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"@id": "http://schema.biothings.io" }, "sms:displayName": "organoid", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Primarycellculture", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Primarycellculture", "rdfs:subClassOf": [ { "@id": "bts:ModelSystemType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "primary cell culture", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Notassigned", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Notassigned", "rdfs:subClassOf": [ { "@id": "bts:IsModelSystem" }, { "@id": "bts:Consortium" }, { "@id": "bts:IsMultiSpecimen" }, { "@id": "bts:ProjectShortName" }, { "@id": "bts:DataSubtype" }, { "@id": "bts:ModelSystemType" }, { "@id": "bts:ResourceType" }, { "@id": "bts:GrantNumber" }, { "@id": "bts:AnalysisType" }, { "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Not assigned", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:manifestColumn", "@type": "rdf:Property", "rdfs:comment": "TBD", "rdfs:label": "manifestColumn", "schema:domainIncludes": [ { "@id": "bts:ModelSystemType" }, { "@id": "bts:IsModelSystem" }, { "@id": "bts:DNAextraction" }, { "@id": "bts:AcquisitionBatchID" }, { "@id": "bts:AcquisitionBatchSize" }, { "@id": "bts:AcquisitionBatchSizeUnit" }, { "@id": "bts:AcquisitionMode" }, { "@id": "bts:AcquisitionSoftware" }, { "@id": "bts:AcquisitionSoftwareVersion" }, { "@id": "bts:Adapters" }, { "@id": "bts:AdjustedCovariates" }, { "@id": "bts:AnalysisType" }, { "@id": "bts:ArrayInformation" }, { "@id": "bts:ArrayManufacturer" }, { "@id": "bts:AssemblyName" }, { "@id": "bts:AssemblyQual" }, { "@id": "bts:AssemblySoftware" }, { "@id": "bts:AssociatedResource" }, { "@id": "bts:BackgroundTrait" }, { "@id": "bts:BatchID" }, { "@id": "bts:BatchLabel" }, { "@id": "bts:CaptivityDuration" }, { "@id": "bts:CaptivityStatus" }, { "@id": "bts:CommonName" }, { "@id": "bts:ConsentGroupID" }, { "@id": "bts:Consortium" }, { "@id": "bts:ConversionRatio" }, { "@id": "bts:ConversionRatioUnits" }, { "@id": "bts:CountryCode" }, { "@id": "bts:DataFile" }, { "@id": "bts:DataModelVersion" }, { "@id": "bts:DataSubtype" }, { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" }, { "@id": "bts:DatabaseLibrary" }, { "@id": "bts:DatabaseName" }, { "@id": "bts:DatabaseSource" }, { "@id": "bts:DatabaseVersion" }, { "@id": "bts:DatabaseWeblink" }, { "@id": "bts:DiagnosisStatus" }, { "@id": "bts:DigestionMethod" }, { "@id": "bts:DigestionReagent" }, { "@id": "bts:DnaBatchID" }, { "@id": "bts:DnaBatchSize" }, { "@id": "bts:DnaBatchSizeUnit" }, { "@id": "bts:Enrichment" }, { "@id": "bts:EnrichmentMethod" }, { "@id": "bts:EnrichmentStrategy" }, { "@id": "bts:EthnicGroupCode" }, { "@id": "bts:ExperimentType" }, { "@id": "bts:ExperimentalBatchSizeUnit" }, { "@id": "bts:ExperimentalFactor" }, { "@id": "bts:ExtractionMethod" }, { "@id": "bts:FieldCenterCode" }, { "@id": "bts:FileFormat" }, { "@id": "bts:FractionIdentifier" }, { "@id": "bts:GasFlowTemperature" }, { "@id": "bts:GasFlowTemperatureUnit" }, { "@id": "bts:GenotypeTechnology" }, { "@id": "bts:HasAssayControl" }, { "@id": "bts:HasIonizationSource" }, { "@id": "bts:Imputation" }, { "@id": "bts:ImputationPanel" }, { "@id": "bts:ImputationSoftware" }, { "@id": "bts:InstrumentModel" }, { "@id": "bts:IonProperty" }, { "@id": "bts:IsobaricLabelingReagent" }, { "@id": "bts:LabelFreeQuantitation" }, { "@id": "bts:LabelQuantitation" }, { "@id": "bts:LensVoltages" }, { "@id": "bts:LensVoltagesUnit" }, { "@id": "bts:LibLayout" }, { "@id": "bts:LibReadsSeqd" }, { "@id": "bts:LibSize" }, { "@id": "bts:LibVector" }, { "@id": "bts:LibraryBatchID" }, { "@id": "bts:LifeStage" }, { "@id": "bts:MeasurementTechnique" }, { "@id": "bts:Mid" }, { "@id": "bts:ModificationParameters" }, { "@id": "bts:MsAnalyteType" }, { "@id": "bts:MsAssayTechnique" }, { "@id": "bts:MsTarget" }, { "@id": "bts:NucleAcidExt" }, { "@id": "bts:NumberContig" }, { "@id": "bts:NumberIndividuals" }, { "@id": "bts:ProcessingBatchID" }, { "@id": "bts:Program" }, { "@id": "bts:ProjectShortName" }, { "@id": "bts:QuantationStrategy" }, { "@id": "bts:ReadLengthUnits" }, { "@id": "bts:ReadmeFile" }, { "@id": "bts:ReagentCatalogNumber" }, { "@id": "bts:ReagentContact" }, { "@id": "bts:ReagentIDs" }, { "@id": "bts:ReagentLotNumber" }, { "@id": "bts:ReagentManufacturer" }, { "@id": "bts:ReagentName" }, { "@id": "bts:ReagentWeblink" }, { "@id": "bts:ReferenceTranscriptID" }, { "@id": "bts:ReportedTrait" }, { "@id": "bts:RepositoryName" }, { "@id": "bts:ResourceType" }, { "@id": "bts:ResultUnit" }, { "@id": "bts:RnaBatchID" }, { "@id": "bts:RnaBatchSize" }, { "@id": "bts:RnaBatchSizeUnit" }, { "@id": "bts:SampleBatchID" }, { "@id": "bts:SampleIntroduction" }, { "@id": "bts:SamplePrepProtocol" }, { "@id": "bts:SampleType" }, { "@id": "bts:SeqMethod" }, { "@id": "bts:SeqPlatform" }, { "@id": "bts:SequencingBatchID" }, { "@id": "bts:SequencingBatchSize" }, { "@id": "bts:SequencingBatchSizeUnit" }, { "@id": "bts:Sop" }, { "@id": "bts:SourceMatID" }, { "@id": "bts:SpeciesAge" }, { "@id": "bts:SpeciesGroup" }, { "@id": "bts:SpeciesName" }, { "@id": "bts:SpecimenAge" }, { "@id": "bts:SpecimenSource" }, { "@id": "bts:SpecimenType" }, { "@id": "bts:Stage" }, { "@id": "bts:StatisticalModel" }, { "@id": "bts:StudyCode" }, { "@id": "bts:StudyKey" }, { "@id": "bts:SummaryFile" }, { "@id": "bts:SummaryStatisticsAssembly" }, { "@id": "bts:TargetGene" }, { "@id": "bts:Taxon" }, { "@id": "bts:TechnologyPlatformVersion" }, { "@id": "bts:TissueVolume" }, { "@id": "bts:TranscriptType" }, { "@id": "bts:TreatmentAmountUnit" }, { "@id": "bts:TreatmentAmountValue" }, { "@id": "bts:TreatmentDurationUnit" }, { "@id": "bts:TreatmentDurationValue" }, { "@id": "bts:TreatmentIDs" }, { "@id": "bts:TreatmentName" }, { "@id": "bts:TreatmentTemperatureUnit" }, { "@id": "bts:TreatmentTemperatureValue" }, { "@id": "bts:UseReadMeFile" }, { "@id": "bts:UseReagent" }, { "@id": "bts:UseSummaryFile" }, { "@id": "bts:UseTreatment" }, { "@id": "bts:VacuumPressure" }, { "@id": "bts:VacuumPressureUnit" }, { "@id": "bts:ValueReported" }, { "@id": "bts:VariantCount" }, { "@id": "bts:VisitCode" }, { "@id": "bts:GrantNumber" }, { "@id": "bts:MetadataType" }, { "@id": "bts:BatchSize" }, { "@id": "bts:CellType" }, { "@id": "bts:FastingState" }, { "@id": "bts:IsPostMortem" }, { "@id": "bts:NucleicAcidSource" }, { "@id": "bts:Organ" }, { "@id": "bts:SamplingAge" }, { "@id": "bts:SpecimenID" }, { "@id": "bts:Tissue" }, { "@id": "bts:TissueWeight" }, { "@id": "bts:Diagnosis" }, { "@id": "bts:Ethnicity" }, { "@id": "bts:FamilyStudyParticipant" }, { "@id": "bts:Race" }, { "@id": "bts:Sex" }, { "@id": "bts:Assay" }, { "@id": "bts:ControlType" }, { "@id": "bts:PlatformLocation" }, { "@id": "bts:Age" }, { "@id": "bts:Cohort" }, { "@id": "bts:HasADLs" }, { "@id": "bts:HasCASI" }, { "@id": "bts:HasCDR" }, { "@id": "bts:HasMMSE" }, { "@id": "bts:HasMoCA" }, { "@id": "bts:IndividualID" }, { "@id": "bts:IsMultiSpecimen" }, { "@id": "bts:Species" }, { "@id": "bts:SpectrometerFrequency" }, { "@id": "bts:DirectionalBSseqLibrary" }, { "@id": "bts:GDNAconc" }, { "@id": "bts:IsStranded" }, { "@id": "bts:LambdaDNAconc" }, { "@id": "bts:LibraryPrep" }, { "@id": "bts:LibraryPreparationMethod" }, { "@id": "bts:LibraryVersion" }, { "@id": "bts:MeanCoverage" }, { "@id": "bts:PcrCycles" }, { "@id": "bts:ReadLength" }, { "@id": "bts:ReadStrandOrigin" }, { "@id": "bts:RunType" }, { "@id": "bts:TotalReads" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "ManifestColumn", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:IsModelSystem", "@type": "rdfs:Class", "rdfs:comment": "Boolean flag indicating whether or not a file has data from a model system", "rdfs:label": "IsModelSystem", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:True" }, { "@id": "bts:False" }, { "@id": "bts:Notassigned" } ], "sms:displayName": "isModelSystem", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:True", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "True", "rdfs:subClassOf": [ { "@id": "bts:IsModelSystem" }, { "@id": "bts:IsMultiSpecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "true", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:False", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "False", "rdfs:subClassOf": [ { "@id": "bts:IsModelSystem" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "False", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DNAextraction", "@type": "rdfs:Class", "rdfs:comment": "DNA extraction kit