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The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.\n", - "rdfs:label" : "slideID", + "rdfs:comment" : "TBD", + "rdfs:label" : "BodyPartEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "slideID", + "sms:displayName" : "BodyPartEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:sourceName", + "@id" : "bts:UnknownEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Intended for non-biological samples, tf the sample is a nanoparticle sample or some chemical substance not derived from a biological material, the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.\n", - "rdfs:label" : "sourceName", + "rdfs:comment" : "TBD", + "rdfs:label" : "UnknownEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "sourceName", + "sms:displayName" : "UnknownEnum", "sms:required" : "sms:false" }, { - 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"rdfs:comment" : "Size of file in bytes.", - "rdfs:label" : "fileSize", + "rdfs:comment" : "TBD", + "rdfs:label" : "SpecimenPreparationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "fileSize", + "sms:displayName" : "SpecimenPreparationMethodEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:DataSubtypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DataSubtypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:dermalSchwannoma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "dermalSchwannoma", - "rdfs:comment" : "Characterization of the manifestation of Dermal schwannoma.", - "@type" : "rdfs:Class", - "sms:displayName" : "dermalSchwannoma" + "sms:displayName" : "DataSubtypeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:benefactorId", + "@id" : "bts:FileFormatEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "The id of the resource from which access control is inherited.", - "rdfs:label" : "benefactorId", + "rdfs:comment" : "TBD", + "rdfs:label" : "FileFormatEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "benefactorId", + "sms:displayName" : "FileFormatEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:MultipleImagingDiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with one or multiple sites being the most relevant result.", + "rdfs:label" : "MultipleImagingDiagnosisEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:spinalSchwannoma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:notimaged" - }, { - "@id" : "bts:absentbyimaging" - }, { - "@id" : "bts:single" - }, { - "@id" : "bts:multiple" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "spinalSchwannoma", - "rdfs:comment" : "Characterization of the manifestation of Spinal schwannoma.", - "@type" : "rdfs:Class", - "sms:displayName" : "spinalSchwannoma" + "sms:displayName" : "MultipleImagingDiagnosisEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:SexEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SexEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:accessType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:PublicAccess" - }, { - "@id" : "bts:OpenAccess" - }, { - "@id" : "bts:ControlledAccess" - } ], - "rdfs:label" : "accessType", - "rdfs:comment" : "Indicates access type / possible procedures needed for access to the resource.", - "@type" : "rdfs:Class", - "sms:displayName" : "accessType" + "sms:displayName" : "SexEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:MRISequenceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MRISequenceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:spinalNeurofibromas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:notimaged" - }, { - "@id" : "bts:absent" - }, { - "@id" : "bts:levels1-3" - }, { - "@id" : "bts:alllevels" - } ], - "rdfs:label" : "spinalNeurofibromas", - "rdfs:comment" : "Characterization of the manifestation of Spinal neurofibromas.", - "@type" : "rdfs:Class", - "sms:displayName" : "spinalNeurofibromas" + "sms:displayName" : "MRISequenceEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:AgeGroupEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AgeGroupEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:opticGlioma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present-asymptomatic" - }, { - "@id" : "bts:present-symptomatic-nottreated" - }, { - "@id" : "bts:present-symptomatic-treated" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "opticGlioma", - "rdfs:comment" : "Characterization of the manifestation of Optic glioma.", - "@type" : "rdfs:Class", - "sms:displayName" : "opticGlioma" + "sms:displayName" : "AgeGroupEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:createdOn", + "@id" : "bts:TumorTreatmentEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to when the resource was created.", - "rdfs:label" : "createdOn", + "rdfs:comment" : "TBD", + "rdfs:label" : "TumorTreatmentEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdOn", + "sms:displayName" : "TumorTreatmentEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:protocolPurpose", + "@id" : "bts:PlatformEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Brief description of the protocol purpose.", - "rdfs:label" : "protocolPurpose", + "rdfs:comment" : "TBD", + "rdfs:label" : "PlatformEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "protocolPurpose", + "sms:displayName" : "PlatformEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:NF1Variant", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "NF1Variant", "rdfs:subClassOf" : [ ], - "@id" : "bts:grantDOI", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "grantDOI", - "rdfs:comment" : "Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity.", - "@type" : "rdfs:Class", - "sms:displayName" : "grantDOI" + "sms:displayName" : "NF1Variant", + "sms:required" : "sms:false" }, { + "@id" : "bts:GenePerturbationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GenePerturbationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:breastCancer", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "breastCancer", - "rdfs:comment" : "Characterization of the manifestation of Breast cancer.", - "@type" : "rdfs:Class", - "sms:displayName" : "breastCancer" + "sms:displayName" : "GenePerturbationEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:reporterSubstance", + "@id" : "bts:TestSummaryEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.", - "rdfs:label" : "reporterSubstance", + "rdfs:comment" : "TBD", + "rdfs:label" : "TestSummaryEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterSubstance", + "sms:displayName" : "TestSummaryEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:SpinalNeuromaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of spinal neurofibromas, combining information on presence and the cervical locations.", + "rdfs:label" : "SpinalNeuromaManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:slideVersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:V1" - }, { - "@id" : "bts:V2" - }, { - "@id" : "bts:V3" - }, { - "@id" : "bts:V4" - } ], - "rdfs:label" : "slideVersion", - "rdfs:comment" : "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "@type" : "rdfs:Class", - "sms:displayName" : "slideVersion" + "sms:displayName" : "SpinalNeuromaManifestationEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:reporterGene", + "@id" : "bts:WorkflowEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.", - "rdfs:label" : "reporterGene", + "rdfs:comment" : "TBD", + "rdfs:label" : "WorkflowEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterGene", + "sms:displayName" : "WorkflowEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:BooleanEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Boolean data as Yes/No enums", + "rdfs:label" : "BooleanEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:nf1Genotype", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:-/-" - }, { - "@id" : "bts:+/-" - }, { - "@id" : "bts:+/+" - }, { - "@id" : "bts:Unknown" - }, { - "@id" : "bts:Unknown" - } ], - "rdfs:label" : "nf1Genotype", - "rdfs:comment" : "Genotype of NF1 gene in the biospecimen from which the data were derived, if known.", - "@type" : "rdfs:Class", - "sms:displayName" : "nf1Genotype" + "sms:displayName" : "BooleanEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:PubertyOnsetEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PubertyOnsetEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:diagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Neurofibromatosistype1" - }, { - "@id" : "bts:Schwannomatosis" - }, { - "@id" : "bts:NF2-relatedschwannomatosis" - }, { - "@id" : "bts:SMARCB1-relatedschwannomatosis" - }, { - "@id" : "bts:LZTR1-relatedschwannomatosis" - }, { - "@id" : "bts:22q-relatedschwannomatosis" - }, { - "@id" : "bts:Schwannomatosis-NOS" - }, { - "@id" : "bts:Schwannomatosis-NEC" - }, { - "@id" : "bts:SporadicSchwannoma" - } ], - "rdfs:label" : "diagnosis", - "rdfs:comment" : "Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.", - "@type" : "rdfs:Class", - "sms:displayName" : "diagnosis" + "sms:displayName" : "PubertyOnsetEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:targetDepth", - "@type" : "rdfs:Class", - "rdfs:comment" : "The targeted read depth prior to sequencing.", - "rdfs:label" : "targetDepth", + "@id" : "bts:GenePerturbationMethodEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GenePerturbationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "targetDepth", + "sms:displayName" : "GenePerturbationMethodEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:accessRequirements", + "@id" : "bts:Data", "@type" : "rdfs:Class", - "rdfs:comment" : "Statement describing access requirements for an entity.", - "rdfs:label" : "accessRequirements", + "rdfs:comment" : "TBD", + "rdfs:label" : "Data", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "accessRequirements", + "sms:displayName" : "Data", "sms:required" : "sms:false" }, { + "@id" : "bts:PlexiformNeurofibromaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of plexiform neurofibromas, combining information on presence and the certainty via MRI imaging technique.", + "rdfs:label" : "PlexiformNeurofibromaManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:creator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "creator", - "rdfs:comment" : "An entity responsible for making the resource.", - "@type" : "rdfs:Class", - "sms:displayName" : "creator" + "sms:displayName" : "PlexiformNeurofibromaManifestationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:BinaryImagingDiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with mainly absent or present being the most relevant result.", + "rdfs:label" : "BinaryImagingDiagnosisEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:age", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "age", - "rdfs:comment" : "A numeric value representing age of the individual. Use with `ageUnit`.