diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index ae6be1a0..69a85956 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -8,2487 +8,1013 @@ }, "@graph": [ { - "@id": "schema:Text", - "@type": [ - "schema:DataType", - "rdfs:Class" + "@id": "bts:Assay", + "@type": "rdfs:Class", + "rdfs:comment": "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]", + "rdfs:label": "Assay", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } ], - "rdfs:comment": "Data type: Text.", - "rdfs:label": "Text" + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Assay", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "schema:Number", - "@type": [ - "schema:DataType", - "rdfs:Class" + "@id": "bts:Device", + "@type": "rdfs:Class", + "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", + "rdfs:label": "Device", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } ], - "rdfs:comment": "Data type: Number.", - "rdfs:label": "Number" + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Device", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "schema:Integer", + "@id": "bts:Sequencing", "@type": "rdfs:Class", - "rdfs:comment": "Data type: Integer.", - "rdfs:label": "Integer", - "rdfs:subClassOf": { - "@id": "schema:Number" - } + "rdfs:comment": "Module for next generation sequencing assays", + "rdfs:label": "Sequencing", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sequencing", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "schema:Thing", + "@id": "bts:Component", "@type": "rdfs:Class", - "rdfs:comment": "Thing", - "rdfs:label": "Thing", + "rdfs:comment": "Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.", + "rdfs:label": "Component", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], "schema:isPartOf": { - "@id": "http://schema.org" - } + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Component", + "sms:required": "sms:true", + "sms:validationRules": [] }, { - "@id": "bts:BiologicalEntity", + "@id": "bts:Patient", "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "BiologicalEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" + "rdfs:comment": "HTAN patient", + "rdfs:label": "Patient", + "rdfs:subClassOf": [ + { + "@id": "bts:IndividualOrganism" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" }, + "sms:displayName": "Patient", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Demographics" + }, + { + "@id": "bts:FamilyHistory" + }, + { + "@id": "bts:Exposure" + }, + { + "@id": "bts:FollowUp" + }, + { + "@id": "bts:Diagnosis" + }, + { + "@id": "bts:Therapy" + }, + { + "@id": "bts:MolecularTest" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParticipantID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )", + "rdfs:label": "HTANParticipantID", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } + }, + "sms:displayName": "HTAN Participant ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))$ warning" + ] }, { - "@id": "bts:OntologyClass", + "@id": "bts:Demographics", "@type": "rdfs:Class", - "rdfs:comment": "a concept or class in an ontology, vocabulary or thesaurus", - "rdfs:label": "OntologyClass", - "rdfs:subClassOf": { - "@id": "schema:Thing" + "rdfs:comment": "Demographic attributes", + "rdfs:label": "Demographics", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" }, + "sms:displayName": "Demographics", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:Ethnicity" + }, + { + "@id": "bts:Gender" + }, + { + "@id": "bts:Race" + }, + { + "@id": "bts:VitalStatus" + }, + { + "@id": "bts:DaystoBirth" + }, + { + "@id": "bts:CountryofResidence" + }, + { + "@id": "bts:AgeIsObfuscated" + }, + { + "@id": "bts:YearOfBirth" + }, + { + "@id": "bts:OccupationDurationYears" + }, + { + "@id": "bts:PrematureAtBirth" + }, + { + "@id": "bts:WeeksGestationatBirth" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:FamilyHistory", + "@type": "rdfs:Class", + "rdfs:comment": "Family cancer