patient_Id,Instance_Id,Treatment_Ref,TumorPahtologyEvent_Ref,AdverseEvent_Code,AdverseEvent_Date,AdverseEvent_EndDate,AdverseEvent_Grade
+L304,1,2,1,Mal à la tete,2007-06-13,2007-07-10,
+,,,,,,,
+Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,,

pivot/OSIRIS_pivot_Analysis.csv

@@ -1,4 +1,8 @@
-patient_id,instance_id,analysis_biologicalsample_instance,analysis_tumorpathologyevent_instance,analysis_code,analysis_type,analysis_analysisdate,technology_technicalprotocol,technology_platformname,technology_platformaccession,technology_dateofexperiment,panel_panelname,analysisprocess_analyticpipelinecode,experiment_on_specimen_algorithmiccellularity,experiment_on_specimen_algorithmicplody,experiment_on_specimen_cpynb_quality_filter_numberofbreakpoints
-L304,1,"ech primary",1,ATX90U,Genomique,2018-02-07,OSIRIS:O6-4,OSIRIS:O7-66,,2017-09-20,OSIRIS:O10-4,v351,50,OSIRIS:O13-2,
-L304,2,"ech 2",2,fgh587,NGS,2018-02-07,OSIRIS:O6-12,OSIRIS:O7-46,,2017-09-19,OSIRIS:O10-0,"RNAseq pipeline v3.2",50,OSIRIS:O13-2,
-L304,3,"ech 2",2,rt52485,Genomique,2018-02-09,OSIRIS:O6-3,OSIRIS:O7-25,,2018-02-09,OSIRIS:O10-0,sbd54dsf57s,,,320
+Patient_Id,Instance_Id,TumorPathologyEvent_Ref,BiologicalSample_Ref,Analysis_Code,Analysis_Type,Analysis_Date,Technology_TechnicalProtocol,Technology_PlatformName,Technology_PlatformAccession,Technology_DateOfExperiment,Panel_Name,AnalysisProcess_AnalyticPipelineCode,OmicAnalysis_AlgorithmicCellularity,OmicAnalysis_AlgorithmicPloidy,OmicAnalysis_NumberOfBreakPoints
+L304,1,1,ech primary,ATX90U,Genomique,2018-02-07,OSIRIS:O6-4,OSIRIS:O7-66,,2017-09-20,OSIRIS:O10-4,v351,50,OSIRIS:O13-2,
+L304,2,2,ech 2,fgh587,NGS,2018-02-07,OSIRIS:O6-12,OSIRIS:O7-46,,2017-09-19,OSIRIS:O10-0,RNAseq pipeline v3.2,50,OSIRIS:O13-2,
+L304,3,2,ech 2,rt52485,Genomique,2018-02-09,OSIRIS:O6-3,OSIRIS:O7-25,,2018-02-09,OSIRIS:O10-0,sbd54dsf57s,,,320
+,,,,,,,,,,,,,,,
+,,,Laetitia: !!valeur = instance_id,,,,,,,,,,Vincent : ces deux colonnes sont génériques à toutes les altérations pour être mises ici ?,,
+,,,,Yec'han : j'ai rajouté comme proposition car nous avons un code unique pour chaque analyse que nous faisons et que l'on retrouve dans nos fichiers de résultats => traçabilité facilitée,,,,,,,,,,,"Vincent : spécifique du CNV, déplacer cette colonne dans le fichier CNV ?"
+,,,Vincent : Il faut mettre la reférence de la colonne Instance_Id du fichier BiologicalSample,,,,,,,,,,,,"Laetitia: c'est ici car c'est un annotation qui concerne l'analyse en totalité. Si on la met dans le fichier CNV, il va falloir la répéter sur toutes les lignes"