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:ageUnit" - } ], - "sms:displayName" : "age" + "sms:displayName" : "BinaryImagingDiagnosisEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:SpeciesEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SpeciesEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:isCellLine", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isCellLine", - "rdfs:comment" : "Whether or not sample source is a cell line (Yes; No)", - "@type" : "rdfs:Class", - "sms:displayName" : "isCellLine" + "sms:displayName" : "SpeciesEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:DiagnosisEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryPreparationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:10x" - }, { - "@id" : "bts:CEL-seq" - }, { - "@id" : "bts:Drop-Seq" - }, { - "@id" : "bts:GTAC@WUSTLin-houseprep" - }, { - "@id" : "bts:IDTxGenExomeResearchPanel" - }, { - "@id" : "bts:IlluminaTruSeqDNANano" - }, { - "@id" : "bts:IlluminaTn5Transposase" - }, { - "@id" : "bts:KAPAHyperPrepKitPCR-free" - }, { - "@id" : "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)" - }, { - "@id" : "bts:KAPAmRNAHyperPrepKit" - }, { - "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" - }, { - "@id" : "bts:Omni-ATAC" - }, { - "@id" : "bts:QuantSeqFWDV2withUDI" - }, { - "@id" : "bts:Smart-seq2" - }, { - "@id" : "bts:Smart-seq4" - }, { - "@id" : "bts:TruSeq" - }, { - "@id" : "bts:TruSeqstandardtotalRNAlibrarykit" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "libraryPreparationMethod", - "rdfs:comment" : "Method by which library was prepared", - "@type" : "rdfs:Class", - "sms:displayName" : "libraryPreparationMethod" + "sms:displayName" : "DiagnosisEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:ProteinExtractSourceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ProteinExtractSourceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:publisher", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "publisher", - "rdfs:comment" : "An entity responsible for making the resource available.", - "@type" : "rdfs:Class", - "sms:displayName" : "publisher" + "sms:displayName" : "ProteinExtractSourceEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:averageBaseQuality", + "@id" : "bts:VitalStatusEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Average base quality collected from samtools", - "rdfs:label" : "averageBaseQuality", + "rdfs:comment" : "TBD", + "rdfs:label" : "VitalStatusEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "averageBaseQuality", + "sms:displayName" : "VitalStatusEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:MosaicismEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MosaicismEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:sex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Male" - }, { - "@id" : "bts:Female" - }, { - "@id" : "bts:Unknown" - }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "sex", - "rdfs:comment" : "Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.", - "@type" : "rdfs:Class", - "sms:displayName" : "sex" + "sms:displayName" : "MosaicismEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:createdBy", + "@id" : "bts:WorkingDistanceUnitEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to the user who created the resource.", - "rdfs:label" : "createdBy", + "rdfs:comment" : "TBD", + "rdfs:label" : "WorkingDistanceUnitEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdBy", + "sms:displayName" : "WorkingDistanceUnitEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:StrandednessEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "StrandednessEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:otherTumors", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "otherTumors", - "rdfs:comment" : "Characterization of the manifestation of other tumors.", - "@type" : "rdfs:Class", - "sms:displayName" : "otherTumors" + "sms:displayName" : "StrandednessEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:OrganismSubstance", + "@type" : "rdfs:Class", + "rdfs:comment" : "This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens.", + "rdfs:label" : "OrganismSubstance", "rdfs:subClassOf" : [ ], - "@id" : "bts:genePerturbationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "genePerturbationType", - "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", - "@type" : "rdfs:Class", - "sms:displayName" : "genePerturbationType" + "sms:displayName" : "OrganismSubstance", + "sms:required" : "sms:false" }, { + "@id" : "bts:BiologicalProcess", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BiologicalProcess", "rdfs:subClassOf" : [ ], - "@id" : "bts:painStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:notaproblem" - }, { - "@id" : "bts:occasional" - }, { - "@id" : "bts:disabling" - } ], - "rdfs:label" : "painStatus", - "rdfs:comment" : "Pain status rating.", - "@type" : "rdfs:Class", - "sms:displayName" : "painStatus" + "sms:displayName" : "BiologicalProcess", + "sms:required" : "sms:false" }, { + "@id" : "bts:ExpressionUnitEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Quantification units for gene expression.", + "rdfs:label" : "ExpressionUnitEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:compoundDose", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "rdfs:label" : "compoundDose", - "rdfs:comment" : "A dose quantity for the treatment compound. To be used with compoundDoseUnit.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:compoundDoseUnit" - } ], - "sms:displayName" : "compoundDose" + "sms:displayName" : "ExpressionUnitEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:OrganEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "OrganEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readDepth", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "readDepth", - "rdfs:comment" : "If available, the coverage statistic as output from bedtools coverage or samtools stats.", - "@type" : "rdfs:Class", - "sms:displayName" : "readDepth" + "sms:displayName" : "OrganEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:InChIKey", + "@id" : "bts:Tumor", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). This is a more reliable identifier than the compound name and should be used if available.\n", - "rdfs:label" : "InChIKey", + "rdfs:comment" : "TBD", + "rdfs:label" : "Tumor", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "InChIKey", + "sms:displayName" : "Tumor", "sms:required" : "sms:false" }, { + "@id" : "bts:WHOPerformanceStatusScores", + "@type" : "rdfs:Class", + "rdfs:comment" : "https://www.ncbi.nlm.nih.gov/books/NBK97482/", + "rdfs:label" : "WHOPerformanceStatusScores", "rdfs:subClassOf" : [ ], - "@id" : "bts:concentrationMaterial", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "concentrationMaterial", - "rdfs:comment" : "Numeric value for concentration of the material", - "@type" : "rdfs:Class", - "sms:displayName" : "concentrationMaterial" + "sms:displayName" : "WHOPerformanceStatusScores", + "sms:required" : "sms:false" }, { - "@id" : "bts:fileCount", + "@id" : "bts:ConcentrationUnit", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of files in the resource collection.", - "rdfs:label" : "fileCount", + "rdfs:comment" : "TBD", + "rdfs:label" : "ConcentrationUnit", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "fileCount", + "sms:displayName" : "ConcentrationUnit", "sms:required" : "sms:false" }, { - "@id" : "bts:assayTarget", + "@id" : "bts:NucleicAcidSourceEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Target of the assay such as a HUGO gene symbol, cell type, or tissue region depending on the capabilities of the assay.", - "rdfs:label" : "assayTarget", + "rdfs:comment" : "TBD", + "rdfs:label" : "NucleicAcidSourceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "assayTarget", + "sms:displayName" : "NucleicAcidSourceEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:ReadPairOrientationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReadPairOrientationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:license", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "license", - "rdfs:comment" : "Link to a license or name of license applicable for the resource.", - "@type" : "rdfs:Class", - "sms:displayName" : "license" + "sms:displayName" : "ReadPairOrientationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:LateralManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging (MRI or other), where lateral information is most relevant.", + "rdfs:label" : "LateralManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readLength", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "readLength", - "rdfs:comment" : "Number of base pairs (bp) sequenced for a read", - "@type" : "rdfs:Class", - "sms:displayName" : "readLength" + "sms:displayName" : "LateralManifestationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:LibraryPrepEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryPrepEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:tumorTreatmentStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:nospecifictherapy" - }, { - "@id" : "bts:chemotherapy" - }, { - "@id" : "bts:surgery" - }, { - "@id" : "bts:radiation" - }, { - "@id" : "bts:targetedtherapy" - }, { - "@id" : "bts:clinicaltrial" - } ], - "rdfs:label" : "tumorTreatmentStatus", - "rdfs:comment" : "Tumor treatment status for the individual.", - "@type" : "rdfs:Class", - "sms:displayName" : "tumorTreatmentStatus" + "sms:displayName" : "LibraryPrepEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Percentiles-2SD", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations corresponding to 3 bins using 2 standard deviations as a cutoff.", + "rdfs:label" : "Percentiles-2SD", "rdfs:subClassOf" : [ ], - "@id" : "bts:studyId", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "studyId", - "rdfs:comment" : "Id of study.", - "@type" : "rdfs:Class", - "sms:displayName" : "studyId" + "sms:displayName" : "Percentiles-2SD", + "sms:required" : "sms:false" }, { - "@id" : "bts:Filename", + "@id" : "bts:Tissue", "@type" : "rdfs:Class", - "rdfs:comment" : "The name of the file.", - "rdfs:label" : "Filename", + "rdfs:comment" : "Tissue is a group of cells that have similar structure and that function together as a unit.", + "rdfs:label" : "Tissue", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Filename", + "sms:displayName" : "Tissue", "sms:required" : "sms:false" }, { + "@id" : "bts:LibraryPreparationMethodEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryPreparationMethodEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:diffuseDermalNeurofibromas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:scattered" - }, { - "@id" : "bts:dense" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "diffuseDermalNeurofibromas", - "rdfs:comment" : "Characterization