history", + "rdfs:label": "FamilyHistory", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } + }, + "sms:displayName": "Family History", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:RelativewithCancerHistory" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:RelationshipType", + "@id": "bts:Exposure", "@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:comment": "Exposure to carcinogens", + "rdfs:label": "Exposure", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Exposure", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:AdoptedDaughter" + "@id": "bts:Component" }, { - "@id": "bts:AdoptedSon" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:AdoptiveBrother" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:AdoptiveFather" + "@id": "bts:SmokingExposure" }, { - "@id": "bts:AdoptiveMother" + "@id": "bts:AlcoholExposure" }, { - "@id": "bts:AdoptiveSister" + "@id": "bts:AsbestosExposure" }, { - "@id": "bts:Aunt" + "@id": "bts:CoalDustExposure" }, { - "@id": "bts:Brother" + "@id": "bts:EnvironmentalTobaccoSmokeExposure" }, { - "@id": "bts:Brother-in-law" + "@id": "bts:RadonExposure" }, { - "@id": "bts:Child" + "@id": "bts:RespirableCrystallineSilicaExposure" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:FollowUp", + "@type": "rdfs:Class", + "rdfs:comment": "Follow up clinical visits", + "rdfs:label": "FollowUp", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Follow Up", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:Cousin" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Daughter" + "@id": "bts:DaystoFollowUp" }, { - "@id": "bts:Daughter-in-law" + "@id": "bts:AdverseEvent" }, { - "@id": "bts:DomesticPartner" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:Father" + "@id": "bts:BarrettsEsophagusGobletCellsPresent" }, { - "@id": "bts:Father-in-law" + "@id": "bts:BMI" }, { - "@id": "bts:FemaleCousin" + "@id": "bts:CauseofResponse" }, { - "@id": "bts:FirstCousin" + "@id": "bts:Comorbidity" }, { - "@id": "bts:FirstCousinOnceRemoved" + "@id": "bts:ComorbidityMethodofDiagnosis" }, { - "@id": "bts:FosterBrother" + "@id": "bts:DaystoAdverseEvent" }, { - "@id": "bts:FosterDaughter" + "@id": "bts:DaystoComorbidity" }, { - "@id": "bts:FosterFather" + "@id": "bts:DiabetesTreatmentType" }, { - "@id": "bts:FosterMother" + "@id": "bts:DiseaseResponse" }, { - "@id": "bts:FosterSister" + "@id": "bts:DLCORefPredictivePercent" }, { - "@id": "bts:FosterSon" + "@id": "bts:ECOGPerformanceStatus" }, { - "@id": "bts:FraternalTwinBrother" + "@id": "bts:FEV1FVCPostBronchPercent" }, { - "@id": "bts:FraternalTwinSibling" + "@id": "bts:FEV1FVCPreBronchPercent" }, { - "@id": "bts:FraternalTwinSister" + "@id": "bts:FEV1RefPostBronchPercent" }, { - "@id": "bts:FullBrother" + "@id": "bts:FEV1RefPreBronchPercent" }, { - "@id": "bts:FullSister" + "@id": "bts:Height" }, { - "@id": "bts:GrandNephew" + "@id": "bts:HepatitisSustainedVirologicalResponse" }, { - "@id": "bts:GrandNiece" + "@id": "bts:HPVPositiveType" }, { - "@id": "bts:Grandchild" + "@id": "bts:KarnofskyPerformanceStatus" }, { - "@id": "bts:Granddaughter" + "@id": "bts:MenopauseStatus" }, { - "@id": "bts:Grandfather" + "@id": "bts:PancreatitisOnsetYear" }, { - "@id": "bts:Grandmother" + "@id": "bts:RefluxTreatmentType" }, { - "@id": "bts:Grandparent" + "@id": "bts:RiskFactor" }, { - "@id": "bts:Grandson" + "@id": "bts:RiskFactorTreatment" }, { - "@id": "bts:GreatGrandchild" + "@id": "bts:ViralHepatitisSerologies" }, { - "@id": "bts:HalfBrother" + "@id": "bts:Weight" }, { - "@id": "bts:HalfSibling" + "@id": "bts:AdverseEventGrade" }, { - "@id": "bts:HalfSister" + "@id": "bts:AIDSRiskFactors" }, { - "@id": "bts:Husband" + "@id": "bts:BodySurfaceArea" }, { - "@id": "bts:IdenticalTwinBrother" + "@id": "bts:CD4Count" }, { - "@id": "bts:IdenticalTwinSibling" + "@id": "bts:CDCHIVRiskFactors" }, { - "@id": "bts:IdenticalTwinSister" + "@id": "bts:DaystoImaging" }, { - "@id": "bts:LegalGuardian" + "@id": "bts:EvidenceofRecurrenceType" }, { - "@id": "bts:MaleCousin" + "@id": "bts:HAARTTreatmentIndicator" }, { - "@id": "bts:MaternalAunt" + "@id": "bts:HIVViralLoad" }, { - "@id": "bts:MaternalFirstCousin" + "@id": "bts:HormonalContraceptiveUse" }, { - "@id": "bts:MaternalFirstCousinOnceRemoved" + "@id": "bts:HysterectomyMarginsInvolved" }, { - "@id": "bts:MaternalGrandfather" + "@id": "bts:HysterectomyType" }, { - "@id": "bts:MaternalGrandmother" + "@id": "bts:ImagingResult" }, { - "@id": "bts:MaternalGrandparent" + "@id": "bts:ImagingType" }, { - "@id": "bts:MaternalGreatAunt" + "@id": "bts:ImmunosuppressiveTreatmentType" }, { - "@id": "bts:MaternalGreatGrandparent" + "@id": "bts:NadirCD4Count" }, { - "@id": "bts:MaternalGreatUncle" + "@id": "bts:PregnancyOutcome" }, { - "@id": "bts:MaternalHalfBrother" + "@id": "bts:RecistTargetedRegionsNumber" }, { - "@id": "bts:MaternalHalfSibling" + "@id": "bts:RecistTargetedRegionsSum" }, { - "@id": "bts:MaternalHalfSister" + "@id": "bts:ScanTracerUsed" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Diagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "Disease diagnosis", + "rdfs:label": "Diagnosis", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Diagnosis", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:MaternalUncle" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Mother" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:Mother-in-law" + "@id": "bts:YearofDiagnosis" }, { - "@id": "bts:NaturalBrother" + "@id": "bts:PrimaryDiagnosis" }, { - "@id": "bts:NaturalChild" + "@id": "bts:SiteofResectionorBiopsy" }, { - "@id": "bts:NaturalDaughter" + "@id": "bts:TissueorOrganofOrigin" }, { - "@id": "bts:NaturalFather" + "@id": "bts:Morphology" }, { - "@id": "bts:NaturalGrandchild" + "@id": "bts:TumorGrade" }, { - "@id": "bts:NaturalGrandfather" + "@id": "bts:ProgressionorRecurrence" }, { - "@id": "bts:NaturalGrandmother" + "@id": "bts:LastKnownDiseaseStatus" }, { - "@id": "bts:NaturalGrandparent" + "@id": "bts:DaystoLastFollowup" }, { - "@id": "bts:NaturalMother" + "@id": "bts:DaystoLastKnownDiseaseStatus" }, { - "@id": "bts:NaturalParent" + "@id": "bts:MethodofDiagnosis" }, { - "@id": "bts:NaturalSibling" + "@id": "bts:PriorMalignancy" }, { - "@id": "bts:NaturalSister" + "@id": "bts:PriorTreatment" }, { - "@id": "bts:NaturalSon" + "@id": "bts:MetastasisatDiagnosis" }, { - "@id": "bts:Nephew" + "@id": "bts:MetastasisatDiagnosisSite" }, { - "@id": "bts:Niece" + "@id": "bts:FirstSymptomPriortoDiagnosis" }, { - "@id": "bts:NieceSecondDegreeRelative" + "@id": "bts:DaystoDiagnosis" }, { - "@id": "bts:Other" + "@id": "bts:PercentTumorInvasion" }, { - "@id": "bts:Parent" + "@id": "bts:ResidualDisease" }, { - "@id": "bts:PaternalAunt" + "@id": "bts:SynchronousMalignancy" }, { - "@id": "bts:PaternalFirstCousin" + "@id": "bts:TumorConfinedtoOrganofOrigin" }, { - "@id": "bts:PaternalFirstCousinOnceRemoved" + "@id": "bts:TumorFocality" }, { - "@id": "bts:PaternalGrandfather" + "@id": "bts:TumorLargestDimensionDiameter" }, { - "@id": "bts:PaternalGrandmother" + "@id": "bts:GrossTumorWeight" }, { - "@id": "bts:PaternalGrandparent" + "@id": "bts:BreslowThickness" }, { - "@id": "bts:PaternalGreatAunt" + "@id": "bts:VascularInvasionPresent" }, { - "@id": "bts:PaternalGreatGrandparent" + "@id": "bts:VascularInvasionType" }, { - "@id": "bts:PaternalGreatUncle" + "@id": "bts:AnaplasiaPresent" }, { - "@id": "bts:PaternalHalfBrother" + "@id": "bts:AnaplasiaPresentType" }, { - "@id": "bts:PaternalHalfSibling" + "@id": "bts:Laterality" }, { - "@id": "bts:PaternalHalfSister" + "@id": "bts:PerineuralInvasionPresent" }, { - "@id": "bts:PaternalUncle" + "@id": "bts:LymphaticInvasionPresent" }, { - "@id": "bts:Refused" + "@id": "bts:LymphNodesPositive" }, { - "@id": "bts:Sibling" + "@id": "bts:LymphNodesTested" }, { - "@id": "bts:Sister" + "@id": "bts:PeritonealFluidCytologicalStatus" }, { - "@id": "bts:Sister-in-law" + "@id": "bts:ClassificationofTumor" }, { - "@id": "bts:Son" + "@id": "bts:BestOverallResponse