diff --git a/GF.jsonld b/GF.jsonld index 76ecfac..f17016d 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -9,7696 +9,7833 @@ }, "@id" : "http://schema.biothings.io/", "@graph" : [ { - "@id" : "bts:IndicatorEnum", + "@id" : "bts:YearsSmoked", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "IndicatorEnum", + "rdfs:comment" : "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label" : "YearsSmoked", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "IndicatorEnum", + "sms:displayName" : "YearsSmoked", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCancerAssessmentTestsEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerAssessmentTestsEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:RelationshipGender", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCancerAssessmentTestsEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:female" + }, { + "@id" : "bts:male" + }, { + "@id" : "bts:unspecified" + } ], + "rdfs:label" : "RelationshipGender", + "rdfs:comment" : "The text term used to describe the gender of the patient's relative with a history of cancer.", + "@type" : "rdfs:Class", + "sms:displayName" : "RelationshipGender" }, { - "@id" : "bts:HereditaryCancerPredispositionSyndromeEnum", + "@id" : "bts:AdjacentSampleIDs", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HereditaryCancerPredispositionSyndromeEnum", + "rdfs:comment" : "List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample", + "rdfs:label" : "AdjacentSampleIDs", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HereditaryCancerPredispositionSyndromeEnum", + "sms:displayName" : "AdjacentSampleIDs", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCarcinomaDetectionMethodTypeEnum", + "@id" : "bts:AdapterSequence", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaDetectionMethodTypeEnum", + "rdfs:comment" : "Base sequence of the sequencing adapter. String", + "rdfs:label" : "AdapterSequence", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaDetectionMethodTypeEnum", + "sms:displayName" : "AdapterSequence", "sms:required" : "sms:false" }, { - "@id" : "bts:CancerAssociatedGeneMutationsEnum", + "@id" : "bts:DaystoDeath", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CancerAssociatedGeneMutationsEnum", + "rdfs:comment" : "Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.", + "rdfs:label" : "DaystoDeath", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CancerAssociatedGeneMutationsEnum", + "sms:displayName" : "DaystoDeath", "sms:required" : "sms:false" }, { - "@id" : "bts:RelativewithCancerHistoryEnum", + "@id" : "bts:SentinelLymphNodeCount", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RelativewithCancerHistoryEnum", + "rdfs:comment" : "Numeric count of sentinel lymph nodes.", + "rdfs:label" : "SentinelLymphNodeCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RelativewithCancerHistoryEnum", + "sms:displayName" : "SentinelLymphNodeCount", "sms:required" : "sms:false" }, { - "@id" : "bts:EthnicityEnum", + "@id" : "bts:StopDaysfromIndex", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "EthnicityEnum", + "rdfs:comment" : "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label" : "StopDaysfromIndex", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EthnicityEnum", + "sms:displayName" : "StopDaysfromIndex", "sms:required" : "sms:false" }, { - "@id" : "bts:ImmersionEnum", + "@id" : "bts:NumberofDrinksPerWeek", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ImmersionEnum", + "rdfs:label" : "NumberofDrinksPerWeek", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ImmersionEnum", + "sms:displayName" : "NumberofDrinksPerWeek", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCancerGenomicTestPerformedEnum", + "@id" : "bts:SentinelNodePositiveAssessmentCount", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerGenomicTestPerformedEnum", + "rdfs:comment" : "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", + "rdfs:label" : "SentinelNodePositiveAssessmentCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCancerGenomicTestPerformedEnum", + "sms:displayName" : "SentinelNodePositiveAssessmentCount", "sms:required" : "sms:false" }, { - "@id" : "bts:FileFormatEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "FileFormatEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:PreservationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FileFormatEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Negative80DegC" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Cryopreservationindryice-deadtissue" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Fresh" + }, { + "@id" : "bts:Cryopreservationinliquidnitrogen-deadtissue" + }, { + "@id" : "bts:Formalinfixedparaffinembedded-FFPE" + }, { + "@id" : "bts:Archival" + }, { + "@id" : "bts:Formalinfixed-buffered" + }, { + "@id" : "bts:Formalinfixed-unbuffered" + }, { + "@id" : "bts:Cryopreserved" + }, { + "@id" : "bts:Frozen" + }, { + "@id" : "bts:Freshdissociatedandsinglecellsorted" + }, { + "@id" : "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + }, { + "@id" : "bts:Methacarnfixedparaffinembedded-MFPE" + }, { + "@id" : "bts:Freshdissociated" + }, { + "@id" : "bts:Freshdissociatedandsinglecellsortedintoplates" + }, { + "@id" : "bts:Cryopreservationinliquidnitrogen-livecells" + }, { + "@id" : "bts:OCT" + }, { + "@id" : "bts:SnapFrozen" + }, { + "@id" : "bts:LiquidNitrogen" + } ], + "rdfs:label" : "PreservationMethod", + "rdfs:comment" : "Text term that represents the method used to preserve the sample.", + "@type" : "rdfs:Class", + "sms:displayName" : "PreservationMethod" }, { - "@id" : "bts:DimensionOrderEnum", + "@id" : "bts:Ecigvapeuse", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "DimensionOrderEnum", + "rdfs:label" : "Ecigvapeuse", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DimensionOrderEnum", + "sms:displayName" : "Ecigvapeuse", "sms:required" : "sms:false" }, { - "@id" : "bts:SexEnum", + "@id" : "bts:PublicationDOI", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SexEnum", + "rdfs:label" : "PublicationDOI", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SexEnum", + "sms:displayName" : "PublicationDOI", "sms:required" : "sms:false" }, { - "@id" : "bts:AlcoholIntensityEnum", + "@id" : "bts:DaystoBirth", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholIntensityEnum", + "rdfs:comment" : "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.", + "rdfs:label" : "DaystoBirth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AlcoholIntensityEnum", + "sms:displayName" : "DaystoBirth", "sms:required" : "sms:false" }, { - "@id" : "bts:ImagingAssayTypeEnum", + "@id" : "bts:TestUnits", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ImagingAssayTypeEnum", + "rdfs:comment" : "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "TestUnits", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ImagingAssayTypeEnum", + "sms:displayName" : "TestUnits", "sms:required" : "sms:false" }, { - "@id" : "bts:PassedQCEnum", + "@id" : "bts:AdjacentBiospecimenIDs", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "PassedQCEnum", + "rdfs:label" : "AdjacentBiospecimenIDs", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PassedQCEnum", + "sms:displayName" : "AdjacentBiospecimenIDs", "sms:required" : "sms:false" }, { - "@id" : "bts:ExtentofTumorResectionEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ExtentofTumorResectionEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastBiopsyProcedureFindingType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ExtentofTumorResectionEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ReverseTranscriptionPrimerEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:Atypicalhyperplasia" + }, { + "@id" : "bts:DCIS" + }, { + "@id" : "bts:LCIS" + }, { + "@id" : "bts:Cancer" + }, { + "@id" : "bts:Nocancer" + } ], + "rdfs:label" : "BreastBiopsyProcedureFindingType", + "rdfs:comment" : "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReverseTranscriptionPrimerEnum", + "sms:displayName" : "BreastBiopsyProcedureFindingType" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:LibraryLayout", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReverseTranscriptionPrimerEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CountryofResidenceEnum", + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:PairedEnd" + }, { + "@id" : "bts:SingleRead" + }, { + "@id" : "bts:Mid-length" + }, { + "@id" : "bts:LongRead" + } ], + "rdfs:label" : "LibraryLayout", + "rdfs:comment" : "Sequencing read type", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CountryofResidenceEnum", + "sms:displayName" : "LibraryLayout" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:SpecimenLaterality", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CountryofResidenceEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TobaccoSmokingStatusEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Bilateral" + }, { + "@id" : "bts:Left" + }, { + "@id" : "bts:Right" + } ], + "rdfs:label" : "SpecimenLaterality", + "rdfs:comment" : "For samples in paired organs, designates the side from which obtained.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TobaccoSmokingStatusEnum", + "sms:displayName" : "SpecimenLaterality" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastCarcinomaHistologyCategory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TobaccoSmokingStatusEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:OncotypeRiskGroupEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OncotypeRiskGroupEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:Infiltratingductalcarcinoma" + }, { + "@id" : "bts:Infiltratinglobularcarcinoma" + }, { + "@id" : "bts:InvasivemammarycarcinomaNOS" + }, { + "@id" : "bts:Invasivemixedductalandlobularcarcinoma" + } ], + "rdfs:label" : "BreastCarcinomaHistologyCategory", + "rdfs:comment" : "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastCarcinomaHistologyCategory" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:SingleCellIsolationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OncotypeRiskGroupEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:MicrofluidicsChip" + }, { + "@id" : "bts:Droplets" + }, { + "@id" : "bts:FACS" + }, { + "@id" : "bts:Plates" + }, { + "@id" : "bts:10x" + }, { + "@id" : "bts:NucleiIsolation" + } ], + "rdfs:label" : "SingleCellIsolationMethod", + "rdfs:comment" : "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", + "@type" : "rdfs:Class", + "sms:displayName" : "SingleCellIsolationMethod" }, { - "@id" : "bts:PathogenicityEnum", + "@id" : "bts:UMIBarcodeOffset", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PathogenicityEnum", + "rdfs:comment" : "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", + "rdfs:label" : "UMIBarcodeOffset", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PathogenicityEnum", + "sms:displayName" : "UMIBarcodeOffset", "sms:required" : "sms:false" }, { - "@id" : "bts:LabTestsforMMRStatusEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LabTestsforMMRStatusEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:DimensionsUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LabTestsforMMRStatusEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" + }, { + "@id" : "bts:mm" + } ], + "rdfs:label" : "DimensionsUnit", + "rdfs:comment" : "Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)", + "@type" : "rdfs:Class", + "sms:displayName" : "DimensionsUnit" }, { - "@id" : "bts:LibraryConstructionMethodEnum", + "@id" : "bts:TypeofSmokeExposure", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryConstructionMethodEnum", + "rdfs:label" : "TypeofSmokeExposure", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryConstructionMethodEnum", + "sms:displayName" : "TypeofSmokeExposure", "sms:required" : "sms:false" }, { - "@id" : "bts:BisulfiteConversionKitEnum", + "@id" : "bts:SizeC", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BisulfiteConversionKitEnum", + "rdfs:comment" : "Number of channels. Integer >= 1", + "rdfs:label" : "SizeC", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BisulfiteConversionKitEnum", + "sms:displayName" : "SizeC", "sms:required" : "sms:false" }, { - "@id" : "bts:TotalVolumeUnitEnum", + "@id" : "bts:SpecializedMolecularTest", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TotalVolumeUnitEnum", + "rdfs:comment" : "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "SpecializedMolecularTest", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TotalVolumeUnitEnum", + "sms:displayName" : "SpecializedMolecularTest", "sms:required" : "sms:false" }, { - "@id" : "bts:BooleanEnum", + "@id" : "bts:Locus", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BooleanEnum", + "rdfs:comment" : "Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.", + "rdfs:label" : "Locus", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BooleanEnum", + "sms:displayName" : "Locus", "sms:required" : "sms:false" }, { - "@id" : "bts:MolecularAnalysisMethodEnum", + "@id" : "bts:PlaneCount", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MolecularAnalysisMethodEnum", + "rdfs:comment" : "Number of Z-planes (not to be confused with downsampled \"\"pyramid\"\"). Integer >=1", + "rdfs:label" : "PlaneCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MolecularAnalysisMethodEnum", + "sms:displayName" : "PlaneCount", "sms:required" : "sms:false" }, { - "@id" : "bts:ClonalityEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ClonalityEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:DissociationMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClonalityEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:gentleMACS" + }, { + "@id" : "bts:Dounce" + }, { + "@id" : "bts:EnzymaticDigestion" + } ], + "rdfs:label" : "DissociationMethod", + "rdfs:comment" : "The tissue dissociation method used for scRNASeq or scATAC-seq assays", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", + "sms:displayName" : "DissociationMethod" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:PRStainingIntensity", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:IschemicTemperatureEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Strong" + }, { + "@id" : "bts:Moderate" + }, { + "@id" : "bts:Weak" + }, { + "@id" : "bts:Weak-Moderate" + }, { + "@id" : "bts:Moderate-Strong" + }, { + "@id" : "bts:Weak-Strong" + } ], + "rdfs:label" : "PRStainingIntensity", + "rdfs:comment" : "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "IschemicTemperatureEnum", + "sms:displayName" : "PRStainingIntensity" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastCarcinomaSurgicalProcedureName", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "IschemicTemperatureEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Radicalmastectomy" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Simplemastectomy" + }, { + "@id" : "bts:Modifiedradicalmastectomy" + }, { + "@id" : "bts:Partialmastectomy" + }, { + "@id" : "bts:Surgerynotperformed" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Lumpectomy" + }, { + "@id" : "bts:Re-excision" + } ], + "rdfs:label" : "BreastCarcinomaSurgicalProcedureName", + "rdfs:comment" : "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastCarcinomaSurgicalProcedureName" }, { - "@id" : "bts:AgeIsObfuscatedEnum", + "@id" : "bts:BreastCarcinomaERStatusPercentageValue", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AgeIsObfuscatedEnum", + "rdfs:comment" : "A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer", + "rdfs:label" : "BreastCarcinomaERStatusPercentageValue", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AgeIsObfuscatedEnum", + "sms:displayName" : "BreastCarcinomaERStatusPercentageValue", "sms:required" : "sms:false" }, { - "@id" : "bts:LaboratoryTestEnum", + "@id" : "bts:BreastCarcinomaPRStatusPercentageValue", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LaboratoryTestEnum", + "rdfs:comment" : "A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer", + "rdfs:label" : "BreastCarcinomaPRStatusPercentageValue", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LaboratoryTestEnum", + "sms:displayName" : "BreastCarcinomaPRStatusPercentageValue", "sms:required" : "sms:false" }, { - "@id" : "bts:SiteofResectionorBiopsyEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SiteofResectionorBiopsyEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:TobaccoSmokingStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SiteofResectionorBiopsyEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:VascularInvasionTypeEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:CurrentReformedSmoker" + }, { + "@id" : "bts:CurrentSmoker" + }, { + "@id" : "bts:CurrentReformedSmokerfor>15yrs" + }, { + "@id" : "bts:DurationNotSpecified" + }, { + "@id" : "bts:Smokinghistorynotdocumented" + }, { + "@id" : "bts:LifelongNon-Smoker" + }, { + "@id" : "bts:CurrentReformedSmokerfor= 1", + "rdfs:label" : "SizeX", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PixelTypeEnum", + "sms:displayName" : "SizeX", "sms:required" : "sms:false" }, { - "@id" : "bts:SpikeInEnum", + "@id" : "bts:GenomeAnnotationURL", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SpikeInEnum", + "rdfs:label" : "GenomeAnnotationURL", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpikeInEnum", + "sms:displayName" : "GenomeAnnotationURL", "sms:required" : "sms:false" }, { - "@id" : "bts:ReadEnum", + "@id" : "bts:OligoBarcodeLowerStrand", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ReadEnum", + "rdfs:label" : "OligoBarcodeLowerStrand", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReadEnum", + "sms:displayName" : "OligoBarcodeLowerStrand", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCarcinomaHER2StatusEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaHER2StatusEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:Read2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHER2StatusEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:CellBarcodeandDNAInsert" + }, { + "@id" : "bts:SampleIndexandDNAInsert" + }, { + "@id" : "bts:DNAInsert" + }, { + "@id" : "bts:SampleIndex" + }, { + "@id" : "bts:CellBarcode" + } ], + "rdfs:label" : "Read2", + "rdfs:comment" : "Read 2 content description", + "@type" : "rdfs:Class", + "sms:displayName" : "Read2" }, { - "@id" : "bts:ClinicalBiospecimenTypeEnum", + "@id" : "bts:TotalReads", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ClinicalBiospecimenTypeEnum", + "rdfs:comment" : "Total number of reads per sample. Integer", + "rdfs:label" : "TotalReads", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClinicalBiospecimenTypeEnum", + "sms:displayName" : "TotalReads", "sms:required" : "sms:false" }, { - "@id" : "bts:RelationshipPrimaryDiagnosisEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "RelationshipPrimaryDiagnosisEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:HistoneVariant", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RelationshipPrimaryDiagnosisEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:mH2A" + }, { + "@id" : "bts:mH2A.1" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:H2A.Z" + }, { + "@id" : "bts:H3.2" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:H3t(H3.4)" + }, { + "@id" : "bts:H3.X" + }, { + "@id" : "bts:H2A.Z.2.2" + }, { + "@id" : "bts:H3.Y" + }, { + "@id" : "bts:H3.5" + }, { + "@id" : "bts:H3.3" + }, { + "@id" : "bts:H3.1" + }, { + "@id" : "bts:H2A-Bbd" + }, { + "@id" : "bts:mH2A.2" + }, { + "@id" : "bts:CENP-A" + }, { + "@id" : "bts:H2A.Z.2" + }, { + "@id" : "bts:H2A.X" + }, { + "@id" : "bts:H2A.Z.1" + } ], + "rdfs:label" : "HistoneVariant", + "rdfs:comment" : "The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.", + "@type" : "rdfs:Class", + "sms:displayName" : "HistoneVariant" }, { - "@id" : "bts:BIRADSMammographyBreastDensityCategoryEnum", + "@id" : "bts:Chewingtobaccodailyusecount", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "BIRADSMammographyBreastDensityCategoryEnum", + "rdfs:label" : "Chewingtobaccodailyusecount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BIRADSMammographyBreastDensityCategoryEnum", + "sms:displayName" : "Chewingtobaccodailyusecount", "sms:required" : "sms:false" }, { - "@id" : "bts:SingleNucleusBufferEnum", + "@id" : "bts:SecondGeneSymbol", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SingleNucleusBufferEnum", + "rdfs:comment" : "The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "SecondGeneSymbol", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SingleNucleusBufferEnum", + "sms:displayName" : "SecondGeneSymbol", "sms:required" : "sms:false" }, { - "@id" : "bts:BiospecimenTypeEnum", + "@id" : "bts:CycleNumber", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "BiospecimenTypeEnum", + "rdfs:label" : "CycleNumber", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BiospecimenTypeEnum", + "sms:displayName" : "CycleNumber", "sms:required" : "sms:false" }, { - "@id" : "bts:AntibioticUseEnum", + "@id" : "bts:GeneSymbol", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AntibioticUseEnum", + "rdfs:comment" : "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "GeneSymbol", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AntibioticUseEnum", + "sms:displayName" : "GeneSymbol", "sms:required" : "sms:false" }, { - "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicatorEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:GenomicCoverageType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:WholeGenome" + }, { + "@id" : "bts:TargetedGenome" + }, { + "@id" : "bts:BeadchipArray" + } ], + "rdfs:label" : "GenomicCoverageType", + "rdfs:comment" : "Genomic coverage", + "@type" : "rdfs:Class", + "sms:displayName" : "GenomicCoverageType" }, { - "@id" : "bts:PreservationMethodEnum", + "@id" : "bts:TargetDepth", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PreservationMethodEnum", + "rdfs:comment" : "Targeted read depth prior to sequencing. Integer", + "rdfs:label" : "TargetDepth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PreservationMethodEnum", + "sms:displayName" : "TargetDepth", "sms:required" : "sms:false" }, { - "@id" : "bts:TumorExtranodalExtensionIndicatorEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TumorExtranodalExtensionIndicatorEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:PixelType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TumorExtranodalExtensionIndicatorEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:TseriesEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:int32" + }, { + "@id" : "bts:int16" + }, { + "@id" : "bts:double" + }, { + "@id" : "bts:float" + }, { + "@id" : "bts:uint16" + }, { + "@id" : "bts:int8" + }, { + "@id" : "bts:uint32" + }, { + "@id" : "bts:bit" + }, { + "@id" : "bts:uint8" + } ], + "rdfs:label" : "PixelType", + "rdfs:comment" : "Data type for each pixel value. E.g. \"\"uint16\"\"", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TseriesEnum", + "sms:displayName" : "PixelType" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:VitalStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TseriesEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Dead" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Alive" + } ], + "rdfs:label" : "VitalStatus", + "rdfs:comment" : "The survival state of the person registered on the protocol.", + "@type" : "rdfs:Class", + "sms:displayName" : "VitalStatus" }, { - "@id" : "bts:DissociationMethodEnum", + "@id" : "bts:ParentID", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DissociationMethodEnum", + "rdfs:comment" : "ID of parent biospecimen", + "rdfs:label" : "ParentID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DissociationMethodEnum", + "sms:displayName" : "ParentID", "sms:required" : "sms:false" }, { - "@id" : "bts:LibraryLayoutEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LibraryLayoutEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:FileFormat", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryLayoutEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:dat" + }, { + "@id" : "bts:Rscript" + }, { + "@id" : "bts:tif" + }, { + "@id" : "bts:bam" + }, { + "@id" : "bts:M" + }, { + "@id" : "bts:7z" + }, { + "@id" : "bts:csv" + }, { + "@id" : "bts:png" + }, { + "@id" : "bts:tar" + }, { + "@id" : "bts:bai" + }, { + "@id" : "bts:OME-TIFF" + }, { + "@id" : "bts:dup" + }, { + "@id" : "bts:hic" + }, { + "@id" : "bts:cellam" + }, { + "@id" : "bts:idat" + }, { + "@id" : "bts:txt" + }, { + "@id" : "bts:raw" + }, { + "@id" : "bts:hdf5" + }, { + "@id" : "bts:bgzip" + }, { + "@id" : "bts:seg" + }, { + "@id" : "bts:rmd" + }, { + "@id" : "bts:scn" + }, { + "@id" : "bts:vcf" + }, { + "@id" : "bts:maf" + }, { + "@id" : "bts:tsv" + }, { + "@id" : "bts:pdf" + }, { + "@id" : "bts:sam" + }, { + "@id" : "bts:bedgraph" + }, { + "@id" : "bts:sra" + }, { + "@id" : "bts:abf" + }, { + "@id" : "bts:fastq" + }, { + "@id" : "bts:pzfx" + }, { + "@id" : "bts:bednarrowPeak" + }, { + "@id" : "bts:fig" + }, { + "@id" : "bts:am" + }, { + "@id" : "bts:gct" + }, { + "@id" : "bts:tagAlign" + }, { + "@id" : "bts:gzip" + }, { + "@id" : "bts:gtf" + }, { + "@id" : "bts:DICOM" + }, { + "@id" : "bts:cloupe" + }, { + "@id" : "bts:czi" + }, { + "@id" : "bts:tiff" + }, { + "@id" : "bts:powerpoint" + }, { + "@id" : "bts:zip" + }, { + "@id" : "bts:bed" + }, { + "@id" : "bts:mex" + }, { + "@id" : "bts:ab1" + }, { + "@id" : "bts:Pythonscript" + }, { + "@id" : "bts:msf" + }, { + "@id" : "bts:mzML" + }, { + "@id" : "bts:svg" + }, { + "@id" : "bts:cel" + }, { + "@id" : "bts:mtx" + }, { + "@id" : "bts:bigwig" + }, { + "@id" : "bts:chp" + }, { + "@id" : "bts:svs" + }, { + "@id" : "bts:wiggle" + }, { + "@id" : "bts:mov" + }, { + "@id" : "bts:bcf" + }, { + "@id" : "bts:hyperlink" + }, { + "@id" : "bts:sdf" + }, { + "@id" : "bts:recal" + }, { + "@id" : "bts:idx" + }, { + "@id" : "bts:sif" + }, { + "@id" : "bts:json" + }, { + "@id" : "bts:avi" + }, { + "@id" : "bts:HEIC" + }, { + "@id" : "bts:gff3" + }, { + "@id" : "bts:bpm" + }, { + "@id" : "bts:bedbroadPeak" + }, { + "@id" : "bts:excel" + }, { + "@id" : "bts:flagstat" + }, { + "@id" : "bts:mpg" + }, { + "@id" : "bts:RData" + }, { + "@id" : "bts:Sentrixdescriptorfile" + }, { + "@id" : "bts:jpg" + }, { + "@id" : "bts:doc" + }, { + "@id" : "bts:bedgappedPeak" + }, { + "@id" : "bts:xml" + }, { + "@id" : "bts:sqlite" + }, { + "@id" : "bts:tranches" + }, { + "@id" : "bts:plink" + }, { + "@id" : "bts:sav" + }, { + "@id" : "bts:locs" + }, { + "@id" : "bts:html" + }, { + "@id" : "bts:md" + }, { + "@id" : "bts:fasta" + } ], + "rdfs:label" : "FileFormat", + "rdfs:comment" : "Format of a file (e.g. txt, csv, fastq, bam, etc.)", + "@type" : "rdfs:Class", + "sms:displayName" : "FileFormat" }, { - "@id" : "bts:BreastCancerAllredEstrogenReceptorScoreEnum", + "@id" : "bts:LinkedMatrices", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCancerAllredEstrogenReceptorScoreEnum", + "rdfs:label" : "LinkedMatrices", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCancerAllredEstrogenReceptorScoreEnum", + "sms:displayName" : "LinkedMatrices", "sms:required" : "sms:false" }, { - "@id" : "bts:PrecancerousConditionTypeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PrecancerousConditionTypeEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholExposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PrecancerousConditionTypeEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes-AlcoholExposure" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:No-AlcoholExposure" + } ], + "rdfs:label" : "AlcoholExposure", + "rdfs:comment" : "Indicate if individual has alcohol exposure", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholExposure" }, { - "@id" : "bts:VariantTypeEnum", + "@id" : "bts:ScRNAseqWorkflowParametersDescription", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "VariantTypeEnum", + "rdfs:label" : "ScRNAseqWorkflowParametersDescription", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "VariantTypeEnum", + "sms:displayName" : "ScRNAseqWorkflowParametersDescription", "sms:required" : "sms:false" }, { - "@id" : "bts:RelationshipTypeEnum", + "@id" : "bts:ExcitationBandwidth", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "RelationshipTypeEnum", + "rdfs:label" : "ExcitationBandwidth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RelationshipTypeEnum", + "sms:displayName" : "ExcitationBandwidth", "sms:required" : "sms:false" }, { - "@id" : "bts:SmokingExposureEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SmokingExposureEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:PriorInvasiveBreastDisease", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SmokingExposureEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:DCIS" + }, { + "@id" : "bts:LCIS" + }, { + "@id" : "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" + } ], + "rdfs:label" : "PriorInvasiveBreastDisease", + "rdfs:comment" : "Text term to indicate prior invasive breast condition in the participant", + "@type" : "rdfs:Class", + "sms:displayName" : "PriorInvasiveBreastDisease" }, { - "@id" : "bts:OvarianCancerPlatinumStatusEnum", + "@id" : "bts:SizeT", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OvarianCancerPlatinumStatusEnum", + "rdfs:comment" : "Number of time points. Integer >= 1", + "rdfs:label" : "SizeT", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OvarianCancerPlatinumStatusEnum", + "sms:displayName" : "SizeT", "sms:required" : "sms:false" }, { - "@id" : "bts:HistoneFamilyEnum", + "@id" : "bts:Intron", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HistoneFamilyEnum", + "rdfs:comment" : "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", + "rdfs:label" : "Intron", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HistoneFamilyEnum", + "sms:displayName" : "Intron", "sms:required" : "sms:false" }, { - "@id" : "bts:ChromosomeEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ChromosomeEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastCancerGenomicTestPerformed", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ChromosomeEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:OvarianCancerHistologicSubtypeEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Oncotype" + }, { + "@id" : "bts:MammaPrint" + }, { + "@id" : "bts:Notperformed" + } ], + "rdfs:label" : "BreastCancerGenomicTestPerformed", + "rdfs:comment" : "Text term that represents the name of the genomic test performed for breast cancer.