Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn,UsedIn\
analysis_results_metadata_template,Template for analysis and results,,"entity, entityID, analysisType, resultType, dataTypeAll, format, dataFormat, workflowFormat, assay, experimentalDesign, hasAlgorithm, algorithm, hasNotebook, notebook, hasProtocol, protocol, hasScript, script, hasSoftware, software, hasLibrary, library, hasParameters, parameters, hasSettings, settings, hasEnvironment, environment, hasOpertaingSystem, operatingSystem, hasProgrammingLanguage, programmingLanguage",,False,Component,,template,Sage Bionetworks, template,False,,Sage Bionetworks,,,
ModelSystemType,Type of model system,"animal, cerebral organoid, immortalized cell line, iPSC, organoid, primary cell culture, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,"study_folder_template, file_annotation_template",
isModelSystem,Boolean flag indicating whether or not a file has data from a model system,"True, False, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ADKP,False,BOOLEAN,Sage Bionetworks,,"study_folder_template, file_annotation_template",
DNAextraction,"DNA extraction kit method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,DSWG, ,Metagenomics,
acquisitionBatchID,"Acquisition 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",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
acquisitionBatchSize,The number of samples,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
acquisitionBatchSizeUnit,The unit of measurement for number of samples in a batch,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
acquisitionMode,"The specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated (full scan, MSn, SIM, MRM, etc.). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1003213,"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,
acquisitionSoftware,"The name of the acquisition software used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,http://purl.obolibrary.org/obo/MS_1001455,"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,
acquisitionSoftwareVersion,"The version number of software used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,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. ",Metabolomics,
adapters,"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters. Example - 'AATGATACGGCGACCACCGAGATCTACACGCT; CAAGCAGAAGACGGCATACGAGAT'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
adjustedCovariates,Any covariates the GWAS is adjusted for. Multiple values can be listed separately by a semicolon (;). Example - age;sex,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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,
analysisType,Type of analysis,"ANOVA,batch effect correction,clustering,data normalization,de-novo assembly,dose response study,enrichment analysis,genome-wide association,mendelian randomization analysis,network analysis,polygenic risk scores, Not assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template",
arrayInformation,"Additional information about the genotyping array. For example, for targeted arrays, please provide the specific type of array. Example - Immunochip",,,,False,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,
arrayManufacturer,"Manufacturer of the genotyping array used for the discovery stage. Separate multiple manufacturers by a semicolon (;). Example - Illumina, Affymetrix, Perlegen",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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,
assemblyName,"Name/version of the assembly provided by the submitter used in the genome browsers and the community. Example - 'HuRef, JCVI_ISG_3_1.0'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
assemblyQual,"Assembly quality. The assembly quality category is based on sets of criteria outlined for each assembly quality category.High Quality- Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.Medium Quality- Many fragments with little to no review of assembly other than reporting of standard assembly statistics.Low Quality- Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to, total assembly size, number of contigs, contig N50/L50, and maximum contig length. Example values - high-quality genome, medium-quality genome, low-quality genome",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
assemblySoftware,"Tool(s) used for assembly, including version number and parameters. Example - 'metaSPAdes;3.11.0; kmer set 21,33,55,77,99,121, default parameters otherwise'. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
associatedResource,"Relevant electronic resources. A related resource that is referenced, cited, or otherwise associated to the sequence. Example - 'http-//www.earthmicrobiome.org/'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
backgroundTrait,Any background trait(s) shared by all individuals in the GWAS (e.g. in both cases and controls). Example - Nicotine dependence,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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,
batchID,"ID used to identify a batch, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
batchLabel,Used to supply batch label information with any string value,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,http://purl.obolibrary.org/obo/MS_4000088, ,Metabolomics,
captivityDuration,"The duration of captivity in months for the individuals in captivity (formatted in months, ex. 72 months).note- Applicable only to animals with captivity status captive.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"https://www.animalaudiograms.org/audiogram_metadata_scheme#:~:text=species%20are%20possible.-,captivity%20duration,-The%20duration%20of", ,Individual_non_Human,
captivityStatus,"The status of the individual with regard to captivity.note- Wild, captive, and stranded values are applicable, especially for marine mammals. Depending on life stage terminology for individual species, other values are possible. Please let the data curation team know.","Captive,Stranded,Wild, Not applicable, Not collected, Not specified, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"https://www.animalaudiograms.org/audiogram_metadata_scheme#:~:text=of%20the%20animal.-,captivity%20status,-The%20status%20of", ,Individual_non_Human,
commonName,"The biological species common name the individual belongs to (ex. ""Horned Lark""). note- As a default, the valid scientific name for the species should be indicated.",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1874,example: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135430. ,Individual_non_Human,
consentGroupID,"Indicate the consent group for the individual, provided by the data contributor's data dictionary",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Individual_Human,
consortium,The name of the consortium,"ELITE, ELITE CDCP, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template",
conversionRatio,The ratio or % detailing how well the bisulfite conversion worked. Provide a value or 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.",bsSeq,
conversionRatioUnits,The units of measurement. Provide a value or 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.",bsSeq,
countryCode,"Indicate the geographic region for the individual (shown as ex. ""840"")",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,INTEGER,https://wits.worldbank.org/countryprofile/metadata/en/country/all, ,Individual_Human,
dataFile,"Name of additional file(s) accompanying the data. The file(s) provide, for example, the name of any raw files generated by the instrument, generated reports from a vendor, an Rscript, or an instructions document. The files can be instrument raw files, converted peak lists such as mzML, MGF, or result files like mzIdentML. The files can be additional documentation submitted alongside the data needed for reuse and sharing purposes. Provide the file names of any additional files submitted alongside the data (ex., an ADAT file). Multiple file names can be separated by (;)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"DSLWG,Proteomics Sample Metadata,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. ","Metabolomics,Metagenomics,Proteomics",