" }, { - "@id": "bts:Son-in-law" + "@id": "bts:MitoticCount" }, { - "@id": "bts:Spouse" + "@id": "bts:AJCCClinicalM" }, { - "@id": "bts:StepChild" + "@id": "bts:AJCCClinicalN" }, { - "@id": "bts:StepSibling" + "@id": "bts:AJCCClinicalStage" }, { - "@id": "bts:Stepbrother" + "@id": "bts:AJCCClinicalT" }, { - "@id": "bts:Stepdaughter" + "@id": "bts:AJCCPathologicM" }, { - "@id": "bts:Stepfather" + "@id": "bts:AJCCPathologicN" }, { - "@id": "bts:Stepmother" + "@id": "bts:AJCCPathologicStage" }, { - "@id": "bts:Stepsister" + "@id": "bts:AJCCPathologicT" }, { - "@id": "bts:Stepson" + "@id": "bts:AJCCStagingSystemEdition" }, { - "@id": "bts:TwinSibling" + "@id": "bts:CogNeuroblastomaRiskGroup" }, { - "@id": "bts:Uncle" + "@id": "bts:CogRhabdomyosarcomaRiskGroup" }, { - "@id": "bts:Unrelated" + "@id": "bts:GleasonGradeGroup" }, { - "@id": "bts:Ward" + "@id": "bts:GleasonGradeTertiary" }, { - "@id": "bts:Wife" + "@id": "bts:GleasonPatternsPercent" }, { - "@id": "bts:Unknown" + "@id": "bts:GreatestTumorDimension" }, { - "@id": "bts:NotReported" + "@id": "bts:IGCCCGStage" + }, + { + "@id": "bts:INPCGrade" + }, + { + "@id": "bts:INPCHistologicGroup" + }, + { + "@id": "bts:INRGStage" + }, + { + "@id": "bts:INSSStage" + }, + { + "@id": "bts:InternationalPrognosticIndex" + }, + { + "@id": "bts:IRSGroup" + }, + { + "@id": "bts:IRSStage" + }, + { + "@id": "bts:ISSStage" + }, + { + "@id": "bts:LymphNodeInvolvedSite" + }, + { + "@id": "bts:MarginDistance" + }, + { + "@id": "bts:MarginsInvolvedSite" + }, + { + "@id": "bts:MedulloblastomaMolecularClassification" + }, + { + "@id": "bts:MicropapillaryFeatures" + }, + { + "@id": "bts:MitosisKaryorrhexisIndex" + }, + { + "@id": "bts:NonNodalRegionalDisease" + }, + { + "@id": "bts:NonNodalTumorDeposits" + }, + { + "@id": "bts:OvarianSpecimenStatus" + }, + { + "@id": "bts:OvarianSurfaceInvolvement" + }, + { + "@id": "bts:PregnantatDiagnosis" + }, + { + "@id": "bts:PrimaryGleasonGrade" + }, + { + "@id": "bts:SecondaryGleasonGrade" + }, + { + "@id": "bts:SupratentorialLocalization" + }, + { + "@id": "bts:TumorDepth" + }, + { + "@id": "bts:WHOCNSGrade" + }, + { + "@id": "bts:WHONTEGrade" } ], - "sms:displayName": "Relationship Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeneOntologyClass", + "@id": "bts:Therapy", "@type": "rdfs:Class", - "rdfs:comment": "an ontology class that describes a functional aspect of a gene, gene prodoct or complex", - "rdfs:label": "GeneOntologyClass", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" - }, + "rdfs:comment": "Clinical therapy or treatment", + "rdfs:label": "Therapy", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:OrganismTaxon", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "OrganismTaxon", - "rdfs:subClassOf": { - "@id": "bts:OntologyClass" }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } + "sms:displayName": "Therapy", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TreatmentorTherapy" + }, + { + "@id": "bts:TreatmentType" + }, + { + "@id": "bts:TreatmentEffect" + }, + { + "@id": "bts:TreatmentOutcome" + }, + { + "@id": "bts:DaystoTreatmentEnd" + }, + { + "@id": "bts:TreatmentAnatomicSite" + }, + { + "@id": "bts:DaystoTreatmentStart" + }, + { + "@id": "bts:InitialDiseaseStatus" + }, + { + "@id": "bts:RegimenorLineofTherapy" + }, + { + "@id": "bts:TherapeuticAgents" + }, + { + "@id": "bts:TreatmentIntentType" + }, + { + "@id": "bts:ChemoConcurrenttoRadiation" + }, + { + "@id": "bts:NumberofCycles" + }, + { + "@id": "bts:ReasonTreatmentEnded" + }, + { + "@id": "bts:TreatmentArm" + }, + { + "@id": "bts:TreatmentDose" + }, + { + "@id": "bts:TreatmentDoseUnits" + }, + { + "@id": "bts:TreatmentEffectIndicator" + }, + { + "@id": "bts:TreatmentFrequency" + } + ], + "sms:validationRules": [] }, { - "@id": "bts:OrganismalEntity", + "@id": "bts:MolecularTest", "@type": "rdfs:Class", - "rdfs:comment": "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities", - "rdfs:label": "OrganismalEntity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, + "rdfs:comment": "Clinical