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "OvarianCancerHistologicSubtypeEnum", + "sms:displayName" : "BreastCancerGenomicTestPerformed" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:EnvironmentalTobaccoSmokeExposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OvarianCancerHistologicSubtypeEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "EnvironmentalTobaccoSmokeExposure", + "rdfs:comment" : "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", + "@type" : "rdfs:Class", + "sms:displayName" : "EnvironmentalTobaccoSmokeExposure" }, { - "@id" : "bts:MicroscopyUnitEnum", + "@id" : "bts:ProtocolLink", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MicroscopyUnitEnum", + "rdfs:comment" : "URL to a free/open protocol resource describing the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", + "rdfs:label" : "ProtocolLink", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MicroscopyUnitEnum", + "sms:displayName" : "ProtocolLink", "sms:required" : "sms:false" }, { - "@id" : "bts:HistoryEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HistoryEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:RelativewithCancerHistory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HistoryEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes-CancerHistoryRelative" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:None" + } ], + "rdfs:label" : "RelativewithCancerHistory", + "rdfs:comment" : "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "@type" : "rdfs:Class", + "sms:displayName" : "RelativewithCancerHistory" }, { - "@id" : "bts:CauseofDeathEnum", + "@id" : "bts:LibraryPrepKitVendor", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CauseofDeathEnum", + "rdfs:comment" : "Vendor of Library Prep Kit. String", + "rdfs:label" : "LibraryPrepKitVendor", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CauseofDeathEnum", + "sms:displayName" : "LibraryPrepKitVendor", "sms:required" : "sms:false" }, { - "@id" : "bts:TestResultEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TestResultEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:PrecancerousConditionType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TestResultEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:CarcinomaNOS" + }, { + "@id" : "bts:Atypicalmelanocyticproliferation" + }, { + "@id" : "bts:Superficialspreading" + }, { + "@id" : "bts:Melanomainsituarisinginagiantcongenitalnevus" + }, { + "@id" : "bts:Invasivemelanoma" + }, { + "@id" : "bts:Invasivemelanoma-acrallentiginous" + }, { + "@id" : "bts:Melanomainsitunototherwiseclassified" + }, { + "@id" : "bts:Milddysplasia" + }, { + "@id" : "bts:Adenocarcinomainsitu-nonmucinous" + }, { + "@id" : "bts:Reservecellhyperplasia" + }, { + "@id" : "bts:Invasivemelanoma-nevoid" + }, { + "@id" : "bts:Nodiagnosispossible" + }, { + "@id" : "bts:Hamartoma" + }, { + "@id" : "bts:Adenocarcinomainsitu-mucinous" + }, { + "@id" : "bts:Squamousmetaplasia-immature" + }, { + "@id" : "bts:Severedysplasia" + }, { + "@id" : "bts:Invasivemelanoma-lentigomaligna" + }, { + "@id" : "bts:Squamousmetaplasia-mature" + }, { + "@id" : "bts:Acral-lentiginous" + }, { + "@id" : "bts:Invasivemelanoma-superficialspreading" + }, { + "@id" : "bts:Atypicaladenomatoushyperplasia" + }, { + "@id" : "bts:Moderatedysplasia" + }, { + "@id" : "bts:AtypicalAdenomatousLungHyperplasia" + }, { + "@id" : "bts:NormalWDA" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Persistentmelanomainsitu" + }, { + "@id" : "bts:PancreaticIntraepithelialNeoplasia" + }, { + "@id" : "bts:DuctalCarcinomaInSitu" + }, { + "@id" : "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" + }, { + "@id" : "bts:Melanocytichyperplasia" + }, { + "@id" : "bts:Melanomainsitu" + }, { + "@id" : "bts:Invasivemelanoma-desmoplastic" + }, { + "@id" : "bts:BenigntumorNOS" + }, { + "@id" : "bts:Lentigomalignatype" + }, { + "@id" : "bts:Scar-noresidualmelanoma" + }, { + "@id" : "bts:Invasivemelanoma-nodulartype" + }, { + "@id" : "bts:ProstaticIntraepithelialNeoplasia" + } ], + "rdfs:label" : "PrecancerousConditionType", + "rdfs:comment" : "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", + "@type" : "rdfs:Class", + "sms:displayName" : "PrecancerousConditionType" }, { - "@id" : "bts:AntigenEnum", + "@id" : "bts:CellBarcodeOffset", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AntigenEnum", + "rdfs:comment" : "Offset in sequence for cell barcode read (in bp): number", + "rdfs:label" : "CellBarcodeOffset", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AntigenEnum", + "sms:displayName" : "CellBarcodeOffset", "sms:required" : "sms:false" }, { - "@id" : "bts:MolecularConsequenceEnum", + "@id" : "bts:UMIBarcodeLength", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MolecularConsequenceEnum", + "rdfs:comment" : "Length of UMI barcode read (in bp): number", + "rdfs:label" : "UMIBarcodeLength", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MolecularConsequenceEnum", + "sms:displayName" : "UMIBarcodeLength", "sms:required" : "sms:false" }, { - "@id" : "bts:ReceptorStatusEnum", + "@id" : "bts:IschemicTime", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ReceptorStatusEnum", + "rdfs:comment" : "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", + "rdfs:label" : "IschemicTime", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ReceptorStatusEnum", + "sms:displayName" : "IschemicTime", "sms:required" : "sms:false" }, { - "@id" : "bts:TumorTissueTypeEnum", + "@id" : "bts:ProgressionorRecurrenceType", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TumorTissueTypeEnum", + "rdfs:label" : "ProgressionorRecurrenceType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TumorTissueTypeEnum", + "sms:displayName" : "ProgressionorRecurrenceType", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastQuadrantSiteEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastQuadrantSiteEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastQuadrantSiteEnum", - "sms:required" : "sms:false" - }, { - "@id" : "bts:PloidyEnum", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Beer" + }, { + "@id" : "bts:Liquor" + }, { + "@id" : "bts:Wine" + } ], + "rdfs:label" : "AlcoholType", + "rdfs:comment" : "Type of alcohol use", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "PloidyEnum", + "sms:displayName" : "AlcoholType" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:MismatchRepairMutation", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PloidyEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "MismatchRepairMutation", + "rdfs:comment" : "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "MismatchRepairMutation" }, { - "@id" : "bts:SpecimenLateralityEnum", + "@id" : "bts:Filename", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SpecimenLateralityEnum", + "rdfs:label" : "Filename", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SpecimenLateralityEnum", + "sms:displayName" : "Filename", "sms:required" : "sms:false" }, { - "@id" : "bts:FamilyMemberVitalStatusIndicatorEnum", + "@id" : "bts:AdapterName", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "FamilyMemberVitalStatusIndicatorEnum", + "rdfs:comment" : "Name of the sequencing adapter. String", + "rdfs:label" : "AdapterName", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FamilyMemberVitalStatusIndicatorEnum", + "sms:displayName" : "AdapterName", "sms:required" : "sms:false" }, { - "@id" : "bts:SequencingPlatformEnum", + "@id" : "bts:CountryofBirth", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SequencingPlatformEnum", + "rdfs:label" : "CountryofBirth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SequencingPlatformEnum", + "sms:displayName" : "CountryofBirth", "sms:required" : "sms:false" }, { - "@id" : "bts:VariantOriginEnum", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "VariantOriginEnum", "rdfs:subClassOf" : [ ], + "@id" : "bts:LibraryConstructionMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "VariantOriginEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:10xV3" + }, { + "@id" : "bts:inDropsV2" + }, { + "@id" : "bts:10xV1.1" + }, { + "@id" : "bts:10xV3.1" + }, { + "@id" : "bts:Drop-seq" + }, { + "@id" : "bts:10xV2" + }, { + "@id" : "bts:10xV1.0" + }, { + "@id" : "bts:Smart-seq2" + }, { + "@id" : "bts:Smart-SeqV4" + }, { + "@id" : "bts:sci-ATAC-seq" + }, { + "@id" : "bts:inDropsV3" + }, { + "@id" : "bts:CEL-seq2" + }, { + "@id" : "bts:TruDrop" + } ], + "rdfs:label" : "LibraryConstructionMethod", + "rdfs:comment" : "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", + "@type" : "rdfs:Class", + "sms:displayName" : "LibraryConstructionMethod" }, { - "@id" : "bts:AnaplasiaPresentTypeEnum", + "@id" : "bts:OtherBiopsyResectionSite", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AnaplasiaPresentTypeEnum", + "rdfs:comment" : "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under Clinical Data Tier 1)", + "rdfs:label" : "OtherBiopsyResectionSite", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AnaplasiaPresentTypeEnum", + "sms:displayName" : "OtherBiopsyResectionSite", "sms:required" : "sms:false" }, { - "@id" : "bts:TranspositionReactionEnum", + "@id" : "bts:MedianPassingReadPercentage", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TranspositionReactionEnum", + "rdfs:comment" : "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", + "rdfs:label" : "MedianPassingReadPercentage", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TranspositionReactionEnum", + "sms:displayName" : "MedianPassingReadPercentage", "sms:required" : "sms:false" }, { - "@id" : "bts:EndBiasEnum", - "@type" : "rdfs:Class", + "rdfs:subClassOf" : [ ], + "@id" : "bts:ReadIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:I1" + }, { + "@id" : "bts:R1" + }, { + "@id" : "bts:R2" + }, { + "@id" : "bts:R1&R2" + }, { + "@id" : "bts:R3" + }, { + "@id" : "bts:NotApplicable" + } ], + "rdfs:label" : "ReadIndicator", "rdfs:comment" : "TBD", - "rdfs:label" : "EndBiasEnum", + "@type" : "rdfs:Class", + "sms:displayName" : "ReadIndicator" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EndBiasEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Alveolartype" + }, { + "@id" : "bts:Classicaltype" + }, { + "@id" : "bts:Pleomorphictype" + } ], + "rdfs:label" : "InvasiveLobularBreastCarcinomaHistologicCategory", + "rdfs:comment" : "The histologic subtype for an infiltrating lobular carcinoma of the breast.", + "@type" : "rdfs:Class", + "sms:displayName" : "InvasiveLobularBreastCarcinomaHistologicCategory" }, { - "@id" : "bts:HistoneVariantEnum", + "rdfs:subClassOf" : [ ], + "@id" : "bts:TumorExtranodalExtensionIndicator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Absent" + }, { + "@id" : "bts:Notapplicable" + }, { + "@id" : "bts:YES" + }, { + "@id" : "bts:unspecified" + }, { + "@id" : "bts:Nosourcedocumentation" + }, { + "@id" : "bts:UNKNOWN" + }, { + "@id" : "bts:Present" + }, { + "@id" : "bts:Present-extensive" + }, { + "@id" : "bts:Notsampledordissected" + }, { + "@id" : "bts:Present-minimal" + }, { + "@id" : "bts:NO" + }, { + "@id" : "bts:Indeterminate" + } ], + "rdfs:label" : "TumorExtranodalExtensionIndicator", + "rdfs:comment" : "The indicator to determine extranodal involvement or extent of the disease.", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "HistoneVariantEnum", + "sms:displayName" : "TumorExtranodalExtensionIndicator" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:ERReceptorStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HistoneVariantEnum", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Borderline" + }, { + "@id" : "bts:Equivocal" + }, { + "@id" : "bts:Indeterminate" + }, { + "@id" : "bts:Negative" + }, { + "@id" : "bts:NotPerformed" + }, { + "@id" : "bts:PerformedbutNotAvailable" + }, { + "@id" : "bts:Positive" + } ], + "rdfs:label" : "ERReceptorStatus", + "rdfs:comment" : "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "ERReceptorStatus" }, { - "@id" : "bts:BreastCarcinomaHistologyCategoryEnum", + "@id" : "bts:Comment", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "BreastCarcinomaHistologyCategoryEnum", + "rdfs:comment" : "Free text field (generally for QC comment)", + "rdfs:label" : "Comment", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHistologyCategoryEnum", + "sms:displayName" : "Comment", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastImagingPerformedTypeEnum", + "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastQuadrantSite", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:Upperouterquadrant" + }, { + "@id" : "bts:Lowerouterquadrant" + }, { + "@id" : "bts:Upperinnerquadrant" + }, { + "@id" : "bts:Lowerinnerquadrant" + }, { + "@id" : "bts:Central" + }, { + "@id" : "bts:Nipple" + } ], + "rdfs:label" : "BreastQuadrantSite", + "rdfs:comment" : "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastQuadrantSite" + }, { + "@id" : "bts:LinkedDatasets", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "BreastImagingPerformedTypeEnum", + "rdfs:label" : "LinkedDatasets", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastImagingPerformedTypeEnum", + "sms:displayName" : "LinkedDatasets", "sms:required" : "sms:false" }, { - "@id" : "bts:AlcoholExposureEnum", + "@id" : "bts:BreastCarcinomaHER2Chromosome17Ratio", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholExposureEnum", + "rdfs:comment" : "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label" : "BreastCarcinomaHER2Chromosome17Ratio", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AlcoholExposureEnum", + "sms:displayName" : "BreastCarcinomaHER2Chromosome17Ratio", "sms:required" : "sms:false" }, { - "@id" : "bts:SlideChargeTypeEnum", + "@id" : "bts:PhysicalSizeY", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SlideChargeTypeEnum", + "rdfs:comment" : "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. 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"rdfs:label" : "AnalyteBiospecimenType", - "rdfs:comment" : "TBD", + "sms:displayName" : "CellBarcodeLength", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ClassBRCA1", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:AnalyteType" - }, { - "@id" : "bts:FixationDuration" - }, { - "@id" : "bts:SlideChargeType" - }, { - "@id" : "bts:SectionThicknessValue" - }, { - "@id" : "bts:SectioningDaysfromIndex" - }, { - "@id" : "bts:ShippingConditionType" - }, { - "@id" : "bts:IschemicTime" - }, { - "@id" : "bts:IschemicTemperature" - } ], - "sms:displayName" : "AnalyteBiospecimenType" + "rdfs:comment" : "TBD", + "rdfs:label" : "ClassBRCA1", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ClassBRCA1", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Exposure" - } ], - "@id" : "bts:Yes-AlcoholExposure", + "@id" : "bts:SectionNumberinSequence", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)", + "rdfs:label" : "SectionNumberinSequence", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Yes-AlcoholExposure", + "sms:displayName" : "SectionNumberinSequence", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SampleCollectionCenter", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "SampleCollectionCenter", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleCollectionCenter", + "sms:required" : "sms:false" + }, { + "@id" : "bts:CopyNumber", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:StartDaysfromIndex" - }, { - "@id" : "bts:SmokingExposure" - }, { - "@id" : "bts:AlcoholExposure" - }, { - "@id" : "bts:EnvironmentalTobaccoSmokeExposure" - }, { - "@id" : "bts:AlcoholDaysPerWeek" - }, { - "@id" : "bts:AlcoholDrinksPerDay" - }, { - "@id" : "bts:AlcoholHistory" - }, { - "@id" : "bts:AlcoholIntensity" - }, { - "@id" : "bts:AlcoholType" - } ], - "sms:displayName" : "Yes-AlcoholExposure" + "rdfs:comment" : "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "CopyNumber", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "CopyNumber", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:File" - } ], - "@id" : "bts:BulkMethylation-seqLevel3", + "@id" : "bts:SectioningDaysfromIndex", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of days from the research participant's index date that the biospecimen was sectioned after collection", + "rdfs:label" : "SectioningDaysfromIndex", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SectioningDaysfromIndex", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Immersion", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BulkMethylation-seqLevel3", - "rdfs:comment" : "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:DMCallingTool" + "schema:rangeIncludes" : [ { + "@id" : "bts:Air" }, { - "@id" : "bts:WorkflowLink" + "@id" : "bts:Oil" }, { - "@id" : "bts:PUC19methylationratio" + "@id" : "bts:Water" }, { - "@id" : "bts:Lambdamethylationratio" + "@id" : "bts:Other" } ], - "sms:displayName" : "BulkMethylation-seqLevel3" + "rdfs:label" : "Immersion", + "rdfs:comment" : "Immersion medium", + "@type" : "rdfs:Class", + "sms:displayName" : "Immersion" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel1", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Pyramid", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel1", - "rdfs:comment" : "TBD", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "Pyramid", + "rdfs:comment" : "Does data file contain pyramid of images", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" + "sms:displayName" : "Pyramid" + }, { + "@id" : "bts:SampleSite", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SampleSite", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleSite", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MismatchRepairSystemStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:MismatchrepairdeficiencyMMRD" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:MismatchrepairproficiencyMMPP" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:MicrosatelliteinstabilityhighMSIH" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:MicrosatellitestableMSS" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:unknownorother" + } ], + "rdfs:label" : "MismatchRepairSystemStatus", + "rdfs:comment" : "The text that best describes the condition or state of MMR (mismatch repair system) in the patient", + "@type" : "rdfs:Class", + "sms:displayName" : "MismatchRepairSystemStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Tseries", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:No" + } ], + "rdfs:label" : "Tseries", + "rdfs:comment" : "Does data file contain a time-series of images", + "@type" : "rdfs:Class", + "sms:displayName" : "Tseries" + }, { + "@id" : "bts:Component", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Component", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Component", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RelativeswithCancerHistoryCount", + "@type" : "rdfs:Class", + "rdfs:comment" : "The number of relatives the patient has with a known history of cancer.", + "rdfs:label" : "RelativeswithCancerHistoryCount", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelativeswithCancerHistoryCount", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholDrinksPerDay", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the average number of alcoholic beverages a person consumes per day.", + "rdfs:label" : "AlcoholDrinksPerDay", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholDrinksPerDay", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:EndBias", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:3Prime" }, { - 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Determines which nucleus the reads originated from", + "@type" : "rdfs:Class", + "sms:displayName" : "NucleusIdentifier" + }, { + "@id" : "bts:Title", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Title", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Title", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ClinicalBiospecimenType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:ConnectiveTissue" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:PeritonealFluid" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:NotReported" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:Saliva" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:TissueNOS" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:Skin" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:unknown" }, { - "@id" : "bts:BatchID" + "@id" : "bts:Feces" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:UninvolvedTissueNOS" }, { - "@id" : "bts:TechnicalReplicateGroup" + "@id" : "bts:Plasma" }, { - "@id" : "bts:DissociationMethod" + "@id" : "bts:Granulocyte" }, { - "@id" : "bts:CryopreservedCellsinSample" + "@id" : "bts:EmbryonicTissue" }, { - "@id" : "bts:SingleCellIsolationMethod" + "@id" : "bts:BuccalMucosa" }, { - "@id" : "bts:TotalNumberofInputCells" + "@id" : "bts:Blood" }, { - "@id" : "bts:InputCellsandNuclei" + "@id" : "bts:MuscleTissue" }, { - "@id" : "bts:ReverseTranscriptionPrimer" + "@id" : "bts:CerebrospinalFluid" }, { - "@id" : "bts:SpikeIn" + "@id" : "bts:SoftTissue" }, { - "@id" : "bts:EndBias" + "@id" : "bts:Urine" }, { - "@id" : "bts:UMIBarcodeOffset" + "@id" : "bts:PleuralFluid" }, { - "@id" : "bts:UMIBarcodeLength" + "@id" : "bts:BoneMarrow" }, { - "@id" : "bts:MedianUMIsperCellNumber" + "@id" : "bts:Serum" }, { - "@id" : "bts:CellBarcodeOffset" + "@id" : "bts:EmbryonicFluid" }, { - "@id" : "bts:CellBarcodeLength" + "@id" : "bts:NerveTissue" }, { - "@id" : "bts:ValidBarcodesCellNumber" + "@id" : "bts:BuffyCoat" } ], - "sms:displayName" : "ScRNA-seqLevel1" + "rdfs:label" : "ClinicalBiospecimenType", + "rdfs:comment" : "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "ClinicalBiospecimenType" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:BreastCancerPatient", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Antigen", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BreastCancerPatient", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "schema:rangeIncludes" : [ { + "@id" : "bts:CA19-9" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:CD79A" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:CD5" }, { - "@id" : "bts:BreastCarcinomaDetectionMethodType" + "@id" : "bts:CD30" }, { - "@id" : "bts:BreastCarcinomaHistologyCategory" + "@id" : "bts:NotReported" }, { - "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + "@id" : "bts:CD20" }, { - "@id" : "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + "@id" : "bts:CD14" }, { - "@id" : "bts:BreastBiopsyProcedureFindingType" + "@id" : "bts:CD19" }, { - "@id" : "bts:BreastQuadrantSite" + "@id" : "bts:unknown" }, { - "@id" : "bts:BreastCancerAssessmentTests" + "@id" : "bts:CD34" }, { - "@id" : "bts:BreastCancerGenomicTestPerformed" + "@id" : "bts:CCND1" }, { - "@id" : "bts:MammaprintRiskGroup" + "@id" : "bts:CD25" }, { - "@id" : "bts:OncotypeRiskGroup" + "@id" : "bts:HLA-DR" }, { - "@id" : "bts:ERReceptorStatus" + "@id" : "bts:Mesothelin" }, { - "@id" : "bts:PRReceptorStatus" + "@id" : "bts:CD10" }, { - "@id" : "bts:BreastCancerAllredEstrogenReceptorScore" + "@id" : "bts:CD56" }, { - "@id" : "bts:PriorInvasiveBreastDisease" + "@id" : "bts:CD3" }, { - "@id" : "bts:BreastCarcinomaERStatusPercentageValue" + "@id" : "bts:NSE" }, { - "@id" : "bts:BreastCarcinomaPRStatusPercentageValue" + "@id" : "bts:CA-125" }, { - "@id" : "bts:HER2BreastCarcinomaCopyNumberTotal" + "@id" : "bts:CD22" }, { - "@id" : "bts:BreastCarcinomaCentromere17CopyNumber" + "@id" : "bts:CD23" }, { - "@id" : "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" + "@id" : "bts:SquamousCellCarcinomaAntigen" }, { - "@id" : "bts:BreastCarcinomaHER2Chromosome17Ratio" + "@id" : "bts:CEA" }, { - "@id" : "bts:BreastCarcinomaSurgicalProcedureName" + "@id" : "bts:CD33" }, { - "@id" : "bts:BreastCarcinomaHER2RatioDiagnosis" + "@id" : "bts:CD138" }, { - "@id" : "bts:BreastCarcinomaHER2Status" + "@id" : "bts:BCL6" }, { - "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicator" + "@id" : "bts:CD7" }, { - "@id" : "bts:ERStainingIntensity" + "@id" : "bts:CD117" }, { - "@id" : "bts:PRStainingIntensity" + "@id" : "bts:CD15" }, { - "@id" : "bts:OncotypeScore" + "@id" : "bts:CD45" + } ], + "rdfs:label" : "Antigen", + "rdfs:comment" : "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Antigen" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:OncotypeRiskGroup", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:BreastImagingPerformedType" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:MultifocalBreastCarcinomaPresentIndicator" + "@id" : "bts:Highrisk" }, { - "@id" : "bts:MulticentricBreastCarcinomaPresentIndicator" + "@id" : "bts:Intermediaterisk" }, { - "@id" : "bts:BIRADSMammographyBreastDensityCategory" + "@id" : "bts:Lowrisk" } ], - "sms:displayName" : "BreastCancerPatient" + "rdfs:label" : "OncotypeRiskGroup", + "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "@type" : "rdfs:Class", + "sms:displayName" : "OncotypeRiskGroup" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:Patient", + "@id" : "bts:ModeofCancerDetection", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Patient", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "schema:rangeIncludes" : [ { + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:StandardofCareScreening" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:ClinicalExaminationofunrelatedcancersymptoms" + }, { + "@id" : "bts:Incidentaloma" + }, { + "@id" : "bts:IntervalCancer" } ], - "sms:displayName" : "Patient" + "rdfs:label" : "ModeofCancerDetection", + "rdfs:comment" : "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", + "@type" : "rdfs:Class", + "sms:displayName" : "ModeofCancerDetection" + }, { + "@id" : "bts:RelationshipType", + "@type" : "rdfs:Class", + "rdfs:comment" : "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.", + "rdfs:label" : "RelationshipType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelationshipType", + "sms:required" : "sms:false" }, { + "@id" : "bts:FeatureReferenceId", + "@type" : "rdfs:Class", + "rdfs:comment" : "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", + "rdfs:label" : "FeatureReferenceId", "rdfs:subClassOf" : [ ], - "@id" : "bts:File", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "File", - "rdfs:comment" : "Basic metadata for a file entity that contains data (whether sequencing, imaging, etc.) will inherit.", + "sms:displayName" : "FeatureReferenceId", + "sms:required" : "sms:false" + }, { + "@id" : "bts:RelationshipAgeatDiagnosis", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "rdfs:comment" : "The age (in years) when the patient's relative was first diagnosed.", + "rdfs:label" : "RelationshipAgeatDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "RelationshipAgeatDiagnosis", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SmokingExposure", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes-SmokingExposure" }, { - "@id" : "bts:Filename" + "@id" : "bts:NotReported" }, { - "@id" : "bts:FileFormat" + "@id" : "bts:No-SmokingExposure" } ], - "sms:displayName" : "File" + "rdfs:label" : "SmokingExposure", + "rdfs:comment" : "Indicate if individual has smoking exposure", + "@type" : "rdfs:Class", + "sms:displayName" : "SmokingExposure" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel2", + "@id" : "bts:AltSampleID", + "@type" : "rdfs:Class", + "rdfs:comment" : "Additional alternative ID associated with a biosample", + "rdfs:label" : "AltSampleID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AltSampleID", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:TestResult", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel2", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" + "schema:rangeIncludes" : [ { + "@id" : "bts:Normal" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:NotReported" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:TestValueReported" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:unknown" }, { - "@id" : "bts:LibraryPrepKitName" + "@id" : "bts:Overexpressed" }, { - "@id" : "bts:LibraryPrepKitVersion" + "@id" : "bts:Intermediate" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:NotApplicable" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:LossofExpression" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:Low" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:High" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:Equivocal" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:CopyNumberReported" }, { - "@id" : "bts:BatchID" + "@id" : "bts:Positive" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:Negative" }, { - "@id" : "bts:TechnicalReplicateGroup" + "@id" : "bts:AbnormalNOS" + } ], + "rdfs:label" : "TestResult", + "rdfs:comment" : "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "TestResult" + }, { + "@id" : "bts:DMCallingTool", + "@type" : "rdfs:Class", + "rdfs:comment" : "Software used for calling differentially methylated CpG (DMC) and/or differentially methylated region (DMR)", + "rdfs:label" : "DMCallingTool", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DMCallingTool", + "sms:required" : "sms:false" + }, { + "@id" : "bts:MedianFractionofReadsinAnnotatedcisDNAElements", + "@type" : "rdfs:Class", + "rdfs:comment" : "Median fraction of reads in annotated cis-DNA elements (FRIADE)", + "rdfs:label" : "MedianFractionofReadsinAnnotatedcisDNAElements", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "MedianFractionofReadsinAnnotatedcisDNAElements", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Zygosity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:DissociationMethod" + "@id" : "bts:NotReported" }, { - "@id" : "bts:CryopreservedCellsinSample" + "@id" : "bts:Heterozygous" }, { - "@id" : "bts:SingleCellIsolationMethod" + "@id" : "bts:Hemizygous" }, { - "@id" : "bts:TotalNumberofInputCells" + "@id" : "bts:Homozygous" }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:ScRNAseqWorkflowType" - }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription" - }, { - "@id" : "bts:WorkflowVersion" - }, { - "@id" : "bts:WorkflowLink" + "@id" : "bts:Nullizygous" + } ], + "rdfs:label" : "Zygosity", + "rdfs:comment" : "The text term used to describe the zygosity of a specific genetic variant.", + "@type" : "rdfs:Class", + "sms:displayName" : "Zygosity" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BreastImagingPerformedType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:GenomicReference" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:GenomicReferenceURL" + "@id" : "bts:Mammogram" }, { - "@id" : "bts:GenomeAnnotationURL" + "@id" : "bts:Ultrasound" }, { - "@id" : "bts:WhitelistCellBarcodeFileLink" + "@id" : "bts:MRI" }, { - "@id" : "bts:CellBarcodeTag" + "@id" : "bts:PET/CT" }, { - "@id" : "bts:UMITag" + "@id" : "bts:CT" }, { - "@id" : "bts:AppliedHardTrimming" + "@id" : "bts:Multipleimagingmodalities" } ], - "sms:displayName" : "ScRNA-seqLevel2" + "rdfs:label" : "BreastImagingPerformedType", + "rdfs:comment" : "The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastImagingPerformedType" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Diagnosis" - } ], - "@id" : "bts:Yes-VascularInvasionPresent", + "@id" : "bts:PackYearsSmoked", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.", + "rdfs:label" : "PackYearsSmoked", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Yes-VascularInvasionPresent", - "rdfs:comment" : "TBD", + "sms:displayName" : "PackYearsSmoked", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TobaccoUseperDay", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:VascularInvasionType" - } ], - "sms:displayName" : "Yes-VascularInvasionPresent" + "rdfs:comment" : "Numeric value that represents the number of times the patient uses tobacco each day.", + "rdfs:label" : "TobaccoUseperDay", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TobaccoUseperDay", + "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SequencingData" - } ], - "@id" : "bts:SingleCellSequencing", + "@id" : "bts:TechnicalReplicateGroup", + "@type" : "rdfs:Class", + "rdfs:comment" : "A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)", + "rdfs:label" : "TechnicalReplicateGroup", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "SingleCellSequencing", + "sms:displayName" : "TechnicalReplicateGroup", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Dilution", + "@type" : "rdfs:Class", "rdfs:comment" : "TBD", + "rdfs:label" : "Dilution", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Dilution", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FOVY", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "rdfs:comment" : "Field of view Y dimension. Floating point value", + "rdfs:label" : "FOVY", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "FOVY", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SiteofResectionorBiopsy", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Tonsillarfossa" }, { - "@id" : "bts:Filename" + "@id" : "bts:Overlappinglesionoflung" }, { - "@id" : "bts:FileFormat" + "@id" : "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:Endometrium" }, { - "@id" : "bts:SampleID" + "@id" : "bts:BoneoflimbNOS" }, { - "@id" : "bts:AltSampleID" + "@id" : "bts:Posteriorwallofnasopharynx" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:SmallintestineNOS" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:Anteriorwallofnasopharynx" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:Thoracicesophagus" }, { - 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"@id" : "bts:Weight" + "@id" : "bts:Posteriorwalloforopharynx" }, { - "@id" : "bts:Gravidity" + "@id" : "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id" : "bts:Parity" + "@id" : "bts:Undescendedtestis" }, { - "@id" : "bts:AgeAtMenarche" + "@id" : "bts:Nasalcavity" }, { - "@id" : "bts:MenstrualCyclePhase" + "@id" : "bts:Cerebralmeninges" }, { - "@id" : "bts:MenopauseStatus" + "@id" : "bts:Overlappinglesionoffloorofmouth" }, { - "@id" : "bts:PrimaryDiagnosis" + "@id" : "bts:Overlappinglesionofcorpusuteri" }, { - "@id" : "bts:AgeatDiagnosis" + "@id" : "bts:LipNOS" }, { - "@id" : "bts:DiagnosisStatusType" + "@id" : "bts:Cheekmucosa" }, { - "@id" : "bts:ClassBRCA1" + "@id" : "bts:UpperlimbNOS" }, { - "@id" : "bts:ClassBRCA2" + "@id" : "bts:Domeofbladder" }, { - "@id" : "bts:TobaccoUse" + "@id" : "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id" : "bts:PackYearsSmoked" + "@id" : "bts:unknownprimarysite" }, { - "@id" : "bts:AlcoholUse" + "@id" : "bts:Posteriormediastinum" }, { - "@id" : "bts:NumberofDrinksPerWeek" + "@id" : "bts:Uretericorifice" }, { - "@id" : "bts:AntibioticUse" + "@id" : "bts:Otherill-definedsites" }, { - "@id" : "bts:SampleCollectionCenter" + "@id" : "bts:Bonemarrow" }, { - "@id" : "bts:SampleCollectionYear" + "@id" : "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" }, { - "@id" : "bts:ERStatus" + "@id" : "bts:LymphnodeNOS" }, { - "@id" : "bts:PRStatus" + "@id" : "bts:Skinofscalpandneck" }, { - "@id" : "bts:HER2Status" - } ], - "sms:displayName" : "CohortCoreTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:TissueBiospecimenType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "TissueBiospecimenType", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" + "@id" : "bts:Retromolararea" }, { - "@id" : "bts:ParentID" + "@id" : "bts:Overlappinglesionofliporalcavityandpharynx" }, { - "@id" : "bts:ParentBiospecimenID" + "@id" : "bts:Overlappinglesionofaccessorysinuses" }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "@id" : "bts:Overlappinglesionofpenis" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:Overlappinglesionofvulva" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:Overlappinglesionofill-definedsites" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:Occipitallobe" }, { - "@id" : "bts:IschemicTime" + "@id" : "bts:Overlappinglesionofeyeandadnexa" }, { - "@id" : "bts:IschemicTemperature" + "@id" : "bts:Lingualtonsil" }, { - "@id" : "bts:SiteofResectionorBiopsy" + "@id" : "bts:GumNOS" }, { - "@id" : "bts:PortionWeight" + "@id" : "bts:Thymus" }, { - "@id" : "bts:TotalVolume" + "@id" : "bts:MalegenitalorgansNOS" }, { - "@id" : "bts:TumorTissueType" + "@id" : "bts:IsletsofLangerhans" }, { - "@id" : "bts:HistologicMorphologyCode" + "@id" : "bts:Isthmusuteri" }, { - "@id" : "bts:PreservationMethod" + "@id" : "bts:Spinalmeninges" }, { - "@id" : "bts:BiospecimenDimension1" + "@id" : "bts:Myometrium" }, { - "@id" : "bts:BiospecimenDimension2" + "@id" : "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id" : "bts:BiospecimenDimension3" + "@id" : "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id" : "bts:SectionNumberinSequence" - } ], - "sms:displayName" : "TissueBiospecimenType" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:FamilyHistory", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "FamilyHistory", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:Anterior2/3oftongueNOS" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:Upperthirdofesophagus" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:MeningesNOS" }, { - "@id" : "bts:RelativewithCancerHistory" - } ], - "sms:displayName" : "FamilyHistory" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:SingleCellSequencing" - } ], - "@id" : "bts:ScRNA-seqLevel4", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNA-seqLevel4", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:Prostategland" }, { - "@id" : "bts:Filename" + "@id" : "bts:Overlappinglesionofsmallintestine" }, { - "@id" : "bts:FileFormat" + "@id" : "bts:Lowergum" }, { - "@id" : "bts:ParticipantID" + "@id" : "bts:Paraspinal" }, { - "@id" : "bts:SampleID" + "@id" : "bts:Appendix" }, { - "@id" : "bts:AltSampleID" + "@id" : "bts:ScrotumNOS" }, { - "@id" : "bts:SequencingPlatform" + "@id" : "bts:Overlappinglesionoflarynx" }, { - "@id" : "bts:NucleicAcidSource" + "@id" : "bts:Mainbronchus" }, { - "@id" : "bts:LibraryConstructionMethod" + "@id" : "bts:Descendedtestis" }, { - "@id" : "bts:LibrarySelectionMethod" + "@id" : "bts:Cloacogeniczone" }, { - "@id" : "bts:LibraryLayout" + "@id" : "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" }, { - "@id" : "bts:LibraryPrepKitName" + "@id" : "bts:Heart" }, { - "@id" : "bts:LibraryPrepKitVersion" + "@id" : "bts:MucosaoflipNOS" }, { - "@id" : "bts:LibraryPrepKitVendor" + "@id" : "bts:Broadligament" }, { - "@id" : "bts:ReadIndicator" + "@id" : "bts:Headofpancreas" }, { - "@id" : "bts:ReadContent" + "@id" : "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id" : "bts:TargetDepth" + "@id" : "bts:Temporallobe" }, { - "@id" : "bts:AdapterName" + "@id" : "bts:Bodyofpenis" }, { - "@id" : "bts:AdapterSequence" + "@id" : "bts:Overlappinglesionofbiliarytract" }, { - "@id" : "bts:BatchID" + "@id" : "bts:Labiumminus" }, { - "@id" : "bts:LaneNumber" + "@id" : "bts:Descendingcolon" }, { - "@id" : "bts:TechnicalReplicateGroup" + "@id" : "bts:Lateralwallofnasopharynx" }, { - "@id" : "bts:DissociationMethod" + "@id" : "bts:Posteriorwallofhypopharynx" }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" + "@id" : "bts:Nipple" }, { - "@id" : "bts:TotalNumberofInputCells" + "@id" : "bts:Jejunum" }, { - "@id" : "bts:InputCellsandNuclei" + "@id" : "bts:Posteriorwallofbladder" }, { - "@id" : "bts:ReverseTranscriptionPrimer" + "@id" : "bts:Laryngealcartilage" }, { - "@id" : "bts:SpikeIn" + "@id" : "bts:Cecum" }, { - "@id" : "bts:EndBias" + "@id" : "bts:Skinoflowerlimbandhip" }, { - "@id" : "bts:DataCategory" + "@id" : "bts:Corpusuteri" }, { - "@id" : "bts:MatrixType" + "@id" : "bts:FemalegenitaltractNOS" }, { - "@id" : "bts:LinkedMatrices" + "@id" : "bts:AbdomenNOS" }, { - "@id" : "bts:CellMedianNumberReads" + "@id" : "bts:Tonsillarpillar" }, { - "@id" : "bts:CellMedianNumberGenes" + "@id" : "bts:Otherspecifiedpartsoffemalegenitalorgans" }, { - "@id" : "bts:CellTotal" + "@id" : "bts:Glottis" }, { - "@id" : "bts:ScRNAseqWorkflowType" + "@id" : "bts:OrbitNOS" }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription" + "@id" : "bts:Skinoftrunk" }, { - "@id" : "bts:WorkflowLink" + "@id" : "bts:VentricleNOS" }, { - "@id" : "bts:WorkflowVersion" + "@id" : "bts:Frontallobe" } ], - "sms:displayName" : "ScRNA-seqLevel4" + "rdfs:label" : "SiteofResectionorBiopsy", + "rdfs:comment" : "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "@type" : "rdfs:Class", + "sms:displayName" : "SiteofResectionorBiopsy" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Patient" - } ], - "@id" : "bts:Demographics", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Clonality", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Demographics", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:Ethnicity" - }, { - "@id" : "bts:Gender" - }, { - "@id" : "bts:Race" - }, { - "@id" : "bts:VitalStatus" - }, { - "@id" : "bts:DaystoBirth" - }, { - "@id" : "bts:CountryofResidence" - }, { - "@id" : "bts:AgeIsObfuscated" + "schema:rangeIncludes" : [ { + "@id" : "bts:Clonal" }, { - "@id" : "bts:YearOfBirth" + "@id" : "bts:Non-clonal" } ], - "sms:displayName" : "Demographics" + "rdfs:label" : "Clonality", + "rdfs:comment" : "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Clonality" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:ScRNA-seqLevel1" - } ], - "@id" : "bts:CEL-seq2", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Sex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "CEL-seq2", - "rdfs:comment" : "Highly-multiplexed plate-based single-cell RNA-Seq assay (so a subtype of scRNA-seq, and some additional metadata parameters are collected)", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" - }, { - "@id" : "bts:Filename" - }, { - "@id" : "bts:FileFormat" - }, { - "@id" : "bts:ParticipantID" - }, { - "@id" : "bts:SampleID" - }, { - "@id" : "bts:AltSampleID" - }, { - "@id" : "bts:SequencingPlatform" - }, { - "@id" : "bts:NucleicAcidSource" - }, { - "@id" : "bts:LibraryConstructionMethod" - }, { - "@id" : "bts:LibrarySelectionMethod" - }, { - "@id" : "bts:LibraryLayout" - }, { - "@id" : "bts:LibraryPrepKitName" - }, { - "@id" : "bts:LibraryPrepKitVersion" - }, { - "@id" : "bts:LibraryPrepKitVendor" - }, { - "@id" : "bts:ReadIndicator" - }, { - "@id" : "bts:ReadContent" - }, { - "@id" : "bts:TargetDepth" - }, { - "@id" : "bts:AdapterName" - }, { - "@id" : "bts:AdapterSequence" - }, { - "@id" : "bts:BatchID" - }, { - "@id" : "bts:LaneNumber" - }, { - "@id" : "bts:TechnicalReplicateGroup" - }, { - "@id" : "bts:DissociationMethod" - }, { - "@id" : "bts:CryopreservedCellsinSample" - }, { - "@id" : "bts:SingleCellIsolationMethod" - }, { - "@id" : "bts:TotalNumberofInputCells" - }, { - "@id" : "bts:InputCellsandNuclei" - }, { - "@id" : "bts:ReverseTranscriptionPrimer" - }, { - "@id" : "bts:SpikeIn" - }, { - "@id" : "bts:EndBias" - }, { - "@id" : "bts:UMIBarcodeOffset" - }, { - "@id" : "bts:UMIBarcodeLength" - }, { - "@id" : "bts:MedianUMIsperCellNumber" - }, { - "@id" : "bts:CellBarcodeOffset" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:CellBarcodeLength" + "@id" : "bts:NotReported" }, { - "@id" : "bts:ValidBarcodesCellNumber" + "@id" : "bts:female" }, { - "@id" : "bts:EmptyWellBarcode" + "@id" : "bts:male" }, { - "@id" : "bts:WellIndex" + "@id" : "bts:unspecified" } ], - "sms:displayName" : "CEL-seq2" + "rdfs:label" : "Sex", + "rdfs:comment" : "Sex of individual", + "@type" : "rdfs:Class", + "sms:displayName" : "Sex" + }, { + "@id" : "bts:YearOfBirth", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label" : "YearOfBirth", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "YearOfBirth", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:Biospecimen", + "@id" : "bts:FOVXUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "Biospecimen", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "@id" : "bts:mm" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:µm" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:nm" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:Å" } ], - "sms:displayName" : "Biospecimen" + "rdfs:label" : "FOVXUnit", + "rdfs:comment" : "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "FOVXUnit" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:BiospecimenDimension1", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Pathogenicity", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BiospecimenDimension1", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" + "schema:rangeIncludes" : [ { + "@id" : "bts:Benign" }, { - "@id" : "bts:BiospecimenType" + "@id" : "bts:LikelyBenign" }, { - "@id" : "bts:TimepointLabel" + "@id" : "bts:LikelyPathogenic" }, { - "@id" : "bts:SpecimenLaterality" + "@id" : "bts:Pathogenic" }, { - "@id" : "bts:DimensionsUnit" + "@id" : "bts:UncertainSignificance" } ], - "sms:displayName" : "BiospecimenDimension1" + "rdfs:label" : "Pathogenicity", + "rdfs:comment" : "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", + "@type" : "rdfs:Class", + "sms:displayName" : "Pathogenicity" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:Biospecimen" - } ], - "@id" : "bts:BloodBiospecimenType", + "@id" : "bts:SmokelessTobaccoQuitAge", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SmokelessTobaccoQuitAge", + "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BloodBiospecimenType", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:BiospecimenID" - }, { - "@id" : "bts:ParentID" - }, { - "@id" : "bts:ParentBiospecimenID" - }, { - "@id" : "bts:AdjacentBiospecimenIDs" - }, { - "@id" : "bts:BiospecimenType" - }, { - "@id" : "bts:TimepointLabel" - }, { - "@id" : "bts:SpecimenLaterality" - }, { - "@id" : "bts:ShippingConditionType" - } ], - "sms:displayName" : "BloodBiospecimenType" + "sms:displayName" : "SmokelessTobaccoQuitAge", + "sms:required" : "sms:false" }, { - "@id" : "bts:YearsSmoked", - "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value (or unknown) to represent the number of years a person has been smoking.", - "rdfs:label" : "YearsSmoked", "rdfs:subClassOf" : [ ], + "@id" : "bts:PixelsBigEndian", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "YearsSmoked", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "PixelsBigEndian", + "rdfs:comment" : "Boolean (True/False)", + "@type" : "rdfs:Class", + "sms:displayName" : "PixelsBigEndian" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:RelationshipGender", + "@id" : "bts:BreastCarcinomaDetectionMethodType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { + "@id" : "bts:Other" + }, { "@id" : "bts:unknown" }, { - "@id" : "bts:NotReported" + "@id" : "bts:ClinicalExam" }, { - "@id" : "bts:female" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:male" + "@id" : "bts:NippleDischarge" }, { - "@id" : "bts:unspecified" + "@id" : "bts:ScreeningMammography" + }, { + "@id" : "bts:ScreeningMRI" + }, { + "@id" : "bts:Selfexam" } ], - "rdfs:label" : "RelationshipGender", - "rdfs:comment" : "The text term used to describe the gender of the patient's relative with a history of cancer.", - "@type" : "rdfs:Class", - "sms:displayName" : "RelationshipGender" - }, { - "@id" : "bts:AdjacentSampleIDs", - "@type" : "rdfs:Class", - "rdfs:comment" : "List of Identifiers (separated by commas) of adjacent biospecimens cut from the same sample", - "rdfs:label" : "AdjacentSampleIDs", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AdjacentSampleIDs", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AdapterSequence", - "@type" : "rdfs:Class", - "rdfs:comment" : "Base sequence of the sequencing adapter. String", - "rdfs:label" : "AdapterSequence", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AdapterSequence", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DaystoDeath", + "rdfs:label" : "BreastCarcinomaDetectionMethodType", + "rdfs:comment" : "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days.", - "rdfs:label" : "DaystoDeath", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "DaystoDeath", - "sms:required" : "sms:false" + "sms:displayName" : "BreastCarcinomaDetectionMethodType" }, { - "@id" : "bts:SentinelLymphNodeCount", + "@id" : "bts:SizeZ", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric count of sentinel lymph nodes.", - "rdfs:label" : "SentinelLymphNodeCount", + "rdfs:comment" : "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label" : "SizeZ", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SentinelLymphNodeCount", + "sms:displayName" : "SizeZ", "sms:required" : "sms:false" }, { - "@id" : "bts:StopDaysfromIndex", + "@id" : "bts:COVID19AntibodyTesting", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", - "rdfs:label" : "StopDaysfromIndex", + "rdfs:comment" : "TBD", + "rdfs:label" : "COVID19AntibodyTesting", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "StopDaysfromIndex", + "sms:displayName" : "COVID19AntibodyTesting", "sms:required" : "sms:false" }, { - "@id" : "bts:NumberofDrinksPerWeek", + "@id" : "bts:BMI", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "NumberofDrinksPerWeek", + "rdfs:label" : "BMI", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NumberofDrinksPerWeek", + "sms:displayName" : "BMI", "sms:required" : "sms:false" }, { - "@id" : "bts:SentinelNodePositiveAssessmentCount", + "@id" : "bts:EmptyWellBarcode", "@type" : "rdfs:Class", - "rdfs:comment" : "The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.", - "rdfs:label" : "SentinelNodePositiveAssessmentCount", + "rdfs:comment" : "Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.", + "rdfs:label" : "EmptyWellBarcode", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SentinelNodePositiveAssessmentCount", + "sms:displayName" : "EmptyWellBarcode", "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:PreservationMethod", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Negative80DegC" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Cryopreservationindryice-deadtissue" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Fresh" - }, { - "@id" : "bts:Cryopreservationinliquidnitrogen-deadtissue" - }, { - "@id" : "bts:Formalinfixedparaffinembedded-FFPE" - }, { - "@id" : "bts:Archival" - }, { - "@id" : "bts:Formalinfixed-buffered" - }, { - "@id" : "bts:Formalinfixed-unbuffered" - }, { - "@id" : "bts:Cryopreserved" - }, { - "@id" : "bts:Frozen" - }, { - "@id" : "bts:Freshdissociatedandsinglecellsorted" - }, { - "@id" : "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" - }, { - "@id" : "bts:Methacarnfixedparaffinembedded-MFPE" - }, { - "@id" : "bts:Freshdissociated" - }, { - "@id" : "bts:Freshdissociatedandsinglecellsortedintoplates" - }, { - "@id" : "bts:Cryopreservationinliquidnitrogen-livecells" - }, { - "@id" : "bts:OCT" - }, { - "@id" : "bts:SnapFrozen" - }, { - "@id" : "bts:LiquidNitrogen" - } ], - "rdfs:label" : "PreservationMethod", - "rdfs:comment" : "Text term that represents the method used to preserve the sample.", - "@type" : "rdfs:Class", - "sms:displayName" : "PreservationMethod" - }, { - "@id" : "bts:Ecigvapeuse", + "@id" : "bts:BreastCarcinomaHER2RatioDiagnosis", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Ecigvapeuse", + "rdfs:comment" : "HER2 ratio of the participant at diagnosis", + "rdfs:label" : "BreastCarcinomaHER2RatioDiagnosis", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Ecigvapeuse", + "sms:displayName" : "BreastCarcinomaHER2RatioDiagnosis", "sms:required" : "sms:false" }, { - "@id" : "bts:PublicationDOI", + "@id" : "bts:TimebetweenWakingandFirstSmoke", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "PublicationDOI", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "PublicationDOI", - "sms:required" : "sms:false" - }, { - "@id" : "bts:DaystoBirth", - "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days.", - "rdfs:label" : "DaystoBirth", + "rdfs:label" : "TimebetweenWakingandFirstSmoke", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DaystoBirth", + "sms:displayName" : "TimebetweenWakingandFirstSmoke", "sms:required" : "sms:false" }, { - "@id" : "bts:TestUnits", + "@id" : "bts:MedianPercentageofMitochondrialReadsperNucleus", "@type" : "rdfs:Class", - "rdfs:comment" : "The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "TestUnits", + "rdfs:comment" : "Contamination from mitochondrial sequences", + "rdfs:label" : "MedianPercentageofMitochondrialReadsperNucleus", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TestUnits", + "sms:displayName" : "MedianPercentageofMitochondrialReadsperNucleus", "sms:required" : "sms:false" }, { - "@id" : "bts:AdjacentBiospecimenIDs", + "@id" : "bts:PhysicalSizeZ", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AdjacentBiospecimenIDs", + "rdfs:comment" : "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label" : "PhysicalSizeZ", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AdjacentBiospecimenIDs", + "sms:displayName" : "PhysicalSizeZ", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastBiopsyProcedureFindingType", + "@id" : "bts:LibrarySelectionMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:Other" + "@id" : "bts:hybridselection" }, { - "@id" : "bts:Atypicalhyperplasia" + "@id" : "bts:PCR" }, { - "@id" : "bts:DCIS" + "@id" : "bts:affinityenrichment" }, { - "@id" : "bts:LCIS" + "@id" : "bts:poly-Tenrichment" }, { - "@id" : "bts:Cancer" + "@id" : "bts:random" }, { - "@id" : "bts:Nocancer" + "@id" : "bts:rRNAdepletion" + }, { + "@id" : "bts:miRNAsizefractionation" + }, { + "@id" : "bts:other" } ], - "rdfs:label" : "BreastBiopsyProcedureFindingType", - "rdfs:comment" : "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", + "rdfs:label" : "LibrarySelectionMethod", + "rdfs:comment" : "How RNA molecules are isolated", "@type" : "rdfs:Class", - "sms:displayName" : "BreastBiopsyProcedureFindingType" + "sms:displayName" : "LibrarySelectionMethod" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:LibraryLayout", + "@id" : "bts:CountryofResidence", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:PairedEnd" + "@id" : "bts:TrinidadandTobago" }, { - "@id" : "bts:SingleRead" + "@id" : "bts:Botswana" }, { - "@id" : "bts:Mid-length" + "@id" : "bts:Malaysia" }, { - "@id" : "bts:LongRead" - } ], - "rdfs:label" : "LibraryLayout", - "rdfs:comment" : "Sequencing read type", - "@type" : "rdfs:Class", - "sms:displayName" : "LibraryLayout" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SpecimenLaterality", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:NotApplicable" + "@id" : "bts:Suriname" }, { - "@id" : "bts:unknown" + "@id" : "bts:Uruguay" }, { - "@id" : "bts:NotReported" + "@id" : "bts:Gibraltar" }, { - "@id" : "bts:Bilateral" + "@id" : "bts:Andorra" }, { - "@id" : "bts:Left" + "@id" : "bts:CaymanIslands" }, { - "@id" : "bts:Right" - } ], - "rdfs:label" : "SpecimenLaterality", - "rdfs:comment" : "For samples in paired organs, designates the side from which obtained.", - "@type" : "rdfs:Class", - "sms:displayName" : "SpecimenLaterality" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastCarcinomaHistologyCategory", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" + "@id" : "bts:Mozambique" }, { - "@id" : "bts:Infiltratingductalcarcinoma" + "@id" : "bts:Dominica" }, { - "@id" : "bts:Infiltratinglobularcarcinoma" + "@id" : "bts:Tajikistan" }, { - "@id" : "bts:InvasivemammarycarcinomaNOS" + "@id" : "bts:Barbados" }, { - "@id" : "bts:Invasivemixedductalandlobularcarcinoma" - } ], - "rdfs:label" : "BreastCarcinomaHistologyCategory", - "rdfs:comment" : "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", - "@type" : "rdfs:Class", - "sms:displayName" : "BreastCarcinomaHistologyCategory" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SingleCellIsolationMethod", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:MicrofluidicsChip" + "@id" : "bts:Seychelles" }, { - "@id" : "bts:Droplets" + "@id" : "bts:Curacao" }, { - "@id" : "bts:FACS" + "@id" : "bts:Coted'Ivoire" }, { - "@id" : "bts:Plates" + "@id" : "bts:Albania" }, { - "@id" : "bts:10x" + "@id" : "bts:China" }, { - "@id" : "bts:NucleiIsolation" - } ], - "rdfs:label" : "SingleCellIsolationMethod", - "rdfs:comment" : "The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)", - "@type" : "rdfs:Class", - "sms:displayName" : "SingleCellIsolationMethod" - }, { - "@id" : "bts:UMIBarcodeOffset", - "@type" : "rdfs:Class", - "rdfs:comment" : "Start position of UMI barcode in the sequence. Values: number, 0 for start of read", - "rdfs:label" : "UMIBarcodeOffset", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "UMIBarcodeOffset", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:DimensionsUnit", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cm" + "@id" : "bts:Oman" }, { - "@id" : "bts:mm" - } ], - "rdfs:label" : "DimensionsUnit", - "rdfs:comment" : "Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)", - "@type" : "rdfs:Class", - "sms:displayName" : "DimensionsUnit" - }, { - "@id" : "bts:TypeofSmokeExposure", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "TypeofSmokeExposure", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "TypeofSmokeExposure", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SizeC", - "@type" : "rdfs:Class", - "rdfs:comment" : "Number of channels. Integer >= 1", - "rdfs:label" : "SizeC", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SizeC", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SpecializedMolecularTest", - "@type" : "rdfs:Class", - "rdfs:comment" : "Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. 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For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "SecondGeneSymbol", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SecondGeneSymbol", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CycleNumber", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CycleNumber", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CycleNumber", - "sms:required" : "sms:false" - }, { - "@id" : "bts:GeneSymbol", - "@type" : "rdfs:Class", - "rdfs:comment" : "The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "GeneSymbol", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "GeneSymbol", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:GenomicCoverageType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:WholeGenome" + "@id" : "bts:Mongolia" }, { - "@id" : "bts:TargetedGenome" + "@id" : "bts:Switzerland" }, { - "@id" : "bts:BeadchipArray" - } ], - "rdfs:label" : "GenomicCoverageType", - "rdfs:comment" : "Genomic coverage", - "@type" : "rdfs:Class", - "sms:displayName" : "GenomicCoverageType" - }, { - "@id" : "bts:TargetDepth", - "@type" : "rdfs:Class", - "rdfs:comment" : "Targeted read depth prior to sequencing. 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"@id" : "bts:gtf" + "@id" : "bts:Slovakia" }, { - "@id" : "bts:DICOM" + "@id" : "bts:Lesotho" }, { - "@id" : "bts:cloupe" + "@id" : "bts:DominicanRepublic" }, { - "@id" : "bts:czi" + "@id" : "bts:SaintPierreandMiquelon" }, { - "@id" : "bts:tiff" + "@id" : "bts:Moldova" }, { - "@id" : "bts:powerpoint" + "@id" : "bts:SanMarino" }, { - "@id" : "bts:zip" + "@id" : "bts:Nauru" }, { - "@id" : "bts:bed" + "@id" : "bts:Luxembourg" }, { - "@id" : "bts:mex" + "@id" : "bts:Monaco" }, { - "@id" : "bts:ab1" + "@id" : "bts:Zimbabwe" }, { - "@id" : "bts:Pythonscript" + "@id" : "bts:SaudiArabia" }, { - "@id" : "bts:msf" + "@id" : "bts:Mauritania" }, { - "@id" : "bts:mzML" + "@id" : "bts:Panama" }, { - "@id" : "bts:svg" + "@id" : "bts:UnitedStates" }, { - "@id" : "bts:cel" + "@id" : "bts:Montserrat" }, { - "@id" : "bts:mtx" + "@id" : "bts:Nicaragua" }, { - "@id" : "bts:bigwig" + "@id" : "bts:FaroeIslands" }, { - "@id" : "bts:chp" + "@id" : "bts:UnitedKingdom" }, { - "@id" : "bts:svs" + "@id" : "bts:Canada" }, { - "@id" : "bts:wiggle" + "@id" : "bts:Ghana" }, { - "@id" : "bts:mov" + "@id" : "bts:Armenia" }, { - "@id" : "bts:bcf" + "@id" : "bts:Bulgaria" }, { - "@id" : "bts:hyperlink" + "@id" : "bts:Egypt" }, { - "@id" : "bts:sdf" + "@id" : "bts:Reunion" }, { - "@id" : "bts:recal" + "@id" : "bts:Cameroon" }, { - "@id" : "bts:idx" + "@id" : "bts:Rwanda" }, { - "@id" : "bts:sif" + "@id" : "bts:Timor-Leste" }, { - "@id" : "bts:json" + "@id" : "bts:Yemen" }, { - "@id" : "bts:avi" + "@id" : "bts:SaintLucia" }, { - "@id" : "bts:HEIC" + "@id" : "bts:Poland" }, { - "@id" : "bts:gff3" + "@id" : "bts:Namibia" }, { - "@id" : "bts:bpm" + "@id" : "bts:Guinea-Bissau" }, { - "@id" : "bts:bedbroadPeak" + "@id" : "bts:Thailand" }, { - "@id" : "bts:excel" + "@id" : "bts:Argentina" }, { - "@id" : "bts:flagstat" + "@id" : "bts:Turkey" }, { - "@id" : "bts:mpg" + "@id" : "bts:Djibouti" }, { - "@id" : "bts:RData" + "@id" : "bts:Greece" }, { - "@id" : "bts:Sentrixdescriptorfile" + "@id" : "bts:Jersey" }, { - "@id" : "bts:jpg" + "@id" : "bts:Mauritius" }, { - "@id" : "bts:doc" + "@id" : "bts:WallisandFutuna" }, { - "@id" : "bts:bedgappedPeak" + "@id" : "bts:Pakistan" }, { - "@id" : "bts:xml" + "@id" : "bts:Ukraine" }, { - "@id" : "bts:sqlite" + "@id" : "bts:StateofPalestine" }, { - "@id" : "bts:tranches" + "@id" : "bts:Ecuador" }, { - "@id" : "bts:plink" + "@id" : "bts:SouthKorea" }, { - "@id" : "bts:sav" + "@id" : "bts:Russia" }, { - "@id" : "bts:locs" + "@id" : "bts:Greenland" }, { - "@id" : "bts:html" + "@id" : "bts:Liechtenstein" }, { - "@id" : "bts:md" + "@id" : "bts:Nigeria" }, { - "@id" : "bts:fasta" + "@id" : "bts:Benin" + }, { + "@id" : "bts:Vanuatu" + }, { + "@id" : "bts:SriLanka" + }, { + "@id" : "bts:Tokelau" + }, { + "@id" : "bts:CzechRepublic(Czechia)" + }, { + "@id" : "bts:MarshallIslands" + }, { + "@id" : "bts:Estonia" + }, { + "@id" : "bts:SaintVincentandtheGrenadines" + }, { + "@id" : "bts:PuertoRico" + }, { + "@id" : "bts:Grenada" + }, { + "@id" : "bts:Guadeloupe" + }, { + "@id" : "bts:SierraLeone" + }, { + "@id" : "bts:Afghanistan" + }, { + "@id" : "bts:Haiti" + }, { + "@id" : "bts:Lithuania" + }, { + "@id" : "bts:Indonesia" + }, { + "@id" : "bts:VirginIslandsBritish" + }, { + "@id" : "bts:VirginIslandsU.S." + }, { + "@id" : "bts:Sudan" + }, { + "@id" : "bts:Morocco" + }, { + "@id" : "bts:Iceland" + }, { + "@id" : "bts:NorthKorea" + }, { + "@id" : "bts:NewCaledonia" + }, { + "@id" : "bts:Brunei" } ], - "rdfs:label" : "FileFormat", - "rdfs:comment" : "Format of a file (e.g. txt, csv, fastq, bam, etc.)", - "@type" : "rdfs:Class", - "sms:displayName" : "FileFormat" - }, { - "@id" : "bts:LinkedMatrices", + "rdfs:label" : "CountryofResidence", + "rdfs:comment" : "Country of Residence at enrollment", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LinkedMatrices", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "LinkedMatrices", - "sms:required" : "sms:false" + "sms:displayName" : "CountryofResidence" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:AlcoholExposure", + "@id" : "bts:BreastCancerAssessmentTests", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes-AlcoholExposure" + "@id" : "bts:Other" }, { - "@id" : "bts:NotReported" + "@id" : "bts:unknown" }, { - "@id" : "bts:No-AlcoholExposure" + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:EstrogenreceptorIHC" + }, { + "@id" : "bts:ProgesteronereceptorIHC" + }, { + "@id" : "bts:HER2IHC" + }, { + "@id" : "bts:HER2FISH-CISH" + }, { + "@id" : "bts:HER2FISH" } ], - "rdfs:label" : "AlcoholExposure", - "rdfs:comment" : "Indicate if individual has alcohol exposure", + "rdfs:label" : "BreastCancerAssessmentTests", + "rdfs:comment" : "Text term to identify assessment tests done in participants during diagnosis", "@type" : "rdfs:Class", - "sms:displayName" : "AlcoholExposure" + "sms:displayName" : "BreastCancerAssessmentTests" }, { - "@id" : "bts:ScRNAseqWorkflowParametersDescription", + "@id" : "bts:EmissionBandwidth", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ScRNAseqWorkflowParametersDescription", + "rdfs:label" : "EmissionBandwidth", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ScRNAseqWorkflowParametersDescription", + "sms:displayName" : "EmissionBandwidth", "sms:required" : "sms:false" }, { - "@id" : "bts:ExcitationBandwidth", + "@id" : "bts:MatrixType", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ExcitationBandwidth", + "rdfs:label" : "MatrixType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ExcitationBandwidth", + "sms:displayName" : "MatrixType", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:PriorInvasiveBreastDisease", + "@id" : "bts:SpikeIn", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:Other" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" + "@id" : "bts:ERCC" }, { - "@id" : "bts:DCIS" + "@id" : "bts:OtherSpikeIn" }, { - "@id" : "bts:LCIS" + "@id" : "bts:NoSpikeIn" }, { - "@id" : "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" + "@id" : "bts:PhiX" } ], - "rdfs:label" : "PriorInvasiveBreastDisease", - "rdfs:comment" : "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label" : "SpikeIn", + "rdfs:comment" : "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", "@type" : "rdfs:Class", - "sms:displayName" : "PriorInvasiveBreastDisease" + "sms:displayName" : "SpikeIn" }, { - "@id" : "bts:SizeT", + "@id" : "bts:TypeofTobaccoUsed", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of time points. Integer >= 1", - "rdfs:label" : "SizeT", + "rdfs:comment" : "TBD", + "rdfs:label" : "TypeofTobaccoUsed", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SizeT", + "sms:displayName" : "TypeofTobaccoUsed", "sms:required" : "sms:false" }, { - "@id" : "bts:Intron", + "@id" : "bts:HistologicMorphologyCode", "@type" : "rdfs:Class", - "rdfs:comment" : "Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.", - "rdfs:label" : "Intron", + "rdfs:comment" : "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", + "rdfs:label" : "HistologicMorphologyCode", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Intron", + "sms:displayName" : "HistologicMorphologyCode", "sms:required" : "sms:false" }, { + "@id" : "bts:PhysicalSizeX", + "@type" : "rdfs:Class", + "rdfs:comment" : "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", + "rdfs:label" : "PhysicalSizeX", "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastCancerGenomicTestPerformed", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Oncotype" - }, { - "@id" : "bts:MammaPrint" - }, { - "@id" : "bts:Notperformed" - } ], - "rdfs:label" : "BreastCancerGenomicTestPerformed", - "rdfs:comment" : "Text term that represents the name of the genomic test performed for breast cancer.", - "@type" : "rdfs:Class", - "sms:displayName" : "BreastCancerGenomicTestPerformed" + "sms:displayName" : "PhysicalSizeX", + "sms:required" : "sms:false" }, { + "@id" : "bts:Ecigvape30dayusenum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Ecigvape30dayusenum", "rdfs:subClassOf" : [ ], - "@id" : "bts:EnvironmentalTobaccoSmokeExposure", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "EnvironmentalTobaccoSmokeExposure", - "rdfs:comment" : "The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.", - "@type" : "rdfs:Class", - "sms:displayName" : "EnvironmentalTobaccoSmokeExposure" + "sms:displayName" : "Ecigvape30dayusenum", + "sms:required" : "sms:false" }, { - "@id" : "bts:ProtocolLink", + "@id" : "bts:CauseofDeathSource", "@type" : "rdfs:Class", - "rdfs:comment" : "URL to a free/open protocol resource describing the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.", - "rdfs:label" : "ProtocolLink", + "rdfs:comment" : "TBD", + "rdfs:label" : "CauseofDeathSource", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ProtocolLink", + "sms:displayName" : "CauseofDeathSource", "sms:required" : "sms:false" }, { + "@id" : "bts:YearofDeath", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value to represent the year of the death of an individual.", + "rdfs:label" : "YearofDeath", "rdfs:subClassOf" : [ ], - "@id" : "bts:RelativewithCancerHistory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes-CancerHistoryRelative" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:None" - } ], - "rdfs:label" : "RelativewithCancerHistory", - "rdfs:comment" : "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "sms:displayName" : "YearofDeath", + "sms:required" : "sms:false" + }, { + "@id" : "bts:LinkedProject", "@type" : "rdfs:Class", - "sms:displayName" : "RelativewithCancerHistory" + "rdfs:comment" : "TBD", + "rdfs:label" : "LinkedProject", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LinkedProject", + "sms:required" : "sms:false" }, { - "@id" : "bts:LibraryPrepKitVendor", + "@id" : "bts:CancerIncidence", "@type" : "rdfs:Class", - "rdfs:comment" : "Vendor of Library Prep Kit. String", - "rdfs:label" : "LibraryPrepKitVendor", + "rdfs:comment" : "TBD", + "rdfs:label" : "CancerIncidence", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryPrepKitVendor", + "sms:displayName" : "CancerIncidence", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:PrecancerousConditionType", + "@id" : "bts:BreastCancerAllredEstrogenReceptorScore", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:CarcinomaNOS" + "@id" : "bts:unknown" }, { - "@id" : "bts:Atypicalmelanocyticproliferation" + "@id" : "bts:10" }, { - "@id" : "bts:Superficialspreading" + "@id" : "bts:0" }, { - "@id" : "bts:Melanomainsituarisinginagiantcongenitalnevus" + "@id" : "bts:4" }, { - "@id" : "bts:Invasivemelanoma" + "@id" : "bts:7" }, { - "@id" : "bts:Invasivemelanoma-acrallentiginous" - }, { - "@id" : "bts:Melanomainsitunototherwiseclassified" - }, { - "@id" : "bts:Milddysplasia" - }, { - "@id" : "bts:Adenocarcinomainsitu-nonmucinous" - }, { - "@id" : "bts:Reservecellhyperplasia" - }, { - "@id" : "bts:Invasivemelanoma-nevoid" - }, { - "@id" : "bts:Nodiagnosispossible" - }, { - "@id" : "bts:Hamartoma" - }, { - "@id" : "bts:Adenocarcinomainsitu-mucinous" - }, { - "@id" : "bts:Squamousmetaplasia-immature" - }, { - "@id" : "bts:Severedysplasia" - }, { - "@id" : "bts:Invasivemelanoma-lentigomaligna" - }, { - "@id" : "bts:Squamousmetaplasia-mature" - }, { - "@id" : "bts:Acral-lentiginous" - }, { - "@id" : "bts:Invasivemelanoma-superficialspreading" + "@id" : "bts:1" }, { - "@id" : "bts:Atypicaladenomatoushyperplasia" + "@id" : "bts:8" }, { - "@id" : "bts:Moderatedysplasia" + "@id" : "bts:2" }, { - "@id" : "bts:AtypicalAdenomatousLungHyperplasia" + "@id" : "bts:5" }, { - "@id" : "bts:NormalWDA" + "@id" : "bts:3" }, { + "@id" : "bts:6" + } ], + "rdfs:label" : "BreastCancerAllredEstrogenReceptorScore", + "rdfs:comment" : "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "@type" : "rdfs:Class", + "sms:displayName" : "BreastCancerAllredEstrogenReceptorScore" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ERStainingIntensity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { "@id" : "bts:Other" }, { - "@id" : "bts:Persistentmelanomainsitu" - }, { - "@id" : "bts:PancreaticIntraepithelialNeoplasia" - }, { - "@id" : "bts:DuctalCarcinomaInSitu" - }, { - "@id" : "bts:PancreaticIntraductalPapillary-MucinousNeoplasm" - }, { - "@id" : "bts:Melanocytichyperplasia" - }, { - "@id" : "bts:Melanomainsitu" + "@id" : "bts:unknown" }, { - "@id" : "bts:Invasivemelanoma-desmoplastic" + "@id" : "bts:Strong" }, { - "@id" : "bts:BenigntumorNOS" + "@id" : "bts:Moderate" }, { - "@id" : "bts:Lentigomalignatype" + "@id" : "bts:Weak" }, { - "@id" : "bts:Scar-noresidualmelanoma" + "@id" : "bts:Weak-Moderate" }, { - "@id" : "bts:Invasivemelanoma-nodulartype" + "@id" : "bts:Moderate-Strong" }, { - "@id" : "bts:ProstaticIntraepithelialNeoplasia" + "@id" : "bts:Weak-Strong" } ], - "rdfs:label" : "PrecancerousConditionType", - "rdfs:comment" : "The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).", - "@type" : "rdfs:Class", - "sms:displayName" : "PrecancerousConditionType" - }, { - "@id" : "bts:CellBarcodeOffset", + "rdfs:label" : "ERStainingIntensity", + "rdfs:comment" : "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", "@type" : "rdfs:Class", - "rdfs:comment" : "Offset in sequence for cell barcode read (in bp): number", - "rdfs:label" : "CellBarcodeOffset", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CellBarcodeOffset", - "sms:required" : "sms:false" + "sms:displayName" : "ERStainingIntensity" }, { - "@id" : "bts:UMIBarcodeLength", + "@id" : "bts:FOVX", "@type" : "rdfs:Class", - "rdfs:comment" : "Length of UMI barcode read (in bp): number", - "rdfs:label" : "UMIBarcodeLength", + "rdfs:comment" : "Field of view X dimension. Floating point", + "rdfs:label" : "FOVX", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "UMIBarcodeLength", + "sms:displayName" : "FOVX", "sms:required" : "sms:false" }, { - "@id" : "bts:IschemicTime", - "@type" : "rdfs:Class", - "rdfs:comment" : "Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.", - "rdfs:label" : "IschemicTime", "rdfs:subClassOf" : [ ], + "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "IschemicTime", - "sms:required" : "sms:false" - }, { - "@id" : "bts:ProgressionorRecurrenceType", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "HormoneTherapyBreastCancerPreventionIndicator", + "rdfs:comment" : "Did the patient receive hormonal therapy for prevention of breast