dataModelVersion,Version of the data model,,,,False,,,ManifestColumn,,ManifestColumn,False,STRING,,,,
dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata","raw,processed,results,normalized,metadata, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template",
dataType,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,file_annotation_template,
dataTypeAll,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,study_folder_template,
databaseLibrary,"The name(s) of the associated database library. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,DSWG, ,Metagenomics,
databaseName,"The name of the search database (nr, SwissProt or est_human, and/or mass spectral library). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"DSLWG,Sage Bionetworks,http://purl.obolibrary.org/obo/MS_1001013","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,Proteomics",
databaseSource,"The name of the organization, project, or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"DSLWG,Sage Bionetworks,http://purl.obolibrary.org/obo/MS_1001012","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,Proteomics",
databaseVersion,"The version of the database. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,DSWG, ,Metagenomics,
databaseWeblink,"An internet address that may provide details of a database or software search, as well as for labs that generate their own search method (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, DSLWG","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,Proteomics",
diagnosisStatus,"Whether the individual has been diagnosed with a condition or disease (physical and/or cognitive), \True"" indicates the individual has been diagnosed""","FALSE,TRUE",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Sage Bionetworks, ,"Individual_Human,Phenotype_human",
digestionMethod,"The type of digestion (ex. in-solution, in-gel)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, DSLWG","A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Proteomics,
digestionReagent,Enzymes or reagents used for digestion.,"2-iodobenzoate,Arg-C,Asp-N,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Glutamyl endopeptidase,Leukocyte elastase,Lys-C,Lys-C/P,No cleavage,NoEnzyme,Not applicable,Not available,Not collected,Not specified,PepsinA,Proline endopeptidase,TrypChymo,Trypsin,Trypsin/P,Unknown,Unspecific cleavage,V8-DE,V8-E",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomics Data Commons, ,Proteomics,
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,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. ","Microbiome,bsSeq",
dnaBatchSize,The number of samples. Provide a value or 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.","Microbiome,bsSeq",
dnaBatchSizeUnit,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,Unknown,Not collected,Not applicable,Not specified",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"Microbiome,bsSeq",
enrichment,"Protocol or reagent used for enrichment (ex. Fe3+NTA-Agarose (Qiagen)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomic Data Commons,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Proteomics,
enrichmentMethod,"The method used for performing an enrichment of specific regions by a restriction enzyme digest. 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. ",bsSeq,
enrichmentStrategy,Type of peptide or protein enrichment,"Acetylome Proteome,Glycoproteome,Lipidome,Metabolome,Not applicable,Not available,Not collected,Not specified,Phosphoproteome,Ubiquitylome,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomic Data Commons,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Proteomics,
ethnicGroupCode,"A coded value specifying the self-declared ethnic origination independent of racial origination, provided by the data contributor's data dictionary",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=23.04d&code=C93563&ns=ncit&type=properties&key=1040179992&b=1&n=0&vse=null,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ","Individual_Human,Phenotype_human",
experimentType,"The type of experiment used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Proteomic Data Commons,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,Proteomics",
experimentalBatchSizeUnit,The unit of measurement for number of samples in a experimental batch,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
experimentalFactor,"Variable aspects of an experiment design that can be used to describe an experiment or set of experiments in an increasingly detailed manner.This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). Example - 'time series design [EFO-0001779]'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
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,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,http://purl.obolibrary.org/obo/OBI_0302884,"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,Microbiome",
fieldCenterCode,Name of the field center,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Individual_Human,
fileFormat,"Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","FASTQ, FASTA, SAM, BAM, CRAM, VCF, BCF, GTF, GFF, GFF3, BED, BigBed, WIG, BigWig, CSV, TSV, MTX, H5AD, LOOM, RDS,PED, MAP, BED_PLINK, TPED, TFAM, BEDGRAPH, NARROWPEAK, BROADPEAK, TAGALIGN, OME-TIFF, ND2, CZI, LSM, H5, HDF5, PARQUET, PDB, MMCIF, JSON, YAML, XML, TXT, XLSX, CSV, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template",
fractionIdentifier,"Number of fractions in the experimental runProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, The Proteomics Sample Metadata Project, MS Ontology Proteomics Data Commons https://pdc.cancer.gov/data-dictionary/dictionary.html","A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Proteomics,
gasFlowTemperature,"e.g., nebulization gas, cone gas, etc.Unit of measure-C, F, K, Not specified",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
gasFlowTemperatureUnit,Unit of gas flow temperature,"C,F,K",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
genotypeTechnology,"Method(s) used to genotype variants in the discovery stage. Separate multiple methods separated by a semicolon (;). Example - genome-wide genotyping array, exome-wide sequencing, targeted genotyping array",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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,
hasAssayControl,"Boolean flag indicating whether or not a specimen is a technical or assay control. Examples include study pools or reference pools, blanks, or internal standards.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,BOOLEAN,Sage Bionetworks, ,Metabolomics,
hasIonizationSource,Were the ionization conditions recorded to enable reproduction of the experiment?,"No,Yes",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,BOOLEAN,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
imputation,Were SNPs imputed for the discovery GWAS?,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, EMBL-EBI", ,Genotyping_Human,
imputationPanel,Panel used for imputation. Example - 1000 Genomes Phase 3,,,,False,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,
imputationSoftware,Imputation software. Example - IMPUTE,,,,False,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,
instrumentModel,"The model of the instrument used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"DSLWG,Proposed minimum metadata relative to mass spectrometry,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 OR use one of these possible values linked belowPossible values are listed under the instrument model term. https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000031&viewMode=All&siblings=false. ","Metabolomics,Metagenomics,Proteomics",
