From 1142cff2621e8adaee10efe08b9865eb039b1f5d Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 1 Nov 2024 14:45:51 +0000 Subject: [PATCH] Github Action: Updated dictionary term files and term pages --- _data/ManifestColumn.csv | 6 +++--- _data/assay_RNAseq_template.csv | 10 +++++----- _data/assay_bsSeq_template.csv | 4 ++-- _data/assay_microbiome_template.csv | 4 ++-- _data/assay_scRNAseq_template.csv | 10 +++++----- _data/assay_whole_genome_sequencing_template.csv | 10 +++++----- _data/libraryPreparationMethod.csv | 1 + _data/readStrandOrigin.csv | 2 ++ _data/repositoryName.csv | 3 ++- _data/resultUnit.csv | 3 ++- _data/sequencing.csv | 4 ++-- _data/transcriptType.csv | 1 + 12 files changed, 32 insertions(+), 26 deletions(-) diff --git a/_data/ManifestColumn.csv b/_data/ManifestColumn.csv index 6263caf..4fec4be 100644 --- a/_data/ManifestColumn.csv +++ b/_data/ManifestColumn.csv @@ -93,8 +93,8 @@ reagentName,The reagent name is an alternative to the Reagent ID.,,STRING,Manife reagentWeblink,An internet address that may provide details of an assay reagent.,,STRING,ManifestColumn,ManifestColumn 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",,STRING,ManifestColumn,ManifestColumn 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",,STRING,ManifestColumn,ManifestColumn -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",STRING,ManifestColumn,ManifestColumn -resultUnit,The unit for the result value,"FPKM,Not applicable,Not collected,Not specified,RPKM,TPM,Unknown",STRING,ManifestColumn,ManifestColumn +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",STRING,ManifestColumn,ManifestColumn +resultUnit,The unit for the result value,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown",STRING,ManifestColumn,ManifestColumn 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",,STRING,ManifestColumn,ManifestColumn rnaBatchSize,The number of samples,,NUMBER,ManifestColumn,ManifestColumn 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",STRING,ManifestColumn,ManifestColumn @@ -125,7 +125,7 @@ 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"")",,STRING,ManifestColumn,ManifestColumn 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",,STRING,ManifestColumn,ManifestColumn tissueVolume,The volume of the tissue sample. Measured in microliters.,,STRING,ManifestColumn,ManifestColumn -transcriptType,The type of transcript reported,"lincRNA,mRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown",STRING,ManifestColumn,ManifestColumn +transcriptType,The type of transcript reported,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown",STRING,ManifestColumn,ManifestColumn 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",NUMBER,ManifestColumn,ManifestColumn treatmentAmountValue,"The Amount Value indicates how much (concentration, mass, volume) of a treatment agent was applied to a sample.",,STRING,ManifestColumn,ManifestColumn treatmentDurationUnit,Unit of treatment duration.,"d.p.c.,Days,Hours,Minutes,Months,Not applicable,Not collected,Not specified,Seconds,Unknown,Weeks,Years",STRING,ManifestColumn,ManifestColumn diff --git a/_data/assay_RNAseq_template.csv b/_data/assay_RNAseq_template.csv index aa17c03..d510753 100644 --- a/_data/assay_RNAseq_template.csv +++ b/_data/assay_RNAseq_template.csv @@ -2,20 +2,20 @@ Attribute,Description,Required,columnType,DependsOn,Source,Parent,Valid Values measurementTechnique,"The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn, readLengthUnits,The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt" -resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" +repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"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" +resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" sampleType,"The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" +transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" valueReported,The count or gene count for the transcript,True,NUMBER,,,ManifestColumn, Component,,False,,,,, Filename,,False,,,,, specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",True,STRING,,sage.annotations-experimentalData.specimenID-0.0.2,ManifestColumn, platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn, isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE" -libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" +libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" 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,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn, readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn, -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, Unknown, Not