molecular test data", + "rdfs:label": "MolecularTest", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } + }, + "sms:displayName": "Molecular Test", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:GeneSymbol" + }, + { + "@id": "bts:MolecularAnalysisMethod" + }, + { + "@id": "bts:TestResult" + }, + { + "@id": "bts:AAChange" + }, + { + "@id": "bts:Antigen" + }, + { + "@id": "bts:ClinicalBiospecimenType" + }, + { + "@id": "bts:BloodTestNormalRangeUpper" + }, + { + "@id": "bts:BloodTestNormalRangeLower" + }, + { + "@id": "bts:CellCount" + }, + { + "@id": "bts:Chromosome" + }, + { + "@id": "bts:Clonality" + }, + { + "@id": "bts:CopyNumber" + }, + { + "@id": "bts:Cytoband" + }, + { + "@id": "bts:Exon" + }, + { + "@id": "bts:HistoneFamily" + }, + { + "@id": "bts:HistoneVariant" + }, + { + "@id": "bts:Intron" + }, + { + "@id": "bts:LaboratoryTest" + }, + { + "@id": "bts:LociAbnormalCount" + }, + { + "@id": "bts:LociCount" + }, + { + "@id": "bts:Locus" + }, + { + "@id": "bts:MismatchRepairMutation" + }, + { + "@id": "bts:MolecularConsequence" + }, + { + "@id": "bts:Pathogenicity" + }, + { + "@id": "bts:Ploidy" + }, + { + "@id": "bts:SecondExon" + }, + { + "@id": "bts:SecondGeneSymbol" + }, + { + "@id": "bts:SpecializedMolecularTest" + }, + { + "@id": "bts:TestAnalyteType" + }, + { + "@id": "bts:TestUnits" + }, + { + "@id": "bts:TestValue" + }, + { + "@id": "bts:Transcript" + }, + { + "@id": "bts:VariantOrigin" + }, + { + "@id": "bts:VariantType" + }, + { + "@id": "bts:Zygosity" + } + ], + "sms:validationRules": [] }, { "@id": "bts:IndividualOrganism", "@type": "rdfs:Class", - "rdfs:comment": null, + "rdfs:comment": "TBD", "rdfs:label": "IndividualOrganism", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Case", - "@type": "rdfs:Class", - "rdfs:comment": "An individual organism that has a patient role in some clinical context.", - "rdfs:label": "Case", - "rdfs:subClassOf": { - "@id": "bts:IndividualOrganism" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PopulationOfIndividualOrganisms", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "PopulationOfIndividualOrganisms", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Biosample", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Biosample", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:DiseaseOrPhenotypicFeature", - "@type": "rdfs:Class", - "rdfs:comment": "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.", - "rdfs:label": "DiseaseOrPhenotypicFeature", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Disease", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Disease", - "rdfs:subClassOf": { - "@id": "bts:DiseaseOrPhenotypicFeature" }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } + "sms:displayName": "Individual Organism", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PhenotypicFeature", + "@id": "bts:File", "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "PhenotypicFeature", - "rdfs:subClassOf": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, + "rdfs:comment": "A type of Information Content Entity specific to OS", + "rdfs:label": "File", + "rdfs:subClassOf": [ + { + "@id": "bts:InformationContentEntity" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Environment", - "@type": "rdfs:Class", - "rdfs:comment": "A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes", - "rdfs:label": "Environment", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } + "sms:displayName": "File", + "sms:required": "sms:false", + "sms:validationRules": [] }, { "@id": "bts:InformationContentEntity", "@type": "rdfs:Class", - "rdfs:comment": "a piece of information that typically describes some piece of biology or is used as support.", + "rdfs:comment": "TBD", "rdfs:label": "InformationContentEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ConfidenceLevel", - "@type": "rdfs:Class", - "rdfs:comment": "Level