Merge pull request #67 from eliteportal/LLFS-rnaseq-updates

added rnaseq valid values for LLFS

EL.data.model.csv

@@ -94,8 +94,8 @@ reagentName,The reagent name is an alternative to the Reagent ID.,,,,False,Manif
 reagentWeblink,An internet address that may provide details of an assay reagent.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human
 referenceTranscriptID,"The ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 reportedTrait,"The trait under investigation. Please describe the trait concisely but with enough detail to be clear to a non-specialist. Avoid the use of abbreviations; if these are necessary, please define them or their source in the readme file. Example - Reticulocyte count",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, EMBL-EBI","A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Genotyping_Human
-repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)","ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
-resultUnit,The unit for the result value,"FPKM,Not applicable,Not collected,Not specified,RPKM,TPM,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
+repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)","ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
+resultUnit,The unit for the result value,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
 rnaBatchID,"Isolation batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"Whole_Genome_Sequencing,scRNAseq"
 rnaBatchSize,The number of samples,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,Sage Bionetworks, ,scRNAseq
 rnaBatchSizeUnit,The unit of measurement for number of samples in a batch,"AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,other,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,scRNAseq
@@ -126,7 +126,7 @@ targetGene,"Targeted gene or locus name for marker gene studies. Provide a value
 taxon,"Taxonomic identifier. The National Center for Biotechnology Information taxon ID (formatted as, ex. ""txid9989"")",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"https://www.ncbi.nlm.nih.gov/taxonomy, http://edamontology.org/data_1179, http://purl.obolibrary.org/obo/TAXRANK_0000010", ,Individual_non_Human
 technologyPlatformVersion,"The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"DSLWG,Sage Bionetworks,http://purl.obolibrary.org/obo/NCIT_C45378","A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 tissueVolume,The volume of the tissue sample. Measured in microliters.,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
-transcriptType,The type of transcript reported,"lincRNA,mRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,ImmPort, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
+transcriptType,The type of transcript reported,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,ImmPort, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq"
 treatmentAmountUnit,Unit of treatment amount.,"AFU,AI,AU/ml,DK units/ml,g/dl,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,other,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,NUMBER,"Sage Bionetworks, ImmPort", ,Genotyping_Human
 treatmentAmountValue,"The Amount Value indicates how much (concentration, mass, volume) of a treatment agent was applied to a sample.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human
 treatmentDurationUnit,Unit of treatment duration.,"d.p.c.,Days,Hours,Minutes,Months,Not applicable,Not collected,Not specified,Seconds,Unknown,Weeks,Years",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human
@@ -198,12 +198,12 @@ gDNAconc,gDNA Concentration in ng. Provide a value or Unknown Not collected Not
 isStranded,Whether or not the library is stranded.,"FALSE,TRUE",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.isStranded-0.0.2,sequencing,False,BOOLEAN,Sage Bionetworks, ,"Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 lambdaDNAconc,Lambda DNA spike-in concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified ,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.lambdaDNAconc-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified.",bsSeq
 libraryPrep,"The general strategy by which the library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified","amplicon, cellHashing, Chromium Single Cell 3', DNALibraryConstruction, EndItDNAEndRepairKit, KapaHyperPrep, lncRNAenrichment, methylSeq, miRNAenrichment, multiome, MULTIseq, PCRfree, polyAselection, proximity ligation, rRNAdepletion, snIsoSeq, SPLITseq, STARRSeq, SureCell, totalRNA, Unknown, Not collected, Not applicable, Not specified",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.libraryPrep-0.0.13,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Metagenomics,Microbiome,Whole_Genome_Sequencing,bsSeq,scRNAseq"
-libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified","10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Unknown, Not collected, Not applicable, Not specified",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.libraryPreparationMethod-0.0.10,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
+libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified","10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Unknown, Not collected, Not applicable, Not specified",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.libraryPreparationMethod-0.0.10,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 libraryVersion,"Library Version- for example, rnaSeq 10x library version. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.libraryVersion-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 meanCoverage,Total number of bases covered by ATAC-seq reads/size of genome. Provide a value or Unknown Not collected Not applicable Not specified,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-qc.meanCoverage-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified.",bsSeq
 pcrCycles,Number of PCR cycles to amplify transposased DNA fragments. Provide a value or Unknown Not collected Not applicable Not specified ,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.pcrCycles-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified.",bsSeq
 readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.readLength-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified.","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
-readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,"forward, reverse, Unknown, Not collected, Not specified, Not applicable",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.readStrandOrigin-0.0.2,sequencing,False,STRING,Sage Bionetworks, ,"Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
+readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.readStrandOrigin-0.0.2,sequencing,False,STRING,Sage Bionetworks, ,"Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 runType,The type of run,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.runType-0.0.2,sequencing,False,STRING,Sage Bionetworks, ,"Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 totalReads,Total number of sequencing reads from a library.,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.totalReads-0.0.2,sequencing,False,STRING,Sage Bionetworks,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified.","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
 assay_RNAseq_template,Template for RNAseq,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,repositoryName,transcriptType,resultUnit,valueReported,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,