pivot/OSIRIS_pivot_Annotation.csv

@@ -1,2 +1,4 @@
-patient_id,instance_id,annotation_alteration_instance,annotation_variationdatabase,annotation_variationid,annotation_mutationpredictionalgorithm,annotation_mutationpredictionvalue,annotation_mutationpredictionscore,annotation_proteinreferencedatabase,annotation_proteinreferencesequenceid,annotation_transcriptreferencedatabase,annotation_transcriptreferencesequenceid,annotation_dnasequencevariation,annotation_aminoacidchange,annotation_genomicsequencevariation,annotation_rnasequencevariation,annotation_aminoacidchangetype
-L304,1,1,COSMIC,COSM760,SIFT,Deleterious,0.35,RefSeq,NP_006209.2,RefSeq,NM_006218.3,c.1624G>A,p.E542K,,,LA6698-0
+Patient_Id,Instance_Id,Alteration_Ref,AlterationType,Annotation_ReferenceType,Annotation_ReferenceDatabase,Annotation_ReferenceId,Annotation_Symbol,Annotation_PfamDomain,Annotation_PfamId,Annotation_MutationPredictionAlgorithm,Annotation_MutationPredictionValue,Annotation_MutationPredictionScore,Annotation_DNARegionName,Annotation_DNASequenceVariation,Annotation_AminoAcidChange,Annotation_GenomicSequenceVariation,Annotation_RNASequenceVariation,Annotation_AminoAcidChangeType,FusionPrimeEnd,Strand
+L304,1,1,,Variant,COSMIC,COSM760,PI3K,"PI3K_rbd; PI3-kinase family, ras-binding domain",pfam00794,SIFT,Deleterious,0.35,exon 2,c.1624G>A,p.E542K,,,LA6698-0,,
+,,,,,,,,,,,,,exon 14,,,,,,,
+,,,Laetitia: doublons avec Annotaion_ReferenceType ?,,,,,,,,,,,,,,,,,

pivot/OSIRIS_pivot_BiologicalSample.csv

@@ -1,3 +1,3 @@
-patient_id,instance_id,biologicalsample_tumorpathologyevent_instance,consent_instance,biologicalsample_sampleid,biologicalsample_parentsampleid,biologicalsample_parentsampleref,biologicalsample_collectdate,biologicalsample_topographycode,biologicalsample_samplenature,biologicalsample_sampleorigin,biologicalsample_storagetemperature,biologicalsample_tumorcellularity
-L304,1,1,1,"ech primary",,cf564,2005-12-27,C34,,OSIRIS:O59-2,"MIABIS:Tissue Frozen",30
-L304,2,2,1,"ech 2",,,2011-02-08,C30,"MIABIS:Tissue FFPE",OSIRIS:O59-2,FFPE,60
+Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Consent_Ref,BiologicalSample_SampleExternalAccession,BiologicalSample_ParentSampleExternalAccession,BiologicalSample_CollectDate,BiologicalSample_TopographyCode,BiologicalSample_Nature,BiologicalSample_Origin,BiologicalSample_StorageTemperature,BiologicalSample_TumorCellularity
+L304,1,1,1,ech primary,,2005-12-27,C34,C4039816,OSIRIS:O59-2,MIABIS:Tissue Frozen,30
+L304,2,2,1,ech 2,ech primary,2011-02-08,C30,C1519524,OSIRIS:O59-2,FFPE,60

pivot/OSIRIS_pivot_Biomarker.csv

@@ -1,2 +1,2 @@
-patient_id,instance_id,biomarker_analysis_instance,biomarker_biomarkercode,biomarker_biomarkerstatus
-L304,1,1,cg6548,++
+Patient_Id,Instance_Id,Analysis_Ref,Biomarker_Code,Biomarker_Value,Biomarker_Unit
+L304,1,1,cg6548,++,

pivot/OSIRIS_pivot_Consent.csv

@@ -1,2 +1,2 @@
-patient_id,instance_id,consent_expirationdate,consent_intrinsicanalysisauth,consent_somaticanalysisauth
-L304,1,2000-11-16,0,1
+Patient_Id,Instance_Id,Consent_Date,Consent_GeneticAnalysisAuthorization
+L304,1,2000-11-16,0