ionProperty,Ion charge state (positive or negative-ion analysis),"Negative,Positive",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
isobaricLabelingReagent,"Reagent set used for isobaric labeling. Examples- iTRAQ113 TMT126Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomics Data Commons,"A data contributor should be able to write in a name OR provide one of these values: Unknown Not collected, Not applicable, Not specified. ",Proteomics,
labelFreeQuantitation,"Type of label-free data analysis strategyProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified","Label-free gene level quantitation,Label-free peptide level quantitation,Label-free protein group level quantitation,Label-free protein level quantitation,Label-free raw feature quantitation,Not applicable,Not available,Not collected,Not specified,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Proteomics Data Commons, ,Proteomics,
labelQuantitation,"Type of labeling usedProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified","AminoxyTMT,DiART,DiLeu,Glyco-TMT,Hydrazide TMT,IodoTMT,IPTL,iTRAQ,iTRAQH,Label Free,Not available,Not collected,Not specified,TMT,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, DSLWG, https://www.ebi.ac.uk/ols/ontologies/pride/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPRIDE_0000514&viewMode=All&siblings=false Proteomics Data Commons https://pdc.cancer.gov/data-dictionary/dictionary.html", ,Proteomics,
lensVoltages,"The skimmer/focusing lens voltages e.g., capillary voltage, etc.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
lensVoltagesUnit,Unit of lens voltages,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
libLayout,"Library layout. Specify whether to expect single, paired, or other configurations of reads. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
libReadsSeqd,"Library reads sequenced. Total number of clones sequenced from the library. Example - '20'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,INTEGER,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
libSize,"Library size. Total number of clones in the library prepared for the project. Example - '50'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,INTEGER,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
libVector,"Library vector. Cloning vector type(s) used in the construction of libraries. Example - 'Bacteriophage P1'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
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,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. ","Microbiome,Whole_Genome_Sequencing,bsSeq,scRNAseq",
lifeStage,The life stage of the individual.note- Other values are possible depending on life stage terminology for individual species. Please let the data curation team know.,"Adult,Juvenile,Post-Juvenile, Not applicable, Not collected, Not specified, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Biological Collections Ontology, https://www.animalaudiograms.org/audiogram_metadata_scheme#:~:text=range%3A%20female%3B%20male-,life%20stage,-The%20life%20stage, https://www.ebi.ac.uk/ols/ontologies/pato", ,Individual_non_Human,
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,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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. ","Biospecimen_human,Genotyping_Human,Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq",
mid,"Multiplex identifiers. Molecular barcodes, called Multiplex Identifiers (MIDs), are used to tag unique samples in a sequencing run specifically. Sequence should be reported in uppercase letters. Example - 'GTGAATAT'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
modificationParameters,"Modification parameters for a search engine run. (ex. PSI- PI http-//www.w3.org/2002/07/owl#Axiom) or used in the peptide identification database search. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001055,"Possible values are listed under modification parameters:https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001055Other, Unknown, Not collected, Not applicable, Not specified. ",Proteomics,
msAnalyteType,"The type of biospecimen subjected to analysis (ex., peptide, protein, metabolite, lipid)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"http://purl.obolibrary.org/obo/NCIT_C156434,http://purl.obolibrary.org/obo/NCIT_C156434 Proteomic Data Commons https://pdc.cancer.gov/data-dictionary/dictionary.html","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,Proteomics",
msAssayTechnique,"Specified the mass spectrometer technique used or the name of the proteomics assay used (ex. DDA)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, DSLWG","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,Proteomics",
msTarget,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay,"Not applicable,Not available,Not collected,Not specified,Targeted,Unknown,Untargeted",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"DSLWG,Sage Bionetworks", ,"Metabolomics,Proteomics",
nucleAcidExt,"Nucleic acid extraction. A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample. (example, https-//mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
numberContig,"Number of contigs. Total number of contigs in the cleaned/submitted assembly that comprise a given genome, SAG, MAG, or UViG. Example - '40'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,INTEGER,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
numberIndividuals,Number of individuals in a group. Example - 2000,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,INTEGER,"Sage Bionetworks, EMBL-EBI", ,Genotyping_Human,
processingBatchID,"Processing 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",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Metabolomics,
program,,"ELITE,AD",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,"study_folder_template,computational_tools_template",
projectShortName,,"LC,ILO,LLFS,LG, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template,
quantationStrategy,"The general strategy used for differential analysis Example - Absolute quantitation analysis, Isobaric label quantitation analysis, LC-MS label-free quantitation analysis,Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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. ",Proteomics,
readLengthUnits,The units of measurement. Provide a value or 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.","Microbiome,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq",
readmeFile,The name of any readme file uploaded to Synapse. Example - example.tsv,,,,False,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,
reagentCatalogNumber,"If the assay reagent is a commercial product, enter the vendor's catalog identifier. If the reagent is a custom preparation enter 'NA'.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
reagentContact,The contact information is particularly helpful when the reagent is not from a commercial vendor.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
reagentIDs,"One or more identifiers, separated by a semicolon (;). The reagent identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort","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,
reagentLotNumber,The lot number is often provided by a reagent source when the reagent is replenished over time.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
reagentManufacturer,"The manufacturer is the source of a reagent and may include commercial vendors as well as non-commercial sources (e.g., collaborating labs).",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
reagentName,The reagent name is an alternative to the Reagent ID.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
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,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,Synapse,UniProt,Other,Unknown,Not collected,Not applicable,Not specified",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq",