of confidence in a statement", - "rdfs:label": "ConfidenceLevel", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EvidenceType", - "@type": "rdfs:Class", - "rdfs:comment": "Class of evidence that supports an association", - "rdfs:label": "EvidenceType", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Publication", - "@type": "rdfs:Class", - "rdfs:comment": "Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.", - "rdfs:label": "Publication", - "rdfs:subClassOf": { - "@id": "bts:InformationContentEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:MolecularEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A gene, gene product, small molecule or macromolecule (including protein complex)", - "rdfs:label": "MolecularEntity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ChemicalSubstance", - "@type": "rdfs:Class", - "rdfs:comment": "May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part", - "rdfs:label": "ChemicalSubstance", - "rdfs:subClassOf": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Drug", - "@type": "rdfs:Class", - "rdfs:comment": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", - "rdfs:label": "Drug", - "rdfs:subClassOf": { - "@id": "bts:ChemicalSubstance" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Metabolite", - "@type": "rdfs:Class", - "rdfs:comment": "Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.", - "rdfs:label": "Metabolite", - "rdfs:subClassOf": { - "@id": "bts:ChemicalSubstance" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:AnatomicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "A subcellular location, cell type or gross anatomical part", - "rdfs:label": "AnatomicalEntity", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:LifeStage", - "@type": "rdfs:Class", - "rdfs:comment": "A stage of development or growth of an organism, including post-natal adult stages", - "rdfs:label": "LifeStage", - "rdfs:subClassOf": { - "@id": "bts:OrganismalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:PlanetaryEntity", - "@type": "rdfs:Class", - "rdfs:comment": "Any entity or process that exists at the level of the whole planet", - "rdfs:label": "PlanetaryEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EnvironmentalProcess", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "EnvironmentalProcess", - "rdfs:subClassOf": { - "@id": "bts:PlanetaryEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:EnvironmentalFeature", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "EnvironmentalFeature", - "rdfs:subClassOf": { - "@id": "bts:PlanetaryEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalEntity", - "@type": "rdfs:Class", - "rdfs:comment": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", - "rdfs:label": "ClinicalEntity", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalTrial", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "ClinicalTrial", - "rdfs:subClassOf": { - "@id": "bts:ClinicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ClinicalIntervention", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "ClinicalIntervention", - "rdfs:subClassOf": { - "@id": "bts:ClinicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Device", - "@type": "rdfs:Class", - "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", - "rdfs:label": "Device", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GenomicEntity", - "@type": "rdfs:Class", - "rdfs:comment": "an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)", - "rdfs:label": "GenomicEntity", - "rdfs:subClassOf": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Genome", - "@type": "rdfs:Class", - "rdfs:comment": "A genome is the sum of genetic material within a cell or virion.", - "rdfs:label": "Genome", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Transcript", - "@type": "rdfs:Class", - "rdfs:comment": "An RNA synthesized on a DNA or RNA template by an RNA