pivot/OSIRIS_pivot_CopyNumber.csv

@@ -1,2 +1,4 @@
-patient_id,instance_id,alteration_in_specimen_analysis_instance,alteration_in_specimen_alterationtype,alteration_chromosome,alteration_genomicstart,alteration_genomicstop,alteration_genomebuild,alteration_cytoband,genome_entity_genomeentitytype,genome_entity_genomeentitydatabase,genome_entity_genomeentityid,genome_entity_genesymbol,segment_copy_number_segmentintensity,segment_copy_number_segmentgenomicstatus,segment_copy_number_copynumber,segment_loh_lossofheterozygosity,validation_validationtype,validation_validationmethod,validation_validationstatus
-L304,1,3,OSIRIS:O15-4,LA21263-1,87751512,88104391,hg19,10q23.31,OSIRIS:O24-1,OSIRIS:O25-1,HGNC:9588,HGNC:9588,33,OSIRIS:O49-2,3,0,OSIRIS:O16-2,"Visual check",OSIRIS:O18-2
+Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Alteration_Chromosome,Alteration_GenomicStart,Alteration_GenomicStop,Alteration_GenomeBuild,Alteration_Cytoband,CNV_SegmentIntensity,CNV_SegmentGenomicStatus,CNV_CopyNumber,CNV_LOH,Validation_Type,Validation_Method,Validation_Status
+L304,1,3,OSIRIS:O15-4,,,,LA21263-1,87751512,88104391,hg19,10q23.31,33,OSIRIS:O49-2,3,0,OSIRIS:O16-2,Visual check,OSIRIS:O18-2
+,,,,,,,,,,,,,,,,,,
+Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,Vincent : Alteration ou Location ?,,,,,,,,,,,,,,,

pivot/OSIRIS_pivot_Drug.csv

@@ -1,3 +1,3 @@
-patient_id,instance_id,drug_treatment_instance,drug_code,drug_drugname
-L304,1,2,c3564,cis-platine
-L304,2,2,f456,Imatinib
+Patient_Id,Instance_Id,Treatment_Ref,Drug_Code,Drug_Name
+L304,1,2,c3564,cis-platine
+L304,2,2,f456,Imatinib

pivot/OSIRIS_pivot_Expression.csv

@@ -1,2 +1,4 @@
-patient_id,instance_id,alteration_in_specimen_analysis_instance,alteration_in_specimen_alterationtype,genome_entity_genomeentitytype,genome_entity_genomeentitydatabase,genome_entity_genomeentityid,genome_entity_genesymbol,gene_expression_expressiondatatype,gene_expression_expressionvalue,gene_expression_expressionpvalue,gene_expression_expressionpvalueadjustmentmethod,validation_validationtype,validation_validationmethod,validation_validationstatus
-L304,,,,,,,,,,,,
+Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,GenomeEntity_Type,GenomeEntity_Database,GenomeEntity_Id,GenomeEntity_Symbol,GeneExpression_DataType,GeneExpression_Value,Validation_Type,Validation_Method,Validation_Status
+L304,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,
+Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,,,,,,,,,,

pivot/OSIRIS_pivot_FamilyCancerHistory.csv

@@ -0,0 +1,3 @@
+Patient_Id,Instance_Id,FamilyCancerHistory_TopographyCode,FamilyCancerHistory_Parentage
+L304,1,C00.5,C0037047
+M521,1,C67.0,

pivot/OSIRIS_pivot_Fusion.csv

@@ -1,2 +1,4 @@
-patient_id,instance_id,alteration_in_specimen_analysis_instance,alteration_in_specimen_alterationtype,fusion_fusiontype,fusion_fusiontranscript,fusion_fusiontranscriptreference,fusion_genesymbol5prime,fusion_fusionregionname5prime,fusion_transcriptreferencesequenceid5prime,fusion_fusionstrand5prime,fusion_fusionpoint5prime,fusion_genesymbol3prime,fusion_fusionregionname3prime,fusion_transcriptreferencesequenceid3prime,fusion_fusionstrand3prime,fusion_fusionpoint3prime,fusion_fusioninframe,fusion_analysis_fusionannotationreferentiel,fusion_analysis_fusionannotationvalue,fusion_qualityfilter_fusionnbspanningpair,fusion_qualityfilter_fusionnbsplitreads,validation_validationtype,validation_validationmethod,validation_validationstatus
-L304,1,2,OSIRIS:O15-3,LOINC:LA26331-1,,,PTEN,exon,NM_123,OSIRIS:O34-1,,,exon,NM_456,OSIRIS:O34-1,,1,OSIRIS:O42-2,,33,5,OSIRIS:O16-3,,OSIRIS:O18-2
+Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Fusion_Type,Fusion_Point5prime,Fusion_Point3prime,Fusion_NbSpanningPair,Fusion_NbSplitReads,Fusion_InFrame,Validation_Type,Validation_Method,Validation_Status
+L304,1,2,OSIRIS:O15-3,,,,LOINC:LA26331-1,,,33,5,1,OSIRIS:O16-3,,OSIRIS:O18-2
+,,,,,,,,,,,,,,,
+Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,,,,,,,,,,