collected, Not specified, Not applicable" +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable" runType,The type of run,True,STRING,,sage.annotations-ngs.runType-0.0.2,ManifestColumn,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown" totalReads,Total number of sequencing reads from a library.,True,STRING,,sage.annotations-experimentalData.totalReads-0.0.2,ManifestColumn, diff --git a/_data/assay_bsSeq_template.csv b/_data/assay_bsSeq_template.csv index 9b27ceb..6982a7b 100644 --- a/_data/assay_bsSeq_template.csv +++ b/_data/assay_bsSeq_template.csv @@ -23,11 +23,11 @@ gDNAconc,gDNA Concentration in ng. Provide a value or Unknown Not collected Not isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE" lambdaDNAconc,Lambda DNA spike-in concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-experimentalData.lambdaDNAconc-0.0.2,ManifestColumn, 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",True,STRING,,sage.annotations-ngs.libraryPrep-0.0.13,ManifestColumn,"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" -libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" +libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" 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,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn, 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,STRING,,sage.annotations-qc.meanCoverage-0.0.2,ManifestColumn, pcrCycles,Number of PCR cycles to amplify transposased DNA fragments. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-experimentalData.pcrCycles-0.0.2,ManifestColumn, readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn, -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, Unknown, Not collected, Not specified, Not applicable" +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable" runType,The type of run,True,STRING,,sage.annotations-ngs.runType-0.0.2,ManifestColumn,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown" totalReads,Total number of sequencing reads from a library.,True,STRING,,sage.annotations-experimentalData.totalReads-0.0.2,ManifestColumn, diff --git a/_data/assay_microbiome_template.csv b/_data/assay_microbiome_template.csv index dd0cda5..6fcac4a 100644 --- a/_data/assay_microbiome_template.csv +++ b/_data/assay_microbiome_template.csv @@ -17,9 +17,9 @@ specimenID,"Identifying string linked to a particular sample or specimen, provid platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn, isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE" 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",True,STRING,,sage.annotations-ngs.libraryPrep-0.0.13,ManifestColumn,"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" -libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" +libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" 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,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn, readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn, -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, Unknown, Not collected, Not specified, Not applicable" +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable" runType,The type of run,True,STRING,,sage.annotations-ngs.runType-0.0.2,ManifestColumn,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown" totalReads,Total number of sequencing reads from a library.,True,STRING,,sage.annotations-experimentalData.totalReads-0.0.2,ManifestColumn, diff --git a/_data/assay_scRNAseq_template.csv b/_data/assay_scRNAseq_template.csv index 5b068b4..c65d31b 100644 --- a/_data/assay_scRNAseq_template.csv +++ b/_data/assay_scRNAseq_template.csv @@ -3,8 +3,8 @@ libraryBatchID,"Library batch identifier, provided by the data contributor to Sa measurementTechnique,"The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn, readLengthUnits,The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt" -resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" +repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"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" +resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" 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,STRING,,,ManifestColumn, rnaBatchSize,The number of samples,False,NUMBER,,,ManifestColumn, rnaBatchSizeUnit,The unit of measurement for number of samples in a batch,True,STRING,,,ManifestColumn,"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" @@ -13,7 +13,7 @@ sequencingBatchID,"Sequencing batch identifier, provided by the data contributor sequencingBatchSize,The