From d1c9ffab167aefb38430e1baebe0e1177aa00b16 Mon Sep 17 00:00:00 2001 From: "Y. Laizet" Date: Tue, 4 Dec 2018 15:48:20 +0100 Subject: [PATCH] Update --- data/ConceptualDomain.tsv | 17 +++++++++-------- data/DataElementConcept.tsv | 12 +++++++----- pivot/OSIRIS_pivot_AdverseEvent.csv | 2 +- pivot/OSIRIS_pivot_Annotation.csv | 13 ++++++++++--- pivot/OSIRIS_pivot_BiologicalSample.csv | 2 +- pivot/OSIRIS_pivot_CopyNumber.csv | 11 ++++++++++- pivot/OSIRIS_pivot_Fusion.csv | 6 ++---- pivot/OSIRIS_pivot_Patient.csv | 4 ++-- pivot/OSIRIS_pivot_TumorPathologyEvent.csv | 2 +- 9 files changed, 43 insertions(+), 26 deletions(-) diff --git a/data/ConceptualDomain.tsv b/data/ConceptualDomain.tsv index 1e4a897..f1cf938 100644 --- a/data/ConceptualDomain.tsv +++ b/data/ConceptualDomain.tsv @@ -53,14 +53,13 @@ HL7:2108-9 European FHIR (HL7) v3 https://www.hl7.org/fhir/v3/Race Enumerated St HL7:2118-8 Middle Eastern or North African FHIR (HL7) v3 https://www.hl7.org/fhir/v3/Race Enumerated String FHIR:Race HL7:2129-5 Arab FHIR (HL7) v3 https://www.hl7.org/fhir/v3/Race Enumerated String FHIR:Race UMLS:C0439673 Unknown UMLS Enumerated String FHIR:Race -UMLS:C0277589 Death of unknown cause UMLS https://uts.nlm.nih.gov/metathesaurus.html#C0277589;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 UMLS:C1707251 Other cancer UMLS https://uts.nlm.nih.gov/metathesaurus.html#C1707251;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 UMLS:C3262234 Other cause UMLS https://uts.nlm.nih.gov/metathesaurus.html#C3262234;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 UMLS:C0679861 Complications of treatment UMLS https://uts.nlm.nih.gov/metathesaurus.html#C0679861;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 UMLS:C0027651 Neoplasm UMLS https://uts.nlm.nih.gov/metathesaurus.html#C0027651;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 -UMLS:C0439673 Unknown UMLS Enumerated String UMLS:C0007465 +UMLS:C0277589 Death of unknown cause UMLS https://uts.nlm.nih.gov/metathesaurus.html#C0277589;0;1;CUI;2016AA;EXACT_MATCH;CUI;*; Enumerated String UMLS:C0007465 UMLS:C2584946 Alive (finding) UMLS Enumerated String OSIRIS:LastNewsStatus -ULMS:C1546956 Patient Outcome - Died UMLS Enumerated String OSIRIS:LastNewsStatus +UMLS:C1546956 Patient Outcome - Died UMLS Enumerated String OSIRIS:LastNewsStatus UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:LastNewsStatus UMLS:C0037047 Sibling UMLS Enumerated String OSIRIS:FamilyCancerHistoryParentage UMLS:C0030551 Parent UMLS Enumerated String OSIRIS:FamilyCancerHistoryParentage @@ -94,7 +93,6 @@ UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:EventType 2 ambulant et capable de se prendre en charge, mais incapable de fournir un travail et alité pendant moins de 50 % de son temps OMS Enumerated String OMS:PerformanceStatus 3 capacité de prise en charge propre beaucoup plus limitée. Passe plus de 50 % de son temps au lit ou dans une chaise. OMS Enumerated String OMS:PerformanceStatus 4 complètement grabataire. Incapable de se prendre en charge. Le patient reste totalement confiné au lit ou dans une chaise. OMS Enumerated String OMS:PerformanceStatus -UMLS:C0439673 Unknown UMLS Enumerated String OMS:PerformanceStatus Tx Tx UICC Enumerated String OSIRIS:T_TNM T0 T0 UICC Enumerated String OSIRIS:T_TNM T1 T1 UICC Enumerated String OSIRIS:T_TNM @@ -146,7 +144,7 @@ RECIST:CR Complete Response RECIST v1.1 Enumerated String OSIRIS:RECIST RECIST:PR Partial Response RECIST v1.1 Enumerated String OSIRIS:RECIST RECIST:SD Stable disease RECIST v1.1 Enumerated String