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assay microbiome template

Template for Microbiome [Source]

Attribute Description Required columnType DependsOn Source Parent Valid Values
dnaBatchID DNA 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
dnaBatchSize The number of samples. Provide a value or Unknown Not collected Not applicable Not specified True STRING ManifestColumn
dnaBatchSizeUnit 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,Unknown,Not collected,Not applicable,Not specified
extractionMethod The name of the process used to separate a desired component of an input material from the remainder. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
libraryBatchID Library 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
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
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
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
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
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
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
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