resourceType,The type of resource being stored and annotated,"experimentalData,metadata,tool,analysis,computationalNotebook,softwareTool,Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template, computational_tools_template",
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,
sampleBatchID,"Sample batch lot 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",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,http://purl.obolibrary.org/obo/MS_1000053, ,Metabolomics,
sampleIntroduction,"The sample introduction and delivery. From GC, from LC, direct infusion without chromatography, direct infusion using dedicated autosampler flow rate. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry","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,
samplePrepProtocol,"An internet address that may provide more details of the protocol information (web link). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"DSLWG,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. ","Metabolomics,Metagenomics,Proteomics",
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,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"ImmPort,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 specifiedThe sample types are adopted from Uberon, Cell and ChEBI ontologies.. ","Genotyping_Human,Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq",
seqMethod,"Sequencing method. Sequencing method used; Example - 'Sanger, pyrosequencing, ABI-solid'. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
seqPlatform,"Sequencing platform information. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,DSWG, ,Metagenomics,
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,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. ","Microbiome,Whole_Genome_Sequencing,bsSeq,scRNAseq",
sequencingBatchSize,The number of samples. Provide a value or 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.","Microbiome,bsSeq,scRNAseq",
sequencingBatchSizeUnit,The unit of measurement for number of samples in a batch. Provide a value or 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.","Microbiome,bsSeq,scRNAseq",
sop,"Relevant standard operating procedures. Standard operating procedures used in the assembly and/or annotation of genomes, metagenomes, or environmental sequences. Example - 'http-//press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/)'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
sourceMatID,"Source material identifiers. A unique identifier assigned to a material sample (as defined by http-//rs.tdwg.org/dwc/terms/materialSampleID and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing.The identifier can refer to the original material collected or any derived sub-samples. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
speciesAge,"Age of individual (formatted in months, ex. ""72 months"").note- Uncertainty about the age might require recording age by specifying a lower and upper estimate in months for the age of the animal.",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, https://www.animalaudiograms.org/audiogram_metadata_scheme#:~:text=species%20are%20possible.-,age,-The%20age%20of", ,Individual_non_Human,
speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62690https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045, ,"file_annotation_template,Individual_non_Human,Phenotype_human",
speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""","Acomys cahirinus, Acomys russatus, Accipiter cooperii, Actitis macularius, Aix sponsa, Anas acuta, Anas carolinensis, Anas platyrhynchos, Antigone canadensis, Archilochus colubris, Artibeus jamaicensis, Baeolophus bicolor, Balaena mysticetus, Blarina brevicauda, Bombycilla cedrorum, Bonasa umbellus, Bos taurus, Branta canadensis, Bubo virginianus, Buteo jamaicensis, Buteo lineatus, Canis latrans, Cardinalis cardinalis, Castor canadensis, Cavia porcellus, Charadrius vociferus, Chinchilla lanigera, Columba livia, Condylura cristata, Corvus brachyrhynchos, Cricetomys ansorgei, Cricetulus barabensis, Cricetulus griseus, Cryptomys damarensis, Cuniculus paca, Cyanocitta cristata, Cygnus olor, Dryobates pubescens, Dumetella carolinensis, Ellobius lutescens, Ellobius talpinus, Eonycteris spelaea, Eptesicus fuscus, Equus caballus, Eremophila alpestris, Fukomys damarensis, Haemorhous mexicanus, Heterocephalus glaber, Hirundo rustica, Homo sapiens, Hydrochoerus hydrochaeris, Hydroprogne caspia, Hylocichla mustelina, Icteria virens, Larus argentatus, Larus delawarensis, Macaca fascicularis, Macaca mulatta, Mareca strepera, Marmota monax, Melanerpes carolinus, Meleagris gallopavo, Melospiza melodia, Meriones unguiculatus, Mesocricetus auratus, Microtus pennsylvanicus, Mimus polyglottos, Molothrus ater, Multi-species, Mus musculus, Myocastor coypus, Myotis lucifugus, Nannospalax galili, Neosciurus carolinensis, Neotoma cinerea, Neotoma floridana, Not applicable, Not collected, Not provided, Not specified, Octodon degus, Odocoileus virginianus, Ondatra zibethicus, Other, Pan troglodytes, Papio anubis, Passer domesticus, Passerina caerulea, Passerina cyanea, Peromyscus gossypinus, Peromyscus leucopus, Peromyscus maniculatus, Phalacrocorax auritus, Phasianus colchicus, Picoides villosus, Pipilo erythrophthalmus, Poecile carolinensis, Quiscalus quiscula, Rattus norvegicus, Rattus rattus, Regulus calendula, Saimiri boliviensis, Sayornis phoebe, Scalopus aquaticus, Sciurus carolinensis, Sciurus niger, Sciurus vulgaris, Scolopax minor, Setophaga citrina, Setophaga coronata, Setophaga dominica, Setophaga petechia, Setophaga pinus, Sialia sialis, Sigmodon hispidus, Sitta carolinensis, Spatula clypeata, Spinus tristis, Spizella passerina, Spizella pusilla, Spizelloides arborea, Struthio camelus, Sturnus vulgaris, Sus scrofa, Sylvilagus floridanus, Tachycineta bicolor, Tamias striatus, Tamiasciurus hudsonicus, Thryothorus ludovicianus, Toxostoma rufum, Troglodytes aedon, Turdus migratorius, Tursiops truncatus, Vicugna pacos, Vireo griseus, Vireo olivaceus, Zalophus californianus, Zenaida macroura, Zonotrichia albicollis, Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045,example: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135430. ,"file_annotation_template,Individual_non_Human",
specimenAge,"The subject's age at the time of specimen extraction is the individual's age (since birth) at the time a given specimen was extracted. Measured as age in years. Other, Unknown, Not collected, Not applicable",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human",
specimenSource,Indicate the biological area of the specimen,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/ccf/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0004537&lang=en&viewMode=PreferredRoots&siblings=false, ,"Biospecimen_human,Biospecimen_non_Human",
specimenType,Type of biological material comprising the Specimen,"blood,Cerebrospinal Fluid (CSF),Not applicable,Not collected,Not specified,organoid,plasma,saliva,serum,sputum,stool,swabs,tissue,Unknown,urine",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, http://purl.obolibrary.org/obo/NCIT_C70713", ,"Biospecimen_human,Biospecimen_non_Human",
stage,Stage of the experimental design.,"Discovery,Not applicable,Not collected,Not specified,Other,Replication,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, EMBL-EBI", ,Genotyping_Human,
statisticalModel,"A brief description of the statistical model used to determine association significance. It is important to distinguish studies that would otherwise appear identical (e.g., the same trait analyzed using additive, dominant, and recessive models). Example - additive model",,,,False,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,
studyCode,"Unique identifier for the study, assigned by the DCC","CDCP,ILO,LC,LG,LLFS,Other",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human",