of the manifestation of Diffuse dermal neurofibromas.", - "@type" : "rdfs:Class", - "sms:displayName" : "diffuseDermalNeurofibromas" + "sms:displayName" : "LibraryPreparationMethodEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:StudyStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "StudyStatusEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readStrandOrigin", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:forward" - }, { - "@id" : "bts:reverse" - } ], - "rdfs:label" : "readStrandOrigin", - "rdfs:comment" : "The strand from which the read originates in a strand-specific protocol", - "@type" : "rdfs:Class", - "sms:displayName" : "readStrandOrigin" + "sms:displayName" : "StudyStatusEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Metadata", + "@type" : "rdfs:Class", + "rdfs:comment" : "Data that provides information about other data", + "rdfs:label" : "Metadata", "rdfs:subClassOf" : [ ], - "@id" : "bts:series", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "series", - "rdfs:comment" : "Title of a custom series that this resource is part of, if any.", - "@type" : "rdfs:Class", - "sms:displayName" : "series" + "sms:displayName" : "Metadata", + "sms:required" : "sms:false" }, { + "@id" : "bts:DiseaseFocusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiseaseFocusEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:ageUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:seconds" - }, { - "@id" : "bts:minutes" - }, { - "@id" : "bts:hours" - }, { - "@id" : "bts:days" - }, { - "@id" : "bts:weeks" - }, { - "@id" : "bts:months" - }, { - "@id" : "bts:years" - } ], - "rdfs:label" : "ageUnit", - "rdfs:comment" : "A time unit that can be used with a given age value, e.g. years.", - "@type" : "rdfs:Class", - "sms:displayName" : "ageUnit" + "sms:displayName" : "DiseaseFocusEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:ChannelEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ChannelEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:progressReportNumber", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:1" - }, { - "@id" : "bts:2" - }, { - "@id" : "bts:3" - }, { - "@id" : "bts:4" - }, { - "@id" : "bts:5" - }, { - "@id" : "bts:6" - }, { - "@id" : "bts:7" - }, { - "@id" : "bts:8" - }, { - "@id" : "bts:9" - }, { - "@id" : "bts:10" - }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "progressReportNumber", - "rdfs:comment" : "Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1", - "@type" : "rdfs:Class", - "sms:displayName" : "progressReportNumber" + "sms:displayName" : "ChannelEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:FundingAgencyEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "FundingAgencyEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:specimenPreparationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:Freshcollected" - }, { - "@id" : "bts:Flashfrozen" - }, { - "@id" : "bts:FFPE" - }, { - "@id" : "bts:Cryopreserved" - }, { - "@id" : "bts:OCT" - }, { - "@id" : "bts:RNAlater" - }, { - "@id" : "bts:formalin-fixed" - }, { - "@id" : "bts:ethanol" - }, { - "@id" : "bts:Viablyfrozen" - } ], - "rdfs:label" : "specimenPreparationMethod", - "rdfs:comment" : "Term that represents preservation of the sample before usage in, e.g. sequencing", - "@type" : "rdfs:Class", - "sms:displayName" : "specimenPreparationMethod" + "sms:displayName" : "FundingAgencyEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Cell", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Cell", "rdfs:subClassOf" : [ ], - "@id" : "bts:isMultiIndividual", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isMultiIndividual", - "rdfs:comment" : "Whether or not a file has data for multiple individuals (Yes; No)", + "sms:displayName" : "Cell", + "sms:required" : "sms:false" + }, { + "@id" : "bts:GenomicReferenceEnum", "@type" : "rdfs:Class", - "sms:displayName" : "isMultiIndividual" + "rdfs:comment" : "TBD", + "rdfs:label" : "GenomicReferenceEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "GenomicReferenceEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:Genotype", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Genotype", "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryStrand", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:FirstStranded" - }, { - "@id" : "bts:SecondStranded" - }, { - "@id" : "bts:Unstranded" - }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "libraryStrand", - "rdfs:comment" : "Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.", - "@type" : "rdfs:Class", - "sms:displayName" : "libraryStrand" + "sms:displayName" : "Genotype", + "sms:required" : "sms:false" }, { + "@id" : "bts:DrugScreen", + "@type" : "rdfs:Class", + "rdfs:comment" : "This is a subset of Assay enum above.", + "rdfs:label" : "DrugScreen", "rdfs:subClassOf" : [ ], - "@id" : "bts:GIST", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "GIST", - "rdfs:comment" : "Characterization of the manifestation of Gastrointestinal stromal tumor (GIST).", - "@type" : "rdfs:Class", - "sms:displayName" : "GIST" + "sms:displayName" : "DrugScreen", + "sms:required" : "sms:false" }, { + "@id" : "bts:DissociationMethodEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DissociationMethodEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:immersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:air" - }, { - "@id" : "bts:oil" - }, { - "@id" : "bts:water" - }, { - "@id" : "bts:other" - } ], - "rdfs:label" : "immersion", - "rdfs:comment" : "Immersion medium", - "@type" : "rdfs:Class", - "sms:displayName" : "immersion" + "sms:displayName" : "DissociationMethodEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:TimeUnit", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TimeUnit", "rdfs:subClassOf" : [ ], - "@id" : "bts:captureArea", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:A" - }, { - "@id" : "bts:B" - }, { - "@id" : "bts:C" - }, { - "@id" : "bts:D" - }, { - "@id" : "bts:A1" - }, { - "@id" : "bts:B1" - }, { - "@id" : "bts:C1" - }, { - "@id" : "bts:D1" - } ], - "rdfs:label" : "captureArea", - "rdfs:comment" : "One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.\n", - "@type" : "rdfs:Class", - "sms:displayName" : "captureArea" + "sms:displayName" : "TimeUnit", + "sms:required" : "sms:false" }, { + "@id" : "bts:Measurement", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Measurement", "rdfs:subClassOf" : [ ], - "@id" : "bts:experimentalFactor", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:braingrowthmeasurement" - }, { - "@id" : "bts:brainvolumemeasurement" - }, { - "@id" : "bts:bodyweight" - }, { - "@id" : "bts:clinicallaboratorymeasurement" - }, { - "@id" : "bts:cognitivefunctionmeasurement" - }, { - "@id" : "bts:gaitmeasurement" - }, { - "@id" : "bts:motordevelopmentmeasurement" - }, { - "@id" : "bts:painmeasurement" - } ], - "rdfs:label" : "experimentalFactor", - "rdfs:comment" : "An ontology concept for experimental factor measured with this data.", - "@type" : "rdfs:Class", - "sms:displayName" : "experimentalFactor" + "sms:displayName" : "Measurement", + "sms:required" : "sms:false" }, { + "@id" : "bts:Material", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Material", "rdfs:subClassOf" : [ ], - "@id" : "bts:stature", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:<5thcentile" - }, { - "@id" : "bts:5th-95thcentile" - }, { - "@id" : "bts:>95thcentile" - } ], - "rdfs:label" : "stature", - "rdfs:comment" : "Stature of the individual.", - "@type" : "rdfs:Class", - "sms:displayName" : "stature" + "sms:displayName" : "Material", + "sms:required" : "sms:false" }, { + "@id" : "bts:ManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:readPair", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "inRange 1 2" ], - "rdfs:label" : "readPair", - "rdfs:comment" : "The read of origin, Read 1 or Read 2", - "@type" : "rdfs:Class", - "sms:displayName" : "readPair" + "sms:displayName" : "ManifestationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:SchwannomaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of schwannomas.", + "rdfs:label" : "SchwannomaManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:workingDistanceUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:angstrom" - }, { - "@id" : "bts:nanometer" - }, { - "@id" : "bts:micrometer" - }, { - "@id" : "bts:millimeter" - }, { - "@id" : "bts:centimeter" - } ], - "rdfs:label" : "workingDistanceUnit", - "rdfs:comment" : "Unit for working distance.", - "@type" : "rdfs:Class", - "sms:displayName" : "workingDistanceUnit" + "sms:displayName" : "SchwannomaManifestationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:OpticGliomaManifestationEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "Enumerations describing the manifestation of optic gliomas, combining information on presence, symptoms, and treatment.", + "rdfs:label" : "OpticGliomaManifestationEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:nonopticGlioma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "nonopticGlioma", - "rdfs:comment" : "Characterization of the manifestation of Nonoptic glioma.", - "@type" : "rdfs:Class", - "sms:displayName" : "nonopticGlioma" + "sms:displayName" : "OpticGliomaManifestationEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:TransplantationType", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TransplantationType", "rdfs:subClassOf" : [ ], - "@id" : "bts:germlineMutationIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:nottested" - }, { - "@id" : "bts:testedbutunknown" - } ], - "rdfs:label" : "germlineMutationIndicator", - "rdfs:comment" : "Indicates a summary testing result for individual's germline mutation only.", - "@type" : "rdfs:Class", - "sms:displayName" : "germlineMutationIndicator" + "sms:displayName" : "TransplantationType", + "sms:required" : "sms:false" }, { - "@id" : "bts:antibodyID", + "@id" : "bts:RunTypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Antibody ID such as RRID if available, otherwise use vendor ID.", - "rdfs:label" : "antibodyID", + "rdfs:comment" : "TBD", + "rdfs:label" : "RunTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "antibodyID", + "sms:displayName" : "RunTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:specimenIDSource", + "@id" : "bts:NotApplicableEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.", - "rdfs:label" : "specimenIDSource", + "rdfs:comment" : "TBD", + "rdfs:label" : "NotApplicableEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "specimenIDSource", + "sms:displayName" : "NotApplicableEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:CellLineModel", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CellLineModel", "rdfs:subClassOf" : [ ], - "@id" : "bts:vestibularSchwannoma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:notimaged" - }, { - "@id" : "bts:absentbyimaging" - }, { - "@id" : "bts:unilateral" - }, { - "@id" : "bts:bilateral" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "vestibularSchwannoma", - "rdfs:comment" : "Characterization of the manifestation of Vestibular schwannoma.", - "@type" : "rdfs:Class", - "sms:displayName" : "vestibularSchwannoma" + "sms:displayName" : "CellLineModel", + "sms:required" : "sms:false" }, { + "@id" : "bts:Resource", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Resource", "rdfs:subClassOf" : [ ], - "@id" : "bts:isPairedEnd", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - } ], - "rdfs:label" : "isPairedEnd", - "rdfs:comment" : "(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).", - "@type" : "rdfs:Class", - "sms:displayName" : "isPairedEnd" + "sms:displayName" : "Resource", + "sms:required" : "sms:false" }, { + "@id" : "bts:MouseModel", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "MouseModel", "rdfs:subClassOf" : [ ], - "@id" : "bts:numberOfSchwannomas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:single" - }, { - "@id" : "bts:scattered" - }, { - "@id" : "bts:dense" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "numberOfSchwannomas", - "rdfs:comment" : "Number of schwannomas.", - "@type" : "rdfs:Class", - "sms:displayName" : "numberOfSchwannomas" + "sms:displayName" : "MouseModel", + "sms:required" : "sms:false" }, { + "@id" : "bts:AssayEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AssayEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:dataStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:DataNotExpected" - }, { - "@id" : "bts:DataPending" - }, { - "@id" : "bts:UnderEmbargo" - }, { - "@id" : "bts:RollingRelease" - }, { - "@id" : "bts:PartiallyAvailable" - }, { - "@id" : "bts:Available" - } ], - "rdfs:label" : "dataStatus", - "rdfs:comment" : "Overall status of data in a study.", - "@type" : "rdfs:Class", - "sms:displayName" : "dataStatus" + "sms:displayName" : "AssayEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:contentSize", + "@id" : "bts:CuratedDataEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "(Files only) File size, usually calculated by the backend.", - "rdfs:label" : "contentSize", + "rdfs:comment" : "TBD", + "rdfs:label" : "CuratedDataEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "contentSize", + "sms:displayName" : "CuratedDataEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:targetCaptureKitID", + "@id" : "bts:NonvestibularSchwannomaManifestationEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.\n", - "rdfs:label" : "targetCaptureKitID", + "rdfs:comment" : "TBD", + "rdfs:label" : "NonvestibularSchwannomaManifestationEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "targetCaptureKitID", + "sms:displayName" : "NonvestibularSchwannomaManifestationEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:aliquotID", + "@id" : "bts:DataStatusEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.", - "rdfs:label" : "aliquotID", + "rdfs:comment" : "TBD", + "rdfs:label" : "DataStatusEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "aliquotID", + "sms:displayName" : "DataStatusEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:Institution", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Institution", "rdfs:subClassOf" : [ ], - "@id" : "bts:initiative", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "initiative", - "rdfs:comment" : "Refers to a funding initiative. Typically handled by the DCC.", - "@type" : "rdfs:Class", - "sms:displayName" : "initiative" + "sms:displayName" : "Institution", + "sms:required" : "sms:false" }, { + "@id" : "bts:ReadStrandOriginEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReadStrandOriginEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:nominalMagnification", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "nominalMagnification", - "rdfs:comment" : "magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens.", - "@type" : "rdfs:Class", - "sms:displayName" : "nominalMagnification" + "sms:displayName" : "ReadStrandOriginEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:PainEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PainEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:genePerturbationTechnology", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:RNAi" - }, { - "@id" : "bts:CRISPR" - }, { - "@id" : "bts:CRERecombinase" - } ], - "rdfs:label" : "genePerturbationTechnology", - "rdfs:comment" : "Technology used to perturb gene", - "@type" : "rdfs:Class", - "sms:displayName" : "genePerturbationTechnology" + "sms:displayName" : "PainEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:relatedResource", + "@id" : "bts:License", "@type" : "rdfs:Class", - "rdfs:comment" : "A related resource.", - "rdfs:label" : "relatedResource", + "rdfs:comment" : "License attached to the data. If indicates UNKNOWN or RESTRICTED-USE, data may not be used without further contact for terms.", + "rdfs:label" : "License", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "relatedResource", + "sms:displayName" : "License", "sms:required" : "sms:false" }, { - "@id" : "bts:specimenID", + "@id" : "bts:PresenceEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen.\n", - "rdfs:label" : "specimenID", + "rdfs:comment" : "Enumeration for binary + unknown for very basic classification of a manifestation in clinical context.", + "rdfs:label" : "PresenceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "specimenID", - "sms:required" : "sms:true" + "sms:displayName" : "PresenceEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:comments", + "@id" : "bts:NeurofibromaManifestationEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Brief free-text comments that may also be important to understanding the resource.", - "rdfs:label" : "comments", + "rdfs:comment" : "Enumerations describing how neurofibromas can manifest more generally.", + "rdfs:label" : "NeurofibromaManifestationEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "comments", + "sms:displayName" : "NeurofibromaManifestationEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:InheritanceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "InheritanceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:fileFormat", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:7z" - }, { - "@id" : "bts:DICOM" - }, { - "@id" : "bts:MATLABdata" - }, { - "@id" : "bts:MATLABscript" - }, { - "@id" : "bts:NWB" - }, { - "@id" : "bts:PAR" - }, { - "@id" : "bts:Pythonscript" - }, { - "@id" : "bts:Rscript" - }, { - "@id" : "bts:RData" - }, { - "@id" : "bts:REC" - }, { - "@id" : "bts:SDAT" - }, { - "@id" : "bts:SPAR" - }, { - "@id" : "bts:Sentrixdescriptorfile" - }, { - "@id" : "bts:ab1" - }, { - "@id" : "bts:abf" - }, { - "@id" : "bts:ai" - }, { - "@id" : "bts:avi" - }, { - "@id" : "bts:bai" - }, { - "@id" : "bts:bam" - }, { - "@id" : "bts:bashscript" - }, { - "@id" : "bts:bcf" - }, { - "@id" : "bts:bed" - }, { - "@id" : "bts:bedbroadPeak" - }, { - "@id" : "bts:bedgappedPeak" - }, { - "@id" : "bts:bednarrowPeak" - }, { - "@id" : "bts:bedgraph" - }, { - "@id" : "bts:bgzip" - }, { - "@id" : "bts:bigwig" - }, { - "@id" : "bts:bpm" - }, { - "@id" : "bts:cel" - }, { - "@id" : "bts:chp" - }, { - "@id" : "bts:cnn" - }, { - "@id" : "bts:cnr" - }, { - "@id" : "bts:cns" - }, { - "@id" : "bts:cram" - }, { - "@id" : "bts:crai" - }, { - "@id" : "bts:csi" - }, { - "@id" : "bts:csv" - }, { - "@id" : "bts:ctab" - }, { - "@id" : "bts:czi" - }, { - "@id" : "bts:dat" - }, { - "@id" : "bts:doc" - }, { - "@id" : "bts:dockerimage" - }, { - "@id" : "bts:dup" - }, { - "@id" : "bts:excel" - }, { - "@id" : "bts:fasta" - }, { - "@id" : "bts:fastq" + }, + "sms:displayName" : "InheritanceEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AccessTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AccessTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AccessTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:GenePerturbationTechnologyEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "GenePerturbationTechnologyEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "GenePerturbationTechnologyEnum", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:ProteinAssayTemplate" + } ], + "@id" : "bts:MassSpecAssayTemplate", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "MassSpecAssayTemplate", + "rdfs:comment" : "Template for raw mass spec-based proteomics data.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:fcs" + "@id" : "bts:Filename" }, { - "@id" : "bts:fig" + "@id" : "bts:fileFormat" }, { - "@id" : "bts:flagstat" + "@id" : "bts:resourceType" }, { - "@id" : "bts:gct" + "@id" : "bts:dataType" }, { - "@id" : "bts:gff3" + "@id" : "bts:dataSubtype" }, { - "@id" : "bts:gtf" + "@id" : "bts:assay" }, { - "@id" : "bts:gzip" + "@id" : "bts:individualID" }, { - "@id" : "bts:hdf5" + "@id" : "bts:species" }, { - "@id" : "bts:hdr" + "@id" : "bts:sex" }, { - "@id" : "bts:hic" + "@id" : "bts:age" }, { - "@id" : "bts:html" + "@id" : "bts:ageUnit" }, { - "@id" : "bts:hyperlink" + "@id" : "bts:diagnosis" }, { - "@id" : "bts:idat" + "@id" : "bts:nf1Genotype" }, { - "@id" : "bts:idx" + "@id" : "bts:nf2Genotype" }, { - "@id" : "bts:img" + "@id" : "bts:tumorType" }, { - "@id" : "bts:jpg" + "@id" : "bts:modelSystemName" }, { - "@id" : "bts:js" + "@id" : "bts:organ" }, { - "@id" : "bts:json" + "@id" : "bts:comments" }, { - "@id" : "bts:locs" + "@id" : "bts:parentSpecimenID" }, { - "@id" : "bts:maf" + "@id" : "bts:specimenID" }, { - "@id" : "bts:md" + "@id" : "bts:aliquotID" }, { - "@id" : "bts:mov" + "@id" : "bts:platform" }, { - "@id" : "bts:msf" + "@id" : "bts:proteinExtractSource" }, { - "@id" : "bts:mtx" + "@id" : "bts:dataCollectionMode" + } ], + "sms:displayName" : "MassSpecAssayTemplate" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:BiologicalAssayDataTemplate" + } ], + "@id" : "bts:ClinicalAssayTemplate", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "ClinicalAssayTemplate", + "rdfs:comment" : "General template for typically tabular **individual-level** data. 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"schema:rangeIncludes" : [ ], - "rdfs:label" : "manifestation", - "rdfs:comment" : "An associated phenotype characteristic.", + "sms:requiresComponent" : "", + "rdfs:label" : "GeneralMeasureDataTemplate", + "rdfs:comment" : "General template for data in tabular form that aggregates tissue-level or cellular-level data.