From ca7afe587e38fdc1ef7632c2274fe52d5a3f81fa Mon Sep 17 00:00:00 2001 From: "Y. Laizet" Date: Tue, 18 Dec 2018 14:14:42 +0100 Subject: [PATCH] move down annotation Pfam properties and update pivot files --- data/DataElementConcept.tsv | 4 ++-- pivot/OSIRIS_pivot_Annotation.csv | 19 ++++++++----------- pivot/OSIRIS_pivot_Expression.csv | 6 ++---- 3 files changed, 12 insertions(+), 17 deletions(-) diff --git a/data/DataElementConcept.tsv b/data/DataElementConcept.tsv index b1fd31d..2e181cd 100644 --- a/data/DataElementConcept.tsv +++ b/data/DataElementConcept.tsv @@ -109,11 +109,11 @@ Variant DNASequenceVariationType Variant_DNASequenceVariationType DNA Sequence V Annotation ReferenceType Annotation_ReferenceType Reference Type Reference Type OSIRIS:Annotation_ReferenceType String optional O90 Annotation ReferenceDatabase Annotation_ReferenceDatabase Reference Database Reference Database OSIRIS:Annotation_ReferenceDatabase String optional O91 Annotation ReferenceValue Annotation_ReferenceValue Reference Value Reference Value String optional O92 -Annotation PfamDomain Annotation_PfamDomain Pfam Domain Pfam Domain String optional Domaines Pfams liés à la position d'altération Pfams domains related to alteration position O58 -Annotation PfamId Annotation_PfamId Pfam Id Pfam Id String optional Identifiant des domaines Pfams liés à la position d'altération Identifier of Pfams domains related to alteration position O59 Annotation MutationPredictionAlgorithm Annotation_MutationPredictionAlgorithm Mutation Prediction Algorithm Mutation Prediction Algorithm OSIRIS:MutationPredictionAlgorithm String optional Algorithme pour prédire l'effet de variation sur la protéine Algorithm to predict the variation effect over the protein O63 Annotation MutationPredictionValue Annotation_MutationPredictionValue Mutation Prediction Value Mutation Prediction Value String optional Prédiction de l'effet de variation sur la protéine Prediction of the variation effect over the protein O64 Annotation MutationPredictionScore Annotation_MutationPredictionScore Mutation Prediction Score Mutation Prediction Score Float optional Niveau de confiance de la prédiction de l'effet de variation sur la protéine Level of confidence of the prediction of the variation effect over the protein O65 +Annotation PfamDomain Annotation_PfamDomain Pfam Domain Pfam Domain String optional Domaines Pfams liés à la position d'altération Pfams domains related to alteration position O58 +Annotation PfamId Annotation_PfamId Pfam Id Pfam Id String optional Identifiant des domaines Pfams liés à la position d'altération Identifier of Pfams domains related to alteration position O59 Annotation DNARegionName Annotation_DNARegionName DNA Region Name DNA Region Name String optional Nom lisible par l'homme de la région d'intérêt liée au transcript (ex: exon1, intron1, UTR3 ') Human readable name for the region of interest related to the transcript (eg: exon1, intron1, UTR3') O66 Annotation DNASequenceVariation Annotation_DNASequenceVariation DNA Sequence Variation DNA Sequence Variation String mandatory Nomenclature HGVS sur le transcript choisi HGVS nomenclature on the chosen transcript O71 c.6964C>T Annotation AminoAcidChange Annotation_AminoAcidChange Amino Acid Change Amino Acid Change String optional Nomenclature HGVS sur le transcript de protéine choisi HGVS nomenclature on the chosen protein transcript O72 p.Arg2322Cys diff --git a/pivot/OSIRIS_pivot_Annotation.csv b/pivot/OSIRIS_pivot_Annotation.csv index b2aa80f..9336808 100644 --- a/pivot/OSIRIS_pivot_Annotation.csv +++ b/pivot/OSIRIS_pivot_Annotation.csv @@ -1,11 +1,8 @@ -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,,,,,,, -,,,,,,,,,,,,,,,,,,,, -,,,,,,,,,,,,,,,,,,,, -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 +Patient_Id,Instance_Id,Alteration_Ref,AlterationOnSample_AlterationType,GenomeEntity_Type,GenomeEntity_Database,GenomeEntity_Id,GenomeEntity_Symbol,Annotation_ReferenceType,Annotation_ReferenceDatabase,Annotation_ReferenceValue,Annotation_MutationPredictionAlgorithm,Annotation_MutationPredictionValue,Annotation_MutationPredictionScore,Annotation_PfamDomain,Annotation_PfamId,Annotation_DNARegionName,Annotation_DNASequenceVariation,Annotation_AminoAcidChange,Annotation_GenomicSequenceVariation,Annotation_RNASequenceVariation,Annotation_AminoAcidChangeType,Annotation_FusionPrimeEnd,Annotation_Strand +L304,1,1,OSIRIS:O15-4,,,,PI3K,OSIRIS:O90-1,COSMIC,COSM760,SIFT,Deleterious,0.35,"PI3K_rbd; PI3-kinase family, ras-binding domain",pfam00794,exon 2,c.1624G>A,p.E542K,,,LA6698-0,, +L304,1,1,Genetic variant,,,,TP53,genome entity,Entrez,123365,,,,,,,,,,,,, +L304,2,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126115,,,,,,exon1,c.73G>T,p.V25F,,,,, +L304,3,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126116,,,,,,exon1,c.73G>T,p.V25F,,,,, +L304,4,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126112,,,,,,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_Expression.csv b/pivot/OSIRIS_pivot_Expression.csv index fca1879..82ce3a9 100644 --- a/pivot/OSIRIS_pivot_Expression.csv +++ b/pivot/OSIRIS_pivot_Expression.csv @@ -1,4 +1,2 @@ -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,,,,,,,,,,,,,,, \ No newline at end of file +Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,GeneExpression_DataType,GeneExpression_Value,Validation_Type,Validation_Method,Validation_Status +L304,,,,,,,,,,, \ No newline at end of file