studyKey,The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA),,,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,ManifestColumn,False,STRING,Sage Bionetworks,,study_folder_template,
summaryFile,The name of any summary statistics file uploaded to Synapse. Example - example.tsv,,,,False,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,
summaryStatisticsAssembly,Genome assembly for the summary statistics. Example - GRCh38,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,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. ",Genotyping_Human,
targetGene,"Targeted gene or locus name for marker gene studies. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics,
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,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,
treatmentDurationValue,Duration of treatment.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
treatmentIDs,"One or more identifiers, separated by a semicolon (;). The treatment identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort","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,
treatmentName,"Treatments refer to in vitro modifications of samples. Three treatment types are supported- agent amount, duration, and temperature.  The treatment name is an alternate identifier to the Treatment ID.",,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
treatmentTemperatureUnit,Unit of treatment temperature.,"C,F,K,Not specified",,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
treatmentTemperatureValue,Value of treatment temperature.,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
useReadMeFile,Was a readme file uploaded to Synapse?,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,Genotyping_Human,
useReagent,Was a reagent applied to the sample?,"FALSE,TRUE",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,BOOLEAN,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
useSummaryFile,Was a summary statitics file uploded to Synapse?,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, EMBL-EBI", ,Genotyping_Human,
useTreatment,Was a treatment applied to the sample?,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,BOOLEAN,"Sage Bionetworks, ImmPort", ,Genotyping_Human,
vacuumPressure,The recorded vacuum pressure value,,,,False,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
vacuumPressureUnit,Unit of vacuum pressure value,"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,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,False,STRING,"Sage Bionetworks, Proposed minimum metadata relative to mass spectrometry", ,Metabolomics,
valueReported,The count or gene count for the transcript,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"RNAseq,Whole_Genome_Sequencing,scRNAseq",
variantCount,The number of variants analysed in the discovery stage (after QC). Example - 52500,,,,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,
visitCode,"Indicate which longitudinal visit for the individual the data comes from, provided by the data contributor's data dictionary",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,NUMBER,Sage Bionetworks, ,Individual_Human,
Component,,,,,False,,,,,Unknown,False,STRING,,,"assay_RNAseq_template,assay_bsSeq_template,assay_metabolomics_template,assay_metagenomics_template,assay_microbiome_template,assay_phenotype_human_template,assay_proteomics_template,assay_scRNAseq_template,assay_whole_genome_sequencing_template,biospecimen_human_template,biospecimen_non_human_template,file_annotation_template,genotyping_human_template,individual_human_template,individual_non_human_template,study_folder_template",
Filename,,,,,False,,,,,Unknown,False,STRING,,,"assay_RNAseq_template,assay_bsSeq_template,assay_metabolomics_template,assay_metagenomics_template,assay_microbiome_template,assay_phenotype_human_template,assay_proteomics_template,assay_scRNAseq_template,assay_whole_genome_sequencing_template,biospecimen_human_template,biospecimen_non_human_template,file_annotation_template,genotyping_human_template,individual_human_template,individual_non_human_template",
accessReqs,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
ackContext,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
acknowledgment,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
acquistionSoftwareVersion,,,,,False,,,,,Unknown,False,STRING,,,assay_metabolomics_template,
batchSizeUnit,,,,,False,,,,,Unknown,False,STRING,,,assay_metabolomics_template,
contributor,,,,,True,,,Unknown,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,computational_tools_template,
displayName,Canonical tool name provided by the tool developer or service provider,,,,True,,,Unknown,Sage Bionetworks,Unknown,False,STRING,Sage Bionetworks,,computational_tools_template,
documentation,,,,,True,,,Unknown,Sage Bionetworks,Unknown,False,STRING,Sage Bionetworks,,computational_tools_template,
experimentalBatchSize,,,,,False,,,,,Unknown,False,INTEGER,,,assay_metabolomics_template,
grantNumber,Grant number including activity code institute code and serial number (e.g. U01MH103392),"U19AG063893,U24AG051129,U19AG023122,UH2AG064706,UH3AG064706,UH2AG064704,UH3AG064704,R01AG061844, Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,study_folder_template,
grants,"Grant number associated with the tool's development. Multiple values permitted, comma separated.",,,,True,,,Unknown,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,computational_tools_template,
institution,,,,,False,,,Unknown,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,computational_tools_template,
isFeatured,,,,,False,,,,,Unknown,False,BOOLEAN,,,"study_folder_template,computational_tools_template",
isReleased,,,,,False,,,,,Unknown,False,BOOLEAN,,,study_folder_template,
metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file","individual,biospecimen,assay,supplementary files,Not Assigned",,,False,ManifestColumn,,ManifestColumn,Sage Bionetworks,Unknown,True,STRING,Sage Bionetworks,,"study_folder_template, file_annotation_template",
methods,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
newsRelease,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
processingBatchSize,,,,,False,,,,,Unknown,False,INTEGER,,,assay_metabolomics_template,
processingBatchSizeUnit,,,,,False,,,,,Unknown,False,STRING,,,assay_metabolomics_template,
project,The ELITE project short name associated with the tool,,,,True,,,Unknown,Sage Bionetworks,Unknown,False,STRING,Sage Bionetworks,,computational_tools_template,
projectFullName,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
relatedStudies,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
sampleBatchSize,,,,,False,,,,,Unknown,False,INTEGER,,,assay_metabolomics_template,
sampleBatchSizeUnit,,,,,False,,,,,Unknown,False,STRING,,,assay_metabolomics_template,
studyAbstract,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyDescription,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyFocus,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyMetadata,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyName,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyType,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
studyWiki,,,,,False,,,,,Unknown,False,STRING,,,study_folder_template,
summary,Textual description of the tool,,,,True,,,Unknown,Sage Bionetworks,Unknown,False,STRING,Sage Bionetworks,,computational_tools_template,
batchSize,The number of samples,,,,False,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.batchSize-0.0.2,batch,False,NUMBER,Sage Bionetworks, ,Metabolomics,