\n", "@type" : "rdfs:Class", - "sms:displayName" : "manifestation" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:aqueductalStenosis", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:present" + "@id" : "bts:Filename" }, { - "@id" : "bts:unknown" + "@id" : "bts:fileFormat" + }, { + "@id" : "bts:resourceType" + }, { + "@id" : "bts:dataType" + }, { + "@id" : "bts:dataSubtype" + }, { + "@id" : "bts:assay" + }, { + "@id" : "bts:individualID" + }, { + "@id" : "bts:species" + }, { + "@id" : "bts:sex" + }, { + "@id" : "bts:age" + }, { + "@id" : "bts:ageUnit" + }, { + "@id" : "bts:diagnosis" + }, { + "@id" : "bts:nf1Genotype" + }, { + "@id" : "bts:nf2Genotype" + }, { + "@id" : "bts:tumorType" + }, { + "@id" : "bts:modelSystemName" + }, { + "@id" : "bts:organ" + }, { + "@id" : "bts:comments" + }, { + "@id" : "bts:parentSpecimenID" + }, { + "@id" : "bts:specimenID" + }, { + "@id" : "bts:aliquotID" + }, { + "@id" : "bts:experimentalFactor" + }, { + "@id" : "bts:experimentalCondition" + }, { + "@id" : "bts:experimentalTimepoint" + }, { + "@id" : "bts:timepointUnit" + }, { + "@id" : "bts:compoundName" + }, { + "@id" : "bts:compoundDose" + }, { + "@id" : "bts:compoundDoseUnit" + }, { + "@id" : "bts:genePerturbed" + }, { + "@id" : "bts:genePerturbationType" + }, { + "@id" : "bts:genePerturbationTechnology" } ], - 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This is an abstract template; \"real\" template subclasses define additional properties appropriate for the type of data file (e.g. imaging vs sequencing).\n", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:CopyNumberVariants" + "@id" : "bts:Filename" }, { - "@id" : "bts:image" + "@id" : "bts:fileFormat" }, { - "@id" : "bts:network" + "@id" : "bts:resourceType" }, { - "@id" : "bts:cellularPhysiology" + "@id" : "bts:dataType" }, { - "@id" : "bts:metabolomics" + "@id" : "bts:dataSubtype" }, { - "@id" : "bts:AnnotatedSomaticVariants" + "@id" : "bts:assay" }, { - "@id" : "bts:AnnotatedGermlineVariants" + "@id" : "bts:individualID" }, { - "@id" : "bts:Weight" + "@id" : "bts:species" }, { - "@id" : "bts:electrophysiology" + "@id" : "bts:sex" }, { - "@id" : "bts:audiotranscript" + "@id" : "bts:age" }, { - "@id" : "bts:dataIndex" + "@id" : "bts:ageUnit" }, { - "@id" : "bts:DescriptiveMetadata" + "@id" : "bts:diagnosis" }, { - "@id" : "bts:StructuralMetadata" + "@id" : "bts:nf1Genotype" }, { - "@id" : "bts:AdministrativeMetadata" + "@id" : "bts:nf2Genotype" }, { - "@id" : "bts:ReferenceMetadata" + "@id" : "bts:tumorType" }, { - "@id" : "bts:StatisticalMetadata" + "@id" : "bts:modelSystemName" }, { - "@id" : "bts:LegalMetadata" + "@id" : "bts:organ" }, { - "@id" : "bts:WorkflowMetadata" - } ], - "rdfs:label" : "dataType", - "rdfs:comment" : "Links an entity to data types that the entity represents/contains. 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This is an abstract template encapsulating data from low-throughput to high-throughput assays, sequencing-based or non-sequencing based (e.g. microarrays, optical genome mapping). In practice, data are more specifically typed and matched to one of the templates below.\n", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:minutes" + "@id" : "bts:Filename" }, { - "@id" : "bts:hours" + "@id" : "bts:fileFormat" }, { - "@id" : "bts:days" + "@id" : "bts:resourceType" }, { - "@id" : "bts:weeks" + "@id" : "bts:dataType" }, { - "@id" : "bts:months" + "@id" : "bts:dataSubtype" }, { - "@id" : "bts:years" - } ], - "rdfs:label" : "timepointUnit", - "rdfs:comment" : "For timed experiments this represents the unit of time measured", - "@type" : "rdfs:Class", - "sms:displayName" : "timepointUnit" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:WHOPerformanceStatus", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:0" + "@id" : "bts:assay" }, { - "@id" : "bts:1" + "@id" : "bts:individualID" }, { - "@id" : "bts:2" + "@id" : "bts:species" }, { - 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Unlike level-2 and level-3 data, individual-level attributes such as age and sex are no longer surfaced on the data file directly.\n", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:combinationscreen" + "@id" : "bts:Filename" }, { - "@id" : "bts:singlemolecule" + "@id" : "bts:fileFormat" }, { - "@id" : "bts:smallmoleculelibraryscreen" - } ], - "rdfs:label" : "drugScreenType", - "rdfs:comment" : "String describing general class of drug screen", - "@type" : "rdfs:Class", - "sms:displayName" : "drugScreenType" - }, { - "@id" : "bts:experimentalCondition", - "@type" : "rdfs:Class", - "rdfs:comment" : "A free-text description of the experimental condition (e.g. 5 mM doxorubicin).", - "rdfs:label" : "experimentalCondition", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "experimentalCondition", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:cafeaulaitMacules", - 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"@id" : "bts:wholegenomesequencing" + "@id" : "bts:unknown" + } ], + "rdfs:label" : "otherTumors", + "rdfs:comment" : "Characterization of the manifestation of other tumors.", + "@type" : "rdfs:Class", + "sms:displayName" : "otherTumors" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:genePerturbationType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "genePerturbationType", + "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", + "@type" : "rdfs:Class", + "sms:displayName" : "genePerturbationType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:painStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notaproblem" }, { - "@id" : "bts:whole-cellpatchclamp" + "@id" : "bts:occasional" }, { - "@id" : "bts:STRprofile" + "@id" : "bts:disabling" } ], - "rdfs:label" : "assay", - "rdfs:comment" : "The technology used to generate the data in this file.", + "rdfs:label" : "painStatus", + "rdfs:comment" : "Pain status rating.", + "@type" : "rdfs:Class", + "sms:displayName" : "painStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:compoundDose", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "rdfs:label" : "compoundDose", + "rdfs:comment" : "A dose quantity for the treatment compound. 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Subproperty of `relatedResource`.", + "rdfs:label" : "series", + "rdfs:comment" : "Title of a custom series that this resource is part of, if any.", "@type" : "rdfs:Class", - "sms:displayName" : "relatedStudies" + "sms:displayName" : "series" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:platform", + "@id" : "bts:ageUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:2DCellTiter-Glo" - }, { - "@id" : "bts:2DIncucyte" - }, { - "@id" : "bts:XF24ExtracellularFluxAnalyzer" - }, { - "@id" : "bts:ZeissLSM" - }, { - "@id" : "bts:ZeissLSM980" - }, { - "@id" : "bts:ZeissLSM700" - }, { - "@id" : "bts:IlluminaNovaSeq6000" - }, { - "@id" : "bts:Agilent44Karray" - }, { - "@id" : "bts:AffymetrixGenome-WideHumanSNP5.0Array" - }, { - "@id" : "bts:IlluminaHumanMethylation450" - }, { - "@id" : "bts:IlluminaHumanOmni1-Quadv1.0" - }, { - "@id" : "bts:VectraH13DImagingSystem" - }, { - "@id" : "bts:IlluminaNextSeq1000" - }, { - "@id" : "bts:IlluminaHiSeqX" - }, { - "@id" : "bts:ChromiumX" - }, { - "@id" : "bts:OrbitrapFusionLumosTribrid" - }, { - "@id" : "bts:IlluminaHiSeq4000" - }, { - "@id" : "bts:EnVision2103MultiplateReader" - }, { - "@id" : "bts:AffymetrixHumanGene1.0STArray" - }, { - "@id" : "bts:IlluminaMiSeq" - }, { - "@id" : "bts:IlluminaWholeGenomeDASL" - }, { - "@id" : "bts:IlluminaGenomeAnalyzerIIx" - }, { - "@id" : "bts:IlluminaInfiniumMethylationEPICBeadChipv1.0(850k)" - }, { - "@id" : "bts:IlluminaHuman660W-Quadv1.0BeadChip" - }, { - "@id" : "bts:SpectramaxMSeries" - }, { - "@id" : "bts:IlluminaNextSeq2000" - }, { - "@id" : "bts:Illumina1M" - }, { - "@id" : "bts:QExativeHF" - }, { - "@id" : "bts:IlluminaNextSeq550" - }, { - "@id" : "bts:AffymetrixU133AB" - }, { - "@id" : "bts:IlluminaHiSeq3000" - }, { - "@id" : "bts:IlluminaHiSeq2500" - }, { - "@id" : "bts:IlluminaMouseWG-6v2.0expressionbeadchip" - }, { - "@id" : "bts:LTQOrbitrapXL" - }, { - "@id" : "bts:IlluminaInfiniumMethylationEPICBeadChipv2.0(935k)" - }, { - "@id" : "bts:IlluminaOmni5M" - }, { - "@id" : "bts:IVISSpectrumInVivoImagingSystem" - }, { - "@id" : "bts:AffymetrixGenome-WideHumanSNP6.0Array" - }, { - "@id" : "bts:LifeVizMicroSystem" - }, { - "@id" : "bts:10xVisiumSpatialGeneExpression" - }, { - "@id" : "bts:MalvernZetasizer" - }, { - "@id" : "bts:NanostringGeoMx" - }, { - "@id" : "bts:IlluminaHumanHap300" - }, { - "@id" : "bts:Vevo3100ImagingSystem" - }, { - "@id" : "bts:IlluminaHumanOmniExpress-24v1.0BeadChip" - }, { - "@id" : "bts:IlluminaHiSeq2000" - }, { - "@id" : "bts:PacBioSequelIIeSystem" - }, { - "@id" : "bts:IlluminaNextSeq500" - }, { - "@id" : "bts:AffymetrixHumanGenomeU133Plus2.0Array" - }, { - "@id" : "bts:Perlegen300Karray" - }, { - "@id" : "bts:IlluminaHumanOmniExpress-24v1.2BeadChip" - }, { - "@id" : "bts:IlluminaOmni2pt5M" - }, { - "@id" : "bts:LI-COROdysseyCLx" - }, { - "@id" : "bts:CherryImagingTRACEPlatform" - }, { - "@id" : "bts:CherryImagingFACEPlatform" + "@id" : "bts:seconds" }, { - "@id" : "bts:PacBioRSII" + "@id" : "bts:minutes" }, { - "@id" : "bts:InfiniumHumanOmniExpressExome" + "@id" : "bts:hours" }, { - "@id" : "bts:LifeVizInfinitySystem" + "@id" : "bts:days" }, { - "@id" : "bts:OlympusDP80" + "@id" : "bts:weeks" }, { - "@id" : "bts:NanostringCounter" + "@id" : "bts:months" }, { - "@id" : "bts:NanoFCM" + "@id" : "bts:years" + } ], + "rdfs:label" : "ageUnit", + "rdfs:comment" : "A time unit that can be used with a given age value, e.g. years.", + "@type" : "rdfs:Class", + "sms:displayName" : "ageUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:progressReportNumber", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:1" }, { - "@id" : "bts:Illuminah650" + "@id" : "bts:2" }, { - "@id" : "bts:BGISEQ-500" + "@id" : "bts:3" }, { - "@id" : "bts:PacBioSequelIISystem" + "@id" : "bts:4" }, { - "@id" : "bts:PromegaGloMaxDiscover" + "@id" : "bts:5" }, { - "@id" : "bts:BionanoIrys" + "@id" : "bts:6" }, { - "@id" : "bts:LeicaAperioAT2" + "@id" : "bts:7" }, { - "@id" : "bts:LeicaS9Stereomicroscope" + "@id" : "bts:8" }, { - "@id" : "bts:PhilipsAchieva3T" + "@id" : "bts:9" }, { - "@id" : "bts:ZenoElectronicWalkway" + "@id" : "bts:10" }, { - "@id" : "bts:BDFACSCalibur" + "@id" : "bts:NotApplicable" + } ], + "rdfs:label" : "progressReportNumber", + "rdfs:comment" : "Indicates milestone the data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1. Also if submitting data associated with first milestone, progressReportNumber =1", + "@type" : "rdfs:Class", + "sms:displayName" : "progressReportNumber" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:specimenPreparationMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Freshcollected" }, { - "@id" : "bts:Pannoramic250Flash" + "@id" : "bts:Flashfrozen" }, { - "@id" : "bts:Scale" + "@id" : "bts:FFPE" }, { - "@id" : "bts:Caliper" + "@id" : "bts:Cryopreserved" }, { - "@id" : "bts:TOOsonixSystemONE-M" + "@id" : "bts:OCT" }, { - "@id" : "bts:MGIT-series" + "@id" : "bts:RNAlater" }, { - "@id" : "bts:VarioskanLUX" + "@id" : "bts:formalin-fixed" }, { - "@id" : "bts:Panorama1.0T" + "@id" : "bts:ethanol" }, { - "@id" : "bts:NotApplicable" + "@id" : "bts:Viablyfrozen" } ], - "rdfs:label" : "platform", - "rdfs:comment" : "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.", + "rdfs:label" : "specimenPreparationMethod", + "rdfs:comment" : "Term that represents preservation of the sample before usage in, e.g. sequencing", "@type" : "rdfs:Class", - "sms:displayName" : "platform" + "sms:displayName" : "specimenPreparationMethod" }, { - "@id" : "bts:studyLeads", - "@type" : "rdfs:Class", - "rdfs:comment" : "Individuals with lead roles in a study.", - "rdfs:label" : "studyLeads", "rdfs:subClassOf" : [ ], + "@id" : "bts:isMultiIndividual", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "studyLeads", - "sms:required" : "sms:true" - }, { - "@id" : "bts:BodyPartEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + } ], + "rdfs:label" : "isMultiIndividual", + "rdfs:comment" : "Whether or not a file has data for multiple individuals (Yes; No)", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BodyPartEnum", + "sms:displayName" : "isMultiIndividual" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:libraryStrand", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BodyPartEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:UnknownEnum", + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:FirstStranded" + }, { + "@id" : "bts:SecondStranded" + }, { + "@id" : "bts:Unstranded" + }, { + "@id" : "bts:NotApplicable" + } ], + "rdfs:label" : "libraryStrand", + "rdfs:comment" : "Strandedness of paired-end RNA-Sequencing data. This is an important parameter for RNA-seq analysis.