pivot/OSIRIS_pivot_Patient.csv

@@ -1,2 +1,5 @@
-patient_id,instance_id,patient_gender,patient_ethnicity,patient_birthdate,patient_deathdate,patient_centerid,patient_causeofdeath,patient_lastnewsdate,patient_lastnewsstatus
-L304,1,M,2043-8,1967-11-08,2017-11-29,IB,UMLS:C0027651,2017-11-29,UMLS:C1546956
+Patient_Id,Instance_Id,Patient_Gender,Patient_Ethnicity,Patient_BirthDate,Patient_DeathDate,Patient_ProviderCenterId,Patient_OriginCenterId,Patient_CauseOfDeath,Patient_LastNewsDate,Patient_LastNewsStatus
+L304,1,M,2043-8,1967-11-08,2017-11-29,IB,IB,UMLS:C0027651,2017-11-29,UMLS:C1546956
+L036,2,,,,,,,,,
+,,,,,,,,,,
+M521,1,F,,1960-10-30,2014-05-16,,,,,

pivot/OSIRIS_pivot_RelatedPathology.csv

@@ -1,2 +1,2 @@
-patient_id,instance_id,relatedpathology_pathologycode,relatedpathology_diagnosisdate,relatedpathology_diagnosisenddate
-L304,1,R60.9,2002-11-14,2003-11-19
+Patient_Id,Instance_Id,RelatedPathology_PathologyCode,RelatedPathology_DiagnosisDate,RelatedPathology_PathologyEndDate
+L304,1,R60.9,2002-11-14,2003-11-19

pivot/OSIRIS_pivot_ResponseEvaluation.csv

@@ -0,0 +1,2 @@
+Patient_Id,Instance_Id,Treatment_Ref,Date,Status
+L304,1,1,,

pivot/OSIRIS_pivot_Treatment.csv

@@ -1,3 +1,3 @@
-patient_id,instance_id,treatment_tumorpathologyevent_instance,treatment_type,treatment_activitycode,treatment_startdate,treatment_enddate,treatment_clinicaltrialcontext,treatment_surgery_resectionquality,treatment_surgery_nature
-L304,1,1,UMLS:C0728940,,2006-01-04,2006-11-23,0,R0,
-L304,2,2,UMLS:C3665472,,2007-01-12,2008-11-17,1,R1,
+Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Treatment_Type,Treatment_LineNumber,Treatment_ActivityCode,Treatment_StartDate,Treatment_EndDate,Treatment_ClinicalTrialContext,Treatment_ClinicalTrialName,Treatment_ClinicalTrialId,Treatment_SurgeryResectionQuality,Treatment_SurgeryNature
+L304,1,1,UMLS:C0728940,2,,2006-01-04,2006-11-23,0,,,R0,
+L304,2,2,UMLS:C3665472,,,2007-01-12,2008-11-17,1,,,R1,

