move down annotation Pfam properties and update pivot files

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

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,,,,,,,,
+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,,,,,,,,,,

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,,,,,,,,,,,,,,,
+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,,,,,,,,,,,