cancer?", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ProgressionorRecurrenceType", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ProgressionorRecurrenceType", - "sms:required" : "sms:false" + "sms:displayName" : "HormoneTherapyBreastCancerPreventionIndicator" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:AlcoholType", + "@id" : "bts:SequencingPlatform", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:Other" + "@id" : "bts:454GSFLXTitanium" }, { - "@id" : "bts:unknown" + "@id" : "bts:ABSOLiD3" + }, { + "@id" : "bts:ABSOLiD4ABSOLiD2" + }, { + "@id" : "bts:CompleteGenomics" + }, { + "@id" : "bts:GridION" + }, { + "@id" : "bts:IlluminaGenomeAnalyzerII" + }, { + "@id" : "bts:IlluminaGenomeAnalyzerIIx" + }, { + "@id" : "bts:IlluminaHiSeq2000" + }, { + "@id" : "bts:IlluminaHiSeq2500" + }, { + "@id" : "bts:IlluminaHiSeq4000" + }, { + "@id" : "bts:IlluminaHiSeqXFive" + }, { + "@id" : "bts:IlluminaHiSeqXTen" + }, { + "@id" : "bts:IlluminaMiSeq" + }, { + "@id" : "bts:IlluminaNextSeq1000" + }, { + "@id" : "bts:IlluminaNextSeq2000" + }, { + "@id" : "bts:IlluminaNextSeq2500" + }, { + "@id" : "bts:IlluminaNextSeq500" + }, { + "@id" : "bts:IlluminaNextSeq550" + }, { + "@id" : "bts:IlluminaNovaSeq6000" + }, { + "@id" : "bts:IonTorrentPGM" + }, { + "@id" : "bts:IonTorrentProton" + }, { + "@id" : "bts:IonTorrentS5" }, { "@id" : "bts:NotReported" }, { - "@id" : "bts:Beer" + "@id" : "bts:NovaSeq6000" }, { - "@id" : "bts:Liquor" + "@id" : "bts:NovaSeqS4" }, { - "@id" : "bts:Wine" + "@id" : "bts:Other" + }, { + "@id" : "bts:OxfordNanoporeminION" + }, { + "@id" : "bts:PacBioRS" + }, { + "@id" : "bts:PacBioSequel2" + }, { + "@id" : "bts:PromethION" + }, { + "@id" : "bts:Revio" + }, { + "@id" : "bts:UltimaGenomicsUG100" + }, { + "@id" : "bts:Unknown" } ], - "rdfs:label" : "AlcoholType", - "rdfs:comment" : "Type of alcohol use", + "rdfs:label" : "SequencingPlatform", + "rdfs:comment" : "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", "@type" : "rdfs:Class", - "sms:displayName" : "AlcoholType" + "sms:displayName" : "SequencingPlatform" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:MismatchRepairMutation", + "@id" : "bts:SlideChargeType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:Other" }, { - "@id" : "bts:No" + "@id" : "bts:Uncharged" }, { - "@id" : "bts:unknown" + "@id" : "bts:Charged" + }, { + "@id" : "bts:Coverslip" + }, { + "@id" : "bts:Notapplicable" } ], - "rdfs:label" : "MismatchRepairMutation", - "rdfs:comment" : "The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "SlideChargeType", + "rdfs:comment" : "A description of the charge on the glass slide.", "@type" : "rdfs:Class", - "sms:displayName" : "MismatchRepairMutation" + "sms:displayName" : "SlideChargeType" }, { - "@id" : "bts:Filename", + "@id" : "bts:COVID19CancerTreatmentFollowup", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Filename", + "rdfs:label" : "COVID19CancerTreatmentFollowup", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Filename", + "sms:displayName" : "COVID19CancerTreatmentFollowup", "sms:required" : "sms:false" }, { - "@id" : "bts:AdapterName", + "@id" : "bts:ChannelName", "@type" : "rdfs:Class", - "rdfs:comment" : "Name of the sequencing adapter. String", - "rdfs:label" : "AdapterName", + "rdfs:comment" : "TBD", + "rdfs:label" : "ChannelName", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AdapterName", + "sms:displayName" : "ChannelName", "sms:required" : "sms:false" }, { - "@id" : "bts:CountryofBirth", + "@id" : "bts:ConcomitantMedicationReceivedType", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "CountryofBirth", + "rdfs:label" : "ConcomitantMedicationReceivedType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CountryofBirth", + "sms:displayName" : "ConcomitantMedicationReceivedType", "sms:required" : "sms:false" }, { + "@id" : "bts:CellTotal", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of sequenced cells. Applies to raw counts matrix only.", + "rdfs:label" : "CellTotal", "rdfs:subClassOf" : [ ], - "@id" : "bts:LibraryConstructionMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:10xV3" - }, { - "@id" : "bts:inDropsV2" - }, { - "@id" : "bts:10xV1.1" - }, { - "@id" : "bts:10xV3.1" - }, { - "@id" : "bts:Drop-seq" - }, { - "@id" : "bts:10xV2" - }, { - "@id" : "bts:10xV1.0" - }, { - "@id" : "bts:Smart-seq2" - }, { - "@id" : "bts:Smart-SeqV4" - }, { - "@id" : "bts:sci-ATAC-seq" - }, { - "@id" : "bts:inDropsV3" - }, { - "@id" : "bts:CEL-seq2" - }, { - "@id" : "bts:TruDrop" - } ], - "rdfs:label" : "LibraryConstructionMethod", - "rdfs:comment" : "Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]", - "@type" : "rdfs:Class", - "sms:displayName" : "LibraryConstructionMethod" - }, { - "@id" : "bts:OtherBiopsyResectionSite", - "@type" : "rdfs:Class", - "rdfs:comment" : "A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under Clinical Data Tier 1)", - "rdfs:label" : "OtherBiopsyResectionSite", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "OtherBiopsyResectionSite", - "sms:required" : "sms:false" - }, { - "@id" : "bts:MedianPassingReadPercentage", - "@type" : "rdfs:Class", - "rdfs:comment" : "Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode", - "rdfs:label" : "MedianPassingReadPercentage", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "MedianPassingReadPercentage", + "sms:displayName" : "CellTotal", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:ReadIndicator", + "@id" : "bts:MolecularAnalysisMethod", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:I1" + "@id" : "bts:WXS" }, { - "@id" : "bts:R1" + "@id" : "bts:WGS" }, { - "@id" : "bts:R2" + "@id" : "bts:ISH" }, { - "@id" : "bts:R1&R2" + "@id" : "bts:NotReported" }, { - "@id" : "bts:R3" + "@id" : "bts:MicrosatelliteAnalysis" }, { - "@id" : "bts:NotApplicable" - } ], - "rdfs:label" : "ReadIndicator", - "rdfs:comment" : "TBD", - "@type" : "rdfs:Class", - "sms:displayName" : "ReadIndicator" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategory", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { "@id" : "bts:unknown" }, { - "@id" : "bts:Datanotavailable" + "@id" : "bts:NotApplicable" }, { - "@id" : "bts:Alveolartype" + "@id" : "bts:TargetedSequencing" }, { - "@id" : "bts:Classicaltype" + "@id" : "bts:NuclearStaining" }, { - "@id" : "bts:Pleomorphictype" - } ], - "rdfs:label" : "InvasiveLobularBreastCarcinomaHistologicCategory", - "rdfs:comment" : "The histologic subtype for an infiltrating lobular carcinoma of the breast.", - "@type" : "rdfs:Class", - "sms:displayName" : "InvasiveLobularBreastCarcinomaHistologicCategory" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:TumorExtranodalExtensionIndicator", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Absent" + "@id" : "bts:FISH" }, { - "@id" : "bts:Notapplicable" + "@id" : "bts:IHC" }, { - "@id" : "bts:YES" + "@id" : "bts:Karyotype" }, { - "@id" : "bts:unspecified" + "@id" : "bts:FlowCytometry" }, { - "@id" : "bts:Nosourcedocumentation" + "@id" : "bts:Other" }, { - "@id" : "bts:UNKNOWN" + "@id" : "bts:RNASequencing" }, { - "@id" : "bts:Present" + "@id" : "bts:SequencingNOS" }, { - "@id" : "bts:Present-extensive" + "@id" : "bts:SouthernBlotting" }, { - "@id" : "bts:Notsampledordissected" + "@id" : "bts:Microarray" }, { - "@id" : "bts:Present-minimal" + "@id" : "bts:ComparativeGenomicHybridization" }, { - "@id" : "bts:NO" + "@id" : "bts:CytogeneticsNOS" }, { - "@id" : "bts:Indeterminate" + "@id" : "bts:RT-PCR" } ], - "rdfs:label" : "TumorExtranodalExtensionIndicator", - "rdfs:comment" : "The indicator to determine extranodal involvement or extent of the disease.", + "rdfs:label" : "MolecularAnalysisMethod", + "rdfs:comment" : "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", "@type" : "rdfs:Class", - "sms:displayName" : "TumorExtranodalExtensionIndicator" + "sms:displayName" : "MolecularAnalysisMethod" }, { + "@id" : "bts:LaneNumber", + "@type" : "rdfs:Class", + "rdfs:comment" : "Basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label" : "LaneNumber", "rdfs:subClassOf" : [ ], - "@id" : "bts:ERReceptorStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Borderline" - }, { - "@id" : "bts:Equivocal" - }, { - "@id" : "bts:Indeterminate" - }, { - "@id" : "bts:Negative" - }, { - "@id" : "bts:NotPerformed" - }, { - "@id" : "bts:PerformedbutNotAvailable" - }, { - "@id" : "bts:Positive" - } ], - "rdfs:label" : "ERReceptorStatus", - "rdfs:comment" : "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "sms:displayName" : "LaneNumber", + "sms:required" : "sms:true" + }, { + "@id" : "bts:ParticipantID", "@type" : "rdfs:Class", - "sms:displayName" : "ERReceptorStatus" + "rdfs:comment" : "ID associated with a patient", + "rdfs:label" : "ParticipantID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ParticipantID", + "sms:required" : "sms:true" }, { - "@id" : "bts:Comment", + "@id" : "bts:COVID19CurrentStatus", "@type" : "rdfs:Class", - "rdfs:comment" : "Free text field (generally for QC comment)", - "rdfs:label" : "Comment", + "rdfs:comment" : "TBD", + "rdfs:label" : "COVID19CurrentStatus", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Comment", + "sms:displayName" : "COVID19CurrentStatus", "sms:required" : "sms:false" }, { + "@id" : "bts:FrameAveraging", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label" : "FrameAveraging", "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastQuadrantSite", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Upperouterquadrant" - }, { - "@id" : "bts:Lowerouterquadrant" - }, { - "@id" : "bts:Upperinnerquadrant" - }, { - "@id" : "bts:Lowerinnerquadrant" - }, { - "@id" : "bts:Central" - }, { - "@id" : "bts:Nipple" - } ], - "rdfs:label" : "BreastQuadrantSite", - "rdfs:comment" : "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", - "@type" : "rdfs:Class", - "sms:displayName" : "BreastQuadrantSite" + "sms:displayName" : "FrameAveraging", + "sms:required" : "sms:false" }, { - "@id" : "bts:LinkedDatasets", + "@id" : "bts:ChannelID", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "LinkedDatasets", + "rdfs:label" : "ChannelID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LinkedDatasets", + "sms:displayName" : "ChannelID", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:subClassOf" : [ ], + "@id" : "bts:BulkMethylationAssayType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Wholegenome" + }, { + "@id" : "bts:TargetedGenome" + }, { + "@id" : "bts:BeadchipArray" + } ], + "rdfs:label" : "BulkMethylationAssayType", + "rdfs:comment" : "Assay types normally determine genomic coverage", "@type" : "rdfs:Class", - "rdfs:comment" : "HER2 chromosome 17 ratio in participants with breast cancer", - "rdfs:label" : "BreastCarcinomaHER2Chromosome17Ratio", + "sms:displayName" : "BulkMethylationAssayType" + }, { + "@id" : "bts:Vendor", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Vendor", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHER2Chromosome17Ratio", + "sms:displayName" : "Vendor", "sms:required" : "sms:false" }, { - "@id" : "bts:PhysicalSizeY", + "@id" : "bts:LociCount", "@type" : "rdfs:Class", - "rdfs:comment" : "Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.", - "rdfs:label" : "PhysicalSizeY", + "rdfs:comment" : "Numeric value used to describe the number of loci tested.", + "rdfs:label" : "LociCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PhysicalSizeY", + "sms:displayName" : "LociCount", "sms:required" : "sms:false" }, { - "@id" : "bts:MetalIsotopeMass", + "@id" : "bts:DaystoRecurrence", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "MetalIsotopeMass", + "rdfs:label" : "DaystoRecurrence", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MetalIsotopeMass", + "sms:displayName" : "DaystoRecurrence", "sms:required" : "sms:false" }, { - "@id" : "bts:BiospecimenDimension2", + "@id" : "bts:AcquisitionMethodOtherSpecify", "@type" : "rdfs:Class", - "rdfs:comment" : "Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", - "rdfs:label" : "BiospecimenDimension2", + "rdfs:comment" : "A custom acquisition method [Text - max length 100 characters]", + "rdfs:label" : "AcquisitionMethodOtherSpecify", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BiospecimenDimension2", + "sms:displayName" : "AcquisitionMethodOtherSpecify", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:Laterality", + "@id" : "bts:ReadLength", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:NotApplicable" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Bilateral" - }, { - "@id" : "bts:Left" - }, { - "@id" : "bts:Right" - } ], - "rdfs:label" : "Laterality", - "rdfs:comment" : "For samples in paired organs, designates the side from which obtained.", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "ReadLength", + "rdfs:comment" : "Length of the sequencing reads. Can be integer, null", "@type" : "rdfs:Class", - "sms:displayName" : "Laterality" + "sms:displayName" : "ReadLength" }, { - "@id" : "bts:MedianFractionofReadsinPeaks", - "@type" : "rdfs:Class", - "rdfs:comment" : "Median fraction of reads in peaks (FRIP)", - "rdfs:label" : "MedianFractionofReadsinPeaks", "rdfs:subClassOf" : [ ], + "@id" : "bts:WellIndex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MedianFractionofReadsinPeaks", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "WellIndex", + "rdfs:comment" : "Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays", + "@type" : "rdfs:Class", + "sms:displayName" : "WellIndex" }, { + "@id" : "bts:BreastCarcinomaCentromere17CopyNumber", + "@type" : "rdfs:Class", + "rdfs:comment" : "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", + "rdfs:label" : "BreastCarcinomaCentromere17CopyNumber", "rdfs:subClassOf" : [ ], - "@id" : "bts:VariantType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Duplication" - }, { - "@id" : "bts:Conversion" - }, { - "@id" : "bts:Chrimerism" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:PartialMethylation" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Substitution" - }, { - "@id" : "bts:Deletion-Insertion" - }, { - "@id" : "bts:Loss" - }, { - "@id" : "bts:Insertion" - }, { - "@id" : "bts:Hypermethylation" - }, { - "@id" : "bts:Alleles" - }, { - "@id" : "bts:Methylation" - }, { - "@id" : "bts:Inversion" - }, { - "@id" : "bts:Extension" - }, { - "@id" : "bts:Mosaicism" - }, { - "@id" : "bts:Deletion" - }, { - "@id" : "bts:Other" - }, { - "@id" : "bts:Rearrangement" - }, { - "@id" : "bts:Translocation" - }, { - "@id" : "bts:Amplification" - }, { - "@id" : "bts:RepeatedSequences" - }, { - "@id" : "bts:Splice" - }, { - "@id" : "bts:Gain" - } ], - "rdfs:label" : "VariantType", - "rdfs:comment" : "The text term used to describe the type of genetic variation.", - "@type" : "rdfs:Class", - "sms:displayName" : "VariantType" + "sms:displayName" : "BreastCarcinomaCentromere17CopyNumber", + "sms:required" : "sms:false" }, { - "@id" : "bts:CigarettesperDay", + "@id" : "bts:NominalMagnification", "@type" : "rdfs:Class", - "rdfs:comment" : "The average number of cigarettes smoked per day.", - "rdfs:label" : "CigarettesperDay", + "rdfs:comment" : "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", + "rdfs:label" : "NominalMagnification", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CigarettesperDay", + "sms:displayName" : "NominalMagnification", "sms:required" : "sms:false" }, { - "@id" : "bts:CellBarcodeTag", + "@id" : "bts:COVID19OccurrenceIndicator", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "CellBarcodeTag", + "rdfs:label" : "COVID19OccurrenceIndicator", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CellBarcodeTag", + "sms:displayName" : "COVID19OccurrenceIndicator", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:ReadContent", + "@id" : "bts:OvarianCancerHistologicSubtype", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:CellBarcodeandDNAInsert" + "@id" : "bts:High-gradeserous" }, { - "@id" : "bts:SampleIndexandDNAInsert" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:DNAInsert" + "@id" : "bts:unknown" }, { - "@id" : "bts:SampleIndex" + "@id" : "bts:Germcell" }, { - "@id" : "bts:CellBarcode" + "@id" : "bts:High-gradeendometrioid" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Low-gradeserous" + }, { + "@id" : "bts:Clearcell" + }, { + "@id" : "bts:Low-gradeendometrioid" + }, { + "@id" : "bts:Mucinous" + }, { + "@id" : "bts:Sex-cordstromal" } ], - "rdfs:label" : "ReadContent", - "rdfs:comment" : "Read content description", + "rdfs:label" : "OvarianCancerHistologicSubtype", + "rdfs:comment" : "Text term to describe the histological subtype of ovarian cancer in the participant", "@type" : "rdfs:Class", - "sms:displayName" : "ReadContent" + "sms:displayName" : "OvarianCancerHistologicSubtype" }, { - "@id" : "bts:DaystoProgressionFree", + "@id" : "bts:TotalVolume", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.", - "rdfs:label" : "DaystoProgressionFree", + "rdfs:comment" : "Numeric value for the total amount of sample or specimen", + "rdfs:label" : "TotalVolume", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DaystoProgressionFree", + "sms:displayName" : "TotalVolume", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:MultifocalBreastCarcinomaPresentIndicator", + "@id" : "bts:TumorTissueType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:Normal" }, { - "@id" : "bts:No" + "@id" : "bts:Normaladjacent" }, { - "@id" : "bts:unknown" + "@id" : "bts:Recurrent" + }, { + "@id" : "bts:Posttherapyneoadjuvant" + }, { + "@id" : "bts:Normaldistant" + }, { + "@id" : "bts:Posttherapyadjuvant" + }, { + "@id" : "bts:Posttherapy" + }, { + "@id" : "bts:Atypia-hyperplasia" + }, { + "@id" : "bts:NotOtherwiseSpecified" + }, { + "@id" : "bts:Metastatic" + }, { + "@id" : "bts:Localrecurrence" + }, { + "@id" : "bts:Premalignant-insitu" + }, { + "@id" : "bts:AdditionalPrimary" + }, { + "@id" : "bts:Premalignant" + }, { + "@id" : "bts:Primary" } ], - "rdfs:label" : "MultifocalBreastCarcinomaPresentIndicator", - "rdfs:comment" : "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.", + "rdfs:label" : "TumorTissueType", + "rdfs:comment" : "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints)", "@type" : "rdfs:Class", - "sms:displayName" : "MultifocalBreastCarcinomaPresentIndicator" + "sms:displayName" : "TumorTissueType" }, { - "@id" : "bts:BiospecimenID", + "@id" : "bts:CellMedianNumberGenes", "@type" : "rdfs:Class", - "rdfs:comment" : " Alias for Sample ID", - "rdfs:label" : "BiospecimenID", + "rdfs:comment" : "Median number of genes detected per cell. Number", + "rdfs:label" : "CellMedianNumberGenes", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BiospecimenID", - "sms:required" : "sms:true" + "sms:displayName" : "CellMedianNumberGenes", + "sms:required" : "sms:false" }, { - "@id" : "bts:BloodTestNormalRangeLower", + "@id" : "bts:Lot", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label" : "BloodTestNormalRangeLower", + "rdfs:comment" : "TBD", + "rdfs:label" : "Lot", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BloodTestNormalRangeLower", + "sms:displayName" : "Lot", "sms:required" : "sms:false" }, { - "@id" : "bts:RuralvsUrban", + "@id" : "bts:COVID19ComplicationsSeverity", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "RuralvsUrban", + "rdfs:label" : "COVID19ComplicationsSeverity", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RuralvsUrban", + "sms:displayName" : "COVID19ComplicationsSeverity", "sms:required" : "sms:false" }, { + "@id" : "bts:ProgressionorRecurrenceAnatomicSite", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ProgressionorRecurrenceAnatomicSite", "rdfs:subClassOf" : [ ], - "@id" : "bts:MulticentricBreastCarcinomaPresentIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "MulticentricBreastCarcinomaPresentIndicator", - "rdfs:comment" : "A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.", - "@type" : "rdfs:Class", - "sms:displayName" : "MulticentricBreastCarcinomaPresentIndicator" + "sms:displayName" : "ProgressionorRecurrenceAnatomicSite", + "sms:required" : "sms:false" }, { - "@id" : "bts:UMITag", + "@id" : "bts:EmissionWavelength", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "UMITag", + "rdfs:label" : "EmissionWavelength", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "UMITag", + "sms:displayName" : "EmissionWavelength", "sms:required" : "sms:false" }, { - "@id" : "bts:CellBarcodeLength", + "@id" : "bts:ImageID", "@type" : "rdfs:Class", - "rdfs:comment" : "Length of cell barcode read (in bp): number", - "rdfs:label" : "CellBarcodeLength", + "rdfs:comment" : "Unique internal image identifier. eg \"\"Image:0\"\". (To be extracted from OME-XML)", + "rdfs:label" : "ImageID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CellBarcodeLength", + "sms:displayName" : "ImageID", "sms:required" : "sms:false" }, { - "@id" : "bts:ClassBRCA1", + "@id" : "bts:LibraryPrepKitName", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ClassBRCA1", + "rdfs:comment" : "Name of Library Prep Kit. String", + "rdfs:label" : "LibraryPrepKitName", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClassBRCA1", - "sms:required" : "sms:false" + "sms:displayName" : "LibraryPrepKitName", + "sms:required" : "sms:true" }, { - "@id" : "bts:SectionNumberinSequence", - "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)", - "rdfs:label" : "SectionNumberinSequence", "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SectionNumberinSequence", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SampleCollectionCenter", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SampleCollectionCenter", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SampleCollectionCenter", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CopyNumber", - "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "CopyNumber", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CopyNumber", - "sms:required" : "sms:false" - }, { - "@id" : "bts:SectioningDaysfromIndex", - "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days from the research participant's index date that the biospecimen was sectioned after collection", - "rdfs:label" : "SectioningDaysfromIndex", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SectioningDaysfromIndex", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Immersion", + "@id" : "bts:SingleNucleusBuffer", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Air" - }, { - "@id" : "bts:Oil" + "@id" : "bts:10x" }, { - "@id" : "bts:Water" + "@id" : "bts:NIB" }, { - "@id" : "bts:Other" + "@id" : "bts:Omni" } ], - "rdfs:label" : "Immersion", - "rdfs:comment" : "Immersion medium", - "@type" : "rdfs:Class", - "sms:displayName" : "Immersion" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Pyramid", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "Pyramid", - "rdfs:comment" : "Does data file contain pyramid of images", + "rdfs:label" : "SingleNucleusBuffer", + "rdfs:comment" : "Nuclei isolation buffer", "@type" : "rdfs:Class", - "sms:displayName" : "Pyramid" + "sms:displayName" : "SingleNucleusBuffer" }, { - "@id" : "bts:SampleSite", + "@id" : "bts:LensNA", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SampleSite", + "rdfs:comment" : "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label" : "LensNA", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SampleSite", + "sms:displayName" : "LensNA", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:MismatchRepairSystemStatus", + "@id" : "bts:PhysicalSizeZUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:MismatchrepairdeficiencyMMRD" + "@id" : "bts:cm" }, { - "@id" : "bts:MismatchrepairproficiencyMMPP" + "@id" : "bts:mm" }, { - "@id" : "bts:MicrosatelliteinstabilityhighMSIH" + "@id" : "bts:µm" }, { - "@id" : "bts:MicrosatellitestableMSS" + "@id" : "bts:nm" }, { - "@id" : "bts:unknownorother" + "@id" : "bts:Å" } ], - "rdfs:label" : "MismatchRepairSystemStatus", - "rdfs:comment" : "The text that best describes the condition or state of MMR (mismatch repair system) in the patient", + "rdfs:label" : "PhysicalSizeZUnit", + "rdfs:comment" : "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", "@type" : "rdfs:Class", - "sms:displayName" : "MismatchRepairSystemStatus" + "sms:displayName" : "PhysicalSizeZUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:Tseries", + "@id" : "bts:HereditaryCancerPredispositionSyndrome", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:SDHassociatedrenalcancer" }, { - "@id" : "bts:No" + "@id" : "bts:Constitutionalmismatchrepairdeficiency" + }, { + "@id" : "bts:Cirrhosisunknownetiology" + }, { + "@id" : "bts:Beckwith-Wiedemann" + }, { + "@id" : "bts:Hereditarymelanoma" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Gorlinsyndrome" + }, { + "@id" : "bts:vonHippel-LindauSyndrome" + }, { + "@id" : "bts:Tuberoussclerosiscomplex" + }, { + "@id" : "bts:RhabdoidtumorpredispositionsyndrometypeI" + }, { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Tyrosinemia" + }, { + "@id" : "bts:Familialgastrointestinalstromaltumor" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:Li-Fraumenisyndrome" + }, { + "@id" : "bts:Fanconianemia" + }, { + "@id" : "bts:Turcotsyndrome" + }, { + "@id" : "bts:Attenuatedfamilialadenomatouspolyposis" + }, { + "@id" : "bts:BAP1mutantdisease" + }, { + "@id" : "bts:Lynchsyndrome" + }, { + "@id" : "bts:Hereditaryparaganglioma–pheochromocytomasyndrome" + }, { + "@id" : "bts:Nevoidbasalcellcarcinomasyndrome" + }, { + "@id" : "bts:MultipleendocrineneoplasiatypeII" + }, { + "@id" : "bts:Rubinstein-Taybisyndrome" + }, { + "@id" : "bts:Cowdensyndrome" + }, { + "@id" : "bts:Hereditaryrenaloncocytoma" + }, { + "@id" : "bts:HereditarypapillaryRCC" + }, { + "@id" : "bts:Peutz–Jegherssyndrome" + }, { + "@id" : "bts:Familialadenomatouspolyposis" + }, { + "@id" : "bts:Biliarydisorder" + }, { + "@id" : "bts:MUTYH-associatedpolyposis" + }, { + "@id" : "bts:RhabdoidtumorpredispositionsyndrometypeII" + }, { + "@id" : "bts:Hereditaryretinoblastoma" + }, { + "@id" : "bts:GlycogenStorageDisease" + }, { + "@id" : "bts:Carneycomplex" + }, { + "@id" : "bts:Hereditarydiffusegastriccancer" + }, { + "@id" : "bts:Juvenilepolyposissyndrome" + }, { + "@id" : "bts:Hereditarymixedpolyposissyndrome" + }, { + "@id" : "bts:Serratedpolyposissyndrome" + }, { + "@id" : "bts:Familialrenalcancer" + }, { + "@id" : "bts:Hereditarypapillaryrenalcellcarcinoma" + }, { + "@id" : "bts:Hereditaryleiomyoma-renalcellcarcinoma" + }, { + "@id" : "bts:MultipleendocrineneoplasiatypeI" + }, { + "@id" : "bts:Birt-Hogg-Dubesyndrome" + }, { + "@id" : "bts:Familialpancreaticcancer" + }, { + "@id" : "bts:Hereditarybreast–ovariancancersyndrome" + }, { + "@id" : "bts:Familialprostatecancer" + }, { + "@id" : "bts:Melanoma–astrocytomasyndrome" + }, { + "@id" : "bts:Alpha-1antitrypsin" } ], - "rdfs:label" : "Tseries", - "rdfs:comment" : "Does data file contain a time-series of images", - "@type" : "rdfs:Class", - "sms:displayName" : "Tseries" - }, { - "@id" : "bts:Component", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Component", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Component", - "sms:required" : "sms:false" - }, { - "@id" : "bts:RelativeswithCancerHistoryCount", - "@type" : "rdfs:Class", - "rdfs:comment" : "The number of relatives the patient has with a known history of cancer.", - "rdfs:label" : "RelativeswithCancerHistoryCount", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RelativeswithCancerHistoryCount", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AlcoholDrinksPerDay", + "rdfs:label" : "HereditaryCancerPredispositionSyndrome", + "rdfs:comment" : "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the average number of alcoholic beverages a person consumes per day.", - "rdfs:label" : "AlcoholDrinksPerDay", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AlcoholDrinksPerDay", - "sms:required" : "sms:false" + "sms:displayName" : "HereditaryCancerPredispositionSyndrome" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:EndBias", + "@id" : "bts:PrimaryDiagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:3Prime" + "@id" : "bts:Pagetdiseaseandintraductalcarcinomaofbreast" }, { - "@id" : "bts:5Prime" + "@id" : "bts:Papillarymicrocarcinoma" }, { - "@id" : "bts:FullLengthTranscript" - } ], - "rdfs:label" : "EndBias", - "rdfs:comment" : "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "@type" : "rdfs:Class", - "sms:displayName" : "EndBias" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SatelliteMetastasisPresentIndicator", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "SatelliteMetastasisPresentIndicator", - "rdfs:comment" : "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", - "@type" : "rdfs:Class", - "sms:displayName" : "SatelliteMetastasisPresentIndicator" - }, { - "@id" : "bts:ParentBiospecimenID", - "@type" : "rdfs:Class", - "rdfs:comment" : "Biospecimen identifier indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", - "rdfs:label" : "ParentBiospecimenID", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "ParentBiospecimenID", - "sms:required" : "sms:false" - }, { - "@id" : "bts:AlcoholUse", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "AlcoholUse", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AlcoholUse", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:NucleusIdentifier", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "NucleusIdentifier", - "rdfs:comment" : "Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from", - "@type" : "rdfs:Class", - "sms:displayName" : "NucleusIdentifier" - }, { - "@id" : "bts:Title", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Title", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "Title", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:ClinicalBiospecimenType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:ConnectiveTissue" + "@id" : "bts:Kaposisarcoma" + }, { + "@id" : "bts:CarcinomaNOS" + }, { + "@id" : "bts:AcutemyeloidleukemiaNOS" + }, { + "@id" : "bts:TumorNOS" + }, { + "@id" : "bts:Renalcelladenocarcinoma" + }, { + "@id" : "bts:MalignantlymphomalymphoblasticNOS" + }, { + "@id" : "bts:Mammarycarcinomainsitu" + }, { + "@id" : "bts:Adenocarcinomainsituintubularadenoma" + }, { + "@id" : "bts:MalignantlymphomasmallBlymphocyticNOS" + }, { + "@id" : "bts:Eosinophilicleukemia" + }, { + "@id" : "bts:AcutelymphoblasticleukemiaNOS" + }, { + "@id" : "bts:MalignantlymphomalymphocyticnodularNOS" + }, { + "@id" : "bts:Basalcellepithelioma" + }, { + "@id" : "bts:Intracysticpapilloma" + }, { + "@id" : "bts:Lobularandductalcarcinoma" + }, { + "@id" : "bts:Cancer" + }, { + "@id" : "bts:Tlymphoblasticleukemia/lymphoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocyte-rich" + }, { + "@id" : "bts:Esophagealintraepithelialneoplasiahighgrade" + }, { + "@id" : "bts:Burkittcellleukemia" + }, { + "@id" : "bts:MonocyticleukemiaNOS" + }, { + "@id" : "bts:AcuteleukemiaNOS" + }, { + "@id" : "bts:Renalmedullarycarcinoma" + }, { + "@id" : "bts:Diffusemelanocytosis" + }, { + "@id" : "bts:Intraductalandlobularcarcinoma" + }, { + "@id" : "bts:MelanoticpsammomatousMPNST" + }, { + "@id" : "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + }, { + "@id" : "bts:Pigmentedadenoma" + }, { + "@id" : "bts:ChronicgranulocyticleukemiaBCR/ABL" + }, { + "@id" : "bts:CervicalintraepithelialneoplasiagradeIII" + }, { + "@id" : "bts:High-gradeserouscarcinoma" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosisgrade1" + }, { + "@id" : "bts:Meningiomamalignant" + }, { + "@id" : "bts:InterstitialcelltumorNOS" + }, { + "@id" : "bts:BronchialadenomaNOS" + }, { + "@id" : "bts:PrecursorT-celllymphoblasticlymphoma" + }, { + "@id" : "bts:Tubularandroblastomawithlipidstorage" + }, { + "@id" : "bts:Combinedlargecellneuroendocrinecarcinoma" + }, { + "@id" : "bts:NephroblastomaNOS" + }, { + "@id" : "bts:Tumorcellsbenign" + }, { + "@id" : "bts:Tumorletbenign" + }, { + "@id" : "bts:Pleomorphiclipoma" + }, { + "@id" : "bts:Adenocarcinomaofanalducts" + }, { + "@id" : "bts:Gastrointestinalstromaltumormalignant" + }, { + "@id" : "bts:Malignantmelanomainjunctionalnevus" + }, { + "@id" : "bts:Rhabdosarcoma" + }, { + "@id" : "bts:EndometrioidadenomaNOS" + }, { + "@id" : "bts:Hodgkinsarcoma" + }, { 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"bts:Paragangliomamalignant" + }, { + "@id" : "bts:ClassicalHodgkinlymphomanodularsclerosisgrade2" + }, { + "@id" : "bts:B-ALL" + }, { + "@id" : "bts:Skinappendagecarcinoma" + }, { + "@id" : "bts:Epithelialtumorbenign" + }, { + "@id" : "bts:Blymphoblasticleukemia/lymphomaNOS" + }, { + "@id" : "bts:HodgkinlymphomanodularsclerosisNOS" + }, { + "@id" : "bts:MalignantlymphomalymphocyticdiffuseNOS" + }, { + "@id" : "bts:Pro-BALL" + }, { + "@id" : "bts:GastrinomaNOS" + }, { + "@id" : "bts:Intraductalcarcinomaclinging" + }, { + "@id" : "bts:Non-invasivelowgradeserouscarcinoma" + }, { + "@id" : "bts:AcutepromyelocyticleukemiaNOS" + }, { + "@id" : "bts:Malignantlymphomanon-HodgkinNOS" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:Melanoticschwannoma" + }, { + "@id" : "bts:SplenicmarginalzonelymphomaNOS" + }, { + "@id" : "bts:Transitionalcellcarcinomainsitu" + }, { + "@id" : "bts:Chronicmonocyticleukemia" + }, { + "@id" : "bts:Gastrincelltumor" + }, { + "@id" : "bts:Papillaryserouscystadenocarcinoma" + }, { + "@id" : "bts:TeratomamalignantNOS" + }, { + "@id" : "bts:ClassicalHodgkinlymphomalymphocytedepletionreticular" + }, { + "@id" : "bts:Tumorcellsuncertainwhetherbenignormalignant" + }, { + "@id" : "bts:Epithelialtumormalignant" + }, { + "@id" : "bts:TubularandroblastomaNOS" + }, { + "@id" : "bts:Papillarycarcinomainsitu" + }, { + "@id" : "bts:PituitarycarcinomaNOS" + }, { + "@id" : "bts:Typicalcarcinoid" + }, { + "@id" : "bts:Non-smallcellcarcinoma" + }, { + "@id" : "bts:MeningiomaNOS" + }, { + "@id" : "bts:EndometrialsarcomaNOS" + }, { + "@id" : "bts:NeuroblastomaNOS" + }, { + "@id" : "bts:BcelllymphomaNOS" + }, { + "@id" : "bts:PeripheralT-celllymphomalargecell" + }, { + "@id" : "bts:RenalcellcarcinomaNOS" + }, { + "@id" : "bts:Renalcellcarcinomaspindlecell" + }, { + "@id" : "bts:Hepatocholangiocarcinoma" + }, { + "@id" : "bts:MalignantlymphomanodularNOS" + }, { + "@id" : "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + }, { + "@id" : 