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "UnknownEnum", + "sms:displayName" : "libraryStrand" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:GIST", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "UnknownEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpecimenPreparationMethodEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "GIST", + "rdfs:comment" : "Characterization of the manifestation of Gastrointestinal stromal tumor (GIST).", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SpecimenPreparationMethodEnum", + "sms:displayName" : "GIST" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:immersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpecimenPreparationMethodEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:FileFormatEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:air" + }, { + "@id" : "bts:oil" + }, { + "@id" : "bts:water" + }, { + "@id" : "bts:other" + } ], + "rdfs:label" : "immersion", + "rdfs:comment" : "Immersion medium", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "FileFormatEnum", + "sms:displayName" : "immersion" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:captureArea", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FileFormatEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MultipleImagingDiagnosisEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:A" + }, { + "@id" : "bts:B" + }, { + "@id" : "bts:C" + }, { + "@id" : "bts:D" + }, { + "@id" : "bts:A1" + }, { + "@id" : "bts:B1" + }, { + "@id" : "bts:C1" + }, { + "@id" : "bts:D1" + } ], + "rdfs:label" : "captureArea", + "rdfs:comment" : "One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.\n", "@type" : "rdfs:Class", - "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with one or multiple sites being the most relevant result.", - "rdfs:label" : "MultipleImagingDiagnosisEnum", + "sms:displayName" : "captureArea" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:experimentalFactor", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MultipleImagingDiagnosisEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SexEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:braingrowthmeasurement" + }, { + "@id" : "bts:brainvolumemeasurement" + }, { + "@id" : "bts:bodyweight" + }, { + "@id" : "bts:clinicallaboratorymeasurement" + }, { + "@id" : "bts:cognitivefunctionmeasurement" + }, { + "@id" : "bts:gaitmeasurement" + }, { + "@id" : "bts:motordevelopmentmeasurement" + }, { + "@id" : "bts:painmeasurement" + } ], + "rdfs:label" : "experimentalFactor", + "rdfs:comment" : "An ontology concept for experimental factor measured with this data.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SexEnum", + "sms:displayName" : "experimentalFactor" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:stature", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SexEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MRISequenceEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:<5thcentile" + }, { + "@id" : "bts:5th-95thcentile" + }, { + "@id" : "bts:>95thcentile" + } ], + "rdfs:label" : "stature", + "rdfs:comment" : "Stature of the individual.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MRISequenceEnum", + "sms:displayName" : "stature" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:readPair", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MRISequenceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AgeGroupEnum", + "sms:required" : "sms:false", + "sms:validationRules" : [ "inRange 1 2" ], + "rdfs:label" : "readPair", + "rdfs:comment" : "The read of origin, Read 1 or Read 2", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AgeGroupEnum", + "sms:displayName" : "readPair" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:workingDistanceUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AgeGroupEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:angstrom" + }, { + "@id" : "bts:nanometer" + }, { + "@id" : "bts:micrometer" + }, { + "@id" : "bts:millimeter" + }, { + "@id" : "bts:centimeter" + } ], + "rdfs:label" : "workingDistanceUnit", + "rdfs:comment" : "Unit for working distance.", + "@type" : "rdfs:Class", + "sms:displayName" : "workingDistanceUnit" }, { - "@id" : "bts:TumorTreatmentEnum", + "rdfs:subClassOf" : [ ], + "@id" : "bts:nonopticGlioma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "nonopticGlioma", + "rdfs:comment" : "Characterization of the manifestation of Nonoptic glioma.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TumorTreatmentEnum", + "sms:displayName" : "nonopticGlioma" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:germlineMutationIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TumorTreatmentEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:nottested" + }, { + "@id" : "bts:testedbutunknown" + } ], + "rdfs:label" : "germlineMutationIndicator", + "rdfs:comment" : "Indicates a summary testing result for individual's germline mutation only.", + "@type" : "rdfs:Class", + "sms:displayName" : "germlineMutationIndicator" }, { - "@id" : "bts:PlatformEnum", + "@id" : "bts:antibodyID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PlatformEnum", + "rdfs:comment" : "Antibody ID such as RRID if available, otherwise use vendor ID.", + "rdfs:label" : "antibodyID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PlatformEnum", + "sms:displayName" : "antibodyID", "sms:required" : "sms:false" }, { - "@id" : "bts:NF1Variant", + "@id" : "bts:specimenIDSource", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NF1Variant", + "rdfs:comment" : "Optional annotation describing where the specimen ID source derived from, e.g. the biobank providing samples or a providing lab.", + "rdfs:label" : "specimenIDSource", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NF1Variant", + "sms:displayName" : "specimenIDSource", "sms:required" : "sms:false" }, { - "@id" : "bts:GenePerturbationEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:vestibularSchwannoma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "GenePerturbationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TestSummaryEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" + }, { + "@id" : "bts:absentbyimaging" + }, { + "@id" : "bts:unilateral" + }, { + "@id" : "bts:bilateral" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "vestibularSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Vestibular schwannoma.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TestSummaryEnum", + "sms:displayName" : "vestibularSchwannoma" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:isPairedEnd", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TestSummaryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpinalNeuromaManifestationEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + } ], + "rdfs:label" : "isPairedEnd", + "rdfs:comment" : "(Legacy/deprecated annotation) Whether or not is paired-end sequencing (Yes; No).", "@type" : "rdfs:Class", - "rdfs:comment" : "Enumerations describing the manifestation of spinal neurofibromas, combining information on presence and the cervical locations.", - "rdfs:label" : "SpinalNeuromaManifestationEnum", + "sms:displayName" : "isPairedEnd" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:numberOfSchwannomas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpinalNeuromaManifestationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:WorkflowEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:single" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "numberOfSchwannomas", + "rdfs:comment" : "Number of schwannomas.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "WorkflowEnum", + "sms:displayName" : "numberOfSchwannomas" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:dataStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "WorkflowEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:DataNotExpected" + }, { + "@id" : "bts:DataPending" + }, { + "@id" : "bts:UnderEmbargo" + }, { + "@id" : "bts:RollingRelease" + }, { + "@id" : "bts:PartiallyAvailable" + }, { + "@id" : "bts:Available" + } ], + "rdfs:label" : "dataStatus", + "rdfs:comment" : "Overall status of data in a study.", + "@type" : "rdfs:Class", + "sms:displayName" : "dataStatus" }, { - "@id" : "bts:BooleanEnum", + "@id" : "bts:contentSize", "@type" : "rdfs:Class", - "rdfs:comment" : "Boolean data as Yes/No enums", - "rdfs:label" : "BooleanEnum", + "rdfs:comment" : "(Files only) File size, usually calculated by the backend.", + "rdfs:label" : "contentSize", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BooleanEnum", + "sms:displayName" : "contentSize", "sms:required" : "sms:false" }, { - "@id" : "bts:PubertyOnsetEnum", + "@id" : "bts:targetCaptureKitID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PubertyOnsetEnum", + "rdfs:comment" : "A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.