cellType,Indicate the cell type.,"A549, arachnoid, astrocytes, B-lymphocytes, CD138+, CD8+ T-Cells, CNON, dopaminergic neurons, Embryonic stem cells, epithelial, epithelial-like, fibroblast, GABAergic neurons, glia, GLUtamatergic neurons, immune cell, iPSC, iPSC-derived astrocytes, iPSC-derived glia, iPSC-derived neuron, iPSC-derived neuronal progenitor cell, iPSC-derived telencephalic organoids, lymphoblast, lymphoblastoid cell line, macrophages, meningioma, microglia, monocytes, monocyte-derived microglia, NCX NES, NeuN-, NeuN+, neural progenitor cell, neuron, oligodendrocyte, peripheral blood mononuclear cell, polygonal, round, schwann, Schwann cell precusor, schwannoma, SH-SY5Y, Not collected, Not specified, Not applicable, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.cellType-0.0.9,biospecimen,False,STRING,"https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2Fcell_type,https://www.ebi.ac.uk/ols/ontologies/ccf/terms?iri=http%3A%2F%2Fpurl.org%2Fccf%2Fcell_type", ,"Biospecimen_human,Biospecimen_non_Human",
fastingState,Was individual fasting when the sample was taken (true/false)?,"FALSE,Not applicable,Not collected,Not specified,TRUE,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.fastingState-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human",
isPostMortem,Was the sample taken after death (true/false)?,"TRUE, FALSE",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.isPostMortem-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human",
nucleicAcidSource,"Specifies the type of nucleic acid (DNA, RNA, Pooled, etc.) found in a sample.","bulk cell,bulk nuclei,mitochondria,Not applicable,Not collected,Not specified,single cell,single nucleus,sorted cells,sorted nuclei,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.nucleicAcidSource-0.0.3,biospecimen,False,STRING,https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=23.04d&ns=ncit&code=C171278&key=1146649015&b=1&n=1, ,"Biospecimen_human,Biospecimen_non_Human",
organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown, plasma, gonadal fat, inguinal fat, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.organ-0.0.4,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C13018, ,"Biospecimen_human,Biospecimen_non_Human",
samplingAge,"The calculated age of the sample, measurement is determined or coded by the data contributor.Other,Unknown, Not collected, Not applicable",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.samplingAge-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human",
specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.specimenID-0.0.2,biospecimen,False,STRING,Sage Bionetworks,n/a (unique to each data contributor). ,"Biospecimen_human,Biospecimen_non_Human,Genotyping_Human,Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq",
tissue,Indicate the tissue the specimen is from,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain, gonadal fat, inguinal fat, kidney, plasma, liver, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissue-0.0.11,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C12801, ,"Biospecimen_human,Biospecimen_non_Human",
tissueWeight,The mass of the tissue specimen. Measured in mg.,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissueWeight-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human",
diagnosis,Indicate the disease or condition.,"AD-DS, Affective Disorder, Alzheimer Disease, Alzheimer disease with psychosis, amyotrophic lateral sclerosis, anxiety, Autism Spectrum Disorder, Bipolar Disorder, Bladder Cancer, Brain Cancer, Breast Cancer, Cervical Cancer, Colon Cancer, control, corticobasal degeneration disorder, CS-DS, dementia, dystonia, essential tremor, Fibrocystic Breast Disease, frontotemporal dementia, gliosis, hypoxia, Juvenile Myelomonocytic Leukemia, Leukemia, Lewy body disease, Longevity, Lung Cancer, Major Depressive Disorder, MCI-DS, mild cognitive impairment, multiple system atrophy, Neurofibromatosis 1, Neurofibromatosis 2, no cognitive impairment, Not Applicable, obesity, obsessive compulsive disorder, Ovary Cancer, Pancreatic Cancer, Parkinson's disease, pathological aging, progressive supranuclear palsy, Prostate Cancer, Schizophrenia, Skin Cancer, Substance Related Disorder, Tourette Syndrome, traumatic brain injury, type 2 diabetes mellitus, vascular dementia, Williams Syndrome",,,False,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.diagnosis-0.0.12,clinical,True,STRING,"https://www.ebi.ac.uk/ols/ontologies/mondo, https://www.ebi.ac.uk/ols/ontologies/maxo, https://www.ebi.ac.uk/ols/ontologies/hp","HPO, MONDO, MAXO codes or labels (not listed for purposes of this RFC), Other, Unknown, Not collected, Not applicable, Not specified. ","Individual_Human,Phenotype_human",
softwareType,,,,,True,,,computational tools,Sage Bionetworks,computational tools,False,STRING,Sage Bionetworks,,computational_tools_template,
toolAccessibility,Whether there are non-monetary restrictions on accessing an online service,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolCmd,"Relevant command, command-line fragment, or option for executing this function/running the tool in this mode",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolComputeRequirements,"Component dependency requirements for application. This includes runtime environments and shared libraries that are not included in the application distribution package, but required to run the application (examples: DirectX, Java or .NET runtime)",,,,False,,,computational tools,schema.org,computational tools,False,STRING,schema.org,,computational_tools_template,
toolCost,Monetary cost of acquiring the software,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDateLastModified,"The date indicating when the tool's entry was most recently modified or updated, providing a timestamp of the latest changes made to the tool's information",,,,False,,,computational tools,schema.org,computational tools,False,STRING,schema.org,,computational_tools_template,
toolDocumentationNote,Comment about the documentation,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDocumentationType,"Type of documentation that is linked to. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDocumentationUrl,Link to documentation on the web for the tool,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDoi,The Digital Object Identifier (DOI) associated with the computational tool,,,,True,,,computational tools,Sage Bionetworks,computational tools,False,STRING,Sage Bionetworks,,computational_tools_template,
toolDownloadNote,Comment about the download,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDownloadType,"The type of data, information, or system that is obtained when the link is resolved",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDownloadUrl,Link to download (or repo providing a download) for the software,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolDownloadVersion,Version information (typically a version number) of the software applicable to this download,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolEntityName,Name of the entities that may be credited,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolEntityRole,Role performed by entity that is credited e.g. Developer,,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolEntityType,Types of entities that may be credited e.g. Person,,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolFunctionNote,"Concise comment about this function, if not apparent from the software description and EDAM annotations",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolHomepage,"Homepage of the software, or some URL that best serves this purpose",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolInputData,"Type of primary input data. Multiple values permitted, comma separated",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolInputFormat,"Allowed format(s) of the input data. Multiple values permitted, comma separated",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolLanguage,"Name of programming language the software source code was written in. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolLicense,"Software or data usage license. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolLinkNote,Comment about the link,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolLinkType,"The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolLinkUrl,A link of some relevance to the software (URL),,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolOperatingSystem,"The operating system supported by a downloadable software package. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolOperation,"The basic operation(s) performed by this software function. Multiple values permitted, comma separated",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolOutputData,"Type of primary output data. Multiple values permitted, comma separated",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,,computational_tools_template