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"bts:Sclerosinghemangioma" + }, { + "@id" : "bts:LymphocyticleukemiaNOS" + }, { + "@id" : "bts:PrecursorcelllymphoblasticleukemiaNOS" + }, { + "@id" : "bts:PapillarycarcinomaNOS" + }, { + "@id" : "bts:Bronchio-alveolarcarcinomamucinous" + }, { + "@id" : "bts:CarcinomainapolypNOS" + }, { + "@id" : "bts:AcutemyeloidleukemiaMLL" + }, { + "@id" : "bts:Tubulocysticrenalcellcarcinoma" + }, { + "@id" : "bts:MelanocytomaNOS" + }, { + "@id" : "bts:ChronicmyelogenousleukemiaPhiladelphiachromosome(Ph1)positive" + }, { + "@id" : "bts:Ewingsarcoma" + }, { + "@id" : "bts:GliomaNOS" + }, { + "@id" : "bts:Bronchial-associatedlymphoidtissuelymphoma" + }, { + "@id" : "bts:Papillotubularadenoma" + }, { + "@id" : "bts:Papillomaofbladder" + }, { + "@id" : "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" + }, { + "@id" : "bts:Carcinomainpleomorphicadenoma" + }, { + "@id" : "bts:Chondrosarcomagrade2/3" }, { - "@id" : "bts:PeritonealFluid" + "@id" : "bts:Neoplasmsecondary" }, { - "@id" : "bts:NotReported" + "@id" : "bts:Rhabdomyosarcomawithganglionicdifferentiation" }, { - "@id" : "bts:Saliva" + "@id" : "bts:Chroniclymphocyticleukemia" }, { - "@id" : "bts:TissueNOS" + "@id" : "bts:Liposarcomawelldifferentiated" }, { - "@id" : "bts:Skin" + "@id" : "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id" : "bts:unknown" + "@id" : "bts:Secretorycarcinomaofbreast" }, { - "@id" : "bts:Feces" + "@id" : "bts:Lobularcarcinomanoninfiltrating" }, { - "@id" : "bts:UninvolvedTissueNOS" + "@id" : "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" }, { - "@id" : "bts:Plasma" + "@id" : "bts:Melanoticneurofibroma" }, { - "@id" : "bts:Granulocyte" + "@id" : "bts:ChronicgranulocyticleukemiaPhiladelphiachromosome(Ph1)positive" }, { - "@id" : "bts:EmbryonicTissue" + "@id" : "bts:Hepatocellularadenoma" }, { - "@id" : "bts:BuccalMucosa" + "@id" : "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id" : "bts:Blood" + "@id" : "bts:ParagangliomaNOS" }, { - "@id" : "bts:MuscleTissue" + "@id" : "bts:DiffuselargeB-celllymphomaNOS" }, { - "@id" : "bts:CerebrospinalFluid" + "@id" : "bts:NevusNOS" }, { - "@id" : "bts:SoftTissue" + "@id" : "bts:Hepatoidcarcinoma" }, { - "@id" : "bts:Urine" + "@id" : "bts:MixedtumormalignantNOS" }, { - "@id" : "bts:PleuralFluid" + "@id" : "bts:Rhabdoidsarcoma" }, { - "@id" : "bts:BoneMarrow" + "@id" : "bts:Tubulolobularcarcinoma" }, { - "@id" : "bts:Serum" + "@id" : "bts:Papillomatosisglandular" }, { - "@id" : "bts:EmbryonicFluid" + "@id" : "bts:Bronchialadenomacarcinoid" }, { - "@id" : "bts:NerveTissue" + "@id" : "bts:Tumorembolus" }, { - "@id" : "bts:BuffyCoat" - } ], - "rdfs:label" : "ClinicalBiospecimenType", - "rdfs:comment" : "The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "@type" : "rdfs:Class", - "sms:displayName" : "ClinicalBiospecimenType" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Antigen", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:CA19-9" + "@id" : "bts:DuctcarcinomaNOS" }, { - "@id" : "bts:CD79A" + "@id" : "bts:RhabdomyosarcomaNOS" }, { - "@id" : "bts:CD5" + "@id" : "bts:LobularcarcinomaNOS" }, { - "@id" : "bts:CD30" + "@id" : "bts:Bronchialadenomacylindroid" }, { - "@id" : "bts:NotReported" + "@id" : "bts:EpidermoidcarcinomaNOS" }, { - "@id" : "bts:CD20" + "@id" : "bts:Papillaryglioneuronaltumor" }, { - "@id" : "bts:CD14" + "@id" : "bts:DuctalcarcinomainsituNOS" }, { - "@id" : "bts:CD19" + "@id" : "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" }, { - "@id" : "bts:unknown" + "@id" : "bts:Glioblastoma" }, { - "@id" : "bts:CD34" + "@id" : "bts:Papillaryandfollicularcarcinoma" }, { - "@id" : "bts:CCND1" + "@id" : "bts:DuctalcarcinomaNOS" }, { - "@id" : "bts:CD25" + "@id" : "bts:Tumorbenign" }, { - "@id" : "bts:HLA-DR" + "@id" : "bts:Pagetdiseasemammary" }, { - "@id" : "bts:Mesothelin" + "@id" : "bts:Diffuseastrocytomalowgrade" }, { - "@id" : "bts:CD10" + "@id" : "bts:Ductcellcarcinoma" }, { - "@id" : "bts:CD56" + "@id" : "bts:Preleukemicsyndrome" }, { - "@id" : "bts:CD3" + "@id" : "bts:Carcinomadiffusetype" }, { - "@id" : "bts:NSE" + "@id" : "bts:Neurosarcoma" }, { - "@id" : "bts:CA-125" + "@id" : "bts:PapillomatosisNOS" }, { - "@id" : "bts:CD22" + "@id" : "bts:Therapyrelatedmyeloidneoplasm" }, { - "@id" : "bts:CD23" + "@id" : "bts:Renalcarcinomacollectingducttype" }, { - "@id" : "bts:SquamousCellCarcinomaAntigen" + "@id" : "bts:NeurofibromaNOS" }, { - "@id" : "bts:CEA" + "@id" : "bts:Meningiomaanaplastic" }, { - "@id" : "bts:CD33" + "@id" : "bts:CementomaNOS" }, { - "@id" : "bts:CD138" + "@id" : "bts:DermatofibromaNOS" }, { - "@id" : "bts:BCL6" + "@id" : "bts:AstrocytomaNOS" }, { - "@id" : "bts:CD7" + "@id" : "bts:Livercelladenoma" }, { - "@id" : "bts:CD117" + "@id" : "bts:TubulovillousadenomaNOS" }, { - "@id" : "bts:CD15" + "@id" : "bts:MelanomaNOS" }, { - "@id" : "bts:CD45" - } ], - "rdfs:label" : "Antigen", - "rdfs:comment" : "The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "@type" : "rdfs:Class", - "sms:displayName" : "Antigen" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:OncotypeRiskGroup", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" + "@id" : "bts:PapillomaNOS" }, { - "@id" : "bts:Datanotavailable" + "@id" : "bts:Esophagealglandulardysplasia(intraepithelialneoplasia)highgrade" }, { - "@id" : "bts:Highrisk" + "@id" : "bts:Tumorcellsmalignant" }, { - "@id" : "bts:Intermediaterisk" + "@id" : "bts:MalignantlymphomadiffuseNOS" }, { - "@id" : "bts:Lowrisk" - } ], - "rdfs:label" : "OncotypeRiskGroup", - "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", - "@type" : "rdfs:Class", - "sms:displayName" : "OncotypeRiskGroup" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:ModeofCancerDetection", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Datanotavailable" + "@id" : "bts:Renalcellcarcinomachromophobetype" }, { - "@id" : "bts:StandardofCareScreening" + "@id" : "bts:Tubularcarcinoid" }, { - "@id" : "bts:ClinicalExaminationofunrelatedcancersymptoms" + "@id" : "bts:Nonpigmentednevus" }, { - "@id" : "bts:Incidentaloma" + "@id" : "bts:Rodentulcer" }, { - "@id" : "bts:IntervalCancer" - } ], - "rdfs:label" : "ModeofCancerDetection", - "rdfs:comment" : "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", - "@type" : "rdfs:Class", - "sms:displayName" : "ModeofCancerDetection" - }, { - "@id" : "bts:RelationshipType", - "@type" : "rdfs:Class", - "rdfs:comment" : "The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.", - "rdfs:label" : "RelationshipType", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RelationshipType", - "sms:required" : "sms:false" - }, { - "@id" : "bts:FeatureReferenceId", - "@type" : "rdfs:Class", - "rdfs:comment" : "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]", - "rdfs:label" : "FeatureReferenceId", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "FeatureReferenceId", - "sms:required" : "sms:false" - }, { - "@id" : "bts:RelationshipAgeatDiagnosis", - "@type" : "rdfs:Class", - "rdfs:comment" : "The age (in years) when the patient's relative was first diagnosed.", - "rdfs:label" : "RelationshipAgeatDiagnosis", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "RelationshipAgeatDiagnosis", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SmokingExposure", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes-SmokingExposure" + "@id" : "bts:HodgkindiseaseNOS" }, { - "@id" : "bts:NotReported" + "@id" : "bts:Acinarcellcarcinoma" }, { - "@id" : "bts:No-SmokingExposure" - } ], - "rdfs:label" : "SmokingExposure", - "rdfs:comment" : "Indicate if individual has smoking exposure", - "@type" : "rdfs:Class", - "sms:displayName" : "SmokingExposure" - }, { - "@id" : "bts:AltSampleID", - "@type" : "rdfs:Class", - "rdfs:comment" : "Additional alternative ID associated with a biosample", - "rdfs:label" : "AltSampleID", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "AltSampleID", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:TestResult", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Normal" + "@id" : "bts:Papillaryadenofibroma" }, { - "@id" : "bts:NotReported" + "@id" : "bts:Oatcellcarcinoma" }, { - "@id" : "bts:TestValueReported" + "@id" : "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id" : "bts:unknown" + "@id" : "bts:SpindlecellcarcinomaNOS" + }, { + "@id" : "bts:Adenocarcinomainpolypoidadenoma" + }, { + "@id" : "bts:Papillaryserousadenocarcinoma" + }, { + "@id" : "bts:SplenicdiffuseredpulpsmallB-celllymphoma" + }, { + "@id" : "bts:ChondromaNOS" + }, { + "@id" : "bts:Bileductadenoma" + }, { + "@id" : "bts:Adenocarcinomainvillousadenoma" }, { - "@id" : "bts:Overexpressed" + "@id" : "bts:SpindlecellmelanomaNOS" }, { - "@id" : "bts:Intermediate" + "@id" : "bts:ClassicalHodgkinlymphomamixedcellularityNOS" }, { - "@id" : "bts:NotApplicable" + "@id" : "bts:Combinedsmallcell-largecarcinoma" }, { - "@id" : "bts:LossofExpression" + "@id" : "bts:Eosinophilcarcinoma" }, { - "@id" : "bts:Low" + "@id" : "bts:PancreaticendocrinetumorNOS" }, { - "@id" : "bts:High" + "@id" : "bts:AdenocarcinomaNOS" }, { - "@id" : "bts:Equivocal" + "@id" : "bts:SarcomaNOS" }, { - "@id" : "bts:CopyNumberReported" + "@id" : "bts:ChronicmyelocyticleukemiaNOS" }, { - "@id" : "bts:Positive" + "@id" : "bts:Adenocarcinomainsitunon-mucinous" }, { - "@id" : "bts:Negative" + "@id" : "bts:ChronicleukemiaNOS" }, { - "@id" : "bts:AbnormalNOS" - } ], - "rdfs:label" : "TestResult", - "rdfs:comment" : "The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. 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"@id" : "bts:unknownprimarysite" + "@id" : "bts:Yes" + } ], + "rdfs:label" : "PassedQC", + "rdfs:comment" : "Did all channels pass QC (if not add free text Comment)", + "@type" : "rdfs:Class", + "sms:displayName" : "PassedQC" + }, { + "@id" : "bts:AgeAtMenarche", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AgeAtMenarche", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeAtMenarche", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ScRNAseqWorkflowType", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ScRNAseqWorkflowType", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ScRNAseqWorkflowType", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Invasivecarcinoma-typecannotbedetermined" }, { - "@id" : "bts:Posteriormediastinum" + "@id" : "bts:Medullarycarcinoma" }, { - "@id" : "bts:Uretericorifice" + "@id" : "bts:Invasivepapillarycarcinoma" }, { - "@id" : "bts:Otherill-definedsites" + "@id" : "bts:Invasivetubularcarcinoma" }, { - "@id" : "bts:Bonemarrow" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + "@id" : "bts:unknown" }, { - "@id" : "bts:LymphnodeNOS" + "@id" : "bts:Invasivecribriformcarcinoma" }, { - "@id" : "bts:Skinofscalpandneck" + "@id" : "bts:Invasivemicropapillarycarcinoma" }, { - "@id" : "bts:Retromolararea" + "@id" : "bts:Tubulolobularcarcinoma" }, { - "@id" : "bts:Overlappinglesionofliporalcavityandpharynx" + "@id" : "bts:Other" }, { - "@id" : "bts:Overlappinglesionofaccessorysinuses" + "@id" : "bts:Classicaltype" }, { - "@id" : "bts:Overlappinglesionofpenis" + "@id" : "bts:Mucinouscarcinoma" + } ], + "rdfs:label" : "InvasiveDuctalBreastCarcinomaHistologicCategory", + "rdfs:comment" : "The histologic subtype for the most common type of invasive breast carcinoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "InvasiveDuctalBreastCarcinomaHistologicCategory" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:TestAnalyteType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:Overlappinglesionofvulva" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Overlappinglesionofill-definedsites" + "@id" : "bts:DNA" }, { - "@id" : "bts:Occipitallobe" + "@id" : "bts:mRNA" }, { - "@id" : "bts:Overlappinglesionofeyeandadnexa" + "@id" : "bts:miRNA" }, { - "@id" : "bts:Lingualtonsil" + "@id" : "bts:ProteinAnalyte" }, { - "@id" : "bts:GumNOS" + "@id" : "bts:TotalRNA" + } ], + "rdfs:label" : "TestAnalyteType", + "rdfs:comment" : "The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "TestAnalyteType" + }, { + "@id" : "bts:DataCategory", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DataCategory", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DataCategory", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Ethnicity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:Thymus" + "@id" : "bts:NotReported" }, { - "@id" : "bts:MalegenitalorgansNOS" + "@id" : "bts:hispanicorlatino" }, { - "@id" : "bts:IsletsofLangerhans" + "@id" : "bts:nothispanicorlatino" }, { - "@id" : "bts:Isthmusuteri" + "@id" : "bts:notallowedtocollect" + } ], + "rdfs:label" : "Ethnicity", + "rdfs:comment" : "An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.", + "@type" : "rdfs:Class", + "sms:displayName" : "Ethnicity" + }, { + "@id" : "bts:WorkingDistance", + "@type" : "rdfs:Class", + "rdfs:comment" : "The working distance of the lens, expressed as a floating point number. Floating point > 0.", + "rdfs:label" : "WorkingDistance", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "WorkingDistance", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FixationDuration", + "@type" : "rdfs:Class", + "rdfs:comment" : "The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)", + "rdfs:label" : "FixationDuration", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "FixationDuration", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:LaboratoryTest", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:AbsoluteNeutrophil" }, { - "@id" : "bts:Spinalmeninges" + "@id" : "bts:Myeloblasts" }, { - "@id" : "bts:Myometrium" + "@id" : "bts:TotalProtein" }, { - "@id" : "bts:Pelvicbonessacrumcoccyxandassociatedjoints" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id" : "bts:Hemoglobin" }, { - "@id" : "bts:Anterior2/3oftongueNOS" + "@id" : "bts:NOS" }, { - "@id" : "bts:Upperthirdofesophagus" + "@id" : "bts:Basophil" }, { - "@id" : "bts:MeningesNOS" + "@id" : "bts:C-ReactiveProtein" }, { - "@id" : "bts:Prostategland" + "@id" : "bts:MProtein" }, { - "@id" : "bts:Overlappinglesionofsmallintestine" + "@id" : "bts:Lambda" }, { - "@id" : "bts:Lowergum" + "@id" : "bts:unknown" }, { - "@id" : "bts:Paraspinal" + "@id" : "bts:CirculatingTumorCells" }, { - "@id" : "bts:Appendix" + "@id" : "bts:Epstein-BarrVirus" }, { - "@id" : "bts:ScrotumNOS" + "@id" : "bts:Promonocytes" }, { - "@id" : "bts:Overlappinglesionoflarynx" + "@id" : "bts:LactateDehydrogenase" }, { - "@id" : "bts:Mainbronchus" + "@id" : "bts:Cellularity" }, { - "@id" : "bts:Descendedtestis" + "@id" : "bts:HumanChorionicGonadotropin" }, { - "@id" : "bts:Cloacogeniczone" + "@id" : "bts:AlphaFetoprotein" }, { - "@id" : "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id" : "bts:Hematocrit" }, { - "@id" : "bts:Heart" + "@id" : "bts:Promyelocytes" }, { - "@id" : "bts:MucosaoflipNOS" + "@id" : "bts:Testosterone" }, { - "@id" : "bts:Broadligament" + "@id" : "bts:Lymphoblasts" }, { - "@id" : "bts:Headofpancreas" + "@id" : "bts:ImmunoglobulinM" }, { - "@id" : "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" + "@id" : "bts:Lymphocytes" }, { - "@id" : "bts:Temporallobe" + "@id" : "bts:Leukocytes" }, { - "@id" : "bts:Bodyofpenis" + "@id" : "bts:HPV-E6/E7" }, { - "@id" : "bts:Overlappinglesionofbiliarytract" + "@id" : "bts:LuteinizingHormone" }, { - "@id" : "bts:Labiumminus" + "@id" : "bts:SegmentedNeutrophil" }, { - "@id" : "bts:Descendingcolon" + "@id" : "bts:ImmunoglobulinG" }, { - "@id" : "bts:Lateralwallofnasopharynx" + "@id" : "bts:Beta2Microglobulin" }, { - "@id" : "bts:Posteriorwallofhypopharynx" + "@id" : "bts:Creatinine" }, { - "@id" : "bts:Nipple" + "@id" : "bts:Glucose" }, { - "@id" : "bts:Jejunum" + "@id" : "bts:SerumFreeImmunoglobulinLightChain" }, { - "@id" : "bts:Posteriorwallofbladder" + "@id" : "bts:Calcium" }, { - "@id" : "bts:Laryngealcartilage" + "@id" : "bts:Metamyelocytes" }, { - "@id" : "bts:Cecum" + "@id" : "bts:Kappa" }, { - "@id" : "bts:Skinoflowerlimbandhip" + "@id" : "bts:Prolymphocytes" }, { - "@id" : "bts:Corpusuteri" + "@id" : "bts:HumanPapillomavirus" }, { - "@id" : "bts:FemalegenitaltractNOS" + "@id" : "bts:Platelets" }, { - "@id" : "bts:AbdomenNOS" + "@id" : "bts:NeutrophilBands" }, { - "@id" : "bts:Tonsillarpillar" + "@id" : "bts:Myelocytes" }, { - "@id" : "bts:Otherspecifiedpartsoffemalegenitalorgans" + "@id" : "bts:Albumin" }, { - "@id" : "bts:Glottis" + "@id" : "bts:BloodUreaNitrogen" }, { - "@id" : "bts:OrbitNOS" + "@id" : "bts:TotalBilirubin" }, { - "@id" : "bts:Skinoftrunk" + "@id" : "bts:Eosinophil" }, { - "@id" : "bts:VentricleNOS" + "@id" : "bts:ImmunoglobulinA" }, { - "@id" : "bts:Frontallobe" + "@id" : "bts:B-cellgenotyping" } ], - "rdfs:label" : "SiteofResectionorBiopsy", - "rdfs:comment" : "The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label" : "LaboratoryTest", + "rdfs:comment" : "The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.", "@type" : "rdfs:Class", - "sms:displayName" : "SiteofResectionorBiopsy" + "sms:displayName" : "LaboratoryTest" }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Clonality", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Clonal" - }, { - "@id" : "bts:Non-clonal" - } ], - "rdfs:label" : "Clonality", - "rdfs:comment" : "The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@id" : "bts:LociAbnormalCount", "@type" : "rdfs:Class", - "sms:displayName" : "Clonality" - }, { + "rdfs:comment" : "Numeric value used to describe the number of loci determined to be abnormal.", + "rdfs:label" : "LociAbnormalCount", "rdfs:subClassOf" : [ ], - "@id" : "bts:Sex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:female" - }, { - "@id" : "bts:male" - }, { - "@id" : "bts:unspecified" - } ], - "rdfs:label" : "Sex", - "rdfs:comment" : "Sex of individual", - "@type" : "rdfs:Class", - "sms:displayName" : "Sex" + "sms:displayName" : "LociAbnormalCount", + "sms:required" : "sms:false" }, { - "@id" : "bts:YearOfBirth", + "@id" : "bts:CatalogNumber", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value to represent the calendar year in which an individual was born.", - "rdfs:label" : "YearOfBirth", + "rdfs:comment" : "TBD", + "rdfs:label" : "CatalogNumber", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "YearOfBirth", + "sms:displayName" : "CatalogNumber", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:FOVXUnit", + "@id" : "bts:ImagingAssayType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:cm" - }, { - "@id" : "bts:mm" - }, { - "@id" : "bts:µm" + "@id" : "bts:MIBI" }, { - "@id" : "bts:nm" + "@id" : "bts:MxIF" }, { - "@id" : "bts:Å" - } ], - "rdfs:label" : "FOVXUnit", - "rdfs:comment" : "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "@type" : "rdfs:Class", - "sms:displayName" : "FOVXUnit" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Pathogenicity", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Benign" + "@id" : "bts:IMC" }, { - "@id" : "bts:LikelyBenign" + "@id" : "bts:NotApplicable" }, { - "@id" : "bts:LikelyPathogenic" + "@id" : "bts:mIHC" }, { - "@id" : "bts:Pathogenic" + "@id" : "bts:H&E" }, { - "@id" : "bts:UncertainSignificance" - } ], - "rdfs:label" : "Pathogenicity", - "rdfs:comment" : "The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).", - "@type" : "rdfs:Class", - "sms:displayName" : "Pathogenicity" - }, { - "@id" : "bts:SmokelessTobaccoQuitAge", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "SmokelessTobaccoQuitAge", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SmokelessTobaccoQuitAge", - "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:PixelsBigEndian", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "PixelsBigEndian", - "rdfs:comment" : "Boolean (True/False)", - "@type" : "rdfs:Class", - "sms:displayName" : "PixelsBigEndian" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastCarcinomaDetectionMethodType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" + "@id" : "bts:IHC" }, { - "@id" : "bts:unknown" + "@id" : "bts:CODEX" }, { - "@id" : "bts:ClinicalExam" + "@id" : "bts:SABER" }, { - "@id" : "bts:Datanotavailable" + "@id" : "bts:MERFISH" }, { - "@id" : "bts:NippleDischarge" + "@id" : "bts:CyCIF" }, { - "@id" : "bts:ScreeningMammography" + "@id" : "bts:t-CyCIF" }, { - "@id" : "bts:ScreeningMRI" + "@id" : "bts:GeoMX-DSP" }, { - "@id" : "bts:Selfexam" - } ], - "rdfs:label" : "BreastCarcinomaDetectionMethodType", - "rdfs:comment" : "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", - "@type" : "rdfs:Class", - "sms:displayName" : "BreastCarcinomaDetectionMethodType" - }, { - "@id" : "bts:SizeZ", - "@type" : "rdfs:Class", - "rdfs:comment" : "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label" : "SizeZ", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "SizeZ", - "sms:required" : "sms:false" + "@id" : "bts:ExSeq" + } ], + "rdfs:label" : "ImagingAssayType", + "rdfs:comment" : "Type of imaging assay", + "@type" : "rdfs:Class", + "sms:displayName" : "ImagingAssayType" }, { - "@id" : "bts:COVID19AntibodyTesting", + "@id" : "bts:NucleiBarcodeRead", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "COVID19AntibodyTesting", + "rdfs:comment" : "Nuclei Barcode Read", + "rdfs:label" : "NucleiBarcodeRead", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "COVID19AntibodyTesting", + "sms:displayName" : "NucleiBarcodeRead", "sms:required" : "sms:false" }, { - "@id" : "bts:BMI", + "@id" : "bts:OligoBarcodeUpperStrand", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "BMI", + "rdfs:label" : "OligoBarcodeUpperStrand", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BMI", + "sms:displayName" : "OligoBarcodeUpperStrand", "sms:required" : "sms:false" }, { - "@id" : "bts:EmptyWellBarcode", + "@id" : "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", "@type" : "rdfs:Class", - "rdfs:comment" : "Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.", - "rdfs:label" : "EmptyWellBarcode", + "rdfs:comment" : "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label" : "BreastCarcinomaHER2Centromere17CopynumberTotal", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EmptyWellBarcode", + "sms:displayName" : "BreastCarcinomaHER2Centromere17CopynumberTotal", "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCarcinomaHER2RatioDiagnosis", - "@type" : "rdfs:Class", - "rdfs:comment" : "HER2 ratio of the participant at diagnosis", - "rdfs:label" : "BreastCarcinomaHER2RatioDiagnosis", "rdfs:subClassOf" : [ ], + "@id" : "bts:BiospecimenType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaHER2RatioDiagnosis", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:FluidsBiospecimenType" + }, { + "@id" : "bts:SputumBiospecimenType" + }, { + "@id" : "bts:TissueBiospecimenType" + }, { + "@id" : "bts:MouthRinseBiospecimenType" + }, { + "@id" : "bts:AscitesBiospecimenType" + }, { + "@id" : "bts:CellsBiospecimenType" + }, { + "@id" : "bts:BloodBiospecimenType" + }, { + "@id" : "bts:AnalyteBiospecimenType" + }, { + "@id" : "bts:BoneMarrowBiospecimenType" + }, { + "@id" : "bts:UrineBiospecimenType" + }, { + "@id" : "bts:StoolBiospecimenType" + } ], + "rdfs:label" : "BiospecimenType", + "rdfs:comment" : "Biospecimen Type", + "@type" : "rdfs:Class", + "sms:displayName" : "BiospecimenType" }, { - "@id" : "bts:TimebetweenWakingandFirstSmoke", + "@id" : "bts:SmokeExposureDuration", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TimebetweenWakingandFirstSmoke", + "rdfs:label" : "SmokeExposureDuration", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TimebetweenWakingandFirstSmoke", + "sms:displayName" : "SmokeExposureDuration", "sms:required" : "sms:false" }, { - "@id" : "bts:MedianPercentageofMitochondrialReadsperNucleus", + "@id" : "bts:MenstrualCyclePhase", "@type" : "rdfs:Class", - "rdfs:comment" : "Contamination from mitochondrial sequences", - "rdfs:label" : "MedianPercentageofMitochondrialReadsperNucleus", + "rdfs:comment" : "TBD", + "rdfs:label" : "MenstrualCyclePhase", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MedianPercentageofMitochondrialReadsperNucleus", + "sms:displayName" : "MenstrualCyclePhase", "sms:required" : "sms:false" }, { - "@id" : "bts:PhysicalSizeZ", + "@id" : "bts:ThresholdforMinimumPassingReads", "@type" : "rdfs:Class", - "rdfs:comment" : "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", - "rdfs:label" : "PhysicalSizeZ", + "rdfs:comment" : "Threshold for calling cells", + "rdfs:label" : "ThresholdforMinimumPassingReads", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PhysicalSizeZ", + "sms:displayName" : "ThresholdforMinimumPassingReads", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:LibrarySelectionMethod", + "@id" : "bts:ShippingConditionType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:hybridselection" + "@id" : "bts:LiquidNitrogen" }, { - "@id" : "bts:PCR" + "@id" : "bts:DryIce" }, { - "@id" : "bts:affinityenrichment" + "@id" : "bts:AmbientPack" }, { - "@id" : "bts:poly-Tenrichment" + "@id" : "bts:ColdPack" }, { - "@id" : "bts:random" + "@id" : "bts:IcePack" }, { - "@id" : "bts:rRNAdepletion" + "@id" : "bts:SpecimenatRoomTemperature" }, { - "@id" : "bts:miRNAsizefractionation" + "@id" : "bts:OtherShippingEnvironment" }, { - "@id" : "bts:other" + "@id" : "bts:NotShipped" } ], - "rdfs:label" : "LibrarySelectionMethod", - "rdfs:comment" : "How RNA molecules are isolated", + "rdfs:label" : "ShippingConditionType", + "rdfs:comment" : "Text descriptor of the shipping environment of a biospecimen.", "@type" : "rdfs:Class", - "sms:displayName" : "LibrarySelectionMethod" + "sms:displayName" : "ShippingConditionType" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:CountryofResidence", + "@id" : "bts:AntibioticUse", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:TrinidadandTobago" - }, { - "@id" : "bts:Botswana" - }, { - "@id" : "bts:Malaysia" - }, { - "@id" : "bts:Suriname" - }, { - "@id" : "bts:Uruguay" - }, { - "@id" : "bts:Gibraltar" - }, { - "@id" : "bts:Andorra" - }, { - "@id" : "bts:CaymanIslands" - }, { - "@id" : "bts:Mozambique" - }, { - "@id" : "bts:Dominica" - }, { - "@id" : "bts:Tajikistan" - }, { - "@id" : "bts:Barbados" - }, { - "@id" : "bts:Seychelles" - }, { - "@id" : "bts:Curacao" - }, { - "@id" : "bts:Coted'Ivoire" - }, { - "@id" : "bts:Albania" - }, { - "@id" : "bts:China" - }, { - "@id" : "bts:Oman" - }, { - "@id" : "bts:Congo" - }, { - "@id" : "bts:Burundi" - }, { - "@id" : "bts:FalklandIslands(Malvinas)" - }, { - "@id" : "bts:Kazakhstan" - }, { - "@id" : "bts:Australia" - }, { - "@id" : "bts:France" - }, { - "@id" : "bts:Bahrain" - }, { - "@id" : "bts:SolomonIslands" - }, { - "@id" : "bts:Tanzania" - }, { - "@id" : "bts:FrenchGuiana" - }, { - "@id" : "bts:FederatedStatesofMicronesia" - }, { - "@id" : "bts:AntiguaandBarbuda" - }, { - "@id" : "bts:Colombia" - }, { - "@id" : "bts:Fiji" - }, { - "@id" : "bts:SaoTomeandPrincipe" - }, { - "@id" : "bts:Brazil" - }, { - "@id" : "bts:Guam" - }, { - "@id" : "bts:SouthAfrica" - }, { - "@id" : "bts:Denmark" - }, { - "@id" : "bts:Kyrgyzstan" - }, { - "@id" : "bts:Tunisia" - }, { - "@id" : "bts:Mexico" - }, { - "@id" : "bts:Martinique" - }, { - "@id" : "bts:BurkinaFaso" - }, { - "@id" : "bts:India" - }, { - "@id" : "bts:Myanmar" - }, { - "@id" : "bts:Malawi" - }, { - "@id" : "bts:Sweden" - }, { - "@id" : "bts:Macau" - }, { - "@id" : "bts:Cambodia" - }, { - "@id" : "bts:EquatorialGuinea" - }, { - "@id" : "bts:Senegal" - }, { - "@id" : "bts:Guernsey" - }, { - "@id" : "bts:Azerbaijan" - }, { - "@id" : "bts:Angola" - }, { - "@id" : "bts:Kuwait" - }, { - "@id" : "bts:PapuaNewGuinea" - }, { - "@id" : "bts:CentralAfricanRepublic" - }, { - "@id" : "bts:Bhutan" - }, { - "@id" : "bts:Uzbekistan" - }, { - "@id" : "bts:Portugal" - }, { - "@id" : "bts:IsleofMan" - }, { - "@id" : "bts:Guatemala" - }, { - "@id" : "bts:SaintHelenaAscensionandTristandaCunha" - }, { - "@id" : "bts:Kiribati" - }, { - "@id" : "bts:Peru" - }, { - "@id" : "bts:SouthSudan" - }, { - "@id" : "bts:NorthMacedonia" - }, { - "@id" : "bts:DemocraticRepublicoftheCongo" - }, { - "@id" : "bts:Belarus" - }, { - "@id" : "bts:Madagascar" - }, { - "@id" : "bts:Singapore" - }, { - "@id" : "bts:Togo" + "@id" : "bts:No" }, { - "@id" : "bts:Gambia" + "@id" : "bts:unknown" }, { - "@id" : "bts:Georgia" + "@id" : "bts:Yes-withinlastmonthh" }, { - "@id" : "bts:Italy" + "@id" : "bts:Yes-withinlast1-6months" }, { - "@id" : "bts:Tuvalu" + "@id" : "bts:Yes-over6monthsago" + } ], + "rdfs:label" : "AntibioticUse", + "rdfs:comment" : "Antibiotic use", + "@type" : "rdfs:Class", + "sms:displayName" : "AntibioticUse" + }, { + "@id" : "bts:ERStatus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ERStatus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ERStatus", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MolecularConsequence", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:TFBindingSiteVariant" }, { - "@id" : "bts:Eswatini" + "@id" : "bts:TranscriptAmplification" }, { - "@id" : "bts:Nepal" + "@id" : "bts:SpliceRegionVariant" }, { - "@id" : "bts:Kenya" + "@id" : "bts:DownstreamGeneVariant" }, { - "@id" : "bts:Niger" + "@id" : "bts:5PrimeUTRVariant" }, { - "@id" : "bts:Israel" + "@id" : "bts:SpliceDonorVariant" }, { - "@id" : "bts:Iran" + "@id" : "bts:SpliceAcceptorVariant" }, { - "@id" : "bts:Liberia" + "@id" : "bts:StopGain" }, { - "@id" : "bts:Mali" + "@id" : "bts:StopRetainedVariant" }, { - "@id" : "bts:Belize" + "@id" : "bts:TFBSAmplification" }, { - "@id" : "bts:Hungary" + "@id" : "bts:3PrimeUTRVariant" }, { - "@id" : "bts:HolySee" + "@id" : "bts:UpstreamGeneVariant" }, { - "@id" : "bts:Serbia" + "@id" : "bts:IntergenicVariant" }, { - "@id" : "bts:Belgium" + "@id" : "bts:RegulatoryRegionAblation" }, { - "@id" : "bts:Bermuda" + "@id" : "bts:NMDTranscriptVariant" }, { - "@id" : "bts:Anguilla" + "@id" : "bts:TranscriptAblation" }, { - "@id" : "bts:Jamaica" + "@id" : "bts:Non-codingTranscriptExonVariant" }, { - "@id" : "bts:Lebanon" + "@id" : "bts:SynonymousVariant" }, { - "@id" : "bts:Svalbard&JanMayenIslands" + "@id" : "bts:RegulatoryRegionVariant" }, { - "@id" : "bts:Cyprus" + "@id" : "bts:StopLost" }, { - "@id" : "bts:Norway" + "@id" : "bts:MaturemiRNAVariant" }, { - "@id" : "bts:Somalia" + "@id" : "bts:InframeInsertion" }, { - "@id" : "bts:Japan" + "@id" : "bts:InframeDeletion" }, { - "@id" : "bts:Guyana" + "@id" : "bts:ProteinAlteringVariant" }, { - "@id" : "bts:Paraguay" + "@id" : "bts:IncompleteTerminalCodonVariant" }, { - "@id" : "bts:NewZealand" + "@id" : "bts:TFBSAblation" }, { - "@id" : "bts:Palau" + "@id" : "bts:IntronVariant" }, { - "@id" : "bts:Laos" + "@id" : "bts:CodingSequenceVariant" }, { - "@id" : "bts:Latvia" + "@id" : "bts:MissenseVariant" }, { - "@id" : "bts:Ethiopia" + "@id" : "bts:FrameshiftVariant" }, { - "@id" : "bts:Cuba" + "@id" : "bts:Non-codingTranscriptVariant" }, { - "@id" : "bts:FrenchPolynesia" + "@id" : "bts:FeatureTruncation" }, { - "@id" : "bts:Slovenia" + "@id" : "bts:RegulatoryRegionAmplification" }, { - "@id" : "bts:Philippines" + "@id" : "bts:StartLost" }, { - "@id" : "bts:Mongolia" + "@id" : "bts:FeatureElongation" + } ], + "rdfs:label" : "MolecularConsequence", + "rdfs:comment" : "The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "MolecularConsequence" + }, { + "@id" : "bts:SampleCollectionYear", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SampleCollectionYear", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleCollectionYear", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:WorkingDistanceUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" }, { - "@id" : "bts:Switzerland" + "@id" : "bts:mm" }, { - "@id" : "bts:Bahamas" + "@id" : "bts:µm" }, { - "@id" : "bts:Samoa" + "@id" : "bts:nm" }, { - "@id" : "bts:ElSalvador" + "@id" : "bts:Å" + } ], + "rdfs:label" : "WorkingDistanceUnit", + "rdfs:comment" : "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "WorkingDistanceUnit" + }, { + "@id" : "bts:PriorSitesofRadiation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PriorSitesofRadiation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PriorSitesofRadiation", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholHistory", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" }, { - "@id" : "bts:Chad" + "@id" : "bts:No" }, { - "@id" : "bts:Honduras" + "@id" : "bts:unknown" }, { - "@id" : "bts:Bangladesh" + "@id" : "bts:NotReported" + } ], + "rdfs:label" : "AlcoholHistory", + "rdfs:comment" : "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholHistory" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AgeIsObfuscated", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:True" }, { - "@id" : "bts:Tonga" + "@id" : "bts:False" + } ], + "rdfs:label" : "AgeIsObfuscated", + "rdfs:comment" : "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", + "@type" : "rdfs:Class", + "sms:displayName" : "AgeIsObfuscated" + }, { + "@id" : "bts:TargetName", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TargetName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TargetName", + "sms:required" : "sms:false" + }, { + "@id" : "bts:TargetCaptureKit", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TargetCaptureKit", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TargetCaptureKit", + "sms:required" : "sms:true" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BisulfiteConversionKit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:ZimoEZDNAMethylationKit" }, { - "@id" : "bts:Croatia" + "@id" : "bts:ZimoEZ-96DNAMethylationShallowKit" }, { - "@id" : "bts:BosniaandHerzegovina" + "@id" : "bts:ZimoEZ-96DNAMethylationDeepKit" }, { - "@id" : "bts:Eritrea" + "@id" : "bts:NEBNextEnzymaticMethyl-seqKit" }, { - "@id" : "bts:SaintKittsandNevis" + "@id" : "bts:AgilentSureSelectXTMethyl-Seq" + } ], + "rdfs:label" : "BisulfiteConversionKit", + "rdfs:comment" : "Name of the kit used in bisulfite conversion", + "@type" : "rdfs:Class", + "sms:displayName" : "BisulfiteConversionKit" + }, { + "@id" : "bts:SecondExon", + "@type" : "rdfs:Class", + "rdfs:comment" : "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", + "rdfs:label" : "SecondExon", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SecondExon", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:HistoneFamily", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:Vietnam" + "@id" : "bts:NotReported" }, { - "@id" : "bts:NorthernMarianaIslands" + "@id" : "bts:H1" }, { - "@id" : "bts:CapeVerde" + "@id" : "bts:H2A" }, { - "@id" : "bts:CookIslands" + "@id" : "bts:H2B" }, { - "@id" : "bts:Turkmenistan" + "@id" : "bts:H3" }, { - "@id" : "bts:WesternSahara" + "@id" : "bts:H4" + } ], + "rdfs:label" : "HistoneFamily", + "rdfs:comment" : "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", + "@type" : "rdfs:Class", + "sms:displayName" : "HistoneFamily" + }, { + "@id" : "bts:BloodTestNormalRangeUpper", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", + "rdfs:label" : "BloodTestNormalRangeUpper", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BloodTestNormalRangeUpper", + "sms:required" : "sms:false" + }, { + "@id" : "bts:LibraryPrepKitVersion", + "@type" : "rdfs:Class", + "rdfs:comment" : "Version of Library Prep Kit. String", + "rdfs:label" : "LibraryPrepKitVersion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryPrepKitVersion", + "sms:required" : "sms:true" + }, { + "@id" : "bts:Immunosuppression", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Immunosuppression", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Immunosuppression", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Authors", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Authors", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Authors", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:OvarianCancerPlatinumStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:Jordan" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:Romania" + "@id" : "bts:Platinum-refractory" }, { - "@id" : "bts:Uganda" + "@id" : "bts:Platinum-sensitive" }, { - "@id" : "bts:Aruba" + "@id" : "bts:Platinum-resistant" + } ], + "rdfs:label" : "OvarianCancerPlatinumStatus", + "rdfs:comment" : "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "OvarianCancerPlatinumStatus" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AlcoholIntensity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:HongKong" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Syria" + "@id" : "bts:Drinker" }, { - "@id" : "bts:Germany" + "@id" : "bts:HeavyDrinker" }, { - "@id" : "bts:Chile" + "@id" : "bts:LifelongNon-Drinker" }, { - "@id" : "bts:Austria" + "@id" : "bts:Non-Drinker" }, { - "@id" : "bts:Gabon" + "@id" : "bts:OccasionalDrinker" + } ], + "rdfs:label" : "AlcoholIntensity", + "rdfs:comment" : "Category