method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "DNAextraction", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "DNAextraction", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AcquisitionBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AcquisitionBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionBatchID", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:AcquisitionBatchSize", "@type": "rdfs:Class", "rdfs:comment": "The number of samples", "rdfs:label": "AcquisitionBatchSize", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionBatchSize", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:AcquisitionBatchSizeUnit", "@type": "rdfs:Class", "rdfs:comment": "The unit of measurement for number of samples in a batch", "rdfs:label": "AcquisitionBatchSizeUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionBatchSizeUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:AcquisitionMode", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AcquisitionMode", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionMode", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AcquisitionSoftware", "@type": "rdfs:Class", "rdfs:comment": "The name of the acquisition software used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "AcquisitionSoftware", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionSoftware", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AcquisitionSoftwareVersion", "@type": "rdfs:Class", "rdfs:comment": "The version number of software used. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "AcquisitionSoftwareVersion", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "acquisitionSoftwareVersion", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Adapters", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "Adapters", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "adapters", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AdjustedCovariates", "@type": "rdfs:Class", "rdfs:comment": "Any covariates the GWAS is adjusted for. Multiple values can be listed separately by a semicolon (;). Example - age;sex", "rdfs:label": "AdjustedCovariates", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "adjustedCovariates", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ANOVA", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ANOVA", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "ANOVA", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Batcheffectcorrection", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Batcheffectcorrection", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "batch effect correction", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Clustering", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Clustering", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "clustering", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Datanormalization", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Datanormalization", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "data normalization", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:De-novoassembly", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "De-novoassembly", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "de-novo assembly", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Doseresponsestudy", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Doseresponsestudy", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "dose response study", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Enrichmentanalysis", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Enrichmentanalysis", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "enrichment analysis", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Genome-wideassociation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Genome-wideassociation", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "genome-wide association", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Mendelianrandomizationanalysis", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Mendelianrandomizationanalysis", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "mendelian randomization analysis", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Networkanalysis", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Networkanalysis", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "network analysis", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Polygenicriskscores", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Polygenicriskscores", "rdfs:subClassOf": [ { "@id": "bts:AnalysisType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "polygenic risk scores", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ArrayInformation", "@type": "rdfs:Class", "rdfs:comment": "Additional information about the genotyping array. For example, for targeted arrays, please provide the specific type of array. Example - Immunochip", "rdfs:label": "ArrayInformation", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "arrayInformation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ArrayManufacturer", "@type": "rdfs:Class", "rdfs:comment": "Manufacturer of the genotyping array used for the discovery stage. Separate multiple manufacturers by a semicolon (;). Example - Illumina, Affymetrix, Perlegen", "rdfs:label": "ArrayManufacturer", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "arrayManufacturer", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:AssemblyName", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AssemblyName", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "assemblyName", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AssemblyQual", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AssemblyQual", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "assemblyQual", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AssemblySoftware", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AssemblySoftware", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "assemblySoftware", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AssociatedResource", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "AssociatedResource", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "associatedResource", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:BackgroundTrait", "@type": "rdfs:Class", "rdfs:comment": "Any background trait(s) shared by all individuals in the GWAS (e.g. in both cases and controls). Example - Nicotine dependence", "rdfs:label": "BackgroundTrait", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "backgroundTrait", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:BatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "BatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "batchID", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:BatchLabel", "@type": "rdfs:Class", "rdfs:comment": "Used to supply batch label information with any string value", "rdfs:label": "BatchLabel", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "batchLabel", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:CaptivityDuration", "@type": "rdfs:Class", "rdfs:comment": "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.", "rdfs:label": "CaptivityDuration", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "captivityDuration", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:CaptivityStatus", "@type": "rdfs:Class", "rdfs:comment": "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.", "rdfs:label": "CaptivityStatus", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Captive" }, { "@id": "bts:Stranded" }, { "@id": "bts:Wild" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:Other" }, { "@id": "bts:unknown" } ], "sms:displayName": "captivityStatus", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Captive", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Captive", "rdfs:subClassOf": [ { "@id": "bts:CaptivityStatus" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Captive", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Stranded", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Stranded", "rdfs:subClassOf": [ { "@id": "bts:CaptivityStatus" }, { "@id": "bts:ReadStrandOrigin" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "stranded", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Wild", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Wild", "rdfs:subClassOf": [ { "@id": "bts:CaptivityStatus" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Wild", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Notapplicable", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Notapplicable", "rdfs:subClassOf": [ { "@id": "bts:MsTarget" }, { "@id": "bts:RunType" }, { "@id": "bts:Stage" }, { "@id": "bts:FastingState" }, { "@id": "bts:ResultUnit" }, { "@id": "bts:SpecimenType" }, { "@id": "bts:Ethnicity" }, { "@id": "bts:Sex" }, { "@id": "bts:CaptivityStatus" }, { "@id": "bts:LifeStage" }, { "@id": "bts:TranscriptType" }, { "@id": "bts:NucleicAcidSource" }, { "@id": "bts:EnrichmentStrategy" }, { "@id": "bts:Cohort" }, { "@id": "bts:DirectionalBSseqLibrary" }, { "@id": "bts:LabelFreeQuantitation" }, { "@id": "bts:SpeciesGroup" }, { "@id": "bts:TreatmentDurationUnit" }, { "@id": "bts:Race" }, { "@id": "bts:ReadStrandOrigin" }, { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" }, { "@id": "bts:DigestionReagent" }, { "@id": "bts:LibraryPreparationMethod" }, { "@id": "bts:Organ" }, { "@id": "bts:LibraryPrep" }, { "@id": "bts:RepositoryName" }, { "@id": "bts:CellType" }, { "@id": "bts:DnaBatchSizeUnit" }, { "@id": "bts:SpeciesName" }, { "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Not applicable", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Notcollected", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Notcollected", "rdfs:subClassOf": [ { "@id": "bts:RunType" }, { "@id": "bts:MsTarget" }, { "@id": "bts:Stage" }, { "@id": "bts:FastingState" }, { "@id": "bts:ResultUnit" }, { "@id": "bts:SpecimenType" }, { "@id": "bts:Ethnicity" }, { "@id": "bts:Sex" }, { "@id": "bts:DirectionalBSseqLibrary" }, { "@id": "bts:CaptivityStatus" }, { "@id": "bts:LifeStage" }, { "@id": "bts:TranscriptType" }, { "@id": "bts:NucleicAcidSource" }, { "@id": "bts:Cohort" }, { "@id": "bts:ReadStrandOrigin" }, { "@id": "bts:EnrichmentStrategy" }, { "@id": "bts:SpeciesGroup" }, { "@id": "bts:TreatmentDurationUnit" }, { "@id": "bts:Race" }, { "@id": "bts:LabelFreeQuantitation" }, { "@id": "bts:LabelQuantitation" }, { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" }, { "@id": "bts:DigestionReagent" }, { "@id": "bts:LibraryPreparationMethod" }, { "@id": "bts:Organ" }, { "@id": "bts:LibraryPrep" }, { "@id": "bts:RepositoryName" }, { "@id": "bts:CellType" }, { "@id": "bts:DnaBatchSizeUnit" }, { "@id": "bts:SpeciesName" }, { "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Not collected", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Notspecified", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Notspecified", "rdfs:subClassOf": [ { "@id": "bts:RunType" }, { "@id": "bts:MsTarget" }, { "@id": "bts:Stage" }, { "@id": "bts:TreatmentTemperatureUnit" }, { "@id": "bts:FastingState" }, { "@id": "bts:ResultUnit" }, { "@id": "bts:SpecimenType" }, { "@id": "bts:Sex" }, { "@id": "bts:CaptivityStatus" }, { "@id": "bts:LifeStage" }, { "@id": "bts:TranscriptType" }, { "@id": "bts:NucleicAcidSource" }, { "@id": "bts:DirectionalBSseqLibrary" }, { "@id": "bts:Cohort" }, { "@id": "bts:ReadStrandOrigin" }, { "@id": "bts:EnrichmentStrategy" }, { "@id": "bts:SpeciesGroup" }, { "@id": "bts:TreatmentDurationUnit" }, { "@id": "bts:LabelFreeQuantitation" }, { "@id": "bts:LabelQuantitation" }, { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" }, { "@id": "bts:DigestionReagent" }, { "@id": "bts:Organ" }, { "@id": "bts:LibraryPreparationMethod" }, { "@id": "bts:LibraryPrep" }, { "@id": "bts:RepositoryName" }, { "@id": "bts:DnaBatchSizeUnit" }, { "@id": "bts:RnaBatchSizeUnit" }, { "@id": "bts:TreatmentAmountUnit" }, { "@id": "bts:VacuumPressureUnit" }, { "@id": "bts:CellType" }, { "@id": "bts:SpeciesName" }, { "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Not specified", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Other", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Other", "rdfs:subClassOf": [ { "@id": "bts:Stage" }, { "@id": "bts:StudyCode" }, { "@id": "bts:Sex" }, { "@id": "bts:CaptivityStatus" }, { "@id": "bts:LifeStage" }, { "@id": "bts:TranscriptType" }, { "@id": "bts:Cohort" }, { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" }, { "@id": "bts:RepositoryName" }, { "@id": "bts:Organ" }, { "@id": "bts:DnaBatchSizeUnit" }, { "@id": "bts:RnaBatchSizeUnit" }, { "@id": "bts:TreatmentAmountUnit" }, { "@id": "bts:CellType" }, { "@id": "bts:SpeciesName" }, { "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "other", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:unknown", "@type": "rdf:Property", "rdfs:comment": "TBD", "rdfs:label": "unknown", "schema:domainIncludes": [ { "@id": "bts:Contributor" }, { "@id": "bts:DisplayName" }, { "@id": "bts:Documentation" }, { "@id": "bts:Grants" }, { "@id": "bts:Institution" }, { "@id": "bts:Project" }, { "@id": "bts:Summary" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Unknown", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:CommonName", "@type": "rdfs:Class", "rdfs:comment": "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.", "rdfs:label": "CommonName", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "commonName", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ConsentGroupID", "@type": "rdfs:Class", "rdfs:comment": "Indicate the consent group for the individual, provided by the data contributor's data dictionary", "rdfs:label": "ConsentGroupID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "consentGroupID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Consortium", "@type": "rdfs:Class", "rdfs:comment": "The name of the consortium", "rdfs:label": "Consortium", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:ELITE" }, { "@id": "bts:ELITECDCP" }, { "@id": "bts:Notassigned" } ], "sms:displayName": "consortium", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ELITE", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ELITE", "rdfs:subClassOf": [ { "@id": "bts:Consortium" }, { "@id": "bts:Program" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "ELITE", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ELITECDCP", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ELITECDCP", "rdfs:subClassOf": [ { "@id": "bts:Consortium" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "ELITE CDCP", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ConversionRatio", "@type": "rdfs:Class", "rdfs:comment": "The ratio or % detailing how well the bisulfite conversion worked. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "ConversionRatio", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "conversionRatio", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ConversionRatioUnits", "@type": "rdfs:Class", "rdfs:comment": "The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "ConversionRatioUnits", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "conversionRatioUnits", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:CountryCode", "@type": "rdfs:Class", "rdfs:comment": "Indicate the geographic region for the individual (shown as ex. \"840\")", "rdfs:label": "CountryCode", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "countryCode", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:DataFile", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "DataFile", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "dataFile", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:DataModelVersion", "@type": "rdfs:Class", "rdfs:comment": "Version of the data model", "rdfs:label": "DataModelVersion", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "dataModelVersion", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DataSubtype", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "DataSubtype", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Raw" }, { "@id": "bts:Processed" }, { "@id": "bts:Results" }, { "@id": "bts:Normalized" }, { "@id": "bts:Metadata" }, { "@id": "bts:Notassigned" } ], "sms:displayName": "dataSubtype", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Raw", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Raw", "rdfs:subClassOf": [ { "@id": "bts:DataSubtype" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "raw", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Processed", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Processed", "rdfs:subClassOf": [ { "@id": "bts:DataSubtype" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "processed", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Results", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Results", "rdfs:subClassOf": [ { "@id": "bts:DataSubtype" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "results", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Normalized", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Normalized", "rdfs:subClassOf": [ { "@id": "bts:DataSubtype" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "normalized", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Metadata", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Metadata", "rdfs:subClassOf": [ { "@id": "bts:ResourceType" }, { "@id": "bts:DataSubtype" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "metadata", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DataType", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "DataType", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Clinical" }, { "@id": "bts:DrugScreen" }, { "@id": "bts:Electrophysiology" }, { "@id": "bts:Epigenetics" }, { "@id": "bts:GeneExpression" }, { "@id": "bts:GenomeAssembly" }, { "@id": "bts:GenomicVariants" }, { "@id": "bts:Imaging" }, { "@id": "bts:Lipidomics" }, { "@id": "bts:Metabolomics" }, { "@id": "bts:Metagenomics" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:Other" }, { "@id": "bts:Phenotype" }, { "@id": "bts:Proteomics" }, { "@id": "bts:unknown" }, { "@id": "bts:WearableData" } ], "sms:displayName": "dataType", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Clinical", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Clinical", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "clinical", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DrugScreen", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "DrugScreen", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "drugScreen", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Electrophysiology", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Electrophysiology", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "electrophysiology", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Epigenetics", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Epigenetics", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "epigenetics", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:GeneExpression", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "GeneExpression", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "geneExpression", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:GenomeAssembly", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "GenomeAssembly", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "genomeAssembly", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:GenomicVariants", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "GenomicVariants", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "genomicVariants", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Imaging", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Imaging", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "imaging", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Lipidomics", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Lipidomics", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "lipidomics", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Metabolomics", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Metabolomics", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "metabolomics", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Metagenomics", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Metagenomics", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "metagenomics", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Phenotype", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Phenotype", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { "@id": "bts:DataTypeAll" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "phenotype", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Proteomics", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Proteomics", "rdfs:subClassOf": [ { "@id": "bts:DataType" }, { 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"rdfs:subClassOf": [ { "@id": "bts:DigestionReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Trypsin", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Trypsin/P", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Trypsin/P", "rdfs:subClassOf": [ { "@id": "bts:DigestionReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Trypsin/P", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Unspecificcleavage", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Unspecificcleavage", "rdfs:subClassOf": [ { "@id": "bts:DigestionReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Unspecific cleavage", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:V8-DE", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "V8-DE", "rdfs:subClassOf": [ { "@id": "bts:DigestionReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "V8-DE", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:V8-E", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "V8-E", "rdfs:subClassOf": [ { "@id": "bts:DigestionReagent" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "V8-E", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DnaBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "DnaBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "dnaBatchID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:DnaBatchSize", "@type": "rdfs:Class", "rdfs:comment": "The number of samples. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "DnaBatchSize", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "dnaBatchSize", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:DnaBatchSizeUnit", "@type": "rdfs:Class", "rdfs:comment": "The unit of measurement for number of samples in a batch", "rdfs:label": "DnaBatchSizeUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:AFU" }, { "@id": "bts:AI" }, { "@id": "bts:AU/ml" }, { "@id": "bts:Bpg/dl" }, { "@id": "bts:DKunits/ml" }, { "@id": "bts:G/l" }, { "@id": "bts:Gm" }, { "@id": "bts:HAU" }, { "@id": "bts:IU" }, { "@id": "bts:Iu/l" }, { "@id": "bts:IU/ml" }, { "@id": "bts:KallikreinInactivatorUnitperMilliliter" }, { "@id": "bts:Kg" }, { "@id": "bts:L" }, { "@id": "bts:M" }, { "@id": 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Examples- iTRAQ113 TMT126Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "IsobaricLabelingReagent", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "isobaricLabelingReagent", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LabelFreeQuantitation", "@type": "rdfs:Class", "rdfs:comment": "Type of label-free data analysis strategyProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "LabelFreeQuantitation", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Label-freegenelevelquantitation" }, { "@id": "bts:Label-freepeptidelevelquantitation" }, { "@id": "bts:Label-freeproteingrouplevelquantitation" }, { "@id": "bts:Label-freeproteinlevelquantitation" }, { "@id": "bts:Label-freerawfeaturequantitation" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notavailable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:unknown" } ], "sms:displayName": "labelFreeQuantitation", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Label-freegenelevelquantitation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Label-freegenelevelquantitation", "rdfs:subClassOf": [ { "@id": "bts:LabelFreeQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label-free gene level quantitation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Label-freepeptidelevelquantitation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Label-freepeptidelevelquantitation", "rdfs:subClassOf": [ { "@id": "bts:LabelFreeQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label-free peptide level quantitation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Label-freeproteingrouplevelquantitation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Label-freeproteingrouplevelquantitation", "rdfs:subClassOf": [ { "@id": "bts:LabelFreeQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label-free protein group level quantitation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Label-freeproteinlevelquantitation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Label-freeproteinlevelquantitation", "rdfs:subClassOf": [ { "@id": "bts:LabelFreeQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label-free protein level quantitation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Label-freerawfeaturequantitation", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Label-freerawfeaturequantitation", "rdfs:subClassOf": [ { "@id": "bts:LabelFreeQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label-free raw feature