\n", + "rdfs:label" : "targetCaptureKitID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PubertyOnsetEnum", + "sms:displayName" : "targetCaptureKitID", "sms:required" : "sms:false" }, { - "@id" : "bts:GenePerturbationMethodEnum", + "@id" : "bts:aliquotID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "GenePerturbationMethodEnum", + "rdfs:comment" : "A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID.", + "rdfs:label" : "aliquotID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "GenePerturbationMethodEnum", + "sms:displayName" : "aliquotID", "sms:required" : "sms:false" }, { - "@id" : "bts:Data", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Data", "rdfs:subClassOf" : [ ], + "@id" : "bts:initiative", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Data", - "sms:required" : "sms:false" - }, { - "@id" : "bts:PlexiformNeurofibromaManifestationEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "initiative", + "rdfs:comment" : "Refers to a funding initiative. Typically handled by the DCC.", "@type" : "rdfs:Class", - "rdfs:comment" : "Enumerations describing the manifestation of plexiform neurofibromas, combining information on presence and the certainty via MRI imaging technique.", - "rdfs:label" : "PlexiformNeurofibromaManifestationEnum", + "sms:displayName" : "initiative" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:nominalMagnification", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PlexiformNeurofibromaManifestationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BinaryImagingDiagnosisEnum", + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "nominalMagnification", + "rdfs:comment" : "magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens.", "@type" : "rdfs:Class", - "rdfs:comment" : "Enumerations describing the manifestation of tumors confirmed via imaging with mainly absent or present being the most relevant result.", - "rdfs:label" : "BinaryImagingDiagnosisEnum", + "sms:displayName" : "nominalMagnification" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:genePerturbationTechnology", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BinaryImagingDiagnosisEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:RNAi" + }, { + "@id" : "bts:CRISPR" + }, { + "@id" : "bts:CRERecombinase" + } ], + "rdfs:label" : "genePerturbationTechnology", + "rdfs:comment" : "Technology used to perturb gene", + "@type" : "rdfs:Class", + "sms:displayName" : "genePerturbationTechnology" }, { - "@id" : "bts:SpeciesEnum", + "@id" : "bts:relatedResource", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SpeciesEnum", + "rdfs:comment" : "A related resource.", + "rdfs:label" : "relatedResource", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpeciesEnum", + "sms:displayName" : "relatedResource", "sms:required" : "sms:false" }, { - "@id" : "bts:DiagnosisEnum", + "@id" : "bts:specimenID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DiagnosisEnum", + "rdfs:comment" : "A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen.\n", + "rdfs:label" : "specimenID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DiagnosisEnum", - "sms:required" : "sms:false" + "sms:displayName" : "specimenID", + "sms:required" : "sms:true" }, { - "@id" : "bts:ProteinExtractSourceEnum", + "@id" : "bts:comments", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ProteinExtractSourceEnum", + "rdfs:comment" : "Brief free-text comments that may also be important to understanding the resource.", + "rdfs:label" : "comments", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ProteinExtractSourceEnum", + "sms:displayName" : "comments", "sms:required" : "sms:false" }, { - "@id" : "bts:VitalStatusEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "VitalStatusEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:fileFormat", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "VitalStatusEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MosaicismEnum", + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:7z" + }, { + "@id" : "bts:DICOM" + }, { + "@id" : "bts:MATLABdata" + }, { + "@id" : "bts:MATLABscript" + }, { + "@id" : "bts:NWB" + }, { + "@id" : "bts:PAR" + }, { + "@id" : "bts:Pythonscript" + }, { + "@id" : "bts:Rscript" + }, { + "@id" : "bts:RData" + }, { + "@id" : "bts:REC" + }, { + "@id" : "bts:SDAT" + }, { + "@id" : "bts:SPAR" + }, { + "@id" : "bts:Sentrixdescriptorfile" + }, { + "@id" : "bts:ab1" + }, { + "@id" : "bts:abf" + }, { + "@id" : "bts:ai" + }, { + "@id" : "bts:avi" + }, { + "@id" : "bts:bai" + }, { + "@id" : "bts:bam" + }, { + "@id" : "bts:bashscript" + }, { + "@id" : "bts:bcf" + }, { + "@id" : "bts:bed" + }, { + "@id" : "bts:bedbroadPeak" + }, { + "@id" : "bts:bedgappedPeak" + }, { + "@id" : "bts:bednarrowPeak" + }, { + "@id" : "bts:bedgraph" + }, { + "@id" : "bts:bgzip" + }, { + "@id" : "bts:bigwig" + }, { + "@id" : "bts:bpm" + }, { + "@id" : "bts:cel" + }, { + "@id" : "bts:chp" + }, { + "@id" : "bts:cnn" + }, { + "@id" : "bts:cnr" + }, { + "@id" : "bts:cns" + }, { + "@id" : "bts:cram" + }, { + "@id" : "bts:crai" + }, { + "@id" : "bts:csi" + }, { + "@id" : "bts:csv" + }, { + "@id" : "bts:ctab" + }, { + "@id" : "bts:czi" + }, { + "@id" : "bts:dat" + }, { + "@id" : "bts:doc" + }, { + "@id" : "bts:dockerimage" + }, { + "@id" : "bts:dup" + }, { + "@id" : "bts:excel" + }, { + "@id" : "bts:fasta" + }, { + "@id" : "bts:fastq" + }, { + "@id" : "bts:fcs" + }, { + "@id" : "bts:fig" + }, { + "@id" : "bts:flagstat" + }, { + "@id" : "bts:gct" + }, { + "@id" : "bts:gff3" + }, { + "@id" : "bts:gtf" + }, { + "@id" : "bts:gzip" + }, { + "@id" : "bts:hdf5" + }, { + "@id" : "bts:hdr" + }, { + "@id" : "bts:hic" + }, { + "@id" : "bts:html" + }, { + "@id" : "bts:hyperlink" + }, { + "@id" : "bts:idat" + }, { + "@id" : "bts:idx" + }, { + "@id" : "bts:img" + }, { + "@id" : "bts:jpg" + }, { + "@id" : "bts:js" + }, { + "@id" : "bts:json" + }, { + "@id" : "bts:locs" + }, { + "@id" : "bts:maf" + }, { + "@id" : "bts:md" + }, { + "@id" : "bts:mov" + }, { + "@id" : "bts:msf" + }, { + "@id" : "bts:mtx" + }, { + "@id" : "bts:mzML" + }, { + "@id" : "bts:nii" + }, { + "@id" : "bts:ome-tiff" + }, { + "@id" : "bts:pdf" + }, { + "@id" : "bts:plink" + }, { + "@id" : "bts:png" + }, { + "@id" : "bts:powerpoint" + }, { + "@id" : "bts:pzfx" + }, { + "@id" : "bts:raw" + }, { + "@id" : "bts:rds" + }, { + "@id" : "bts:recal" + }, { + "@id" : "bts:rmd" + }, { + "@id" : "bts:sam" + }, { + "@id" : "bts:sav" + }, { + "@id" : "bts:sdf" + }, { + "@id" : "bts:seg" + }, { + "@id" : "bts:sf" + }, { + "@id" : "bts:sif" + }, { + "@id" : "bts:sqlite" + }, { + "@id" : "bts:sra" + }, { + "@id" : "bts:svg" + }, { + "@id" : "bts:svs" + }, { + "@id" : "bts:tagAlign" + }, { + "@id" : "bts:tar" + }, { + "@id" : "bts:tbi" + }, { + "@id" : "bts:tif" + }, { + "@id" : "bts:tom" + }, { + "@id" : "bts:tranches" + }, { + "@id" : "bts:tsv" + }, { + "@id" : "bts:txt" + }, { + "@id" : "bts:vcf" + }, { + "@id" : "bts:wiggle" + }, { + "@id" : "bts:xml" + }, { + "@id" : "bts:yaml" + }, { + "@id" : "bts:zip" + } ], + "rdfs:label" : "fileFormat", + "rdfs:comment" : "Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MosaicismEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "MosaicismEnum", - "sms:required" : "sms:false" + "sms:displayName" : "fileFormat" }, { - "@id" : "bts:WorkingDistanceUnitEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "WorkingDistanceUnitEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:nf2Genotype", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "WorkingDistanceUnitEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:StrandednessEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:-/-" + }, { + "@id" : "bts:+/-" + }, { + "@id" : "bts:+/+" + }, { + "@id" : "bts:Unknown" + }, { + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "nf2Genotype", + "rdfs:comment" : "Genotype of NF2 gene in the biospecimen from which the data were derived, if known", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "StrandednessEnum", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "StrandednessEnum", - "sms:required" : "sms:false" + "sms:displayName" : "nf2Genotype" }, { - "@id" : "bts:OrganismSubstance", - "@type" : "rdfs:Class", - "rdfs:comment" : "This preferred root in the UBERON ontology is meant to cover organism-produced substances (bodily secretions and excreta) commonly used as assay specimens.", - "rdfs:label" : "OrganismSubstance", "rdfs:subClassOf" : [ ], + "@id" : "bts:peripheralNeuropathy", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OrganismSubstance", - "sms:required" : "sms:false" - }, { - "@id" : "bts:BiologicalProcess", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "peripheralNeuropathy", + "rdfs:comment" : "Characterization of the manifestation of Peripheral neuropathy.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BiologicalProcess", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "BiologicalProcess", - "sms:required" : "sms:false" + "sms:displayName" : "peripheralNeuropathy" }, { - "@id" : "bts:ExpressionUnitEnum", + "@id" : "bts:Component", "@type" : "rdfs:Class", - "rdfs:comment" : "Quantification units for gene expression.", - "rdfs:label" : "ExpressionUnitEnum", + "rdfs:comment" : "Type of metadata template; provide the same one for all items/rows.", + "rdfs:label" : "Component", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ExpressionUnitEnum", - "sms:required" : "sms:false" + "sms:displayName" : "Component", + "sms:required" : "sms:true" }, { - "@id" : "bts:OrganEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OrganEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:scoliosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OrganEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:Tumor", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "scoliosis", + "rdfs:comment" : "Characterization of the manifestation of Scoliosis.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Tumor", + "sms:displayName" : "scoliosis" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:species", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Tumor", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Rattusnorvegicus" + }, { + "@id" : "bts:Gallusgallus" + }, { + "@id" : "bts:Pantroglodytes" + }, { + "@id" : "bts:Musmusculus(humanized)" + }, { + "@id" : "bts:Homosapiens" + }, { + "@id" : "bts:Daniorerio" + }, { + "@id" : "bts:Drosophilamelanogaster" + }, { + "@id" : "bts:Rhesusmacaque" + }, { + "@id" : "bts:Susscrofa" + }, { + "@id" : "bts:Oryctolaguscuniculus" + }, { + "@id" : "bts:Musmusculus" + } ], + "rdfs:label" : "species", + "rdfs:comment" : "The name of a species (typically a taxonomic group) of organism.", + "@type" : "rdfs:Class", + "sms:displayName" : "species" }, { - "@id" : "bts:WHOPerformanceStatusScores", + "@id" : "bts:concreteType", "@type" : "rdfs:Class", - "rdfs:comment" : "https://www.ncbi.nlm.nih.gov/books/NBK97482/", - "rdfs:label" : "WHOPerformanceStatusScores", + "rdfs:comment" : "Refers to the class model the data platform uses for representing the resource. This is a low-level field set by the platform and is not a user annotation.", + "rdfs:label" : "concreteType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "WHOPerformanceStatusScores", + "sms:displayName" : "concreteType", "sms:required" : "sms:false" }, { - "@id" : "bts:ConcentrationUnit", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ConcentrationUnit", "rdfs:subClassOf" : [ ], + "@id" : "bts:transplantationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ConcentrationUnit", - "sms:required" : "sms:false" - }, { - "@id" : "bts:NucleicAcidSourceEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:allograft" + }, { + "@id" : "bts:xenograft" + }, { + "@id" : "bts:autograft" + }, { + "@id" : "bts:isograft" + } ], + "rdfs:label" : "transplantationType", + "rdfs:comment" : "Type of transplantation involved in the experiment, derived from MESH", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "NucleicAcidSourceEnum", + "sms:displayName" : "transplantationType" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:yearPublished", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NucleicAcidSourceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReadPairOrientationEnum", + "sms:required" : "sms:false", + "sms:validationRules" : [ "int" ], + "schema:rangeIncludes" : [ ], + "rdfs:label" : "yearPublished", + "rdfs:comment" : "Year in which the resource was published/generally made available.