pivot/OSIRIS_pivot_TumorPathologyEvent.csv

@@ -1,3 +1,3 @@
-patient_id,instance_id,tumorpathologyevent_parent_instance,tumorpathologyevent_type,tumorpathologyevent_startdate,tumorpathologyevent_performancestatus,tumorpathologyevent_g8,tumorpathologyevent_t,tumorpathologyevent_n,tumorpathologyevent_m,tumorpathologyevent_tnmversion,tumorpathologyevent_tnmtype,tumorpathologyevent_histologicalgradetype,tumorpathologyevent_histologicalgradevalue,tumorpathologyevent_stadetype,tumorpathologyevent_stadevalue,tumorpathologyevent_diagnosisdate,tumorpathologyevent_topographycode,tumorpathologyevent_morphologycode,tumorpathologyevent_laterality
-L304,1,,UMLS:C0677930,2005-11-17,1,6,T0,N1mi,M1,,c,,,,,2005-11-17,C00.8,8002/3,UMLS:C0238767
-L304,2,1,UMLS:C0521158,2010-11-18,1,6,T1,N2,M1,,p,,,,,2010-11-18,C11.1,8000-1,UMLS:C0439673
+Patient_Id,Instance_Id,TumorPathologyEvent_ParentRef,TumorPathologyEvent_Type,TumorPathologyEvent_StartDate,TumorPathologyEvent_PerformanceStatus,TumorPathologyEvent_G8,TumorPathologyEvent_T,TumorPathologyEvent_N,TumorPathologyEvent_M,TumorPathologyEvent_TNMVersion,TumorPathologyEvent_TNMType,TumorPathologyEvent_HistologicalGradeType,TumorPathologyEvent_HistologicalGradeValue,TumorPathologyEvent_StadeType,TumorPathologyEvent_StadeValue,TumorPathologyEvent_DiagnosisDate,TumorPathologyEvent_TopographyCode,TumorPathologyEvent_MorphologyCode,TumorPathologyEvent_Laterality
+L304,1,,UMLS:C0677930,2005-11-17,1,6,T0,N1mi,M1,,c,,,,,2005-11-17,C00.8,8002/3,UMLS:C0238767
+L304,2,1,UMLS:C0521158,2010-11-18,1,6,T1,N2,M1,,p,,,,,2010-11-18,C11.1,8000-1,UMLS:C0439673

pivot/OSIRIS_pivot_Variant.csv

@@ -1,3 +1,5 @@
-patient_id,instance_id,alteration_in_specimen_analysis_instance,alteration_in_specimen_alterationtype,alteration_chromosome,alteration_genomicstart,alteration_genomicstop,alteration_genomebuild,alteration_cytoband,genome_entity_genomeentitytype,genome_entity_genomeentitydatabase,genome_entity_genomeentityid,genome_entity_genesymbol,reference_variant_referenceallele,reference_variant_alternativeallele,reference_variant_dnasequencevariationtype,reference_variant_pfamdomain,reference_variant_pfamid,reference_variant_dnaregionname,variant_in_specimen_positioncoverage,variant_in_specimen_variantcoverage,variant_in_specimen_strandbias,variant_in_specimen_genomicsourceclass,variant_in_specimen_allelicstate,variant_in_specimen_moleculartumorboardconclusion,variant_in_specimen_clinicaltumorboardconclusion,variant_in_specimen_proposedfororientation,validation_validationtype,validation_validationmethod,validation_validationstatus
-L304,1,1,OSIRIS:O15-5,LA21256-5,178916948,178916948,hg19,,OSIRIS:O24-1,OSIRIS:O25-1,HGNC:8975,HGNC:8975,T,A,LOINC:LA6690-7,"PI3K_rbd; PI3-kinase family, ras-binding domain",pfam00794,exon,31,6,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O81-2,OSIRIS:O82-2,0,OSIRIS:O16-2,biblio,OSIRIS:O18-1
-L304,2,2,OSIRIS:O15-5,LA21263-1,45,896,hg19,,,,,HGNC:11998,A,T,LOINC:LA6690-7,,,exon,785,456,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O81-2,OSIRIS:O82-2,0,OSIRIS:O16-1,,OSIRIS:O18-1
+Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Alteration_Chromosome,Alteration_GenomicStart,Alteration_GenomicStop,Alteration_GenomeBuild,Alteration_Cytoband,Variant_ReferenceAllele,Variant_AlternativeAllele,Variant_DNASequenceVariationType,VariantInSample_PositionReadDepth,VariantInSample_VariantReadDepth,VariantInSample_StrandBias,VariantInSample_GenomicSourceClass,VariantInSample_AllelicState,Validation_Type,Validation_Method,Validation_Status
+L304,1,1,OSIRIS:O15-5,,,,LA21256-5,178916948,178916948,hg19,,T,A,LOINC:LA6690-7,31,6,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O16-2,biblio,OSIRIS:O18-1
+L304,2,2,OSIRIS:O15-5,,,,LA21263-1,45,896,hg19,,A,T,LOINC:LA6690-7,785,456,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O16-1,,OSIRIS:O18-1
+,,,,,,,,,,,,,,,,,,,,,,
+Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,,Vincent : Alteration ou Location ?,,,,,,,,,,,,,,,