number of samples. Provide a value or Unknown Not collected Not applicable Not specified,True,STRING,,,ManifestColumn, sequencingBatchSizeUnit,The unit of measurement for number of samples in a batch. Provide a value or Unknown Not collected Not applicable Not specified,True,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" +transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" valueReported,The count or gene count for the transcript,True,NUMBER,,,ManifestColumn, Component,,False,,,,, Filename,,False,,,,, @@ -21,9 +21,9 @@ specimenID,"Identifying string linked to a particular sample or specimen, provid platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn, isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE" 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",True,STRING,,sage.annotations-ngs.libraryPrep-0.0.13,ManifestColumn,"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" -libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" +libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" 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,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn, readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn, -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, Unknown, Not collected, Not specified, Not applicable" +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable" runType,The type of run,True,STRING,,sage.annotations-ngs.runType-0.0.2,ManifestColumn,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown" totalReads,Total number of sequencing reads from a library.,True,STRING,,sage.annotations-experimentalData.totalReads-0.0.2,ManifestColumn, diff --git a/_data/assay_whole_genome_sequencing_template.csv b/_data/assay_whole_genome_sequencing_template.csv index a8a1053..f2f6bb0 100644 --- a/_data/assay_whole_genome_sequencing_template.csv +++ b/_data/assay_whole_genome_sequencing_template.csv @@ -3,13 +3,13 @@ libraryBatchID,"Library batch identifier, provided by the data contributor to Sa measurementTechnique,"The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn, readLengthUnits,The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt" -resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" +repositoryName,"The public repository name for the transcript (for example, Ensembl or NCBI Gene)",True,STRING,,,ManifestColumn,"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" +resultUnit,The unit for the result value,True,STRING,,,ManifestColumn,"FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown" 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,STRING,,,ManifestColumn, sampleType,"The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,,ManifestColumn, sequencingBatchID,"Sequencing 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,STRING,,,ManifestColumn, 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,STRING,,,ManifestColumn, -transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" +transcriptType,The type of transcript reported,True,STRING,,,ManifestColumn,"lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown" valueReported,The count or gene count for the transcript,True,NUMBER,,,ManifestColumn, Component,,False,,,,, Filename,,False,,,,, @@ -17,9 +17,9 @@ specimenID,"Identifying string linked to a particular sample or specimen, provid platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-experimentalData.platformLocation-0.0.2,ManifestColumn, isStranded,Whether or not the library is stranded.,True,BOOLEAN,,sage.annotations-ngs.isStranded-0.0.2,ManifestColumn,"FALSE,TRUE" 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",True,STRING,,sage.annotations-ngs.libraryPrep-0.0.13,ManifestColumn,"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" -libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" +libraryPreparationMethod,"Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",True,STRING,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,ManifestColumn,"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" 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,STRING,,sage.annotations-ngs.libraryVersion-0.0.2,ManifestColumn, readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,True,STRING,,sage.annotations-ngs.readLength-0.0.2,ManifestColumn, -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, Unknown, Not collected, Not specified, Not applicable" +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,True,STRING,,sage.annotations-ngs.readStrandOrigin-0.0.2,ManifestColumn,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable" runType,The