Merge pull request #68 from eliteportal/update-dictionary

Github Action: Updated dictionary term files and term pages

_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

_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,

_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,

_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,