toolOutputFormat,"Allowed format(s) of the output data. Multiple values permitted, comma separated",,,,True,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolPackageDependencies,"Specifies the software libraries, frameworks, or other components that a tool or package relies on for its proper functioning. This attribute helps users understand the prerequisites needed for installation and usage of the tool within a given computational environment",,,,False,,,computational tools,CWL,computational tools,False,STRING,CWL,,computational_tools_template,
toolPackageDependenciesPresent,Indicates whether the required package dependencies for tool are present,,,,True,,,computational tools,CWL,computational tools,False,BOOLEAN,CWL,,computational_tools_template,
toolPubmedId,The pubMed identifer associated with the development of the tool,,,,False,,,computational tools,Sage Bionetworks,computational tools,False,STRING,Sage Bionetworks,,computational_tools_template,
toolReleaseDate,The release date of a product or product model. This can be used to distinguish the exact variant of a product,,,,True,,,computational tools,schema.org,computational tools,False,STRING,schema.org,,computational_tools_template,
toolTopic,"General scientific domain the software serves, or other general category. Multiple values permitted, comma separated",,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
toolType,"A type of application software: a discrete software entity can have more than one type. Multiple values permitted, comma separated",,,,True,,,computational tools,Sage Bionetworks,computational tools,True,STRING,Sage Bionetworks,,computational_tools_template,
toolVersion,Version information (typically a version number) of the software applicable to this entry,,,,False,,,computational tools,biotoolsschema,computational tools,False,STRING,biotoolsschema,,computational_tools_template,
ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Not applicable,Not collected,Other ethnicity,Prefer not to answer,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicity-0.0.2,demographics,False,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249", ,"Individual_Human,Phenotype_human",
familyStudyParticipant,Indicates whether or not a file has data from a human participant involved in a family study (ex. LLFS),"Yes, No, Not Assigned",,,False,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicityfamilyStudyParticipant-0.0.2,demographics,False,STRING,Sage Bionetworks,,"Individual_Human,Phenotype_human,file_annotation_template",
race,Race of individual,"American Indian or Alaska Native,Ashkenazi Jewish,Asian,Black or African American,Multiracial,Native Hawaiian or Pacific Islander,Not collected,Not applicable,Other race,Prefer not to answer,Unknown,White",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.race-0.0.2,demographics,True,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249, https://jamanetwork.com/pages/inclusive-language, https://thesaurus.cancer.gov/ncitbrowser/pages/home.jsf?version=23.04d", ,"Individual_Human,Phenotype_human",
sex,The biological sex of the individual,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.sex-0.0.2,demographics,False,STRING,"Sage Bionetworks,http://purl.obolibrary.org/obo/NCIT_C28421,https://www.synapse.org/#!Synapse:syn25878249", ,"Individual_Human,Individual_non_Human,Phenotype_human",
assay,The analysis or technology used to generate the data in this file,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway, Not collected, Not specified, Not applicable, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.assay-0.0.26,experimentalData,False,STRING,Sage Bionetworks, ,Biospecimen_non_Human,
controlType,"Control samples suitable for normalization and batch correction.Possible example values - GIS, GoldenWest, NIST SRM 1950, AIBL pool,Baker pool,water plus Baker ISTD, study pool, internal standards, Other, Unknown, Not collected, Not applicable, Not specified","AIBL pool, Baker pool, blank injection, GIS, GoldenWest, NIST SRM 1950, qc mix, Replicate, study pool, water plus Baker ISTD",,,False,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.controlType-0.0.5,experimentalData,False,STRING,https://doi.org/10.1101/2020.05.19.105197 https://doi.org/10.1038/sdata.2017.140 https://www-s.nist.gov/srmors/view_detail.cfm?srm=1950 Sage Bionetworks DSLWG,"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,
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,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.platformLocation-0.0.2,experimentalData,True,STRING,"DSLWG,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. ","Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq",
age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",,,,True,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
cohort,Name of the cohort the individual belongs to,"Arivale Scientific Wellness Study (SWS), Cardiovascular Health Study (CHS), Centenarian, Denmark Family, Not applicable, Not collected, Not specified, Other, Study of Osteoporotic Fractures (SOF), SuperAgers Family Study, The Health Aging and Body Composition Studay (HealthABC), The Osteoporotic Fractures in Men (MrOS) Study, Unknown, US Family",,,False,ManifestColumn,,ManifestColumn,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",individual,True,STRING,Sage Bionetworks, ,"Individual_Human,Individual_non_Human,Phenotype_human",
hasADLs,The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs),"Yes, No",,,False,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
hasCASI,The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI),"Yes, No",,,False,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
hasCDR,The datafile and/or individualID includes cognitive variables and/or scores from the The Clinical Dementia Rating (CDR),"Yes, No",,,False,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
hasMMSE,The datafile and/or individualID includes cognitive variables and/or scores from the Mini-Mental State Examination (MMSE),"Yes, No",,,False,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
hasMoCA,The datafile and/or individualID includes cognitive variables and/or scores from the Montreal Cognitive Assessment (MoCA),"Yes, No",,,False,ManifestColumn,,ManifestColumn,,individual,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. ","Individual_Human,Phenotype_human",
individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.individualID-0.0.2,individual,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human,Individual_Human,Individual_non_Human,Phenotype_human",
isMultiSpecimen,Boolean flag indicating whether or not a file has data for multiple specimens,"true,fasle,Not assigned",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING,Sage Bionetworks,,"study_folder_template,Individual_Human,Individual_non_Human,Biospecimen_human, Biospecimen_non_Human,Phenotype_human,file_annotation_template",
species,The name of a species (typically a taxonomic group) of organism.,"Cross-Species Avian,Cross-Species Mammalian,Human,Mouse",,,True,ManifestColumn,,ManifestColumn,Sage Bionetworks,individual,True,STRING,Sage Bionetworks,,study_folder_template,
spectrometerFrequency,The frequency at which a spectrometer causes hydrogen atoms to resonate (in MHz),,,,False,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.spectrometerFrequency-0.0.2,mass spectrometry,False,NUMBER,Sage Bionetworks, ,Metabolomics,
directionalBSseqLibrary,Indicates whether or not the bisulfiteSeq library is directional,"TRUE, FALSE, Unknown, Not collected, Not applicable, Not specified",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.directionalBSseqLibrary-0.0.2,sequencing,False,STRING,Sage Bionetworks, ,bsSeq,
gDNAconc,gDNA Concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.gDNAconc-0.0.3,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,
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, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Qiagen Rneasy Extraction 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, 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,,,
assay_bsSeq_template,Template for bsSeq,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,dnaBatchID,dnaBatchSize,dnaBatchSizeUnit,libraryBatchID,libraryPrep,libraryPreparationMethod,libraryVersion,sequencingBatchID,sequencingBatchSize,sequencingBatchSizeUnit,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,directionalBSseqLibrary,gDNAconc,lambdaDNAconc,pcrCycles,meanCoverage,conversionRatio,conversionRatioUnits,enrichmentMethod,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_metabolomics_template,Template for Metabolomics,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,instrumentModel,samplePrepProtocol,dataFile,databaseSource,databaseWeblink,databaseName,msTarget,msAssayTechnique,msAnalyteType,sampleIntroduction,extractionMethod,acquisitionMode,acquisitionSoftware,acquistionSoftwareVersion,spectrometerFrequency,hasIonizationSource,ionProperty,vacuumPressure,vacuumPressureUnit,lensVoltages,lensVoltagesUnit,gasFlowTemperature,gasFlowTemperatureUnit,hasAssayControl,controlType,experimentalBatchSize,experimentalBatchSizeUnit,batchSize,batchSizeUnit,batchID,batchLabel,sampleBatchID,sampleBatchSize,sampleBatchSizeUnit,acquisitionBatchID,acquisitionBatchSize,acquisitionBatchSizeUnit,processingBatchID,processingBatchSize,processingBatchSizeUnit,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_metagenomics_template,Template for Metagenomics,,"Filename,specimenID,sampleType,experimentType,measurementTechnique,technologyPlatformVersion,platformLocation,instrumentModel,samplePrepProtocol,dataFile,databaseSource,databaseWeblink,databaseName,databaseVersion,databaseLibrary,libraryPrep,libSize,mid,assemblyName,nucleAcidExt,sourceMatID,libReadsSeqd,numberContig,libLayout,assemblyQual,libVector,adapters,assemblySoftware,experimentalFactor,associatedResource,sop,targetGene,seqMethod,seqPlatform,DNAextraction,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_microbiome_template,Template for Microbiome,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,extractionMethod,libraryBatchID,sequencingBatchID,sequencingBatchSize,sequencingBatchSizeUnit,dnaBatchID,dnaBatchSize,dnaBatchSizeUnit,libraryPrep,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_phenotype_human_template,Template for Phenotype_human,,"Filename,individualID,cohort,speciesGroup,sex,race,ethnicity,ethnicGroupCode,age,diagnosisStatus,diagnosis,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_proteomics_template,Template for Proteomics,,"Filename,specimenID,sampleType,experimentType,measurementTechnique,technologyPlatformVersion,platformLocation,instrumentModel,samplePrepProtocol,dataFile,databaseSource,databaseWeblink,databaseName,modificationParameters,quantationStrategy,labelQuantitation,labelFreeQuantitation,isobaricLabelingReagent,msTarget,msAssayTechnique,msAnalyteType,digestionMethod,digestionReagent,fractionIdentifier,enrichmentStrategy,enrichment,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_scRNAseq_template,Template for scRNAseq,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,repositoryName,transcriptType,resultUnit,valueReported,rnaBatchID,rnaBatchSize,rnaBatchSizeUnit,libraryBatchID,sequencingBatchID,sequencingBatchSize,sequencingBatchSizeUnit,libraryPrep,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
assay_whole_genome_sequencing_template,Template for Whole_Genome_Sequencing,,"Filename,specimenID,sampleType,measurementTechnique,technologyPlatformVersion,platformLocation,referenceTranscriptID,repositoryName,transcriptType,resultUnit,valueReported,rnaBatchID,libraryBatchID,sequencingBatchID,libraryPrep,libraryPreparationMethod,libraryVersion,isStranded,readStrandOrigin,readLength,readLengthUnits,runType,totalReads,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
biospecimen_human_template,Template for Biospecimen_human,,"Filename,individualID,specimenID,isMultiSpecimen,specimenType,measurementTechnique,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
biospecimen_non_human_template,Template for Biospecimen_non_Human,,"Filename,individualID,specimenID,isMultiSpecimen,specimenType,assay,specimenAge,samplingAge,organ,tissue,tissueVolume,tissueWeight,specimenSource,nucleicAcidSource,cellType,fastingState,isPostMortem,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
computational_tools_template,Annotations for computational tools on the ELITE Portal,,"displayName,program,institution,toolType,softwareType,grants,contributor,summary,documentation,resourceType,isFeatured,project,toolAccessibility,toolCmd,toolComputeRequirements,toolCost,toolDateLastModified,toolDocumentationNote,toolDocumentationType,toolDocumentationUrl,toolDownloadNote,toolDownloadType,toolDownloadUrl,toolDownloadVersion,toolEntityName,toolEntityRole,toolEntityType,toolFunctionNote,toolHomepage,toolInputData,toolInputFormat,toolLanguage,toolLicense,toolLinkNote,toolLinkType,toolLinkUrl,toolOperatingSystem,toolOperation,toolOutputData,toolOutputFormat,toolPackageDependencies,toolPackageDependenciesPresent,toolPubmedId,toolReleaseDate,toolTopic,toolVersion,toolDoi",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
file_annotation_template,Base annotations for files in synapse,,"Filename, individualID, specimenID, isMultiSpecimen, speciesName, speciesGroup, familyStudyParticipant, assay, fileFormat, consortium, projectShortName, studyKey, grant, resourceType, dataType, dataSubtype, metadataType, analysisType, isModelSystem, ModelSystemType, Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
genotyping_human_template,Template for Genotyping_Human,,"Filename,specimenID,stage,numberIndividuals,sampleType,useReagent,reagentIDs,reagentName,reagentManufacturer,reagentCatalogNumber,reagentLotNumber,reagentWeblink,reagentContact,useTreatment,treatmentIDs,treatmentName,treatmentAmountValue,treatmentAmountUnit,treatmentDurationValue,treatmentDurationUnit,treatmentTemperatureValue,treatmentTemperatureUnit,measurementTechnique,genotypeTechnology,arrayManufacturer,arrayInformation,imputation,imputationPanel,imputationSoftware,variantCount,statisticalModel,adjustedCovariates,reportedTrait,backgroundTrait,useReadMeFile,readmeFile,useSummaryFile,summaryFile,summaryStatisticsAssembly,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
individual_human_template,Template for Individual_Human,,"Filename,individualID,cohort,studyCode,fieldCenterCode,visitCode,countryCode,consentGroupID,speciesGroup,sex,race,ethnicity,ethnicGroupCode,age,diagnosisStatus,diagnosis,hasMoCA,hasCASI,hasCDR,hasMMSE,hasADLs,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
individual_non_human_template,Template for Individual_non_Human,,"Filename,individualID,studyCode,taxon,speciesGroup,speciesName,commonName,sex,lifeStage,speciesAge,captivityStatus,captivityDuration,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,
study_folder_template,Annotations for study folders,,"studyKey,studyName,projectShortName,projectFullName,dataTypeAll,species,specimenType,studyAbstract,studyDescription,studyFocus,program,grantNumber,studyWiki,acknowledgment,methods,relatedStudies,studyType,isModelSystem,isFeatured,ackContext,studyMetadata,accessReqs,isReleased,newsRelease,metadataType,Component",,False,Component,,template,Sage Bionetworks,template,False,,Sage Bionetworks,,,