OSIRIS:RECIST RECIST:PD Progressive Disease RECIST v1.1 Enumerated String OSIRIS:RECIST -UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:RECIST +RECIST:NE Not evaluable RECIST v1.1 Enumerated String OSIRIS:RECIST OSIRIS:C39-1 CKIT OSIRIS Enumerated String OSIRIS:BiomarkerCode OSIRIS:C39-2 b-catenine OSIRIS Enumerated String OSIRIS:BiomarkerCode OSIRIS:C39-3 CKIT/DOG1 OSIRIS Enumerated String OSIRIS:BiomarkerCode @@ -211,6 +209,7 @@ R2 Gross residual disease ICGC Enumerated String OSIRIS:SurgeryResectionQuality UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:SurgeryResectionQuality UMLS:C0005767 Blood NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0005767 Enumerated String OSIRIS:SampleNature UMLS:C0032105 Plasma NCI https://ncim-stage.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20Metathesaurus&code=C0032105 Enumerated String OSIRIS:SampleNature +UMLS:C1321301 Peripheral Blood Mononuclear Cell NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0085983 Enumerated String OSIRIS:SampleNature UMLS:C0085983 Tumor Cell Line NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0085983 Enumerated String OSIRIS:SampleNature UMLS:C1548793 Frozen Specimen NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C1548793 Enumerated String OSIRIS:SampleNature UMLS:C1519524 Paraffin Embedded Tissue (FFPE) NCI Enumerated String OSIRIS:SampleNature @@ -218,12 +217,14 @@ UMLS:C0042036 Urine NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?d UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:SampleNature OSIRIS:O59-1 Normal OSIRIS Enumerated String OSIRIS:SampleOrigin OSIRIS:O59-2 Tumoral OSIRIS Enumerated String OSIRIS:SampleOrigin +UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:SampleOrigin OSIRIS:C60-1 Room temperature MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature OSIRIS:C60-2 Between 2 °C and 10 °C MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature OSIRIS:C60-3 Between -18 °C and -35 °C MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature OSIRIS:C60-4 Between -60 °C and -85 °C MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature OSIRIS:C60-5 Liquid nitrogen, -150 °C to -196 °C MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature OSIRIS:C60-6 Other MIABIS-2.0-15 https://github.com/MIABIS/miabis/wiki/Structured-data-and-lists#miabis-20-15 Enumerated String OSIRIS:StorageTemperature +UMLS:C0439673 Unknown UMLS Enumerated String OSIRIS:StorageTemperature OSIRIS:O6-1 ChIP-on-Chip OSIRIS Enumerated String OSIRIS:TechnicalProtocol OSIRIS:O6-2 ChIP-seq OSIRIS Enumerated String OSIRIS:TechnicalProtocol OSIRIS:O6-3 DNA microarray OSIRIS Enumerated String OSIRIS:TechnicalProtocol @@ -402,9 +403,6 @@ LOINC:LA26331-1 translocation LOINC http://r.details.loinc.org/LOINC/81289-1.htm OSIRIS:O28-1 readthrough OSIRIS Enumerated String OSIRIS:FusionType OSIRIS:O94-1 + OSIRIS Enumerated String OSIRIS:Strand OSIRIS:O94-2 - OSIRIS Enumerated String OSIRIS:Strand -OSIRIS:O42-1 ChimerDb OSIRIS Enumerated String OSIRIS:FusionAnnotationReferentiel -OSIRIS:O42-2 Oncofuse OSIRIS Enumerated String OSIRIS:FusionAnnotationReferentiel -OSIRIS:O42-3 Mittelman DB OSIRIS Enumerated String OSIRIS:FusionAnnotationReferentiel OSIRIS:O49-1 Amplification OSIRIS Enumerated String OSIRIS:SegmentGenomicStatus OSIRIS:O49-2 Gain OSIRIS Enumerated String OSIRIS:SegmentGenomicStatus OSIRIS:O49-3 Normal OSIRIS Enumerated String OSIRIS:SegmentGenomicStatus @@ -434,6 +432,9 @@ OSIRIS:O91-3 SwissProt OSIRIS Enumerated String OSIRIS:Annotation_ReferenceData OSIRIS:O91-4 