to describe the patient's current level of alcohol use as self-reported by the patient.", + "@type" : "rdfs:Class", + "sms:displayName" : "AlcoholIntensity" + }, { + "@id" : "bts:Transcript", + "@type" : "rdfs:Class", + "rdfs:comment" : "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "Transcript", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Transcript", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EducationLevel", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "EducationLevel", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "EducationLevel", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:DimensionOrder", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:XYZCT" }, { - "@id" : "bts:Kosovo" + "@id" : "bts:XYZTC" }, { - "@id" : "bts:Qatar" + "@id" : "bts:XYCTZ" }, { - "@id" : "bts:Comoros" + "@id" : "bts:XYCZT" }, { - "@id" : "bts:Mayotte" + "@id" : "bts:XYTZC" }, { - "@id" : "bts:Spain" + "@id" : "bts:ZYX" + } ], + "rdfs:label" : "DimensionOrder", + "rdfs:comment" : "The order in which the individual planes of data are interleaved.", + "@type" : "rdfs:Class", + "sms:displayName" : "DimensionOrder" + }, { + "@id" : "bts:Parity", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of pregnancies carried over the threshold of viability", + "rdfs:label" : "Parity", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Parity", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholDaysPerWeek", + "@type" : "rdfs:Class", + "rdfs:comment" : "Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.", + "rdfs:label" : "AlcoholDaysPerWeek", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholDaysPerWeek", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:AnalyteType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:TissueSectionAnalyte" }, { - "@id" : "bts:Libya" + "@id" : "bts:SerumAnalyte" }, { - "@id" : "bts:CostaRica" + "@id" : "bts:PBMCsorPlasmaorSerumAnalyte" }, { - "@id" : "bts:Bolivia" + "@id" : "bts:Plasma" }, { - "@id" : "bts:Taiwan" + "@id" : "bts:TissueBlockAnalyte" }, { - "@id" : "bts:Iraq" + "@id" : "bts:cfDNAAnalyte" }, { - "@id" : "bts:Finland" + "@id" : "bts:DNAAnalyte" }, { - "@id" : "bts:Netherlands" + "@id" : "bts:RNAAnalyte" }, { - "@id" : "bts:Venezuela" + "@id" : "bts:cDNALibrariesAnalyte" }, { - "@id" : "bts:Malta" + "@id" : "bts:PBMCs" }, { - "@id" : "bts:Niue" + "@id" : "bts:TotalRNAAnalyte" + } ], + "rdfs:label" : "AnalyteType", + "rdfs:comment" : "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "@type" : "rdfs:Class", + "sms:displayName" : "AnalyteType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:FOVYUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" }, { - "@id" : "bts:Algeria" + "@id" : "bts:mm" }, { - "@id" : "bts:Guinea" + "@id" : "bts:µm" }, { - "@id" : "bts:Ireland" + "@id" : "bts:nm" }, { - "@id" : "bts:Montenegro" + "@id" : "bts:Å" + } ], + "rdfs:label" : "FOVYUnit", + "rdfs:comment" : "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "FOVYUnit" + }, { + "@id" : "bts:AgeatDiagnosis", + "@type" : "rdfs:Class", + "rdfs:comment" : "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label" : "AgeatDiagnosis", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeatDiagnosis", + "sms:required" : "sms:false" + }, { + "@id" : "bts:Cytoband", + "@type" : "rdfs:Class", + "rdfs:comment" : "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "Cytoband", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Cytoband", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PeaksCallingSoftware", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PeaksCallingSoftware", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PeaksCallingSoftware", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:SecondhandSmokeasChild", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" }, { - "@id" : "bts:UnitedArabEmirates" + "@id" : "bts:No" }, { - "@id" : "bts:Maldives" + "@id" : "bts:unknown" }, { - "@id" : "bts:Zambia" + "@id" : "bts:NotReported" + } ], + "rdfs:label" : "SecondhandSmokeasChild", + "rdfs:comment" : "The text term used to indicate whether the patient was exposed to secondhand smoke as a child.", + "@type" : "rdfs:Class", + "sms:displayName" : "SecondhandSmokeasChild" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:PhysicalSizeXUnit", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:cm" }, { - "@id" : "bts:Slovakia" + "@id" : "bts:mm" }, { - "@id" : "bts:Lesotho" + "@id" : "bts:µm" }, { - "@id" : "bts:DominicanRepublic" + "@id" : "bts:nm" }, { - "@id" : "bts:SaintPierreandMiquelon" + "@id" : "bts:Å" + } ], + "rdfs:label" : "PhysicalSizeXUnit", + "rdfs:comment" : "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "@type" : "rdfs:Class", + "sms:displayName" : "PhysicalSizeXUnit" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:CancerAssociatedGeneMutations", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:PMS2mutation" }, { - "@id" : "bts:Moldova" + "@id" : "bts:POT1mutation" }, { - "@id" : "bts:SanMarino" + "@id" : "bts:TP53mutation" }, { - "@id" : "bts:Nauru" + "@id" : "bts:H3K27Mmutation" }, { - "@id" : "bts:Luxembourg" + "@id" : "bts:SMARCA4mutation" }, { - "@id" : "bts:Monaco" + "@id" : "bts:SDHDmutation" }, { - "@id" : "bts:Zimbabwe" + "@id" : "bts:BRCA1mutation" }, { - "@id" : "bts:SaudiArabia" + "@id" : "bts:CHKmutation" }, { - "@id" : "bts:Mauritania" + "@id" : "bts:RB1mutation" }, { - "@id" : "bts:Panama" + "@id" : "bts:H3G34R/Vmutation" }, { - "@id" : "bts:UnitedStates" + "@id" : "bts:SDHCmutation" }, { - "@id" : "bts:Montserrat" + "@id" : "bts:SDHBmutation" }, { - "@id" : "bts:Nicaragua" + "@id" : "bts:TSC2mutation" }, { - "@id" : "bts:FaroeIslands" + "@id" : "bts:NotReported" }, { - "@id" : "bts:UnitedKingdom" + "@id" : "bts:HOXB13mutation" }, { - "@id" : "bts:Canada" + "@id" : "bts:NF1mutation" }, { - "@id" : "bts:Ghana" + "@id" : "bts:VHLmutation" }, { - "@id" : "bts:Armenia" + "@id" : "bts:BAP1mutation" }, { - "@id" : "bts:Bulgaria" + "@id" : "bts:SETD2mutation" }, { - "@id" : "bts:Egypt" + "@id" : "bts:BRCA1and2mutation" }, { - "@id" : "bts:Reunion" + "@id" : "bts:unknown" }, { - "@id" : "bts:Cameroon" + "@id" : "bts:PTENmutation" }, { - "@id" : "bts:Rwanda" + "@id" : "bts:NotApplicable" }, { - "@id" : "bts:Timor-Leste" + "@id" : "bts:STK11mutation" }, { - "@id" : "bts:Yemen" + "@id" : "bts:PAX5mutation" }, { - "@id" : "bts:SaintLucia" + "@id" : "bts:RETmutation" }, { - "@id" : "bts:Poland" + "@id" : "bts:NF2mutation" }, { - "@id" : "bts:Namibia" + "@id" : "bts:ETV6mutation" }, { - "@id" : "bts:Guinea-Bissau" + "@id" : "bts:PolDmutation" }, { - "@id" : "bts:Thailand" + "@id" : "bts:IKZF1mutation" }, { - "@id" : "bts:Argentina" + "@id" : "bts:PALB2mutation" }, { - "@id" : "bts:Turkey" + "@id" : "bts:SDHAF2mutation" }, { - "@id" : "bts:Djibouti" + "@id" : "bts:EGFRmutation" }, { - "@id" : "bts:Greece" + "@id" : "bts:PDGFRAmutation" }, { - "@id" : "bts:Jersey" + "@id" : "bts:ARFmutation" }, { - "@id" : "bts:Mauritius" + "@id" : "bts:PTCHmutation" }, { - "@id" : "bts:WallisandFutuna" + "@id" : "bts:PRKAR1Amutation" }, { - "@id" : "bts:Pakistan" + "@id" : "bts:MUTYHmutation" }, { - "@id" : "bts:Ukraine" + "@id" : "bts:MSH6mutation" }, { - "@id" : "bts:StateofPalestine" + "@id" : "bts:CDKN2Aandp14ARFmutation" }, { - "@id" : "bts:Ecuador" + "@id" : "bts:GREM1mutation" }, { - "@id" : "bts:SouthKorea" + "@id" : "bts:MAXmutation" }, { - "@id" : "bts:Russia" + "@id" : "bts:FHmutation" }, { - "@id" : "bts:Greenland" + "@id" : "bts:PHOX2Bmutation" }, { - "@id" : "bts:Liechtenstein" + "@id" : "bts:CDH1mutation" }, { - "@id" : "bts:Nigeria" + "@id" : "bts:MSH2mutation" }, { - "@id" : "bts:Benin" + "@id" : "bts:MLH1mutation" }, { - "@id" : "bts:Vanuatu" + "@id" : "bts:METmutation" }, { - "@id" : "bts:SriLanka" + "@id" : "bts:ATRXmutation" }, { - "@id" : "bts:Tokelau" + "@id" : "bts:KRASmutation" }, { - "@id" : "bts:CzechRepublic(Czechia)" + "@id" : "bts:KITmutation" }, { - "@id" : "bts:MarshallIslands" + "@id" : "bts:PolEmutation" }, { - "@id" : "bts:Estonia" + "@id" : "bts:TSC1mutation" }, { - "@id" : "bts:SaintVincentandtheGrenadines" + "@id" : "bts:BLMmutation" }, { - "@id" : "bts:PuertoRico" + "@id" : "bts:ATMmutation" }, { - "@id" : "bts:Grenada" + "@id" : "bts:ACVR1mutation" }, { - "@id" : "bts:Guadeloupe" + "@id" : "bts:FLCNmutation" }, { - "@id" : "bts:SierraLeone" + "@id" : "bts:MEN1mutation" }, { - "@id" : "bts:Afghanistan" + "@id" : "bts:TMEM127mutation" }, { - "@id" : "bts:Haiti" + "@id" : "bts:BRAFmutation" }, { - "@id" : "bts:Lithuania" + "@id" : "bts:ROS1mutation" }, { - "@id" : "bts:Indonesia" + "@id" : "bts:SMAD4mutation" }, { - "@id" : "bts:VirginIslandsBritish" + "@id" : "bts:ALKmutation" }, { - "@id" : "bts:VirginIslandsU.S." + "@id" : "bts:BMPR1Amutation" }, { - "@id" : "bts:Sudan" + "@id" : "bts:APCmutation" }, { - "@id" : "bts:Morocco" + "@id" : "bts:BRCA2mutation" }, { - "@id" : "bts:Iceland" + "@id" : "bts:SMARCB1mutation" }, { - "@id" : "bts:NorthKorea" + "@id" : "bts:CDKN2Amutation" }, { - "@id" : "bts:NewCaledonia" + "@id" : "bts:RAD51Cmutation" }, { - "@id" : "bts:Brunei" + "@id" : "bts:p14ARFmutation" } ], - "rdfs:label" : "CountryofResidence", - "rdfs:comment" : "Country of Residence at enrollment", + "rdfs:label" : "CancerAssociatedGeneMutations", + "rdfs:comment" : "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", "@type" : "rdfs:Class", - "sms:displayName" : "CountryofResidence" + "sms:displayName" : "CancerAssociatedGeneMutations" }, { + "@id" : "bts:ParentDataFileID", + "@type" : "rdfs:Class", + "rdfs:comment" : "Optional, Synapse ID of a parent data file from which this data file is derived.", + "rdfs:label" : "ParentDataFileID", "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastCancerAssessmentTests", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:EstrogenreceptorIHC" - }, { - "@id" : "bts:ProgesteronereceptorIHC" - }, { - "@id" : "bts:HER2IHC" - }, { - "@id" : "bts:HER2FISH-CISH" - }, { - "@id" : "bts:HER2FISH" - } ], - "rdfs:label" : "BreastCancerAssessmentTests", - "rdfs:comment" : "Text term to identify assessment tests done in participants during diagnosis", + "sms:displayName" : "ParentDataFileID", + "sms:required" : "sms:false" + }, { + "@id" : "bts:FOVnumber", "@type" : "rdfs:Class", - "sms:displayName" : "BreastCancerAssessmentTests" + "rdfs:comment" : "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label" : "FOVnumber", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "FOVnumber", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ProportionofMinimumCpGCoverage10X", + "@type" : "rdfs:Class", + "rdfs:comment" : "(For whole genome sequencing or targeted sequencing) Proportion of all reference bases for that achieves 10X or greater coverage per CpG.", + "rdfs:label" : "ProportionofMinimumCpGCoverage10X", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ProportionofMinimumCpGCoverage10X", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ChannelMetadataFilename", + "@type" : "rdfs:Class", + "rdfs:comment" : "Full path of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label" : "ChannelMetadataFilename", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ChannelMetadataFilename", + "sms:required" : "sms:false" }, { - "@id" : "bts:EmissionBandwidth", + "@id" : "bts:Secondhandsmokeexposureyears", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "EmissionBandwidth", + "rdfs:label" : "Secondhandsmokeexposureyears", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EmissionBandwidth", + "sms:displayName" : "Secondhandsmokeexposureyears", "sms:required" : "sms:false" }, { - "@id" : "bts:MatrixType", + "rdfs:subClassOf" : [ ], + "@id" : "bts:Read3", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:CellBarcodeandDNAInsert" + }, { + "@id" : "bts:SampleIndexandDNAInsert" + }, { + "@id" : "bts:DNAInsert" + }, { + "@id" : "bts:SampleIndex" + }, { + "@id" : "bts:CellBarcode" + } ], + "rdfs:label" : "Read3", + "rdfs:comment" : "Read 3 content description", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "MatrixType", + "sms:displayName" : "Read3" + }, { + "@id" : "bts:CellMedianNumberReads", + "@type" : "rdfs:Class", + "rdfs:comment" : "Median number of reads per cell. Number", + "rdfs:label" : "CellMedianNumberReads", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MatrixType", + "sms:displayName" : "CellMedianNumberReads", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:SpikeIn", + "@id" : "bts:Gender", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:ERCC" + "@id" : "bts:unknown" }, { - "@id" : "bts:OtherSpikeIn" + "@id" : "bts:NotReported" }, { - "@id" : "bts:NoSpikeIn" + "@id" : "bts:female" }, { - "@id" : "bts:PhiX" + "@id" : "bts:male" + }, { + "@id" : "bts:unspecified" } ], - "rdfs:label" : "SpikeIn", - "rdfs:comment" : "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", + "rdfs:label" : "Gender", + "rdfs:comment" : "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", "@type" : "rdfs:Class", - "sms:displayName" : "SpikeIn" + "sms:displayName" : "Gender" }, { - "@id" : "bts:TypeofTobaccoUsed", + "@id" : "bts:WorkflowVersion", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TypeofTobaccoUsed", + "rdfs:label" : "WorkflowVersion", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TypeofTobaccoUsed", + "sms:displayName" : "WorkflowVersion", "sms:required" : "sms:false" }, { - "@id" : "bts:HistologicMorphologyCode", + "@id" : "bts:MenopauseStatus", "@type" : "rdfs:Class", - "rdfs:comment" : "Histologic Morphology Code, based on ICD-O-3. Any valid ICD-O-3 morphology code. See https://seer.cancer.gov/icd-o-3/ and https://seer.cancer.gov/icd-o-3/sitetype.icdo3.20200629.xlsx. Examples: 80510", - "rdfs:label" : "HistologicMorphologyCode", + "rdfs:comment" : "TBD", + "rdfs:label" : "MenopauseStatus", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HistologicMorphologyCode", + "sms:displayName" : "MenopauseStatus", "sms:required" : "sms:false" }, { - "@id" : "bts:PhysicalSizeX", + "@id" : "bts:SubCycleNumber", "@type" : "rdfs:Class", - "rdfs:comment" : "Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.", - "rdfs:label" : "PhysicalSizeX", + "rdfs:comment" : "TBD", + "rdfs:label" : "SubCycleNumber", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PhysicalSizeX", + "sms:displayName" : "SubCycleNumber", "sms:required" : "sms:false" }, { - "@id" : "bts:Ecigvape30dayusenum", + "@id" : "bts:GenomicReferenceURL", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Ecigvape30dayusenum", + "rdfs:label" : "GenomicReferenceURL", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Ecigvape30dayusenum", + "sms:displayName" : "GenomicReferenceURL", "sms:required" : "sms:false" }, { - "@id" : "bts:CauseofDeathSource", + "@id" : "bts:GenomicReference", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "CauseofDeathSource", + "rdfs:label" : "GenomicReference", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CauseofDeathSource", + "sms:displayName" : "GenomicReference", "sms:required" : "sms:false" }, { - "@id" : "bts:YearofDeath", + "@id" : "bts:PUC19methylationratio", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value to represent the year of the death of an individual.", - "rdfs:label" : "YearofDeath", + "rdfs:comment" : "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label" : "PUC19methylationratio", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "YearofDeath", - "sms:required" : "sms:false" + "sms:displayName" : "PUC19methylationratio", + "sms:required" : "sms:true" }, { - "@id" : "bts:LinkedProject", + "@id" : "bts:Lambdamethylationratio", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "LinkedProject", + "rdfs:comment" : "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label" : "Lambdamethylationratio", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LinkedProject", + "sms:displayName" : "Lambdamethylationratio", + "sms:required" : "sms:true" + }, { + "@id" : "bts:SizeY", + "@type" : "rdfs:Class", + "rdfs:comment" : "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label" : "SizeY", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SizeY", "sms:required" : "sms:false" }, { - "@id" : "bts:CancerIncidence", + "@id" : "bts:CellCount", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "CancerIncidence", + "rdfs:comment" : "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "CellCount", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CancerIncidence", + "sms:displayName" : "CellCount", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:BreastCancerAllredEstrogenReceptorScore", + "@id" : "bts:AnaplasiaPresentType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -7706,4298 +7843,4162 @@ "schema:rangeIncludes" : [ { "@id" : "bts:unknown" }, { - "@id" : "bts:10" - }, { - "@id" : "bts:0" - }, { - "@id" : "bts:4" - }, { - "@id" : "bts:7" + "@id" : "bts:NotReported" }, { - "@id" : "bts:1" + "@id" : "bts:Equivocal" }, { - "@id" : "bts:8" + "@id" : "bts:Absent" }, { - "@id" : "bts:2" + "@id" : "bts:Present" }, { - "@id" : "bts:5" + "@id" : "bts:Diffuse" }, { - "@id" : "bts:3" + "@id" : "bts:Focal" }, { - "@id" : "bts:6" + "@id" : "bts:Sclerosis" } ], - "rdfs:label" : "BreastCancerAllredEstrogenReceptorScore", - "rdfs:comment" : "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label" : "AnaplasiaPresentType", + "rdfs:comment" : "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", "@type" : "rdfs:Class", - "sms:displayName" : "BreastCancerAllredEstrogenReceptorScore" + "sms:displayName" : "AnaplasiaPresentType" + }, { + "@id" : "bts:SampleID", + "@type" : "rdfs:Class", + "rdfs:comment" : " ID associated with a biosample", + "rdfs:label" : "SampleID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SampleID", + "sms:required" : "sms:true" }, { + "@id" : "bts:ExcitationWavelength", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ExcitationWavelength", "rdfs:subClassOf" : [ ], - "@id" : "bts:ERStainingIntensity", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ExcitationWavelength", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:BIRADSMammographyBreastDensityCategory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Other" - }, { "@id" : "bts:unknown" }, { - "@id" : "bts:Strong" - }, { - "@id" : "bts:Moderate" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:Weak" + "@id" : "bts:Predominantlyfatty" }, { - "@id" : "bts:Weak-Moderate" + "@id" : "bts:Scatteredfibroglandulardensities" }, { - "@id" : "bts:Moderate-Strong" + "@id" : "bts:Heterogeneouslydense" }, { - "@id" : "bts:Weak-Strong" + "@id" : "bts:Extremelydense" } ], - "rdfs:label" : "ERStainingIntensity", - "rdfs:comment" : "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label" : "BIRADSMammographyBreastDensityCategory", + "rdfs:comment" : "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", "@type" : "rdfs:Class", - "sms:displayName" : "ERStainingIntensity" + "sms:displayName" : "BIRADSMammographyBreastDensityCategory" }, { - "@id" : "bts:FOVX", + "@id" : "bts:Weight", "@type" : "rdfs:Class", - "rdfs:comment" : "Field of view X dimension. Floating point", - "rdfs:label" : "FOVX", + "rdfs:comment" : "TBD", + "rdfs:label" : "Weight", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FOVX", + "sms:displayName" : "Weight", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicator", + "@id" : "bts:OvarianCancerSurgicalOutcome", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:NotApplicable" + "@id" : "bts:Other" }, { - "@id" : "bts:Yes" + "@id" : "bts:unknown" + }, { + "@id" : "bts:Datanotavailable" + }, { + "@id" : "bts:R0resection" + }, { + "@id" : "bts:Optimalcytoreduction" + }, { + "@id" : "bts:Sub-optimalcytoreduction" + } ], + "rdfs:label" : "OvarianCancerSurgicalOutcome", + "rdfs:comment" : "Text term that describes the kind of surgical treatment administered.", + "@type" : "rdfs:Class", + "sms:displayName" : "OvarianCancerSurgicalOutcome" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:RelationshipPrimaryDiagnosis", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:ProstateCancer" + }, { + "@id" : "bts:TesticularCancer" + }, { + "@id" : "bts:Cancer" + }, { + "@id" : "bts:KaposiSarcoma" + }, { + "@id" : "bts:BoneCancer" + }, { + "@id" : "bts:LiverCancer" + }, { + "@id" : "bts:CNSCancer" + }, { + "@id" : "bts:UterineCancer" + }, { + "@id" : "bts:NotReported" + }, { + "@id" : "bts:LymphNodeCancer" + }, { + "@id" : "bts:RectalCancer" }, { - "@id" : "bts:No" + "@id" : "bts:WilmsTumor" }, { "@id" : "bts:unknown" - } ], - "rdfs:label" : "HormoneTherapyBreastCancerPreventionIndicator", - "rdfs:comment" : "Did the patient receive hormonal therapy for prevention of breast cancer?", - "@type" : "rdfs:Class", - "sms:displayName" : "HormoneTherapyBreastCancerPreventionIndicator" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SequencingPlatform", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:454GSFLXTitanium" }, { - "@id" : "bts:ABSOLiD3" + "@id" : "bts:Osteosarcoma" }, { - "@id" : "bts:ABSOLiD4ABSOLiD2" + "@id" : "bts:Chondrosarcoma" }, { - "@id" : "bts:CompleteGenomics" + "@id" : "bts:Mesothelioma" }, { - "@id" : "bts:GridION" + "@id" : "bts:GastricCancer" }, { - "@id" : "bts:IlluminaGenomeAnalyzerII" + "@id" : "bts:CervicalCancer" }, { - "@id" : "bts:IlluminaGenomeAnalyzerIIx" + "@id" : "bts:EwingSarcoma" }, { - "@id" : "bts:IlluminaHiSeq2000" + "@id" : "bts:Glioblastoma" }, { - "@id" : "bts:IlluminaHiSeq2500" + "@id" : "bts:SkinCancer" }, { - "@id" : "bts:IlluminaHiSeq4000" + "@id" : "bts:TonsillarCancer" }, { - "@id" : "bts:IlluminaHiSeqXFive" + "@id" : "bts:BileDuctCancer" }, { - "@id" : "bts:IlluminaHiSeqXTen" + "@id" : "bts:TongueCancer" }, { - "@id" : "bts:IlluminaMiSeq" + "@id" : "bts:LaryngealCancer" }, { - "@id" : "bts:IlluminaNextSeq1000" + "@id" : "bts:Melanoma" }, { - "@id" : "bts:IlluminaNextSeq2000" + "@id" : "bts:HematologicCancer" }, { - "@id" : "bts:IlluminaNextSeq2500" + "@id" : "bts:ThroatCancer" }, { - "@id" : "bts:IlluminaNextSeq500" + "@id" : "bts:ColorectalCancer" }, { - "@id" : "bts:IlluminaNextSeq550" + "@id" : "bts:KidneyCancer" }, { - "@id" : "bts:IlluminaNovaSeq6000" + "@id" : "bts:SpleenCancer" }, { - "@id" : "bts:IonTorrentPGM" + "@id" : "bts:BreastCancer" }, { - "@id" : "bts:IonTorrentProton" + "@id" : "bts:Leukemia" }, { - "@id" : "bts:IonTorrentS5" + "@id" : "bts:Sarcoma" }, { - "@id" : "bts:NotReported" + "@id" : "bts:BloodCancer" }, { - "@id" : "bts:NovaSeq6000" + "@id" : "bts:Neuroblastoma" }, { - "@id" : "bts:NovaSeqS4" + "@id" : "bts:GynecologicCancer" }, { - "@id" : "bts:Other" + "@id" : "bts:Rhabdomyosarcoma" }, { - "@id" : "bts:OxfordNanoporeminION" + "@id" : "bts:PancreasCancer" }, { - "@id" : "bts:PacBioRS" + "@id" : "bts:AdrenalGlandCancer" }, { - "@id" : "bts:PacBioSequel2" + "@id" : "bts:ThyroidCancer" }, { - "@id" : "bts:PromethION" + "@id" : "bts:MultipleMyeloma" }, { - "@id" : "bts:Revio" + "@id" : "bts:LungCancer" }, { - "@id" : "bts:UltimaGenomicsUG100" + "@id" : "bts:BasalCellCancer" }, { - "@id" : "bts:Unknown" - } ], - "rdfs:label" : "SequencingPlatform", - "rdfs:comment" : "A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.", - "@type" : "rdfs:Class", - "sms:displayName" : "SequencingPlatform" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:SlideChargeType", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" + "@id" : "bts:BrainCancer" }, { - "@id" : "bts:Uncharged" + "@id" : "bts:EsophagealCancer" }, { - "@id" : "bts:Charged" + "@id" : "bts:Lymphoma" }, { - "@id" : "bts:Coverslip" + "@id" : "bts:OvarianCancer" }, { - "@id" : "bts:Notapplicable" + "@id" : "bts:GallbladderCancer" + }, { + "@id" : "bts:HeadandNeckCancer" + }, { + "@id" : "bts:BladderCancer" } ], - "rdfs:label" : "SlideChargeType", - "rdfs:comment" : "A description of the charge on the glass slide.", + "rdfs:label" : "RelationshipPrimaryDiagnosis", + "rdfs:comment" : "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", "@type" : "rdfs:Class", - "sms:displayName" : "SlideChargeType" + "sms:displayName" : "RelationshipPrimaryDiagnosis" }, { - "@id" : "bts:COVID19CancerTreatmentFollowup", + "@id" : "bts:AppliedHardTrimming", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "COVID19CancerTreatmentFollowup", + "rdfs:label" : "AppliedHardTrimming", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "COVID19CancerTreatmentFollowup", + "sms:displayName" : "AppliedHardTrimming", "sms:required" : "sms:false" }, { - "@id" : "bts:ChannelName", + "@id" : "bts:AAChange", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ChannelName", + "rdfs:comment" : "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "AAChange", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ChannelName", + "sms:displayName" : "AAChange", "sms:required" : "sms:false" }, { - "@id" : "bts:ConcomitantMedicationReceivedType", - "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "ConcomitantMedicationReceivedType", "rdfs:subClassOf" : [ ], + "@id" : "bts:NucleicAcidSource", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ConcomitantMedicationReceivedType", - "sms:required" : "sms:false" - }, { - "@id" : "bts:CellTotal", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:SingleCell" + }, { + "@id" : "bts:SingleNucleus" + }, { + "@id" : "bts:BulkNuclei" + }, { + "@id" : "bts:BulkWholeCell" + }, { + "@id" : "bts:Micro-region" + } ], + "rdfs:label" : "NucleicAcidSource", + "rdfs:comment" : "The source of the input nucleic molecule", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of sequenced cells. Applies to raw counts matrix only.", - "rdfs:label" : "CellTotal", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "CellTotal", - "sms:required" : "sms:false" + "sms:displayName" : "NucleicAcidSource" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:MolecularAnalysisMethod", + "@id" : "bts:ExtentofTumorResection", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:WXS" - }, { - "@id" : "bts:WGS" + "@id" : "bts:Minor" }, { - "@id" : "bts:ISH" + "@id" : "bts:OpenBiopsy" }, { "@id" : "bts:NotReported" }, { - "@id" : "bts:MicrosatelliteAnalysis" + "@id" : "bts:GrossTotalResection" }, { "@id" : "bts:unknown" }, { "@id" : "bts:NotApplicable" }, { - "@id" : "bts:TargetedSequencing" + "@id" : "bts:Segmental" }, { - "@id" : "bts:NuclearStaining" + "@id" : "bts:NTR" }, { - "@id" : "bts:FISH" + "@id" : "bts:Suboptimaldebulking" }, { - "@id" : "bts:IHC" + "@id" : "bts:SubtotalResection" }, { - "@id" : "bts:Karyotype" + "@id" : "bts:Other" }, { - "@id" : "bts:FlowCytometry" + "@id" : "bts:Partialdebulking" }, { - "@id" : "bts:Other" + "@id" : "bts:Suboptimal" }, { - "@id" : "bts:RNASequencing" + "@id" : "bts:Optimaldebulking" }, { - "@id" : "bts:SequencingNOS" + "@id" : "bts:ExtensiveSubtotal" + } ], + "rdfs:label" : "ExtentofTumorResection", + "rdfs:comment" : "The degree to which the lesion has been cut out, or resected.", + "@type" : "rdfs:Class", + "sms:displayName" : "ExtentofTumorResection" + }, { + "@id" : "bts:TimepointLabel", + "@type" : "rdfs:Class", + "rdfs:comment" : "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", + "rdfs:label" : "TimepointLabel", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TimepointLabel", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Ploidy", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" }, { - "@id" : "bts:SouthernBlotting" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Microarray" + "@id" : "bts:Aneuploid" }, { - "@id" : "bts:ComparativeGenomicHybridization" + "@id" : "bts:Diploid" }, { - "@id" : "bts:CytogeneticsNOS" + "@id" : "bts:Hyperdiploid" }, { - "@id" : "bts:RT-PCR" + "@id" : "bts:Hypodiploid" + }, { + "@id" : "bts:NearDiploid" + }, { + "@id" : "bts:Tetraploid" } ], - "rdfs:label" : "MolecularAnalysisMethod", - "rdfs:comment" : "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "rdfs:label" : "Ploidy", + "rdfs:comment" : "Text term used to describe the number of sets of homologous chromosomes.", "@type" : "rdfs:Class", - "sms:displayName" : "MolecularAnalysisMethod" + "sms:displayName" : "Ploidy" }, { - "@id" : "bts:LaneNumber", + "@id" : "bts:PortionWeight", "@type" : "rdfs:Class", - "rdfs:comment" : "Basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", - "rdfs:label" : "LaneNumber", + "rdfs:comment" : "Numeric value that represents the sample portion weight, measured in milligrams.", + "rdfs:label" : "PortionWeight", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LaneNumber", - "sms:required" : "sms:true" + "sms:displayName" : "PortionWeight", + "sms:required" : "sms:false" }, { - "@id" : "bts:ParticipantID", + "@id" : "bts:DaystoProgression", "@type" : "rdfs:Class", - "rdfs:comment" : "ID associated with a patient", - "rdfs:label" : "ParticipantID", + "rdfs:comment" : "Number of days between the date used for index and the date the patient's disease progressed.", + "rdfs:label" : "DaystoProgression", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ParticipantID", - "sms:required" : "sms:true" + "sms:displayName" : "DaystoProgression", + "sms:required" : "sms:false" }, { - "@id" : "bts:COVID19CurrentStatus", + "@id" : "bts:RRIDidentifier", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "COVID19CurrentStatus", + "rdfs:label" : "RRIDidentifier", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "COVID19CurrentStatus", + "sms:displayName" : "RRIDidentifier", "sms:required" : "sms:false" }, { - "@id" : "bts:FrameAveraging", + "@id" : "bts:ClassBRCA2", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", - "rdfs:label" : "FrameAveraging", + "rdfs:comment" : "TBD", + "rdfs:label" : "ClassBRCA2", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FrameAveraging", + "sms:displayName" : "ClassBRCA2", "sms:required" : "sms:false" }, { - "@id" : "bts:ChannelID", + "@id" : "bts:WhitelistCellBarcodeFileLink", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ChannelID", + "rdfs:label" : "WhitelistCellBarcodeFileLink", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ChannelID", + "sms:displayName" : "WhitelistCellBarcodeFileLink", "sms:required" : "sms:false" }, { + "@id" : "bts:StartDaysfromIndex", + "@type" : "rdfs:Class", + "rdfs:comment" : "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", + "rdfs:label" : "StartDaysfromIndex", "rdfs:subClassOf" : [ ], - "@id" : "bts:BulkMethylationAssayType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:Wholegenome" - }, { - "@id" : "bts:TargetedGenome" - }, { - "@id" : "bts:BeadchipArray" - } ], - "rdfs:label" : "BulkMethylationAssayType", - "rdfs:comment" : "Assay types normally determine genomic coverage", - "@type" : "rdfs:Class", - "sms:displayName" : "BulkMethylationAssayType" + "sms:displayName" : "StartDaysfromIndex", + "sms:required" : "sms:false" }, { - "@id" : "bts:Vendor", + "@id" : "bts:Ecigvapetimesperday", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Vendor", + "rdfs:label" : "Ecigvapetimesperday", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Vendor", + "sms:displayName" : "Ecigvapetimesperday", "sms:required" : "sms:false" }, { - "@id" : "bts:LociCount", - "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the number of loci tested.", - "rdfs:label" : "LociCount", "rdfs:subClassOf" : [ ], + "@id" : "bts:FamilyMemberVitalStatusIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LociCount", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "FamilyMemberVitalStatusIndicator", + "rdfs:comment" : "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", + "@type" : "rdfs:Class", + "sms:displayName" : "FamilyMemberVitalStatusIndicator" }, { - "@id" : "bts:DaystoRecurrence", + "@id" : "bts:SectionThicknessValue", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "DaystoRecurrence", + "rdfs:comment" : "Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).", + "rdfs:label" : "SectionThicknessValue", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DaystoRecurrence", + "sms:displayName" : "SectionThicknessValue", "sms:required" : "sms:false" }, { - "@id" : "bts:AcquisitionMethodOtherSpecify", + "@id" : "bts:SoftwareandVersion", "@type" : "rdfs:Class", - "rdfs:comment" : "A custom acquisition method [Text - max length 100 characters]", - "rdfs:label" : "AcquisitionMethodOtherSpecify", + "rdfs:comment" : "TBD", + "rdfs:label" : "SoftwareandVersion", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AcquisitionMethodOtherSpecify", + "sms:displayName" : "SoftwareandVersion", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:ReadLength", + "@id" : "bts:KnownGeneticPredispositionMutation", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "ReadLength", - "rdfs:comment" : "Length of the sequencing reads. Can be integer, null", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" + }, { + "@id" : "bts:No" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "KnownGeneticPredispositionMutation", + "rdfs:comment" : "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", "@type" : "rdfs:Class", - "sms:displayName" : "ReadLength" + "sms:displayName" : "KnownGeneticPredispositionMutation" }, { + "@id" : "bts:TotalDNAInput", + "@type" : "rdfs:Class", + "rdfs:comment" : "A sample amount used for the total number of reads, in microgram or nanogram.", + "rdfs:label" : "TotalDNAInput", "rdfs:subClassOf" : [ ], - "@id" : "bts:WellIndex", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "WellIndex", - "rdfs:comment" : "Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays", - "@type" : "rdfs:Class", - "sms:displayName" : "WellIndex" + "sms:displayName" : "TotalDNAInput", + "sms:required" : "sms:false" }, { - "@id" : "bts:BreastCarcinomaCentromere17CopyNumber", + "@id" : "bts:BiospecimenDimension1", "@type" : "rdfs:Class", - "rdfs:comment" : "Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.", - "rdfs:label" : "BreastCarcinomaCentromere17CopyNumber", + "rdfs:comment" : "First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", + "rdfs:label" : "BiospecimenDimension1", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BreastCarcinomaCentromere17CopyNumber", + "sms:displayName" : "BiospecimenDimension1", "sms:required" : "sms:false" }, { - "@id" : "bts:NominalMagnification", + "@id" : "bts:NucleiBarcodeLength", "@type" : "rdfs:Class", - "rdfs:comment" : "The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)", - "rdfs:label" : "NominalMagnification", + "rdfs:comment" : "Nuclei