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReadPairOrientationEnum", + "sms:displayName" : "yearPublished" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:fundingAgency", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReadPairOrientationEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:LateralManifestationEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "fundingAgency", + "rdfs:comment" : "Refers to the funding organization for the generated resource. 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The E-Tag changes every time an entity is updated it is used to detect when a client's current representation of an entity is out-of-date.", + "rdfs:label" : "etag", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "StudyStatusEnum", + "sms:displayName" : "etag", "sms:required" : "sms:false" }, { - "@id" : "bts:Metadata", + "@id" : "bts:runtimePlatform", "@type" : "rdfs:Class", - "rdfs:comment" : "Data that provides information about other data", - "rdfs:label" : "Metadata", + "rdfs:comment" : "Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).", + "rdfs:label" : "runtimePlatform", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Metadata", + "sms:displayName" : "runtimePlatform", "sms:required" : "sms:false" }, { - "@id" : "bts:DiseaseFocusEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DiseaseFocusEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:MPNST", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - 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"@id" : "bts:modelSystemName" + "@id" : "bts:IlluminaNextSeq1000" }, { - "@id" : "bts:organ" + "@id" : "bts:IlluminaHiSeqX" }, { - "@id" : "bts:comments" + "@id" : "bts:ChromiumX" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:OrbitrapFusionLumosTribrid" }, { - "@id" : "bts:specimenID" + "@id" : "bts:IlluminaHiSeq4000" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:EnVision2103MultiplateReader" }, { - "@id" : "bts:platform" + "@id" : "bts:AffymetrixHumanGene1.0STArray" }, { - "@id" : "bts:nucleicAcidSource" + "@id" : "bts:IlluminaMiSeq" }, { - "@id" : "bts:specimenPreparationMethod" + "@id" : "bts:IlluminaWholeGenomeDASL" }, { - "@id" : "bts:specimenType" + "@id" : "bts:IlluminaGenomeAnalyzerIIx" }, { - "@id" : "bts:runType" + "@id" : "bts:IlluminaInfiniumMethylationEPICBeadChipv1.0(850k)" }, { - "@id" : "bts:libraryStrand" + "@id" : "bts:IlluminaHuman660W-Quadv1.0BeadChip" }, { - "@id" : "bts:libraryPrep" + "@id" : "bts:SpectramaxMSeries" }, { - "@id" : "bts:libraryPreparationMethod" + "@id" : "bts:IlluminaNextSeq2000" }, { - "@id" : "bts:readPair" + "@id" : "bts:Illumina1M" }, { - "@id" : "bts:readLength" + "@id" : "bts:QExativeHF" }, { - "@id" : "bts:readDepth" + "@id" : "bts:IlluminaNextSeq550" }, { - "@id" : "bts:targetDepth" + "@id" : "bts:AffymetrixU133AB" }, { - "@id" : "bts:batchID" + "@id" : "bts:IlluminaHiSeq3000" }, { - "@id" : "bts:bisulfiteConversionKitID" - } ], - "sms:displayName" : "EpigeneticsAssayTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:BiologicalAssayDataTemplate" - } ], - "@id" : "bts:ProcessedVariantCallsTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ProcessedVariantCallsTemplate", - "rdfs:comment" : "Template for describing either simple germline/somatic variant calls output data (VCF/MAF) as well as structural variants (e.g. CNVs).", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:IlluminaHiSeq2500" }, { - "@id" : "bts:Filename" + "@id" : "bts:IlluminaMouseWG-6v2.0expressionbeadchip" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:LTQOrbitrapXL" }, { - "@id" : "bts:resourceType" + "@id" : "bts:IlluminaInfiniumMethylationEPICBeadChipv2.0(935k)" }, { - "@id" : "bts:dataType" + "@id" : "bts:IlluminaOmni5M" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:IVISSpectrumInVivoImagingSystem" }, { - "@id" : "bts:assay" + "@id" : "bts:AffymetrixGenome-WideHumanSNP6.0Array" }, { - "@id" : "bts:individualID" + "@id" : "bts:LifeVizMicroSystem" }, { - "@id" : "bts:species" + "@id" : "bts:10xVisiumSpatialGeneExpression" }, { - "@id" : "bts:sex" + "@id" : "bts:MalvernZetasizer" }, { - "@id" : "bts:age" + "@id" : "bts:NanostringGeoMx" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:IlluminaHumanHap300" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:Vevo3100ImagingSystem" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:IlluminaHumanOmniExpress-24v1.0BeadChip" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:IlluminaHiSeq2000" }, { - "@id" : "bts:tumorType" + "@id" : "bts:PacBioSequelIIeSystem" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:IlluminaNextSeq500" }, { - "@id" : "bts:organ" + "@id" : "bts:AffymetrixHumanGenomeU133Plus2.0Array" }, { - "@id" : "bts:comments" + "@id" : "bts:Perlegen300Karray" }, { - "@id" : "bts:isFilteredReads" + "@id" : "bts:IlluminaHumanOmniExpress-24v1.2BeadChip" }, { - "@id" : "bts:workflow" + "@id" : "bts:IlluminaOmni2pt5M" }, { - "@id" : "bts:workflowLink" + "@id" : "bts:LI-COROdysseyCLx" }, { - "@id" : "bts:auxiliaryAsset" - } ], - "sms:displayName" : "ProcessedVariantCallsTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Template" - } ], - "@id" : "bts:NonBiologicalAssayDataTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "NonBiologicalAssayDataTemplate", - "rdfs:comment" : "A template for describing deposited data artifacts (i.e. files) from an experimental assay that main involves non-biological samples. \n", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:CherryImagingTRACEPlatform" }, { - "@id" : "bts:resourceType" + "@id" : "bts:CherryImagingFACEPlatform" }, { - "@id" : "bts:dataType" + "@id" : "bts:PacBioRSII" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:InfiniumHumanOmniExpressExome" }, { - "@id" : "bts:assay" - } ], - "sms:displayName" : "NonBiologicalAssayDataTemplate" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:PortalDataset", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "PortalDataset", - "rdfs:comment" : "A slightly more specialized dataset concept intended for the specific scope of the NF Portal; see https://nf.synapse.org/Explore/Datasets. \n", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ ], - "sms:displayName" : "PortalDataset" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:BiologicalAssayDataTemplate" - } ], - "@id" : "bts:FlowCytometryTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "FlowCytometryTemplate", - "rdfs:comment" : "Template for flow cytometry assay", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:LifeVizInfinitySystem" }, { - "@id" : "bts:Filename" + "@id" : "bts:OlympusDP80" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:NanostringCounter" }, { - "@id" : "bts:resourceType" + "@id" : "bts:NanoFCM" }, { - "@id" : "bts:dataType" + "@id" : "bts:Illuminah650" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:BGISEQ-500" }, { - "@id" : "bts:assay" + "@id" : "bts:PacBioSequelIISystem" }, { - "@id" : "bts:individualID" + "@id" : "bts:PromegaGloMaxDiscover" }, { - "@id" : "bts:species" + "@id" : "bts:BionanoIrys" }, { - "@id" : "bts:sex" + "@id" : "bts:LeicaAperioAT2" }, { - "@id" : "bts:age" + "@id" : "bts:LeicaS9Stereomicroscope" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:PhilipsAchieva3T" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:ZenoElectronicWalkway" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:BDFACSCalibur" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:Pannoramic250Flash" }, { - "@id" : "bts:tumorType" + "@id" : "bts:Scale" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:Caliper" }, { - "@id" : "bts:organ" + "@id" : "bts:TOOsonixSystemONE-M" }, { - "@id" : "bts:comments" + "@id" : "bts:MGIT-series" }, { - "@id" : "bts:platform" + "@id" : "bts:VarioskanLUX" }, { - "@id" : "bts:cellType" + "@id" : "bts:Panorama1.0T" }, { - "@id" : "bts:auxiliaryAsset" + "@id" : "bts:NotApplicable" } ], - "sms:displayName" : "FlowCytometryTemplate" + "rdfs:label" : "platform", + "rdfs:comment" : "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.", + "@type" : "rdfs:Class", + "sms:displayName" : "platform" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Template" - } ], - "@id" : "bts:WorkflowReport", + "@id" : "bts:studyLeads", + "@type" : "rdfs:Class", + "rdfs:comment" : "Individuals with lead roles in a study.", + "rdfs:label" : "studyLeads", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "WorkflowReport", - "rdfs:comment" : "Template used for miscellaneous workflow reports and accessory files", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:resourceType" - }, { - "@id" : "bts:assay" - }, { - "@id" : "bts:fileFormat" - }, { - "@id" : "bts:relatedDataset" - }, { - "@id" : "bts:workflow" - }, { - "@id" : "bts:workflowLink" - } ], - "sms:displayName" : "WorkflowReport" + "sms:displayName" : "studyLeads", + "sms:required" : "sms:true" }, { "@id" : "bts:autograft", "@type" : "rdfs:Class", diff --git a/modules/Data/Data.yaml b/modules/Data/Data.yaml index f36a41f8..43a81867 100644 --- a/modules/Data/Data.yaml +++ b/modules/Data/Data.yaml @@ -109,7 +109,7 @@ enums: meaning: http://edamontology.org/data_0955 - DataSubtype: + DataSubtypeEnum: permissible_values: normalized: description: A data set that is produced as the output of a normalization data transformation. diff --git a/modules/props.yaml b/modules/props.yaml index 56c86dd4..eeeefcb5 100644 --- a/modules/props.yaml +++ b/modules/props.yaml @@ -283,7 +283,7 @@ slots: description: 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. - range: DataSubtype + range: DataSubtypeEnum required: true dataType: annotations: