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ylaizet committed Dec 4, 2018
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17 changes: 9 additions & 8 deletions data/ConceptualDomain.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -211,19 +209,22 @@ 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
UMLS:C0042036 Urine NCI https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0042036 Enumerated String OSIRIS:SampleNature
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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
12 changes: 7 additions & 5 deletions data/DataElementConcept.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion pivot/OSIRIS_pivot_AdverseEvent.csv
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@@ -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,,,,,,,
13 changes: 10 additions & 3 deletions pivot/OSIRIS_pivot_Annotation.csv
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@@ -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 ?,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,
,,,,,,,,,,,,,,,,,,,,
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,,,,,,,,
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