Barcode Length", + "rdfs:label" : "NucleiBarcodeLength", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NominalMagnification", + "sms:displayName" : "NucleiBarcodeLength", "sms:required" : "sms:false" }, { - "@id" : "bts:COVID19OccurrenceIndicator", + "@id" : "bts:HER2BreastCarcinomaCopyNumberTotal", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "COVID19OccurrenceIndicator", + "rdfs:comment" : "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", + "rdfs:label" : "HER2BreastCarcinomaCopyNumberTotal", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "COVID19OccurrenceIndicator", + "sms:displayName" : "HER2BreastCarcinomaCopyNumberTotal", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:OvarianCancerHistologicSubtype", + "@id" : "bts:MammaprintRiskGroup", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:High-gradeserous" - }, { - "@id" : "bts:Datanotavailable" - }, { "@id" : "bts:unknown" }, { - "@id" : "bts:Germcell" - }, { - "@id" : "bts:High-gradeendometrioid" - }, { - "@id" : "bts:Other" - }, { - "@id" : "bts:Low-gradeserous" - }, { - "@id" : "bts:Clearcell" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:Low-gradeendometrioid" + "@id" : "bts:Highrisk" }, { - "@id" : "bts:Mucinous" + "@id" : "bts:Intermediaterisk" }, { - "@id" : "bts:Sex-cordstromal" + "@id" : "bts:Lowrisk" } ], - "rdfs:label" : "OvarianCancerHistologicSubtype", - "rdfs:comment" : "Text term to describe the histological subtype of ovarian cancer in the participant", + "rdfs:label" : "MammaprintRiskGroup", + "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", "@type" : "rdfs:Class", - "sms:displayName" : "OvarianCancerHistologicSubtype" + "sms:displayName" : "MammaprintRiskGroup" }, { - "@id" : "bts:TotalVolume", + "@id" : "bts:Height", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value for the total amount of sample or specimen", - "rdfs:label" : "TotalVolume", + "rdfs:comment" : "TBD", + "rdfs:label" : "Height", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TotalVolume", + "sms:displayName" : "Height", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:TumorTissueType", + "@id" : "bts:Race", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:Normal" - }, { - "@id" : "bts:Normaladjacent" - }, { - "@id" : "bts:Recurrent" - }, { - "@id" : "bts:Posttherapyneoadjuvant" - }, { - "@id" : "bts:Normaldistant" - }, { - "@id" : "bts:Posttherapyadjuvant" - }, { - "@id" : "bts:Posttherapy" + "@id" : "bts:americanindianoralaskanative" }, { - "@id" : "bts:Atypia-hyperplasia" + "@id" : "bts:NotReported" }, { - "@id" : "bts:NotOtherwiseSpecified" + "@id" : "bts:white" }, { - "@id" : "bts:Metastatic" + "@id" : "bts:unknown" }, { - "@id" : "bts:Localrecurrence" + "@id" : "bts:blackorafricanamerican" }, { - "@id" : "bts:Premalignant-insitu" + "@id" : "bts:notallowedtocollect" }, { - "@id" : "bts:AdditionalPrimary" + "@id" : "bts:asian" }, { - "@id" : "bts:Premalignant" + "@id" : "bts:Other" }, { - "@id" : "bts:Primary" + "@id" : "bts:nativehawaiianorotherpacificislander" } ], - "rdfs:label" : "TumorTissueType", - "rdfs:comment" : "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints)", + "rdfs:label" : "Race", + "rdfs:comment" : "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", "@type" : "rdfs:Class", - "sms:displayName" : "TumorTissueType" + "sms:displayName" : "Race" }, { - "@id" : "bts:CellMedianNumberGenes", + "@id" : "bts:BiospecimenDimension3", "@type" : "rdfs:Class", - "rdfs:comment" : "Median number of genes detected per cell. Number", - "rdfs:label" : "CellMedianNumberGenes", + "rdfs:comment" : "Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", + "rdfs:label" : "BiospecimenDimension3", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CellMedianNumberGenes", + "sms:displayName" : "BiospecimenDimension3", "sms:required" : "sms:false" }, { - "@id" : "bts:Lot", + "@id" : "bts:OncotypeScore", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "Lot", + "rdfs:comment" : "OncotypeDX recurrence score", + "rdfs:label" : "OncotypeScore", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Lot", + "sms:displayName" : "OncotypeScore", "sms:required" : "sms:false" }, { - "@id" : "bts:COVID19ComplicationsSeverity", + "@id" : "bts:InputCellsandNuclei", "@type" : "rdfs:Class", - "rdfs:comment" : "TBD", - "rdfs:label" : "COVID19ComplicationsSeverity", + "rdfs:comment" : "Number of cells and number of nuclei input; entry format: number, number", + "rdfs:label" : "InputCellsandNuclei", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "COVID19ComplicationsSeverity", + "sms:displayName" : "InputCellsandNuclei", "sms:required" : "sms:false" }, { - "@id" : "bts:ProgressionorRecurrenceAnatomicSite", + "rdfs:subClassOf" : [ ], + "@id" : "bts:PRReceptorStatus", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:unknown" + }, { + "@id" : "bts:Borderline" + }, { + "@id" : "bts:Equivocal" + }, { + "@id" : "bts:Indeterminate" + }, { + "@id" : "bts:Negative" + }, { + "@id" : "bts:NotPerformed" + }, { + "@id" : "bts:PerformedbutNotAvailable" + }, { + "@id" : "bts:Positive" + } ], + "rdfs:label" : "PRReceptorStatus", + "rdfs:comment" : "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "@type" : "rdfs:Class", + "sms:displayName" : "PRReceptorStatus" + }, { + "@id" : "bts:Fluorophore", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ProgressionorRecurrenceAnatomicSite", + "rdfs:label" : "Fluorophore", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ProgressionorRecurrenceAnatomicSite", + "sms:displayName" : "Fluorophore", "sms:required" : "sms:false" }, { - "@id" : "bts:EmissionWavelength", + "@id" : "bts:Typeofsmokeexposurecumulativeyears", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "EmissionWavelength", + "rdfs:label" : "Typeofsmokeexposurecumulativeyears", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EmissionWavelength", + "sms:displayName" : "Typeofsmokeexposurecumulativeyears", "sms:required" : "sms:false" }, { - "@id" : "bts:ImageID", + "@id" : "bts:Clone", "@type" : "rdfs:Class", - "rdfs:comment" : "Unique internal image identifier. eg \"\"Image:0\"\". (To be extracted from OME-XML)", - "rdfs:label" : "ImageID", + "rdfs:comment" : "TBD", + "rdfs:label" : "Clone", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ImageID", + "sms:displayName" : "Clone", "sms:required" : "sms:false" }, { - "@id" : "bts:LibraryPrepKitName", + "@id" : "bts:DiagnosisStatusType", "@type" : "rdfs:Class", - "rdfs:comment" : "Name of Library Prep Kit. String", - "rdfs:label" : "LibraryPrepKitName", + "rdfs:comment" : "TBD", + "rdfs:label" : "DiagnosisStatusType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryPrepKitName", - "sms:required" : "sms:true" + "sms:displayName" : "DiagnosisStatusType", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:SingleNucleusBuffer", + "@id" : "bts:Age", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:10x" - }, { - "@id" : "bts:NIB" - }, { - "@id" : "bts:Omni" - } ], - "rdfs:label" : "SingleNucleusBuffer", - "rdfs:comment" : "Nuclei isolation buffer", + "sms:required" : "sms:true", + "sms:validationRules" : [ "regex match ^\\d*\\.?\\d*$|^unknown$" ], + "rdfs:label" : "Age", + "rdfs:comment" : "Age of individual as a positive number such as 40 or 56.5. 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Floating point value > 0.", - "rdfs:label" : "LensNA", + "rdfs:comment" : "TBD", + "rdfs:label" : "TobaccoUse", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LensNA", + "sms:displayName" : "TobaccoUse", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:PhysicalSizeZUnit", + "@id" : "bts:Zstack", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cm" - }, { - "@id" : "bts:mm" - }, { - "@id" : "bts:µm" - }, { - "@id" : "bts:nm" - }, { - "@id" : "bts:Å" - } ], - "rdfs:label" : "PhysicalSizeZUnit", - "rdfs:comment" : "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "Zstack", + "rdfs:comment" : "Does data file contain a Z-stack of images", "@type" : "rdfs:Class", - "sms:displayName" : "PhysicalSizeZUnit" + "sms:displayName" : "Zstack" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:HereditaryCancerPredispositionSyndrome", + "@id" : "bts:Chromosome", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:SDHassociatedrenalcancer" + "@id" : "bts:chr7" }, { - "@id" : "bts:Constitutionalmismatchrepairdeficiency" + "@id" : "bts:chr15" }, { - "@id" : "bts:Cirrhosisunknownetiology" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Beckwith-Wiedemann" + "@id" : "bts:chr3" }, { - "@id" : "bts:Hereditarymelanoma" + "@id" : "bts:chr1" }, { - "@id" : "bts:NotReported" + "@id" : "bts:chr18" }, { - "@id" : "bts:Gorlinsyndrome" + "@id" : "bts:unknown" }, { - "@id" : "bts:vonHippel-LindauSyndrome" + "@id" : "bts:chrY" }, { - "@id" : "bts:Tuberoussclerosiscomplex" + "@id" : "bts:chr22" }, { - "@id" : "bts:RhabdoidtumorpredispositionsyndrometypeI" + "@id" : "bts:chr14" }, { - "@id" : "bts:unknown" + "@id" : "bts:chr12" }, { - "@id" : "bts:Tyrosinemia" + "@id" : "bts:chr11" }, { - "@id" : "bts:Familialgastrointestinalstromaltumor" + "@id" : "bts:chr17" }, { - "@id" : "bts:NotApplicable" + "@id" : "bts:chrM" }, { - "@id" : "bts:Li-Fraumenisyndrome" + "@id" : "bts:chr4" }, { - "@id" : "bts:Fanconianemia" + "@id" : "bts:chr21" }, { - "@id" : "bts:Turcotsyndrome" + "@id" : "bts:chr6" }, { - "@id" : "bts:Attenuatedfamilialadenomatouspolyposis" + "@id" : "bts:chr10" }, { - "@id" : "bts:BAP1mutantdisease" + "@id" : "bts:chr16" }, { - "@id" : "bts:Lynchsyndrome" + "@id" : "bts:chrX" }, { - "@id" : "bts:Hereditaryparaganglioma–pheochromocytomasyndrome" + "@id" : "bts:chr23" }, { - "@id" : "bts:Nevoidbasalcellcarcinomasyndrome" + "@id" : "bts:chr8" }, { - "@id" : "bts:MultipleendocrineneoplasiatypeII" + "@id" : "bts:chr2" }, { - "@id" : "bts:Rubinstein-Taybisyndrome" + "@id" : "bts:chr13" }, { - "@id" : "bts:Cowdensyndrome" + "@id" : "bts:chr19" }, { - "@id" : "bts:Hereditaryrenaloncocytoma" + "@id" : "bts:chr20" }, { - "@id" : "bts:HereditarypapillaryRCC" + "@id" : "bts:chr5" }, { - "@id" : "bts:Peutz–Jegherssyndrome" + "@id" : "bts:chr9" + } ], + "rdfs:label" : "Chromosome", + "rdfs:comment" : "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "@type" : "rdfs:Class", + "sms:displayName" : "Chromosome" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:MutationalSignatures", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Signature19" }, { - "@id" : "bts:Familialadenomatouspolyposis" + "@id" : "bts:Signature1A" }, { - "@id" : "bts:Biliarydisorder" + "@id" : "bts:Iggenehypermutation" }, { - "@id" : "bts:MUTYH-associatedpolyposis" + "@id" : "bts:alteredactivityoftheerror-pronepolymerasePOLε(POLE)" }, { - "@id" : "bts:RhabdoidtumorpredispositionsyndrometypeII" + "@id" : "bts:Signature3" }, { - "@id" : "bts:Hereditaryretinoblastoma" + "@id" : "bts:Signature20" }, { - "@id" : "bts:GlycogenStorageDisease" + "@id" : "bts:NotReported" }, { - "@id" : "bts:Carneycomplex" + "@id" : "bts:Signature17" }, { - "@id" : "bts:Hereditarydiffusegastriccancer" + "@id" : "bts:Signature4" }, { - "@id" : "bts:Juvenilepolyposissyndrome" + "@id" : "bts:Datanotavailable" }, { - "@id" : "bts:Hereditarymixedpolyposissyndrome" + "@id" : "bts:Signature5" }, { - "@id" : "bts:Serratedpolyposissyndrome" + "@id" : "bts:Signature9" }, { - "@id" : "bts:Familialrenalcancer" + "@id" : "bts:unknown" }, { - "@id" : "bts:Hereditarypapillaryrenalcellcarcinoma" + "@id" : "bts:Signature14" }, { - "@id" : "bts:Hereditaryleiomyoma-renalcellcarcinoma" + "@id" : "bts:Signature13" }, { - "@id" : "bts:MultipleendocrineneoplasiatypeI" + "@id" : "bts:NotApplicable" }, { - "@id" : "bts:Birt-Hogg-Dubesyndrome" + "@id" : "bts:Signature12" }, { - "@id" : "bts:Familialpancreaticcancer" + "@id" : "bts:Signature8" }, { - "@id" : "bts:Hereditarybreast–ovariancancersyndrome" + "@id" : "bts:ActivationInducedDeaminases(AID)associatedmutations" }, { - "@id" : "bts:Familialprostatecancer" + "@id" : "bts:Signature7" }, { - "@id" : "bts:Melanoma–astrocytomasyndrome" + "@id" : "bts:microsatelliteinstability(additionsanddeletions)" }, { - "@id" : "bts:Alpha-1antitrypsin" + "@id" : "bts:AlkylatingAgents(Temozolomide)inducedmutations" + }, { + "@id" : "bts:localizedsubstitutionhypermutation(kataegis)" + }, { + "@id" : "bts:Signature16" + }, { + "@id" : "bts:Signature6" + }, { + "@id" : "bts:Other" + }, { + "@id" : "bts:Signature21" + }, { + "@id" : "bts:DNAMMRDeficiency" + }, { + "@id" : "bts:APOBECenzymesassociatedmutations" + }, { + "@id" : "bts:Tobaccouseassociatedmutations" + }, { + "@id" : "bts:transcriptionalstrandbias" + }, { + "@id" : "bts:Signature1B" + }, { + "@id" : "bts:Signature10" + }, { + "@id" : "bts:UVlightinducedmutations" + }, { + "@id" : "bts:Signature18" + }, { + "@id" : "bts:Signature11" + }, { + "@id" : "bts:Signature2" + }, { + "@id" : "bts:methylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" + }, { + "@id" : "bts:Signature15" + }, { + "@id" : "bts:ageofcancerdiagnosis" } ], - "rdfs:label" : "HereditaryCancerPredispositionSyndrome", - "rdfs:comment" : "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "rdfs:label" : "MutationalSignatures", + "rdfs:comment" : "Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. 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", "@type" : "rdfs:Class", - "sms:displayName" : "HereditaryCancerPredispositionSyndrome" + "sms:displayName" : "MutationalSignatures" }, { + "@id" : "bts:CancerIncidenceLocation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CancerIncidenceLocation", "rdfs:subClassOf" : [ ], - "@id" : "bts:PrimaryDiagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Pagetdiseaseandintraductalcarcinomaofbreast" - }, { - "@id" : "bts:Papillarymicrocarcinoma" - }, { - "@id" : "bts:Kaposisarcoma" - }, { - "@id" : "bts:CarcinomaNOS" - }, { - "@id" : "bts:AcutemyeloidleukemiaNOS" - }, { - "@id" : "bts:TumorNOS" - }, { - "@id" : "bts:Renalcelladenocarcinoma" + "sms:displayName" : "CancerIncidenceLocation", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Assay" + } ], + "@id" : "bts:ImagingLevel2", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "ImagingLevel2", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - 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}, - "sms:displayName" : "ThresholdforMinimumPassingReads", - "sms:required" : "sms:false" + "sms:displayName" : "Demographics" }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:ShippingConditionType", + "rdfs:subClassOf" : [ { + "@id" : "bts:ScRNA-seqLevel1" + } ], + "@id" : "bts:CEL-seq2", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:LiquidNitrogen" + "sms:requiresComponent" : "", + "rdfs:label" : "CEL-seq2", + "rdfs:comment" : "Highly-multiplexed plate-based single-cell RNA-Seq assay (so a subtype of scRNA-seq, and some additional metadata parameters are collected)", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" }, { - "@id" : "bts:DryIce" + "@id" : "bts:Filename" }, { - "@id" : "bts:AmbientPack" + "@id" : "bts:FileFormat" }, { - "@id" : "bts:ColdPack" + "@id" : "bts:ParticipantID" }, { - "@id" : "bts:IcePack" + "@id" : "bts:SampleID" }, { - "@id" : "bts:SpecimenatRoomTemperature" + "@id" : "bts:AltSampleID" }, { - 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"@id" : "bts:StopLost" + "@id" : "bts:EmptyWellBarcode" }, { - "@id" : "bts:MaturemiRNAVariant" + "@id" : "bts:WellIndex" + } ], + "sms:displayName" : "CEL-seq2" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:Biospecimen", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "Biospecimen", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" }, { - "@id" : "bts:InframeInsertion" + "@id" : "bts:ParentID" }, { - "@id" : "bts:InframeDeletion" + "@id" : "bts:ParentBiospecimenID" }, { - "@id" : "bts:ProteinAlteringVariant" + "@id" : "bts:AdjacentBiospecimenIDs" }, { - "@id" : "bts:IncompleteTerminalCodonVariant" + "@id" : "bts:BiospecimenType" }, { - "@id" : "bts:TFBSAblation" + "@id" : "bts:TimepointLabel" }, { - "@id" : "bts:IntronVariant" + "@id" : "bts:SpecimenLaterality" + } ], + "sms:displayName" : "Biospecimen" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:BiospecimenDimension1", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BiospecimenDimension1", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" }, { - "@id" : "bts:CodingSequenceVariant" + "@id" : "bts:ParentID" }, { - "@id" : "bts:MissenseVariant" + "@id" : "bts:ParentBiospecimenID" }, { - "@id" : "bts:FrameshiftVariant" + "@id" : "bts:AdjacentBiospecimenIDs" }, { - "@id" : "bts:Non-codingTranscriptVariant" + "@id" : "bts:BiospecimenType" }, { - "@id" : "bts:FeatureTruncation" + "@id" : "bts:TimepointLabel" }, { - "@id" : "bts:RegulatoryRegionAmplification" + "@id" : "bts:SpecimenLaterality" }, { - "@id" : "bts:StartLost" + "@id" : "bts:DimensionsUnit" + } ], + "sms:displayName" : "BiospecimenDimension1" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Biospecimen" + } ], + "@id" : "bts:BloodBiospecimenType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BloodBiospecimenType", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:BiospecimenID" }, { - "@id" : "bts:FeatureElongation" + "@id" : "bts:ParentID" + }, { + "@id" : "bts:ParentBiospecimenID" + }, { + "@id" : "bts:AdjacentBiospecimenIDs" + }, { + "@id" : "bts:BiospecimenType" + }, { + "@id" : "bts:TimepointLabel" + }, { + "@id" : "bts:SpecimenLaterality" + }, { + "@id" : "bts:ShippingConditionType" } ], - 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Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", + "sms:displayName" : "BloodBiospecimenType" + }, { + "@id" : "bts:IndicatorEnum", "@type" : "rdfs:Class", - "sms:displayName" : "MolecularConsequence" + "rdfs:comment" : "TBD", + "rdfs:label" : "IndicatorEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "IndicatorEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:SampleCollectionYear", + "@id" : "bts:BreastCancerAssessmentTestsEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SampleCollectionYear", + "rdfs:label" : "BreastCancerAssessmentTestsEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SampleCollectionYear", + "sms:displayName" : "BreastCancerAssessmentTestsEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:HereditaryCancerPredispositionSyndromeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HereditaryCancerPredispositionSyndromeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:WorkingDistanceUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cm" - }, { - "@id" : "bts:mm" - }, { - "@id" : "bts:µm" - }, { - "@id" : "bts:nm" - }, { - "@id" : "bts:Å" - } ], - "rdfs:label" : "WorkingDistanceUnit", - "rdfs:comment" : "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "sms:displayName" : "HereditaryCancerPredispositionSyndromeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaDetectionMethodTypeEnum", "@type" : "rdfs:Class", - "sms:displayName" : "WorkingDistanceUnit" + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaDetectionMethodTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaDetectionMethodTypeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:PriorSitesofRadiation", + "@id" : "bts:CancerAssociatedGeneMutationsEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "PriorSitesofRadiation", + "rdfs:label" : "CancerAssociatedGeneMutationsEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PriorSitesofRadiation", + "sms:displayName" : "CancerAssociatedGeneMutationsEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:RelativewithCancerHistoryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "RelativewithCancerHistoryEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:AlcoholHistory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - } ], - "rdfs:label" : "AlcoholHistory", - "rdfs:comment" : "A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.", + "sms:displayName" : "RelativewithCancerHistoryEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:EthnicityEnum", "@type" : "rdfs:Class", - "sms:displayName" : "AlcoholHistory" + "rdfs:comment" : "TBD", + "rdfs:label" : "EthnicityEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "EthnicityEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:ImmersionEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ImmersionEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:AgeIsObfuscated", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:True" - }, { - "@id" : "bts:False" - } ], - "rdfs:label" : "AgeIsObfuscated", - "rdfs:comment" : "The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.", - "@type" : "rdfs:Class", - "sms:displayName" : "AgeIsObfuscated" + "sms:displayName" : "ImmersionEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:TargetName", + "@id" : "bts:BreastCancerGenomicTestPerformedEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TargetName", + "rdfs:label" : "BreastCancerGenomicTestPerformedEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TargetName", + "sms:displayName" : "BreastCancerGenomicTestPerformedEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:TargetCaptureKit", + "@id" : "bts:FileFormatEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TargetCaptureKit", + "rdfs:label" : "FileFormatEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TargetCaptureKit", - "sms:required" : "sms:true" + "sms:displayName" : "FileFormatEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:DimensionOrderEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "DimensionOrderEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:BisulfiteConversionKit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:ZimoEZDNAMethylationKit" - }, { - "@id" : "bts:ZimoEZ-96DNAMethylationShallowKit" - }, { - "@id" : "bts:ZimoEZ-96DNAMethylationDeepKit" - }, { - "@id" : "bts:NEBNextEnzymaticMethyl-seqKit" - }, { - "@id" : "bts:AgilentSureSelectXTMethyl-Seq" - } ], - "rdfs:label" : "BisulfiteConversionKit", - "rdfs:comment" : "Name of the kit used in bisulfite conversion", - "@type" : "rdfs:Class", - "sms:displayName" : "BisulfiteConversionKit" + "sms:displayName" : "DimensionOrderEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:SecondExon", + "@id" : "bts:SexEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.", - "rdfs:label" : "SecondExon", + "rdfs:comment" : "TBD", + "rdfs:label" : "SexEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SecondExon", + "sms:displayName" : "SexEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:AlcoholIntensityEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholIntensityEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:HistoneFamily", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:H1" - }, { - "@id" : "bts:H2A" - }, { - "@id" : "bts:H2B" - }, { - "@id" : "bts:H3" - }, { - "@id" : "bts:H4" - } ], - "rdfs:label" : "HistoneFamily", - "rdfs:comment" : "The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.", - "@type" : "rdfs:Class", - "sms:displayName" : "HistoneFamily" + "sms:displayName" : "AlcoholIntensityEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:BloodTestNormalRangeUpper", + "@id" : "bts:ImagingAssayTypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.", - "rdfs:label" : "BloodTestNormalRangeUpper", + "rdfs:comment" : "TBD", + "rdfs:label" : "ImagingAssayTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BloodTestNormalRangeUpper", + "sms:displayName" : "ImagingAssayTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:LibraryPrepKitVersion", + "@id" : "bts:PassedQCEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Version of Library Prep Kit. String", - "rdfs:label" : "LibraryPrepKitVersion", + "rdfs:comment" : "TBD", + "rdfs:label" : "PassedQCEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "LibraryPrepKitVersion", - "sms:required" : "sms:true" + "sms:displayName" : "PassedQCEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Immunosuppression", + "@id" : "bts:ExtentofTumorResectionEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Immunosuppression", + "rdfs:label" : "ExtentofTumorResectionEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Immunosuppression", + "sms:displayName" : "ExtentofTumorResectionEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Authors", + "@id" : "bts:ReverseTranscriptionPrimerEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Authors", + "rdfs:label" : "ReverseTranscriptionPrimerEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Authors", + "sms:displayName" : "ReverseTranscriptionPrimerEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:CountryofResidenceEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "CountryofResidenceEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:OvarianCancerPlatinumStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Platinum-refractory" - }, { - "@id" : "bts:Platinum-sensitive" - }, { - "@id" : "bts:Platinum-resistant" - } ], - "rdfs:label" : "OvarianCancerPlatinumStatus", - "rdfs:comment" : "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", - "@type" : "rdfs:Class", - "sms:displayName" : "OvarianCancerPlatinumStatus" + "sms:displayName" : "CountryofResidenceEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:TobaccoSmokingStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TobaccoSmokingStatusEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:AlcoholIntensity", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Drinker" - }, { - "@id" : "bts:HeavyDrinker" - }, { - "@id" : "bts:LifelongNon-Drinker" - }, { - "@id" : "bts:Non-Drinker" - }, { - "@id" : "bts:OccasionalDrinker" - } ], - "rdfs:label" : "AlcoholIntensity", - "rdfs:comment" : "Category to describe the patient's current level of alcohol use as self-reported by the patient.", - "@type" : "rdfs:Class", - "sms:displayName" : "AlcoholIntensity" + "sms:displayName" : "TobaccoSmokingStatusEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Transcript", + "@id" : "bts:OncotypeRiskGroupEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "Transcript", + "rdfs:comment" : "TBD", + "rdfs:label" : "OncotypeRiskGroupEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Transcript", + "sms:displayName" : "OncotypeRiskGroupEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:EducationLevel", + "@id" : "bts:PathogenicityEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "EducationLevel", + "rdfs:label" : "PathogenicityEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "EducationLevel", + "sms:displayName" : "PathogenicityEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:LabTestsforMMRStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LabTestsforMMRStatusEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:DimensionOrder", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:XYZCT" - }, { - "@id" : "bts:XYZTC" - }, { - "@id" : "bts:XYCTZ" - }, { - "@id" : "bts:XYCZT" - }, { - "@id" : "bts:XYTZC" - }, { - "@id" : "bts:ZYX" - } ], - "rdfs:label" : "DimensionOrder", - "rdfs:comment" : "The order in which the individual planes of data are interleaved.", - "@type" : "rdfs:Class", - "sms:displayName" : "DimensionOrder" + "sms:displayName" : "LabTestsforMMRStatusEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Parity", + "@id" : "bts:LibraryConstructionMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of pregnancies carried over the threshold of viability", - "rdfs:label" : "Parity", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryConstructionMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Parity", + "sms:displayName" : "LibraryConstructionMethodEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:AlcoholDaysPerWeek", + "@id" : "bts:BisulfiteConversionKitEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.", - "rdfs:label" : "AlcoholDaysPerWeek", + "rdfs:comment" : "TBD", + "rdfs:label" : "BisulfiteConversionKitEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AlcoholDaysPerWeek", + "sms:displayName" : "BisulfiteConversionKitEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:TotalVolumeUnitEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TotalVolumeUnitEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:AnalyteType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:TissueSectionAnalyte" - }, { - "@id" : "bts:SerumAnalyte" - }, { - "@id" : "bts:PBMCsorPlasmaorSerumAnalyte" - }, { - "@id" : "bts:Plasma" - }, { - "@id" : "bts:TissueBlockAnalyte" - }, { - "@id" : "bts:cfDNAAnalyte" - }, { - "@id" : "bts:DNAAnalyte" - }, { - "@id" : "bts:RNAAnalyte" - }, { - "@id" : "bts:cDNALibrariesAnalyte" - }, { - "@id" : "bts:PBMCs" - }, { - "@id" : "bts:TotalRNAAnalyte" - } ], - "rdfs:label" : "AnalyteType", - "rdfs:comment" : "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "@type" : "rdfs:Class", - "sms:displayName" : "AnalyteType" + "sms:displayName" : "TotalVolumeUnitEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:BooleanEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BooleanEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:FOVYUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cm" - }, { - "@id" : "bts:mm" - }, { - "@id" : "bts:µm" - }, { - "@id" : "bts:nm" - }, { - "@id" : "bts:Å" - } ], - "rdfs:label" : "FOVYUnit", - "rdfs:comment" : "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "@type" : "rdfs:Class", - "sms:displayName" : "FOVYUnit" + "sms:displayName" : "BooleanEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:AgeatDiagnosis", + "@id" : "bts:MolecularAnalysisMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Age at the time of diagnosis expressed in number of days since birth.", - "rdfs:label" : "AgeatDiagnosis", + "rdfs:comment" : "TBD", + "rdfs:label" : "MolecularAnalysisMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AgeatDiagnosis", + "sms:displayName" : "MolecularAnalysisMethodEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Cytoband", + "@id" : "bts:ClonalityEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "Cytoband", + "rdfs:comment" : "TBD", + "rdfs:label" : "ClonalityEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Cytoband", + "sms:displayName" : "ClonalityEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:PeaksCallingSoftware", + "@id" : "bts:InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "PeaksCallingSoftware", + "rdfs:label" : "InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PeaksCallingSoftware", + "sms:displayName" : "InvasiveDuctalBreastCarcinomaHistologicCategoryEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:IschemicTemperatureEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "IschemicTemperatureEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:SecondhandSmokeasChild", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - } ], - "rdfs:label" : "SecondhandSmokeasChild", - "rdfs:comment" : "The text term used to indicate whether the patient was exposed to secondhand smoke as a child.", + "sms:displayName" : "IschemicTemperatureEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AgeIsObfuscatedEnum", "@type" : "rdfs:Class", - "sms:displayName" : "SecondhandSmokeasChild" + "rdfs:comment" : "TBD", + "rdfs:label" : "AgeIsObfuscatedEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AgeIsObfuscatedEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:LaboratoryTestEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LaboratoryTestEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:PhysicalSizeXUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:cm" - }, { - "@id" : "bts:mm" - }, { - "@id" : "bts:µm" - }, { - "@id" : "bts:nm" - }, { - "@id" : "bts:Å" - } ], - "rdfs:label" : "PhysicalSizeXUnit", - "rdfs:comment" : "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "sms:displayName" : "LaboratoryTestEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SiteofResectionorBiopsyEnum", "@type" : "rdfs:Class", - "sms:displayName" : "PhysicalSizeXUnit" + "rdfs:comment" : "TBD", + "rdfs:label" : "SiteofResectionorBiopsyEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SiteofResectionorBiopsyEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:VascularInvasionTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VascularInvasionTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:CancerAssociatedGeneMutations", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:PMS2mutation" - }, { - "@id" : "bts:POT1mutation" - }, { - "@id" : "bts:TP53mutation" - }, { - "@id" : "bts:H3K27Mmutation" - }, { - "@id" : "bts:SMARCA4mutation" - }, { - "@id" : "bts:SDHDmutation" - }, { - "@id" : "bts:BRCA1mutation" - }, { - "@id" : "bts:CHKmutation" - }, { - "@id" : "bts:RB1mutation" - }, { - "@id" : "bts:H3G34R/Vmutation" - }, { - "@id" : "bts:SDHCmutation" - }, { - "@id" : "bts:SDHBmutation" - }, { - "@id" : "bts:TSC2mutation" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:HOXB13mutation" - }, { - "@id" : "bts:NF1mutation" - }, { - "@id" : "bts:VHLmutation" - }, { - "@id" : "bts:BAP1mutation" - }, { - "@id" : "bts:SETD2mutation" - }, { - "@id" : "bts:BRCA1and2mutation" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:PTENmutation" - }, { - "@id" : "bts:NotApplicable" - }, { - "@id" : "bts:STK11mutation" - }, { - "@id" : "bts:PAX5mutation" - }, { - "@id" : "bts:RETmutation" - }, { - "@id" : "bts:NF2mutation" - }, { - "@id" : "bts:ETV6mutation" - }, { - "@id" : "bts:PolDmutation" - }, { - "@id" : "bts:IKZF1mutation" - }, { - "@id" : "bts:PALB2mutation" - }, { - "@id" : "bts:SDHAF2mutation" - }, { - "@id" : "bts:EGFRmutation" - }, { - "@id" : "bts:PDGFRAmutation" - }, { - "@id" : "bts:ARFmutation" - }, { - "@id" : "bts:PTCHmutation" - }, { - "@id" : "bts:PRKAR1Amutation" - }, { - "@id" : "bts:MUTYHmutation" - }, { - "@id" : "bts:MSH6mutation" - }, { - "@id" : "bts:CDKN2Aandp14ARFmutation" - }, { - "@id" : "bts:GREM1mutation" - }, { - "@id" : "bts:MAXmutation" - }, { - "@id" : "bts:FHmutation" - }, { - "@id" : "bts:PHOX2Bmutation" - }, { - "@id" : "bts:CDH1mutation" - }, { - "@id" : "bts:MSH2mutation" - }, { - "@id" : "bts:MLH1mutation" - }, { - "@id" : "bts:METmutation" - }, { - "@id" : "bts:ATRXmutation" - }, { - "@id" : "bts:KRASmutation" - }, { - "@id" : "bts:KITmutation" - }, { - "@id" : "bts:PolEmutation" - }, { - "@id" : "bts:TSC1mutation" - }, { - "@id" : "bts:BLMmutation" - }, { - "@id" : "bts:ATMmutation" - }, { - "@id" : "bts:ACVR1mutation" - }, { - "@id" : "bts:FLCNmutation" - }, { - "@id" : "bts:MEN1mutation" - }, { - "@id" : "bts:TMEM127mutation" - }, { - "@id" : "bts:BRAFmutation" - }, { - "@id" : "bts:ROS1mutation" - }, { - "@id" : "bts:SMAD4mutation" - }, { - "@id" : "bts:ALKmutation" - }, { - "@id" : "bts:BMPR1Amutation" - }, { - "@id" : "bts:APCmutation" - }, { - "@id" : "bts:BRCA2mutation" - }, { - "@id" : "bts:SMARCB1mutation" - }, { - "@id" : "bts:CDKN2Amutation" - }, { - "@id" : "bts:RAD51Cmutation" - }, { - "@id" : "bts:p14ARFmutation" - } ], - "rdfs:label" : "CancerAssociatedGeneMutations", - "rdfs:comment" : "Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history", + "sms:displayName" : "VascularInvasionTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:StainingIntensityEnum", "@type" : "rdfs:Class", - "sms:displayName" : "CancerAssociatedGeneMutations" + "rdfs:comment" : "TBD", + "rdfs:label" : "StainingIntensityEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "StainingIntensityEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:ParentDataFileID", + "@id" : "bts:MutationalSignaturesEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Optional, Synapse