type of run,True,STRING,,sage.annotations-ngs.runType-0.0.2,ManifestColumn,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown" totalReads,Total number of sequencing reads from a library.,True,STRING,,sage.annotations-experimentalData.totalReads-0.0.2,ManifestColumn, diff --git a/_data/libraryPreparationMethod.csv b/_data/libraryPreparationMethod.csv index d85869a..76d73cf 100644 --- a/_data/libraryPreparationMethod.csv +++ b/_data/libraryPreparationMethod.csv @@ -15,6 +15,7 @@ Key,Key Description,columnType,Source,Parent TruSeq,,STRING,,ManifestColumn Ultralow Methyl-Seq,,STRING,,ManifestColumn Illumina DNA PCR-Free Prep Kit,,STRING,,ManifestColumn + Qiagen PreAnalytiX PAXgene Blood miRNA Kit,,STRING,,ManifestColumn Unknown,,STRING,,ManifestColumn Not collected,,STRING,,ManifestColumn Not applicable,,STRING,,ManifestColumn diff --git a/_data/readStrandOrigin.csv b/_data/readStrandOrigin.csv index f7c6328..b4c990d 100644 --- a/_data/readStrandOrigin.csv +++ b/_data/readStrandOrigin.csv @@ -1,6 +1,8 @@ Key,Key Description,columnType,Source,Parent forward,,STRING,,ManifestColumn reverse,,STRING,,ManifestColumn + stranded,,STRING,,ManifestColumn + unstranded,,STRING,,ManifestColumn Unknown,,STRING,,ManifestColumn Not collected,,STRING,,ManifestColumn Not specified,,STRING,,ManifestColumn diff --git a/_data/repositoryName.csv b/_data/repositoryName.csv index 4a38a20..ddba5f1 100644 --- a/_data/repositoryName.csv +++ b/_data/repositoryName.csv @@ -6,7 +6,8 @@ ENA,,STRING,,ManifestColumn Ensembl,,STRING,,ManifestColumn FlowRepository,,STRING,,ManifestColumn GenBank,,STRING,,ManifestColumn -GEO,,STRING,,ManifestColumn +GENCODEv38 GRCh38,,STRING,,ManifestColumn + GEO,,STRING,,ManifestColumn GISAID,,STRING,,ManifestColumn IEDB,,STRING,,ManifestColumn ImmPort,,STRING,,ManifestColumn diff --git a/_data/resultUnit.csv b/_data/resultUnit.csv index 6a2c629..decf937 100644 --- a/_data/resultUnit.csv +++ b/_data/resultUnit.csv @@ -1,6 +1,7 @@ Key,Key Description,columnType,Source,Parent FPKM,,STRING,,ManifestColumn -Not applicable,,STRING,,ManifestColumn +raw count,,STRING,,ManifestColumn + Not applicable,,STRING,,ManifestColumn Not collected,,STRING,,ManifestColumn Not specified,,STRING,,ManifestColumn RPKM,,STRING,,ManifestColumn diff --git a/_data/sequencing.csv b/_data/sequencing.csv index 49ab372..b46e593 100644 --- a/_data/sequencing.csv +++ b/_data/sequencing.csv @@ -4,11 +4,11 @@ gDNAconc,gDNA Concentration in ng. Provide a value or Unknown Not collected Not isStranded,Whether or not the library is stranded.,"FALSE,TRUE",BOOLEAN,ManifestColumn,sequencing lambdaDNAconc,Lambda DNA spike-in concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified ,,STRING,ManifestColumn,sequencing 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",STRING,ManifestColumn,sequencing -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",STRING,ManifestColumn,sequencing +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",STRING,ManifestColumn,sequencing 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",,STRING,ManifestColumn,sequencing meanCoverage,Total number of bases covered by ATAC-seq reads/size of genome. Provide a value or Unknown Not collected Not applicable Not specified,,STRING,ManifestColumn,sequencing pcrCycles,Number of PCR cycles to amplify transposased DNA fragments. Provide a value or Unknown Not collected Not applicable Not specified ,,STRING,ManifestColumn,sequencing readLength,The length of the read. Provide a value or Unknown Not collected Not applicable Not specified ,,STRING,ManifestColumn,sequencing -readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,"forward, reverse, Unknown, Not collected, Not specified, Not applicable",STRING,ManifestColumn,sequencing +readStrandOrigin,The strand from which the read originates in a strand-specific protocol.,"forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable",STRING,ManifestColumn,sequencing runType,The type of run,"Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown",STRING,ManifestColumn,sequencing totalReads,Total number of sequencing reads from a library.,,STRING,ManifestColumn,sequencing diff --git a/_data/transcriptType.csv b/_data/transcriptType.csv index 6a4b2c8..b68d9fc 100644 --- a/_data/transcriptType.csv +++ b/_data/transcriptType.csv @@ -1,6 +1,7 @@ Key,Key Description,columnType,Source,Parent lincRNA,,STRING,,ManifestColumn mRNA,,STRING,,ManifestColumn +total RNA minus rRNA,,STRING,,ManifestColumn Not applicable,,STRING,,ManifestColumn Not collected,,STRING,,ManifestColumn Not specified,,STRING,,ManifestColumn