quantitation", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LabelQuantitation", "@type": "rdfs:Class", "rdfs:comment": "Type of labeling usedProvide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "LabelQuantitation", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:AminoxyTMT" }, { "@id": "bts:DiART" }, { "@id": "bts:DiLeu" }, { "@id": "bts:Glyco-TMT" }, { "@id": "bts:HydrazideTMT" }, { "@id": "bts:IodoTMT" }, { "@id": "bts:IPTL" }, { "@id": "bts:ITRAQ" }, { "@id": "bts:ITRAQH" }, { "@id": "bts:LabelFree" }, { "@id": "bts:Notavailable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:TMT" }, { "@id": "bts:unknown" } ], "sms:displayName": "labelQuantitation", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AminoxyTMT", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "AminoxyTMT", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "AminoxyTMT", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DiART", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "DiART", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "DiART", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:DiLeu", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "DiLeu", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "DiLeu", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Glyco-TMT", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Glyco-TMT", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Glyco-TMT", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:HydrazideTMT", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "HydrazideTMT", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Hydrazide TMT", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:IodoTMT", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "IodoTMT", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "IodoTMT", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:IPTL", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "IPTL", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "IPTL", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ITRAQ", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ITRAQ", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "iTRAQ", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ITRAQH", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ITRAQH", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "iTRAQH", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LabelFree", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "LabelFree", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Label Free", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:TMT", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "TMT", "rdfs:subClassOf": [ { "@id": "bts:LabelQuantitation" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "TMT", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LensVoltages", "@type": "rdfs:Class", "rdfs:comment": "The skimmer/focusing lens voltages e.g., capillary voltage, etc.", "rdfs:label": "LensVoltages", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "lensVoltages", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LensVoltagesUnit", "@type": "rdfs:Class", "rdfs:comment": "Unit of lens voltages", "rdfs:label": "LensVoltagesUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "lensVoltagesUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LibLayout", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "LibLayout", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "libLayout", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LibReadsSeqd", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "LibReadsSeqd", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "libReadsSeqd", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LibSize", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "LibSize", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "libSize", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LibVector", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "LibVector", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "libVector", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LibraryBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "LibraryBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "libraryBatchID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LifeStage", "@type": "rdfs:Class", "rdfs:comment": "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.", "rdfs:label": "LifeStage", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Adult" }, { "@id": "bts:Juvenile" }, { "@id": "bts:Post-Juvenile" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:Other" }, { "@id": "bts:unknown" } ], "sms:displayName": "lifeStage", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Adult", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Adult", "rdfs:subClassOf": [ { "@id": "bts:LifeStage" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Adult", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Juvenile", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Juvenile", "rdfs:subClassOf": [ { "@id": "bts:LifeStage" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Juvenile", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Post-Juvenile", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Post-Juvenile", "rdfs:subClassOf": [ { "@id": "bts:LifeStage" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Post-Juvenile", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:MeasurementTechnique", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "MeasurementTechnique", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "measurementTechnique", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Mid", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "Mid", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "mid", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ModificationParameters", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "ModificationParameters", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "modificationParameters", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:MsAnalyteType", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "MsAnalyteType", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "msAnalyteType", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:MsAssayTechnique", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "MsAssayTechnique", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "msAssayTechnique", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:MsTarget", "@type": "rdfs:Class", "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay", "rdfs:label": "MsTarget", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Notapplicable" }, { "@id": "bts:Notavailable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:Targeted" }, { "@id": "bts:unknown" }, { "@id": "bts:Untargeted" } ], "sms:displayName": "msTarget", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Targeted", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Targeted", "rdfs:subClassOf": [ { "@id": "bts:MsTarget" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Targeted", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Untargeted", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Untargeted", "rdfs:subClassOf": [ { "@id": "bts:MsTarget" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Untargeted", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:NucleAcidExt", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "NucleAcidExt", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "nucleAcidExt", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:NumberContig", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "NumberContig", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "numberContig", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:NumberIndividuals", "@type": "rdfs:Class", "rdfs:comment": "Number of individuals in a group. Example - 2000", "rdfs:label": "NumberIndividuals", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "numberIndividuals", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ProcessingBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "ProcessingBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "processingBatchID", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Program", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Program", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:ELITE" }, { "@id": "bts:AD" } ], "sms:displayName": "program", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AD", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "AD", "rdfs:subClassOf": [ { "@id": "bts:Program" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "AD", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ProjectShortName", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ProjectShortName", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:LC" }, { "@id": "bts:ILO" }, { "@id": "bts:LLFS" }, { "@id": "bts:LG" }, { "@id": "bts:Notassigned" } ], "sms:displayName": "projectShortName", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:LC", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "LC", "rdfs:subClassOf": [ { "@id": "bts:ProjectShortName" }, { "@id": "bts:StudyCode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "LC", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ILO", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "ILO", "rdfs:subClassOf": [ { "@id": "bts:ProjectShortName" }, { "@id": "bts:StudyCode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "ILO", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LLFS", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "LLFS", "rdfs:subClassOf": [ { "@id": "bts:ProjectShortName" }, { "@id": "bts:StudyCode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "LLFS", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:LG", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "LG", "rdfs:subClassOf": [ { "@id": "bts:ProjectShortName" }, { "@id": "bts:StudyCode" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "LG", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:QuantationStrategy", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "QuantationStrategy", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "quantationStrategy", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ReadLengthUnits", "@type": "rdfs:Class", "rdfs:comment": "The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "ReadLengthUnits", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "readLengthUnits", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ReadmeFile", "@type": "rdfs:Class", "rdfs:comment": "The name of any readme file uploaded to Synapse. Example - example.tsv", "rdfs:label": "ReadmeFile", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "readmeFile", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ReagentCatalogNumber", "@type": "rdfs:Class", "rdfs:comment": "If the assay reagent is a commercial product, enter the vendor's catalog identifier. 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"@id": "bts:ResultUnit", "@type": "rdfs:Class", "rdfs:comment": "The unit for the result value", "rdfs:label": "ResultUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:FPKM" }, { "@id": "bts:Rawcount" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:RPKM" }, { "@id": "bts:TPM" }, { "@id": "bts:unknown" } ], "sms:displayName": "resultUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:FPKM", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "FPKM", "rdfs:subClassOf": [ { "@id": "bts:ResultUnit" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "FPKM", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Rawcount", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Rawcount", "rdfs:subClassOf": [ { "@id": 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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", "rdfs:label": "RnaBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "rnaBatchID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:RnaBatchSize", "@type": "rdfs:Class", "rdfs:comment": "The number of samples", "rdfs:label": "RnaBatchSize", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "rnaBatchSize", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:RnaBatchSizeUnit", "@type": "rdfs:Class", "rdfs:comment": "The unit of measurement for number of samples in a batch", "rdfs:label": "RnaBatchSizeUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:AFU" }, { "@id": "bts:AI" }, { "@id": "bts:AU/ml" }, { "@id": "bts:Bpg/dl" }, { "@id": "bts:DKunits/ml" }, { "@id": "bts:G/l" }, { "@id": "bts:Gm" }, { "@id": "bts:HAU" }, { "@id": "bts:IU" }, { "@id": "bts:Iu/l" }, { "@id": "bts:IU/ml" }, { "@id": "bts:KallikreinInactivatorUnitperMilliliter" }, { "@id": "bts:Kg" }, { "@id": "bts:L" }, { "@id": "bts:M" }, { "@id": "bts:Mg" }, { "@id": "bts:Mg/dl" }, { "@id": "bts:Mg/l" }, { "@id": "bts:Mg/ml" }, { "@id": "bts:Miu/ml" }, { "@id": "bts:Ml" }, { "@id": "bts:MM" }, { "@id": "bts:MOI" }, { "@id": "bts:Ng" }, { "@id": "bts:Ng/dl" }, { "@id": "bts:Ng/ml" }, { "@id": "bts:Ng/nl" }, { "@id": "bts:Ng/ul" }, { "@id": "bts:Nl" }, { "@id": "bts:NM" }, { "@id": "bts:Notspecified" }, { "@id": "bts:NPX" }, { "@id": "bts:Opticaldensity" }, { "@id": "bts:Other" }, { "@id": "bts:PFU" }, { "@id": "bts:PFUe" }, { "@id": "bts:Pg" }, { "@id": "bts:Pg/mgcreatinine" }, { "@id": "bts:Pg/ml" }, { "@id": "bts:Pg/nl" }, { "@id": "bts:Pg/ul" }, { "@id": "bts:Pl" }, { "@id": "bts:PM" }, { "@id": "bts:Pound" }, { "@id": "bts:TCID50" }, { "@id": "bts:Ug" }, { "@id": "bts:Ug/dl" }, { "@id": "bts:Ug/l" }, { "@id": "bts:Ug/ml" }, { "@id": "bts:Ug/ul" }, { "@id": "bts:Uiu/ml" }, { "@id": "bts:Ul" }, { "@id": "bts:UM" }, { "@id": "bts:Umol/l" }, { "@id": "bts:Units/ml" } ], "sms:displayName": "rnaBatchSizeUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SampleBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SampleBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sampleBatchID", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:SampleIntroduction", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SampleIntroduction", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sampleIntroduction", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SamplePrepProtocol", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SamplePrepProtocol", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "samplePrepProtocol", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SampleType", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SampleType", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sampleType", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SeqMethod", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SeqMethod", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "seqMethod", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SeqPlatform", "@type": "rdfs:Class", "rdfs:comment": "Sequencing platform information. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified", "rdfs:label": "SeqPlatform", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "seqPlatform", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SequencingBatchID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SequencingBatchID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sequencingBatchID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SequencingBatchSize", "@type": "rdfs:Class", "rdfs:comment": "The number of samples. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "SequencingBatchSize", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sequencingBatchSize", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SequencingBatchSizeUnit", "@type": "rdfs:Class", "rdfs:comment": "The unit of measurement for number of samples in a batch. Provide a value or Unknown Not collected Not applicable Not specified", "rdfs:label": "SequencingBatchSizeUnit", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sequencingBatchSizeUnit", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Sop", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "Sop", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sop", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SourceMatID", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "SourceMatID", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "sourceMatID", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SpeciesAge", "@type": "rdfs:Class", "rdfs:comment": "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.", "rdfs:label": "SpeciesAge", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "speciesAge", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:SpeciesGroup", "@type": "rdfs:Class", "rdfs:comment": "The taxonomic ranking including both species and subspecies the individual belongs