UniProt OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase OSIRIS:O96-1 Cosmic OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase OSIRIS:O96-2 dbSNP OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase +OSIRIS:O42-1 ChimerDb OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase +OSIRIS:O42-2 Oncofuse OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase +OSIRIS:O42-3 Mittelman DB OSIRIS Enumerated String OSIRIS:Annotation_ReferenceDatabase LOINC:LA6692-3 Deletion LOINC http://r.details.loinc.org/LOINC/48006-1.html Enumerated String OSIRIS:AminoAcidChangeType LOINC:LA6686-5 Duplication LOINC http://r.details.loinc.org/LOINC/48006-1.html Enumerated String OSIRIS:AminoAcidChangeType LOINC:LA6694-9 Frameshift LOINC http://r.details.loinc.org/LOINC/48006-1.html Enumerated String OSIRIS:AminoAcidChangeType diff --git a/data/DataElementConcept.tsv b/data/DataElementConcept.tsv index 6842b44..468145d 100644 --- a/data/DataElementConcept.tsv +++ b/data/DataElementConcept.tsv @@ -15,7 +15,7 @@ RelatedPathology PathologyCode RelatedPathology_PathologyCode Pathology Code Cod RelatedPathology DiagnosisDate RelatedPathology_DiagnosisDate Diagnosis Date Date Date mandatory if ObjectClass is set Date du diagnostic de la pathologie associée Date of diagnosis for the related disease. C14 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). Date of the end of the related disease (if occuring and known) C15 FamilyCancerHistory TopographyCode FamilyCancerHistory_TopographyCode Topography Code Code Localisation ICDO3:Topography String mandatory if ObjectClass is set Code international de la localisation de l'antécédent carcinologique International code for the localization of the oncologic primary site C17 -FamilyCancerHistory Parentage FamilyCancerHistory_Parentage Parentage Parentage OSIRIS:FamilyCancerHistoryParentage ld mandatory if ObjectClass is set Lien de parenté Family relationship C77 +FamilyCancerHistory Parentage FamilyCancerHistory_Parentage Parentage Parentage OSIRIS:FamilyCancerHistoryParentage String mandatory if ObjectClass is set Lien de parenté Family relationship C77 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). 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...) C20 TumorPathologyEvent StartDate TumorPathologyEvent_StartDate Start Date Date de début de l'événement Date mandatory Date de début de l'événement tumoral ou de la maladie Date of start of cancer event or disease C21 TumorPathologyEvent EndDate TumorPathologyEvent_EndDate End Date Date de fin de l'événement Date optional Date de fin de l'événement tumoral ou de la maladie Date of end of cancer event or disease C82 @@ -47,7 +47,7 @@ Treatment LineNumber Treatment_LineNumber Line Number Numéro de ligne String o Treatment ActivityCode Treatment_ActivityCode Activity Code Codification de l'acte CCAM String optional Code CCAM de l'acte CCAM code of the medical act C42 Treatment StartDate Treatment_StartDate Start Date Date de début Date mandatory if ObjectClass is set Date de début du traitement Date of treatment start C43 Treatment EndDate Treatment_EndDate End Date Date de fin Date mandatory if ObjectClass is set Date de fin du traitement Date of treatment end C44 -Treatment ClinicalTrialContext Treatment_ClinicalTrialContext Clinical Trial Context Clinical trial (Yes | No) Boolean optional Traitement effectué dans un contexte d'étude clinique Treatment performed in a clinical study setting C45 +Treatment ClinicalTrialContext Treatment_ClinicalTrialContext Clinical Trial Context Clinical