polymerase", - "rdfs:label": "Transcript", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Exon", - "@type": "rdfs:Class", - "rdfs:comment": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing", - "rdfs:label": "Exon", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:CodingSequence", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "CodingSequence", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:MacromolecularMachine", - "@type": "rdfs:Class", - "rdfs:comment": "A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.", - "rdfs:label": "MacromolecularMachine", - "rdfs:subClassOf": { - "@id": "bts:GenomicEntity" - }, + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneOrGeneProduct", - "@type": "rdfs:Class", - "rdfs:comment": "a union of genes or gene products. Frequently an identifier for one will be used as proxy for another", - "rdfs:label": "GeneOrGeneProduct", - "rdfs:subClassOf": { - "@id": "bts:MacromolecularMachine" }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } + "sms:displayName": "Information Content Entity", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:Gene", + "@id": "bts:Filename", "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Gene", - "rdfs:subClassOf": { - "@id": "bts:GeneOrGeneProduct" - }, + "rdfs:comment": "Name of a file", + "rdfs:label": "Filename", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneProduct", - "@type": "rdfs:Class", - "rdfs:comment": "The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules", - "rdfs:label": "GeneProduct", - "rdfs:subClassOf": { - "@id": "bts:GeneOrGeneProduct" }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } + "sms:displayName": "Filename", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex search ^.+\\/\\S*$" + ] }, { - "@id": "bts:Protein", + "@id": "bts:FileFormat", "@type": "rdfs:Class", - "rdfs:comment": "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA", - "rdfs:label": "Protein", - "rdfs:subClassOf": { - "@id": "bts:GeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GeneProductIsoform", - "@type": "rdfs:Class", - "rdfs:comment": "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.", - "rdfs:label": "GeneProductIsoform", - "rdfs:subClassOf": { - "@id": "bts:GeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ProteinIsoform", - "@type": "rdfs:Class", - "rdfs:comment": "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/", - "rdfs:label": "ProteinIsoform", - "rdfs:subClassOf": { - "@id": "bts:Protein" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:RnaProduct", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "RnaProduct", - "rdfs:subClassOf": { - "@id": "bts:GeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:RnaProductIsoform", - "@type": "rdfs:Class", - "rdfs:comment": "Represents a protein that is a specific isoform of the canonical or reference RNA", - "rdfs:label": "RnaProductIsoform", - "rdfs:subClassOf": { - "@id": "bts:RnaProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:NoncodingRnaProduct", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "NoncodingRnaProduct", - "rdfs:subClassOf": { - "@id": "bts:RnaProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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"@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Occurrent", - "@type": "rdfs:Class", - "rdfs:comment": "A processual entity", - "rdfs:label": "Occurrent", - "rdfs:subClassOf": { - "@id": "schema:Thing" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:BiologicalProcessOrActivity", - "@type": "rdfs:Class", - "rdfs:comment": "Either an individual molecular activity, or a collection of causally connected molecular activities", - "rdfs:label": "BiologicalProcessOrActivity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:MolecularActivity", - "@type": "rdfs:Class", - "rdfs:comment": "An execution of a molecular function carried out by a gene product or macromolecular