to.", "rdfs:label": "SpeciesGroup", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Amphibian" }, { "@id": "bts:Bird" }, { "@id": "bts:Fish" }, { "@id": "bts:Invertebrate" }, { "@id": "bts:Mammal" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notspecified" }, { "@id": "bts:Reptile" }, { "@id": "bts:unknown" } ], "sms:displayName": "speciesGroup", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:Amphibian", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Amphibian", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Amphibian", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Bird", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Bird", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Bird", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Fish", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Fish", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Fish", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Invertebrate", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Invertebrate", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Invertebrate", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Mammal", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Mammal", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Mammal", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Reptile", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Reptile", "rdfs:subClassOf": [ { "@id": "bts:SpeciesGroup" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Reptile", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:SpeciesName", "@type": "rdfs:Class", "rdfs:comment": "The scientific name of the species (typically a taxonomic group, ex. \"Eremophila alpestris) the individual belongs to.\"\"\"", "rdfs:label": "SpeciesName", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Acomyscahirinus" }, { "@id": "bts:Acomysrussatus" }, { "@id": "bts:Accipitercooperii" }, { "@id": "bts:Actitismacularius" }, { "@id": "bts:Aixsponsa" }, { "@id": "bts:Anasacuta" }, { "@id": "bts:Anascarolinensis" }, { "@id": "bts:Anasplatyrhynchos" }, { "@id": 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"bts:Cygnusolor" }, { "@id": "bts:Dryobatespubescens" }, { "@id": "bts:Dumetellacarolinensis" }, { "@id": "bts:Ellobiuslutescens" }, { "@id": "bts:Ellobiustalpinus" }, { "@id": "bts:Eonycterisspelaea" }, { "@id": "bts:Eptesicusfuscus" }, { "@id": "bts:Equuscaballus" }, { "@id": "bts:Eremophilaalpestris" }, { "@id": "bts:Fukomysdamarensis" }, { "@id": "bts:Haemorhousmexicanus" }, { "@id": "bts:Heterocephalusglaber" }, { "@id": "bts:Hirundorustica" }, { "@id": "bts:Homosapiens" }, { "@id": "bts:Hydrochoerushydrochaeris" }, { "@id": "bts:Hydroprognecaspia" }, { "@id": "bts:Hylocichlamustelina" }, { "@id": "bts:Icteriavirens" }, { "@id": "bts:Larusargentatus" }, { "@id": "bts:Larusdelawarensis" }, { "@id": "bts:Macacafascicularis" }, { "@id": "bts:Macacamulatta" }, { "@id": "bts:Marecastrepera" }, { "@id": "bts:Marmotamonax" }, { "@id": "bts:Melanerpescarolinus" }, { "@id": "bts:Meleagrisgallopavo" }, { "@id": "bts:Melospizamelodia" }, { "@id": "bts:Merionesunguiculatus" }, { "@id": 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cahirinus", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Acomysrussatus", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Acomysrussatus", "rdfs:subClassOf": [ { "@id": "bts:SpeciesName" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Acomys russatus", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Accipitercooperii", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Accipitercooperii", "rdfs:subClassOf": [ { "@id": "bts:SpeciesName" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Accipiter cooperii", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Actitismacularius", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Actitismacularius", "rdfs:subClassOf": [ { "@id": "bts:SpeciesName" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Actitis macularius", "sms:required": 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Multiple values permitted, comma separated", "rdfs:label": "ToolDocumentationType", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDocumentationType", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolDocumentationUrl", "@type": "rdfs:Class", "rdfs:comment": "Link to documentation on the web for the tool", "rdfs:label": "ToolDocumentationUrl", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDocumentationUrl", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolDoi", "@type": "rdfs:Class", "rdfs:comment": "The Digital Object Identifier (DOI) associated with the computational tool", "rdfs:label": "ToolDoi", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDoi", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolDownloadNote", "@type": "rdfs:Class", "rdfs:comment": "Comment about the download", "rdfs:label": "ToolDownloadNote", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDownloadNote", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolDownloadType", "@type": "rdfs:Class", "rdfs:comment": "The type of data, information, or system that is obtained when the link is resolved", "rdfs:label": "ToolDownloadType", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDownloadType", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolDownloadUrl", "@type": "rdfs:Class", "rdfs:comment": "Link to download (or repo providing a download) for the software", "rdfs:label": "ToolDownloadUrl", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDownloadUrl", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolDownloadVersion", "@type": "rdfs:Class", "rdfs:comment": "Version information (typically a version number) of the software applicable to this download", "rdfs:label": "ToolDownloadVersion", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolDownloadVersion", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolEntityName", "@type": "rdfs:Class", "rdfs:comment": "Name of the entities that may be credited", "rdfs:label": "ToolEntityName", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolEntityName", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolEntityRole", "@type": "rdfs:Class", "rdfs:comment": "Role performed by entity that is credited e.g. Developer", "rdfs:label": "ToolEntityRole", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolEntityRole", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolEntityType", "@type": "rdfs:Class", "rdfs:comment": "Types of entities that may be credited e.g. Person", "rdfs:label": "ToolEntityType", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolEntityType", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolFunctionNote", "@type": "rdfs:Class", "rdfs:comment": "Concise comment about this function, if not apparent from the software description and EDAM annotations", "rdfs:label": "ToolFunctionNote", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolFunctionNote", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolHomepage", "@type": "rdfs:Class", "rdfs:comment": "Homepage of the software, or some URL that best serves this purpose", "rdfs:label": "ToolHomepage", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolHomepage", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolInputData", "@type": "rdfs:Class", "rdfs:comment": "Type of primary input data. Multiple values permitted, comma separated", "rdfs:label": "ToolInputData", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolInputData", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolInputFormat", "@type": "rdfs:Class", "rdfs:comment": "Allowed format(s) of the input data. Multiple values permitted, comma separated", "rdfs:label": "ToolInputFormat", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolInputFormat", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolLanguage", "@type": "rdfs:Class", "rdfs:comment": "Name of programming language the software source code was written in. Multiple values permitted, comma separated", "rdfs:label": "ToolLanguage", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolLanguage", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolLicense", "@type": "rdfs:Class", "rdfs:comment": "Software or data usage license. Multiple values permitted, comma separated", "rdfs:label": "ToolLicense", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolLicense", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolLinkNote", "@type": "rdfs:Class", "rdfs:comment": "Comment about the link", "rdfs:label": "ToolLinkNote", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolLinkNote", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolLinkType", "@type": "rdfs:Class", "rdfs:comment": "The type of data, information or system that is obtained when the