trial (Yes | No) String optional Traitement effectué dans un contexte d'étude clinique Treatment performed in a clinical study setting C45 Treatment ClinicalTrialName Treatment_ClinicalTrialName Clinical Trial Name Nom de l'essai clinique String optional, mandatory if ClinicalTrialContext is 'Yes' Nom de l'étude clinique Name of the clinical study 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 NCT identifier of the clinical study C76 Treatment SurgeryResectionQuality Treatment_SurgeryResectionQuality Surgery Resection Quality Qualité de la résection (anapath) OSIRIS:SurgeryResectionQuality String optional Qualité de la résection (anapath) Quality of resection (anapath) C46 @@ -58,8 +58,8 @@ AdverseEvent EndDate AdverseEvent_EndDate End Date Date de fin Date optional Da AdverseEvent Grade AdverseEvent_Grade Grade Grade String mandatory if ObjectClass is set Grade de l'évenement indésirable Grade of the adverse event C80 Drug Code Drug_Code Code Code molécule ATC String mandatory if ObjectClass is set Code de la classification thérapeutique (5ème niveau si possible) Therapeutic classification code (5th level if possible) C51 Drug Name Drug_Name Name Nom de la molécule String mandatory if ObjectClass is set Nom de la molécule Name of the molecule C52 -BiologicalSample SampleExternalAccession BiologicalSample_SampleExternalAccession Sample External Accession Id unique de l'échantillon String mandatory if ObjectClass is set Identifiant unique de l'échantillon Unique identifier of the sample C53 -BiologicalSample Parent Sample External Accession BiologicalSample_ParentSampleExternalAccession Identifiant unique de l'échantillon parent String optional Identifiant unique de l'échantillon parent (s'il en existe un, exemple N°histo) Unique identifier of the parent sample (if there is one, example histo#) C54 +BiologicalSample ExternalAccession BiologicalSample_ExternalAccession Sample External Accession Id unique de l'échantillon String mandatory if ObjectClass is set Identifiant unique de l'échantillon Unique identifier of the sample C53 +BiologicalSample ParentExternalAccession BiologicalSample_ParentExternalAccession Parent sample External Accession Identifiant unique de l'échantillon parent String optional Identifiant unique de l'échantillon parent (s'il en existe un, exemple N°histo) Unique identifier of the parent sample (if there is one, example histo#) C54 BiologicalSample CollectDate BiologicalSample_CollectDate Collect Date Date du prélèvement Date mandatory if ObjectClass is set Date du prélèvement Date of sampling C56 BiologicalSample TopographyCode BiologicalSample_TopographyCode Topography Code Code Localisation ICDO3:Topography String mandatory if ObjectClass is set Code de la localisation tumorale Code of tumor localization C57 BiologicalSample Nature BiologicalSample_Nature Nature Nature de l'échantillon OSIRIS:SampleNature String mandatory if ObjectClass is set Nature de l'échantillon Nature of the sample C58 @@ -93,7 +93,9 @@ GenomeEntity Id GenomeEntity_Id Id Id String mandatory Identifiant de l'entité GenomeEntity Symbol GenomeEntity_Symbol Symbol Symbol String mandatory if gene Symbole Hugo du gène Hugo gene symbol O27 Fusion Type Fusion_Type Type Type OSIRIS:FusionType String optional Type de l'événement de fusion. Par exemple: translocation, readthrough Type of the fusion event. For eg: translocation, readthrough O28 Fusion Point5prime Fusion_Point5prime Point 5 prime Point 5 prime String mandatory Position du point de fusion sur le partenaire en 5 prime Position of the fusion