ID of a parent data file from which this data file is derived.", - "rdfs:label" : "ParentDataFileID", + "rdfs:comment" : "TBD", + "rdfs:label" : "MutationalSignaturesEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ParentDataFileID", + "sms:displayName" : "MutationalSignaturesEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:FOVnumber", + "@id" : "bts:PriorInvasiveBreastDiseaseEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label" : "FOVnumber", + "rdfs:comment" : "TBD", + "rdfs:label" : "PriorInvasiveBreastDiseaseEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "FOVnumber", + "sms:displayName" : "PriorInvasiveBreastDiseaseEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:ProportionofMinimumCpGCoverage10X", + "@id" : "bts:MismatchRepairSystemStatusEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "(For whole genome sequencing or targeted sequencing) Proportion of all reference bases for that achieves 10X or greater coverage per CpG.", - "rdfs:label" : "ProportionofMinimumCpGCoverage10X", + "rdfs:comment" : "TBD", + "rdfs:label" : "MismatchRepairSystemStatusEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ProportionofMinimumCpGCoverage10X", + "sms:displayName" : "MismatchRepairSystemStatusEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:ChannelMetadataFilename", + "@id" : "bts:AnalyteTypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Full path of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label" : "ChannelMetadataFilename", + "rdfs:comment" : "TBD", + "rdfs:label" : "AnalyteTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ChannelMetadataFilename", + "sms:displayName" : "AnalyteTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Secondhandsmokeexposureyears", + "@id" : "bts:ModeofCancerDetectionEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Secondhandsmokeexposureyears", + "rdfs:label" : "ModeofCancerDetectionEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Secondhandsmokeexposureyears", + "sms:displayName" : "ModeofCancerDetectionEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:BreastBiopsyProcedureFindingTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastBiopsyProcedureFindingTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Read3", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:CellBarcodeandDNAInsert" - }, { - "@id" : "bts:SampleIndexandDNAInsert" - }, { - "@id" : "bts:DNAInsert" - }, { - "@id" : "bts:SampleIndex" - }, { - "@id" : "bts:CellBarcode" - } ], - "rdfs:label" : "Read3", - "rdfs:comment" : "Read 3 content description", + "sms:displayName" : "BreastBiopsyProcedureFindingTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:AlcoholTypeEnum", "@type" : "rdfs:Class", - "sms:displayName" : "Read3" + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AlcoholTypeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:CellMedianNumberReads", + "@id" : "bts:VitalStatusEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Median number of reads per cell. Number", - "rdfs:label" : "CellMedianNumberReads", + "rdfs:comment" : "TBD", + "rdfs:label" : "VitalStatusEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CellMedianNumberReads", + "sms:displayName" : "VitalStatusEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:InvasiveLobularBreastCarcinomaHistologicCategoryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "InvasiveLobularBreastCarcinomaHistologicCategoryEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Gender", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:female" - }, { - "@id" : "bts:male" - }, { - "@id" : "bts:unspecified" - } ], - "rdfs:label" : "Gender", - "rdfs:comment" : "Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]", + "sms:displayName" : "InvasiveLobularBreastCarcinomaHistologicCategoryEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:DimensionsUnitEnum", "@type" : "rdfs:Class", - "sms:displayName" : "Gender" + "rdfs:comment" : "TBD", + "rdfs:label" : "DimensionsUnitEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "DimensionsUnitEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:WorkflowVersion", + "@id" : "bts:PrimaryDiagnosisEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "WorkflowVersion", + "rdfs:label" : "PrimaryDiagnosisEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "WorkflowVersion", + "sms:displayName" : "PrimaryDiagnosisEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:MenopauseStatus", + "@id" : "bts:TestAnalyteTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "MenopauseStatus", + "rdfs:label" : "TestAnalyteTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "MenopauseStatus", + "sms:displayName" : "TestAnalyteTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:SubCycleNumber", + "@id" : "bts:ZygosityEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SubCycleNumber", + "rdfs:label" : "ZygosityEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SubCycleNumber", + "sms:displayName" : "ZygosityEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:GenomicReferenceURL", + "@id" : "bts:NucleicAcidSourceEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "GenomicReferenceURL", + "rdfs:label" : "NucleicAcidSourceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "GenomicReferenceURL", + "sms:displayName" : "NucleicAcidSourceEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:GenomicReference", + "@id" : "bts:OvarianCancerSurgicalOutcomeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "GenomicReference", + "rdfs:label" : "OvarianCancerSurgicalOutcomeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "GenomicReference", + "sms:displayName" : "OvarianCancerSurgicalOutcomeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:PUC19methylationratio", + "@id" : "bts:SequencingStrategy", "@type" : "rdfs:Class", - "rdfs:comment" : "Methylation ratio of mostly methylated pUC19 control, as a percentage", - "rdfs:label" : "PUC19methylationratio", + "rdfs:comment" : "TBD", + "rdfs:label" : "SequencingStrategy", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PUC19methylationratio", - "sms:required" : "sms:true" + "sms:displayName" : "SequencingStrategy", + "sms:required" : "sms:false" }, { - "@id" : "bts:Lambdamethylationratio", + "@id" : "bts:RaceEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Methylation ratio of mostly unmethylated lambda control, as a percentage", - "rdfs:label" : "Lambdamethylationratio", + "rdfs:comment" : "TBD", + "rdfs:label" : "RaceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Lambdamethylationratio", - "sms:required" : "sms:true" + "sms:displayName" : "RaceEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:SizeY", + "@id" : "bts:BreastCarcinomaSurgicalProcedureNameEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label" : "SizeY", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaSurgicalProcedureNameEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SizeY", + "sms:displayName" : "BreastCarcinomaSurgicalProcedureNameEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:CellCount", + "@id" : "bts:SmokingFrequencyEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "CellCount", + "rdfs:comment" : "TBD", + "rdfs:label" : "SmokingFrequencyEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CellCount", + "sms:displayName" : "SmokingFrequencyEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:PixelTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PixelTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:AnaplasiaPresentType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Equivocal" - }, { - "@id" : "bts:Absent" - }, { - "@id" : "bts:Present" - }, { - "@id" : "bts:Diffuse" - }, { - "@id" : "bts:Focal" - }, { - "@id" : "bts:Sclerosis" - } ], - "rdfs:label" : "AnaplasiaPresentType", - "rdfs:comment" : "The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.", + "sms:displayName" : "PixelTypeEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:SpikeInEnum", "@type" : "rdfs:Class", - "sms:displayName" : "AnaplasiaPresentType" + "rdfs:comment" : "TBD", + "rdfs:label" : "SpikeInEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "SpikeInEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:SampleID", + "@id" : "bts:ReadEnum", "@type" : "rdfs:Class", - "rdfs:comment" : " ID associated with a biosample", - "rdfs:label" : "SampleID", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReadEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SampleID", - "sms:required" : "sms:true" + "sms:displayName" : "ReadEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:BreastCarcinomaHER2StatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaHER2StatusEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BreastCarcinomaHER2StatusEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:ClinicalBiospecimenTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ClinicalBiospecimenTypeEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "ClinicalBiospecimenTypeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:ExcitationWavelength", + "@id" : "bts:RelationshipPrimaryDiagnosisEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ExcitationWavelength", + "rdfs:label" : "RelationshipPrimaryDiagnosisEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ExcitationWavelength", + "sms:displayName" : "RelationshipPrimaryDiagnosisEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:BIRADSMammographyBreastDensityCategoryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BIRADSMammographyBreastDensityCategoryEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:BIRADSMammographyBreastDensityCategory", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Predominantlyfatty" - }, { - "@id" : "bts:Scatteredfibroglandulardensities" - }, { - "@id" : "bts:Heterogeneouslydense" - }, { - "@id" : "bts:Extremelydense" - } ], - "rdfs:label" : "BIRADSMammographyBreastDensityCategory", - "rdfs:comment" : "The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.", - "@type" : "rdfs:Class", - "sms:displayName" : "BIRADSMammographyBreastDensityCategory" + "sms:displayName" : "BIRADSMammographyBreastDensityCategoryEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Weight", + "@id" : "bts:SingleNucleusBufferEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Weight", + "rdfs:label" : "SingleNucleusBufferEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Weight", + "sms:displayName" : "SingleNucleusBufferEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:BiospecimenTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BiospecimenTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:OvarianCancerSurgicalOutcome", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Other" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:R0resection" - }, { - "@id" : "bts:Optimalcytoreduction" - }, { - "@id" : "bts:Sub-optimalcytoreduction" - } ], - "rdfs:label" : "OvarianCancerSurgicalOutcome", - "rdfs:comment" : "Text term that describes the kind of surgical treatment administered.", - "@type" : "rdfs:Class", - "sms:displayName" : "OvarianCancerSurgicalOutcome" + "sms:displayName" : "BiospecimenTypeEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:AntibioticUseEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AntibioticUseEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:RelationshipPrimaryDiagnosis", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:ProstateCancer" - }, { - "@id" : "bts:TesticularCancer" - }, { - "@id" : "bts:Cancer" - }, { - "@id" : "bts:KaposiSarcoma" - }, { - "@id" : "bts:BoneCancer" - }, { - "@id" : "bts:LiverCancer" - }, { - "@id" : "bts:CNSCancer" - }, { - "@id" : "bts:UterineCancer" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:LymphNodeCancer" - }, { - "@id" : "bts:RectalCancer" - }, { - "@id" : "bts:WilmsTumor" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Osteosarcoma" - }, { - "@id" : "bts:Chondrosarcoma" - }, { - "@id" : "bts:Mesothelioma" - }, { - "@id" : "bts:GastricCancer" - }, { - "@id" : "bts:CervicalCancer" - }, { - "@id" : "bts:EwingSarcoma" - }, { - "@id" : "bts:Glioblastoma" - }, { - "@id" : "bts:SkinCancer" - }, { - "@id" : "bts:TonsillarCancer" - }, { - "@id" : "bts:BileDuctCancer" - }, { - "@id" : "bts:TongueCancer" - }, { - "@id" : "bts:LaryngealCancer" - }, { - "@id" : "bts:Melanoma" - }, { - "@id" : "bts:HematologicCancer" - }, { - "@id" : "bts:ThroatCancer" - }, { - "@id" : "bts:ColorectalCancer" - }, { - "@id" : "bts:KidneyCancer" - }, { - "@id" : "bts:SpleenCancer" - }, { - "@id" : "bts:BreastCancer" - }, { - "@id" : "bts:Leukemia" - }, { - "@id" : "bts:Sarcoma" - }, { - "@id" : "bts:BloodCancer" - }, { - "@id" : "bts:Neuroblastoma" - }, { - "@id" : "bts:GynecologicCancer" - }, { - "@id" : "bts:Rhabdomyosarcoma" - }, { - "@id" : "bts:PancreasCancer" - }, { - "@id" : "bts:AdrenalGlandCancer" - }, { - "@id" : "bts:ThyroidCancer" - }, { - "@id" : "bts:MultipleMyeloma" - }, { - "@id" : "bts:LungCancer" - }, { - "@id" : "bts:BasalCellCancer" - }, { - "@id" : "bts:BrainCancer" - }, { - "@id" : "bts:EsophagealCancer" - }, { - "@id" : "bts:Lymphoma" - }, { - "@id" : "bts:OvarianCancer" - }, { - "@id" : "bts:GallbladderCancer" - }, { - "@id" : "bts:HeadandNeckCancer" - }, { - "@id" : "bts:BladderCancer" - } ], - "rdfs:label" : "RelationshipPrimaryDiagnosis", - "rdfs:comment" : "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", - "@type" : "rdfs:Class", - "sms:displayName" : "RelationshipPrimaryDiagnosis" + "sms:displayName" : "AntibioticUseEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:AppliedHardTrimming", + "@id" : "bts:HormoneTherapyBreastCancerPreventionIndicatorEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "AppliedHardTrimming", + "rdfs:label" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AppliedHardTrimming", + "sms:displayName" : "HormoneTherapyBreastCancerPreventionIndicatorEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:AAChange", + "@id" : "bts:PreservationMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "rdfs:label" : "AAChange", + "rdfs:comment" : "TBD", + "rdfs:label" : "PreservationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "AAChange", + "sms:displayName" : "PreservationMethodEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:TumorExtranodalExtensionIndicatorEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TumorExtranodalExtensionIndicatorEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:NucleicAcidSource", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:SingleCell" - }, { - "@id" : "bts:SingleNucleus" - }, { - "@id" : "bts:BulkNuclei" - }, { - "@id" : "bts:BulkWholeCell" - }, { - "@id" : "bts:Micro-region" - } ], - "rdfs:label" : "NucleicAcidSource", - "rdfs:comment" : "The source of the input nucleic molecule", - "@type" : "rdfs:Class", - "sms:displayName" : "NucleicAcidSource" + "sms:displayName" : "TumorExtranodalExtensionIndicatorEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:TseriesEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TseriesEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:ExtentofTumorResection", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Minor" - }, { - "@id" : "bts:OpenBiopsy" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:GrossTotalResection" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotApplicable" - }, { - "@id" : "bts:Segmental" - }, { - "@id" : "bts:NTR" - }, { - "@id" : "bts:Suboptimaldebulking" - }, { - "@id" : "bts:SubtotalResection" - }, { - "@id" : "bts:Other" - }, { - "@id" : "bts:Partialdebulking" - }, { - "@id" : "bts:Suboptimal" - }, { - "@id" : "bts:Optimaldebulking" - }, { - "@id" : "bts:ExtensiveSubtotal" - } ], - "rdfs:label" : "ExtentofTumorResection", - "rdfs:comment" : "The degree to which the lesion has been cut out, or resected.", - "@type" : "rdfs:Class", - "sms:displayName" : "ExtentofTumorResection" + "sms:displayName" : "TseriesEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:TimepointLabel", + "@id" : "bts:DissociationMethodEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label" : "TimepointLabel", + "rdfs:comment" : "TBD", + "rdfs:label" : "DissociationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TimepointLabel", + "sms:displayName" : "DissociationMethodEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:LibraryLayoutEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryLayoutEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Ploidy", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Aneuploid" - }, { - "@id" : "bts:Diploid" - }, { - "@id" : "bts:Hyperdiploid" - }, { - "@id" : "bts:Hypodiploid" - }, { - "@id" : "bts:NearDiploid" - }, { - "@id" : "bts:Tetraploid" - } ], - "rdfs:label" : "Ploidy", - "rdfs:comment" : "Text term used to describe the number of sets of homologous chromosomes.", - "@type" : "rdfs:Class", - "sms:displayName" : "Ploidy" + "sms:displayName" : "LibraryLayoutEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:PortionWeight", + "@id" : "bts:BreastCancerAllredEstrogenReceptorScoreEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value that represents the sample portion weight, measured in milligrams.", - "rdfs:label" : "PortionWeight", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCancerAllredEstrogenReceptorScoreEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "PortionWeight", + "sms:displayName" : "BreastCancerAllredEstrogenReceptorScoreEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:DaystoProgression", + "@id" : "bts:PrecancerousConditionTypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days between the date used for index and the date the patient's disease progressed.", - "rdfs:label" : "DaystoProgression", + "rdfs:comment" : "TBD", + "rdfs:label" : "PrecancerousConditionTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DaystoProgression", + "sms:displayName" : "PrecancerousConditionTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:RRIDidentifier", + "@id" : "bts:VariantTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "RRIDidentifier", + "rdfs:label" : "VariantTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "RRIDidentifier", + "sms:displayName" : "VariantTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:ClassBRCA2", + "@id" : "bts:RelationshipTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "ClassBRCA2", + "rdfs:label" : "RelationshipTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "ClassBRCA2", + "sms:displayName" : "RelationshipTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:WhitelistCellBarcodeFileLink", + "@id" : "bts:SmokingExposureEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "WhitelistCellBarcodeFileLink", + "rdfs:label" : "SmokingExposureEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "WhitelistCellBarcodeFileLink", + "sms:displayName" : "SmokingExposureEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:StartDaysfromIndex", + "@id" : "bts:OvarianCancerPlatinumStatusEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'", - "rdfs:label" : "StartDaysfromIndex", + "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianCancerPlatinumStatusEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "StartDaysfromIndex", + "sms:displayName" : "OvarianCancerPlatinumStatusEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Ecigvapetimesperday", + "@id" : "bts:HistoneFamilyEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Ecigvapetimesperday", + "rdfs:label" : "HistoneFamilyEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Ecigvapetimesperday", + "sms:displayName" : "HistoneFamilyEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:ChromosomeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ChromosomeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:FamilyMemberVitalStatusIndicator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "FamilyMemberVitalStatusIndicator", - "rdfs:comment" : "The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)", - "@type" : "rdfs:Class", - "sms:displayName" : "FamilyMemberVitalStatusIndicator" + "sms:displayName" : "ChromosomeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:SectionThicknessValue", + "@id" : "bts:OvarianCancerHistologicSubtypeEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).", - "rdfs:label" : "SectionThicknessValue", + "rdfs:comment" : "TBD", + "rdfs:label" : "OvarianCancerHistologicSubtypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SectionThicknessValue", + "sms:displayName" : "OvarianCancerHistologicSubtypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:SoftwareandVersion", + "@id" : "bts:MicroscopyUnitEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "SoftwareandVersion", + "rdfs:label" : "MicroscopyUnitEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "SoftwareandVersion", + "sms:displayName" : "MicroscopyUnitEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:HistoryEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "HistoryEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:KnownGeneticPredispositionMutation", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" - }, { - "@id" : "bts:No" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "KnownGeneticPredispositionMutation", - "rdfs:comment" : "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", - "@type" : "rdfs:Class", - "sms:displayName" : "KnownGeneticPredispositionMutation" + "sms:displayName" : "HistoryEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:TotalDNAInput", + "@id" : "bts:CauseofDeathEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "A sample amount used for the total number of reads, in microgram or nanogram.", - "rdfs:label" : "TotalDNAInput", + "rdfs:comment" : "TBD", + "rdfs:label" : "CauseofDeathEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TotalDNAInput", + "sms:displayName" : "CauseofDeathEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:BiospecimenDimension1", + "@id" : "bts:TestResultEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", - "rdfs:label" : "BiospecimenDimension1", + "rdfs:comment" : "TBD", + "rdfs:label" : "TestResultEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BiospecimenDimension1", + "sms:displayName" : "TestResultEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:NucleiBarcodeLength", + "@id" : "bts:AntigenEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Nuclei Barcode Length", - "rdfs:label" : "NucleiBarcodeLength", + "rdfs:comment" : "TBD", + "rdfs:label" : "AntigenEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "NucleiBarcodeLength", + "sms:displayName" : "AntigenEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:HER2BreastCarcinomaCopyNumberTotal", + "@id" : "bts:MolecularConsequenceEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.", - "rdfs:label" : "HER2BreastCarcinomaCopyNumberTotal", + "rdfs:comment" : "TBD", + "rdfs:label" : "MolecularConsequenceEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "HER2BreastCarcinomaCopyNumberTotal", + "sms:displayName" : "MolecularConsequenceEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:ReceptorStatusEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ReceptorStatusEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:MammaprintRiskGroup", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Highrisk" - }, { - "@id" : "bts:Intermediaterisk" - }, { - "@id" : "bts:Lowrisk" - } ], - "rdfs:label" : "MammaprintRiskGroup", - "rdfs:comment" : "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", - "@type" : "rdfs:Class", - "sms:displayName" : "MammaprintRiskGroup" + "sms:displayName" : "ReceptorStatusEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Height", + "@id" : "bts:TumorTissueTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Height", + "rdfs:label" : "TumorTissueTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Height", + "sms:displayName" : "TumorTissueTypeEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:BreastQuadrantSiteEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastQuadrantSiteEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Race", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:americanindianoralaskanative" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:white" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:blackorafricanamerican" - }, { - "@id" : "bts:notallowedtocollect" - }, { - "@id" : "bts:asian" - }, { - "@id" : "bts:Other" - }, { - "@id" : "bts:nativehawaiianorotherpacificislander" - } ], - "rdfs:label" : "Race", - "rdfs:comment" : "An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.", + "sms:displayName" : "BreastQuadrantSiteEnum", + "sms:required" : "sms:false" + }, { + "@id" : "bts:PloidyEnum", "@type" : "rdfs:Class", - "sms:displayName" : "Race" + "rdfs:comment" : "TBD", + "rdfs:label" : "PloidyEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PloidyEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:BiospecimenDimension3", + "@id" : "bts:SpecimenLateralityEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the \"\"dimensions_unit\"\" CDE", - "rdfs:label" : "BiospecimenDimension3", + "rdfs:comment" : "TBD", + "rdfs:label" : "SpecimenLateralityEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "BiospecimenDimension3", + "sms:displayName" : "SpecimenLateralityEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:OncotypeScore", + "@id" : "bts:FamilyMemberVitalStatusIndicatorEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "OncotypeDX recurrence score", - "rdfs:label" : "OncotypeScore", + "rdfs:comment" : "TBD", + "rdfs:label" : "FamilyMemberVitalStatusIndicatorEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "OncotypeScore", + "sms:displayName" : "FamilyMemberVitalStatusIndicatorEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:InputCellsandNuclei", + "@id" : "bts:SequencingPlatformEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Number of cells and number of nuclei input; entry format: number, number", - "rdfs:label" : "InputCellsandNuclei", + "rdfs:comment" : "TBD", + "rdfs:label" : "SequencingPlatformEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "InputCellsandNuclei", + "sms:displayName" : "SequencingPlatformEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:VariantOriginEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "VariantOriginEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:PRReceptorStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Borderline" - }, { - "@id" : "bts:Equivocal" - }, { - "@id" : "bts:Indeterminate" - }, { - "@id" : "bts:Negative" - }, { - "@id" : "bts:NotPerformed" - }, { - "@id" : "bts:PerformedbutNotAvailable" - }, { - "@id" : "bts:Positive" - } ], - "rdfs:label" : "PRReceptorStatus", - "rdfs:comment" : "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", - "@type" : "rdfs:Class", - "sms:displayName" : "PRReceptorStatus" + "sms:displayName" : "VariantOriginEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:Fluorophore", + "@id" : "bts:AnaplasiaPresentTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Fluorophore", + "rdfs:label" : "AnaplasiaPresentTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Fluorophore", + "sms:displayName" : "AnaplasiaPresentTypeEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Typeofsmokeexposurecumulativeyears", + "@id" : "bts:TranspositionReactionEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Typeofsmokeexposurecumulativeyears", + "rdfs:label" : "TranspositionReactionEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Typeofsmokeexposurecumulativeyears", + "sms:displayName" : "TranspositionReactionEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Clone", + "@id" : "bts:EndBiasEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "Clone", + "rdfs:label" : "EndBiasEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Clone", + "sms:displayName" : "EndBiasEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:DiagnosisStatusType", + "@id" : "bts:HistoneVariantEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "DiagnosisStatusType", + "rdfs:label" : "HistoneVariantEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "DiagnosisStatusType", + "sms:displayName" : "HistoneVariantEnum", "sms:required" : "sms:false" }, { - "@id" : "bts:Age", + "@id" : "bts:BreastCarcinomaHistologyCategoryEnum", "@type" : "rdfs:Class", - "rdfs:comment" : "Age of individual", - "rdfs:label" : "Age", + "rdfs:comment" : "TBD", + "rdfs:label" : "BreastCarcinomaHistologyCategoryEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "Age", - "sms:required" : "sms:true" + "sms:displayName" : "BreastCarcinomaHistologyCategoryEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:TobaccoUse", + "@id" : "bts:BreastImagingPerformedTypeEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "TobaccoUse", + "rdfs:label" : "BreastImagingPerformedTypeEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "TobaccoUse", + "sms:displayName" : "BreastImagingPerformedTypeEnum", "sms:required" : "sms:false" }, { + "@id" : "bts:AlcoholExposureEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "AlcoholExposureEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Zstack", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "Zstack", - "rdfs:comment" : "Does data file contain a Z-stack of images", - "@type" : "rdfs:Class", - "sms:displayName" : "Zstack" + "sms:displayName" : "AlcoholExposureEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:SlideChargeTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SlideChargeTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:Chromosome", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:chr7" - }, { - "@id" : "bts:chr15" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:chr3" - }, { - "@id" : "bts:chr1" - }, { - "@id" : "bts:chr18" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:chrY" - }, { - "@id" : "bts:chr22" - }, { - "@id" : "bts:chr14" - }, { - "@id" : "bts:chr12" - }, { - "@id" : "bts:chr11" - }, { - "@id" : "bts:chr17" - }, { - "@id" : "bts:chrM" - }, { - "@id" : "bts:chr4" - }, { - "@id" : "bts:chr21" - }, { - "@id" : "bts:chr6" - }, { - "@id" : "bts:chr10" - }, { - "@id" : "bts:chr16" - }, { - "@id" : "bts:chrX" - }, { - "@id" : "bts:chr23" - }, { - "@id" : "bts:chr8" - }, { - "@id" : "bts:chr2" - }, { - "@id" : "bts:chr13" - }, { - "@id" : "bts:chr19" - }, { - "@id" : "bts:chr20" - }, { - "@id" : "bts:chr5" - }, { - "@id" : "bts:chr9" - } ], - "rdfs:label" : "Chromosome", - "rdfs:comment" : "The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", - "@type" : "rdfs:Class", - "sms:displayName" : "Chromosome" + "sms:displayName" : "SlideChargeTypeEnum", + "sms:required" : "sms:false" }, { + "@id" : "bts:ShippingConditionTypeEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "ShippingConditionTypeEnum", "rdfs:subClassOf" : [ ], - "@id" : "bts:MutationalSignatures", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:Signature19" - }, { - "@id" : "bts:Signature1A" - }, { - "@id" : "bts:Iggenehypermutation" - }, { - "@id" : "bts:alteredactivityoftheerror-pronepolymerasePOLε(POLE)" - }, { - "@id" : "bts:Signature3" - }, { - "@id" : "bts:Signature20" - }, { - "@id" : "bts:NotReported" - }, { - "@id" : "bts:Signature17" - }, { - "@id" : "bts:Signature4" - }, { - "@id" : "bts:Datanotavailable" - }, { - "@id" : "bts:Signature5" - }, { - "@id" : "bts:Signature9" - }, { - "@id" : "bts:unknown" - }, { - "@id" : "bts:Signature14" - }, { - "@id" : "bts:Signature13" - }, { - "@id" : "bts:NotApplicable" - }, { - "@id" : "bts:Signature12" - }, { - "@id" : "bts:Signature8" - }, { - "@id" : "bts:ActivationInducedDeaminases(AID)associatedmutations" - }, { - "@id" : "bts:Signature7" - }, { - "@id" : "bts:microsatelliteinstability(additionsanddeletions)" - }, { - "@id" : "bts:AlkylatingAgents(Temozolomide)inducedmutations" - }, { - "@id" : "bts:localizedsubstitutionhypermutation(kataegis)" - }, { - "@id" : "bts:Signature16" - }, { - "@id" : "bts:Signature6" - }, { - "@id" : "bts:Other" - }, { - "@id" : "bts:Signature21" - }, { - "@id" : "bts:DNAMMRDeficiency" - }, { - "@id" : "bts:APOBECenzymesassociatedmutations" - }, { - "@id" : "bts:Tobaccouseassociatedmutations" - }, { - "@id" : "bts:transcriptionalstrandbias" - }, { - "@id" : "bts:Signature1B" - }, { - "@id" : "bts:Signature10" - }, { - "@id" : "bts:UVlightinducedmutations" - }, { - "@id" : "bts:Signature18" - }, { - "@id" : "bts:Signature11" - }, { - "@id" : "bts:Signature2" - }, { - "@id" : "bts:methylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" - }, { - "@id" : "bts:Signature15" - }, { - "@id" : "bts:ageofcancerdiagnosis" - } ], - "rdfs:label" : "MutationalSignatures", - "rdfs:comment" : "Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done. ", - "@type" : "rdfs:Class", - "sms:displayName" : "MutationalSignatures" + "sms:displayName" : "ShippingConditionTypeEnum", + "sms:required" : "sms:false" }, { - "@id" : "bts:CancerIncidenceLocation", + "@id" : "bts:SingleCellIsolationMethodEnum", "@type" : "rdfs:Class", "rdfs:comment" : "TBD", - "rdfs:label" : "CancerIncidenceLocation", + "rdfs:label" : "SingleCellIsolationMethodEnum", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "CancerIncidenceLocation", + "sms:displayName" : "SingleCellIsolationMethodEnum", "sms:required" : "sms:false" }, { "@id" : "bts:Skinofupperlimbandshoulder", diff --git a/modules/slots.yaml b/modules/slots.yaml index 7ac55f9..fd82cd4 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -30,8 +30,9 @@ slots: Age: title: Age required: true - description: Age of individual + description: Age of individual as a positive number such as 40 or 56.5. If not available, cannot leave blank and must use "unknown". annotations: + validationRules: regex match ^\d*\.?\d*$|^unknown$ AgeAtMenarche: title: Age At Menarche required: false