link is resolved. Multiple values permitted, comma separated", "rdfs:label": "ToolLinkType", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolLinkType", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolLinkUrl", "@type": "rdfs:Class", "rdfs:comment": "A link of some relevance to the software (URL)", "rdfs:label": "ToolLinkUrl", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolLinkUrl", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolOperatingSystem", "@type": "rdfs:Class", "rdfs:comment": "The operating system supported by a downloadable software package. Multiple values permitted, comma separated", "rdfs:label": "ToolOperatingSystem", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolOperatingSystem", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolOperation", "@type": "rdfs:Class", "rdfs:comment": "The basic operation(s) performed by this software function. Multiple values permitted, comma separated", "rdfs:label": "ToolOperation", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolOperation", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolOutputData", "@type": "rdfs:Class", "rdfs:comment": "Type of primary output data. Multiple values permitted, comma separated", "rdfs:label": "ToolOutputData", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolOutputData", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolOutputFormat", "@type": "rdfs:Class", "rdfs:comment": "Allowed format(s) of the output data. Multiple values permitted, comma separated", "rdfs:label": "ToolOutputFormat", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolOutputFormat", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolPackageDependencies", "@type": "rdfs:Class", "rdfs:comment": "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", "rdfs:label": "ToolPackageDependencies", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolPackageDependencies", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolPackageDependenciesPresent", "@type": "rdfs:Class", "rdfs:comment": "Indicates whether the required package dependencies for tool are present", "rdfs:label": "ToolPackageDependenciesPresent", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolPackageDependenciesPresent", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolPubmedId", "@type": "rdfs:Class", "rdfs:comment": "The pubMed identifer associated with the development of the tool", "rdfs:label": "ToolPubmedId", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolPubmedId", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolReleaseDate", "@type": "rdfs:Class", "rdfs:comment": "The release date of a product or product model. This can be used to distinguish the exact variant of a product", "rdfs:label": "ToolReleaseDate", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolReleaseDate", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolTopic", "@type": "rdfs:Class", "rdfs:comment": "General scientific domain the software serves, or other general category. Multiple values permitted, comma separated", "rdfs:label": "ToolTopic", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolTopic", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:ToolType", "@type": "rdfs:Class", "rdfs:comment": "A type of application software: a discrete software entity can have more than one type. Multiple values permitted, comma separated", "rdfs:label": "ToolType", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolType", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:ToolVersion", "@type": "rdfs:Class", "rdfs:comment": "Version information (typically a version number) of the software applicable to this entry", "rdfs:label": "ToolVersion", "rdfs:subClassOf": [ { "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "toolVersion", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Ethnicity", "@type": "rdfs:Class", "rdfs:comment": "Ethnicity of individual", "rdfs:label": "Ethnicity", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:HispanicorLatino" }, { "@id": "bts:NotHispanicorLatino" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Otherethnicity" }, { "@id": "bts:Prefernottoanswer" }, { "@id": "bts:unknown" } ], "sms:displayName": "ethnicity", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:HispanicorLatino", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "HispanicorLatino", "rdfs:subClassOf": [ { "@id": "bts:Ethnicity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Hispanic or Latino", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:NotHispanicorLatino", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "NotHispanicorLatino", "rdfs:subClassOf": [ { "@id": "bts:Ethnicity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Not Hispanic or Latino", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Otherethnicity", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Otherethnicity", "rdfs:subClassOf": [ { "@id": "bts:Ethnicity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Other ethnicity", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Prefernottoanswer", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Prefernottoanswer", "rdfs:subClassOf": [ { "@id": "bts:Ethnicity" }, { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Prefer not to answer", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:FamilyStudyParticipant", "@type": "rdfs:Class", "rdfs:comment": "Indicates whether or not a file has data from a human participant involved in a family study (ex. LLFS)", "rdfs:label": "FamilyStudyParticipant", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Yes" }, { "@id": "bts:No" }, { "@id": "bts:NotAssigned" } ], "sms:displayName": "familyStudyParticipant", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Race", "@type": "rdfs:Class", "rdfs:comment": "Race of individual", "rdfs:label": "Race", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:AmericanIndianorAlaskaNative" }, { "@id": "bts:AshkenaziJewish" }, { "@id": "bts:Asian" }, { "@id": "bts:BlackorAfricanAmerican" }, { "@id": "bts:Multiracial" }, { "@id": "bts:NativeHawaiianorPacificIslander" }, { "@id": "bts:Notcollected" }, { "@id": "bts:Notapplicable" }, { "@id": "bts:Otherrace" }, { "@id": "bts:Prefernottoanswer" }, { "@id": "bts:unknown" }, { "@id": "bts:White" } ], "sms:displayName": "race", "sms:required": "sms:true", "sms:validationRules": [] }, { "@id": "bts:AmericanIndianorAlaskaNative", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "AmericanIndianorAlaskaNative", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "American Indian or Alaska Native", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:AshkenaziJewish", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "AshkenaziJewish", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Ashkenazi Jewish", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Asian", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Asian", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Asian", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:BlackorAfricanAmerican", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "BlackorAfricanAmerican", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Black or African American", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Multiracial", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Multiracial", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Multiracial", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:NativeHawaiianorPacificIslander", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "NativeHawaiianorPacificIslander", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Native Hawaiian or Pacific Islander", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Otherrace", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "Otherrace", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "Other race", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:White", "@type": "rdfs:Class", "rdfs:comment": "TBD", "rdfs:label": "White", "rdfs:subClassOf": [ { "@id": "bts:Race" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "sms:displayName": "White", "sms:required": "sms:false", "sms:validationRules": [] }, { "@id": "bts:Sex", "@type": "rdfs:Class", "rdfs:comment": "The biological sex of the individual", "rdfs:label": "Sex", "rdfs:subClassOf": [ { "@id": "bts:manifestColumn" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { "@id": "bts:Female" }, { "@id": "bts:Male" }, { "@id": "bts:Notapplicable" }, { "@id": 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