point on the 5 prime partner O35 +Fusion Chromosome5prime Fusion_Chromosome5prime Chromosome 5 prime Chromosome 5 prime OSIRIS:Chromosome String mandatory Chromosome du point de fusion sur le partenaire en 5 prime O97 Fusion Point3prime Fusion_Point3prime Point 3 prime Point 3 prime Integer mandatory Position du point de fusion sur le partenaire en 3 prime Position of the fusion point on the 3 prime partner O40 +Fusion Chromosome3prime Fusion_Chromosome3prime Chromosome 3 prime Chromosome 3 prime OSIRIS:Chromosome String mandatory Chromosome du point de fusion sur le partenaire en 3 prime O98 Fusion InFrame Fusion_InFrame In Frame In Frame Boolean optional Indiquez si la fusion est dans le cadre de lecture Specify whether the fusion is in frame O41 Fusion NbSpanningPair Fusion_NbSpanningPair Nb Spanning Pair Nb Spanning Pair Integer mandatory Nombre de paires de reads couvrant la fusion Number of reads pairs spanning the fusion O44 Fusion NbSplitReads Fusion_NbSplitReads Nb Split Reads Nb Split Reads Integer optional Nombre de reads contenant le point de fusion Number of reads containing the fusion point O46 @@ -127,4 +129,4 @@ VariantInSample StrandBias VariantInSample_StrandBias Strand Bias Strand Bias B VariantInSample GenomicSourceClass VariantInSample_GenomicSourceClass Genomic Source Class Genomic Source Class LOINC:LL378-1 String mandatory Classe génomique du variant (par exemple: constitutionel, somatique et prénatal) 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 Niveau d'occurrence allélique d'une variation de séquence d'ADN Level of allelic occurrence of a DNA Sequence Variation O80 GeneExpression DataType GeneExpression_DataType Data Type Data Type OSIRIS:ExpressionDataType String mandatory Type de la valeur d'expression correspondant au niveau de traitement des données Type of the expression value corresponding to the level of data processing O84 -GeneExpression Value GeneExpression_Value Value Value Float mandatory Valeur numérique de l'expression Numerical value for expression O85 +GeneExpression Value GeneExpression_Value Value Value Float mandatory Valeur numérique de l'expression Numerical value for expression O85 \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_AdverseEvent.csv b/pivot/OSIRIS_pivot_AdverseEvent.csv index a7e2022..ebdb9aa 100644 --- a/pivot/OSIRIS_pivot_AdverseEvent.csv +++ b/pivot/OSIRIS_pivot_AdverseEvent.csv @@ -1,4 +1,4 @@ -Patient_Id,Instance_Id,Treatment_Ref,TumorPahtologyEvent_Ref,AdverseEvent_Code,AdverseEvent_Date,AdverseEvent_EndDate,AdverseEvent_Grade +Patient_Id,Instance_Id,Treatment_Ref,TumorPathologyEvent_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,,,,,,, \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_Annotation.csv b/pivot/OSIRIS_pivot_Annotation.csv index 520349e..b2aa80f 100644 --- a/pivot/OSIRIS_pivot_Annotation.csv +++ b/pivot/OSIRIS_pivot_Annotation.csv @@ -1,4 +1,11 @@ -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,, +Patient_Id,Instance_Id,Alteration_Ref,AlterationOnSample_AlterationType,Annotation_ReferenceType,Annotation_ReferenceDatabase,Annotation_ReferenceValue,Annotation_Symbol,Annotation_PfamDomain,Annotation_PfamId,Annotation_MutationPredictionAlgorithm,Annotation_MutationPredictionValue,Annotation_MutationPredictionScore,Annotation_DNARegionName,Annotation_DNASequenceVariation,Annotation_AminoAcidChange,Annotation_GenomicSequenceVariation,Annotation_RNASequenceVariation,Annotation_AminoAcidChangeType,Annotation_FusionPrimeEnd,Annotation_Strand +L304,1,1,OSIRIS:O15-4,OSIRIS:O90-1,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 ?,,,,,,,,,,,,,,,,, \ No newline at end of file +,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,, +L304,1,1,Genetic variant,genome entity,Entrez,123365,TP53,,,,,,,,,,,,, +L304,2,1,Genetic variant,exonic variant transcript,Refseq,NM_001126115,TP53,,,,,,exon1,c.73G>T,p.V25F,,,,, +L304,3,1,Genetic variant,exonic variant transcript,Refseq,NM_001126116,TP53,,,,,,exon1,c.73G>T,p.V25F,,,,, +L304,4,1,Genetic variant,exonic variant transcript,Refseq,NM_001126112,TP53,,,,,,exon5,c.469G>T,p.V157F,,,,, +L304,5,1,Genetic variant,,,,TP53,,,SIFT,Deleterious,0.35,,,,,,,, +L304,6,1,Genetic variant,,,,TP53,,,Polyphen,Deleterious,0.7,,,,,,,, \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_BiologicalSample.csv b/pivot/OSIRIS_pivot_BiologicalSample.csv index 58ec630..2fe56f8 100644 --- a/pivot/OSIRIS_pivot_BiologicalSample.csv +++ b/pivot/OSIRIS_pivot_BiologicalSample.csv @@ -1,3 +1,3 @@ -Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Consent_Ref,BiologicalSample_SampleExternalAccession,BiologicalSample_ParentSampleExternalAccession,BiologicalSample_CollectDate,BiologicalSample_TopographyCode,BiologicalSample_Nature,BiologicalSample_Origin,BiologicalSample_StorageTemperature,BiologicalSample_TumorCellularity +Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Consent_Ref,BiologicalSample_ExternalAccession,BiologicalSample_ParentExternalAccession,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 \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_CopyNumber.csv b/pivot/OSIRIS_pivot_CopyNumber.csv index 522938b..d9a1f0c 100644 --- a/pivot/OSIRIS_pivot_CopyNumber.csv +++ b/pivot/OSIRIS_pivot_CopyNumber.csv @@ -1,4 +1,13 @@ 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 ?,,,,,,,,,,,,,,, \ No newline at end of file +Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,Vincent : Alteration ou Location ?,,,,,,,,,,,,,,, +,,,,,solution actuelle,,chr1,1,10,,,,,2,,,, +,,,,,,,chr1,11,30,,,,,5,,,, +,,,,,,,chr1,1,60,,,,,,1,,, +,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,, +,,,,,meilleure solution pour les requetes,,chr1,1,10,,,,,2,1,,, +,,,,,,,chr1,11,30,,,,,5,1,,, +,,,,,,,chr1,30,60,,,,,2,1,,, \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_Fusion.csv b/pivot/OSIRIS_pivot_Fusion.csv index 069f607..9fdb65f 100644 --- a/pivot/OSIRIS_pivot_Fusion.csv +++ b/pivot/OSIRIS_pivot_Fusion.csv @@ -1,4 +1,2 @@ -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,,,,,,,,,,,,,,, \ No newline at end of file +Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Fusion_Type,Fusion_Chromosome5prime,Fusion_Point5prime,Fusion_Chromosome3prime,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 \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_Patient.csv b/pivot/OSIRIS_pivot_Patient.csv index a652596..0bfa33e 100644 --- a/pivot/OSIRIS_pivot_Patient.csv +++ b/pivot/OSIRIS_pivot_Patient.csv @@ -1,3 +1,3 @@ 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,,,,,,,,, +L304,1,HL7:M,2043-8,1967-11-08,2017-11-29,IB,IB,UMLS:C0027651,2017-11-29,UMLS:C1546956 +L036,2,,,,,,,,, \ No newline at end of file diff --git a/pivot/OSIRIS_pivot_TumorPathologyEvent.csv b/pivot/OSIRIS_pivot_TumorPathologyEvent.csv index fa351c6..3dd198d 100644 --- a/pivot/OSIRIS_pivot_TumorPathologyEvent.csv +++ b/pivot/OSIRIS_pivot_TumorPathologyEvent.csv @@ -1,3 +1,3 @@ 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 \ No newline at end of file +L304,2,1,UMLS:C0521158,2010-11-18,6,6,T1,N2,M1,,p,,,,,2010-11-18,C11.1,8000-1,UMLS:C0439673 \ No newline at end of file