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dataset template

Annotations for datasets on the ELITE Portal [Download]

Attribute Description Required columnType DependsOn Source Parent Valid Values
dataType The category or format of data generated or collected in an experiment, describing the kind of information the dataset contains (for example, genomics, imaging, proteomics, or behavioral data). True STRING_LIST Sage Bionetworks ManifestColumn clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData
measurementTechnique The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn Bisulfite sequencing,Clinical data,Genome-wide association study,High-performance liquid chromatography tandem mass spectrometry,Liquid chromatography mass spectrometry,Liquid chromatography tandem mass spectrometry,Mass spectrometry,Metabolomics,MetaX-processed metabolomics data,Proximity extension assay,RNA sequencing,Single-cell RNA sequencing,Shotgun metagenomic sequencing,Single nucleotide polymorphism array,Tandem Mass Tag proteomics,Whole-genome sequencing,Unknown,Other,Not collected,Not applicable,Not specified
specimenType Type of biological material sample taken from a biological entity for research purposes True STRING_LIST ManifestColumn blood, brain, buffy coat, cell line, cells, nervous system, organoid, plasma, saliva, serum, skin, stool, tissue, urine, Not applicable, Not collected, Not specified, Other, Unknown
studyKey The short acronym for a study name in a URL-friendly format (ex. LLFS_Metabolomics OR ELPSCRNA) True STRING Sage Bionetworks ManifestColumn
contributor True STRING Sage Bionetworks
project The ELITE project short name associated with the tool True STRING Sage Bionetworks ILO BU, ILO TGEN, LC, LG, LLFS, NECS APOE, Not assigned
alternateName An altername name that can be used for search and discovery improvement. False STRING SageBionetworks
conditionsOfAccess Additional requirements a user may need outside of Data Use Modifiers. This could include additional registration updating profile information joining a Synapse Team or using specific authentication methods like 2FA or RAS. Omit property if not applicable/unknown. False STRING SageBionetworks
countryOfOrigin Origin of individuals from which data were generated. Omit if not applicable/unknown. False STRING SageBionetworks
creator Main researchers involved in producing the data in priority order. Usually matches the project PI(s) and data lead(s) responsible for conception and initial content creation. For tools this is the manufacturer or developer of the instrument. Expects properly formatted name of the organization or person (e.g. NF-OSI" or "Robert Allaway") not an id. See https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/creator/." True STRING_LIST SageBionetworks
croissant_file_s3_object Link to croissant file for dataset. False STRING SageBionetworks
dataRestriction Indicates the restriction level of files/folders. True STRING SageBionetworks Controlled, Registered, Open
dataUseModifiers List of data use ontology (DUO) terms that are true for dataset which describes the allowable scope and terms for data use. Most datasets allow "General Research Use" unless otherwise specified. False STRING_LIST SageBionetworks Clinical Care Use,Collaboration Required,Disease Specific Research,Ethics Approval Required,General Research Use,Genetic Studies Only,Geographical Restriction,Health or Medical or Biomedical Research,Institution Specific Restriction,No General Methods Research,No Restriction,Non-Commercial Use Only,Not-for-Profit Non-Commercial Use Only,Not-for-Profit Organisation Use Only,Population Origins or Ancestry Research Only,Population Origins or Ancestry Research Prohibited,Project Specific Restriction,Publication Moratorium,Publication Required,Research Specific Restrictions,Return to Database or Resource,Time Limit on Use,User Specific Restriction
datasetType The classification of a dataset based on its role, scope, or purpose within a study. True STRING SageBionetworks experimental, publication
datePublished Date the dataset was published or made available on Synapse formatted as YYYY-MM-DD. Maps to schema.org datePublished. False STRING SageBionetworks
individualCount Number of unique individuals included in the dataset (whether as individual-level or as aggregate data). Omit if not applicable/unknown. False INTEGER SageBionetworks
keywords Typically between 1 to 5 informative terms or phrases that help users find the dataset. True STRING_LIST SageBionetworks
license License attached to the data. If indicates UNKNOWN or RESTRICTED-USE. Data may not be used without further contact for terms. True STRING_LIST SageBionetworks CC BY-NC,CC BY-NC 4.0,CC BY-NC 3.0,CC BY-NC 2.5,CC BY-NC 2.0,CC BY-NC 1.0,CC BY-NC-ND,CC BY-NC-ND 4.0,CC BY-NC-ND 3.0,CC BY-NC-ND 2.5,CC BY-NC-ND 2.0,CC BY-NC-ND 1.0,CC BY-NC-SA,CC BY-NC-SA 4.0,CC BY-NC-SA 3.0,CC BY-NC-SA 2.5,CC BY-NC-SA 2.0,CC BY-NC-SA 1.0,CC BY-ND,CC BY-ND 4.0,CC BY-ND 3.0,CC BY-ND 2.5,CC BY-ND 2.0,CC BY-ND 1.0,CC BY-SA,CC BY-SA 4.0,CC BY-SA 3.0,CC BY-SA 2.5,CC BY-SA 2.0,CC BY-SA 1.0,CC-0,CC0 1.0,CC-BY,CC-BY 4.0,CC-BY 3.0,CC-BY 2.5,CC-BY 2.0,CC-BY 1.0,ODC-BY,ODC-BY 1.0,ODC-ODbL,ODC-ODbL 1.0,ODC-PDDL,ODC-PDDL 1.0,Public Domain,UNKNOWN
subject Applicable subject term(s) for dataset cataloging; use the Library of Congress Subject Headings (LCSH) scheme. False STRING_LIST SageBionetworks
assay The analysis or technology used to generate the data in this file True STRING_LIST sage.annotations-experimentalData.assay-0.0.26 ManifestColumn 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
species The name of a species (typically a taxonomic group) of organism. True STRING Sage Bionetworks ManifestColumn Cross-Species Avian,Cross-Species Mammalian,Human,Mouse