complex.", - "rdfs:label": "MolecularActivity", - "rdfs:subClassOf": { - "@id": "bts:BiologicalProcessOrActivity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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"@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:Cell", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "Cell", - "rdfs:subClassOf": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:CellLine", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "CellLine", - "rdfs:subClassOf": { - "@id": "bts:Biosample" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:GrossAnatomicalStructure", - "@type": "rdfs:Class", - "rdfs:comment": null, - "rdfs:label": "GrossAnatomicalStructure", - "rdfs:subClassOf": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - } - }, - { - "@id": "bts:ensembl", - "@type": "rdf:Property", - "rdfs:comment": "Ensembl ID for gene, protein or transcript", - "rdfs:label": "ensembl", - "schema:domainIncludes": [ - { - "@id": "bts:Transcript" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:hgnc", - "@type": "rdf:Property", - "rdfs:comment": "HGNC ID for gene", - "rdfs:label": "hgnc", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:entrez", - "@type": "rdf:Property", - "rdfs:comment": "Entrez ID for gene", - "rdfs:label": "entrez", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:refseq", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "refseq", - "schema:domainIncludes": [ - { - "@id": "bts:Transcript" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:omim", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "omim", - "schema:domainIncludes": [ - { - "@id": "bts:Disease" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Integer" - } - }, - { - "@id": "bts:umls", - "@type": "rdf:Property", - "rdfs:comment": "Refseq ID for gene, protein or transcript", - "rdfs:label": "umls", - "schema:domainIncludes": { - "@id": "bts:Disease" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "schema:Text" - } - }, - { - "@id": "bts:homologousTo", - "@type": "rdf:Property", - "rdfs:comment": "Shared ancestry between protein or gene", - "rdfs:label": "homologousTo", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - 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"@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesAbundanceOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest", - "rdfs:label": "decreasesAbundanceOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest", - "rdfs:label": "affectsActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest", - "rdfs:label": "increasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesActivityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest", - "rdfs:label": "decreasesActivityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest", - "rdfs:label": "affectsExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest", - "rdfs:label": "increasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesExpressionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest", - "rdfs:label": "decreasesExpressionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other ", - "rdfs:label": "affectsFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other ", - "rdfs:label": "increasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesFoldingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other ", - "rdfs:label": "decreasesFoldingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest", - "rdfs:label": "affectsLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest", - "rdfs:label": "increasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesLocalizationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest", - "rdfs:label": "decreasesLocalizationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest", - "rdfs:label": "affectsMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "increasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMetabolicProcessingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest", - "rdfs:label": "decreasesMetabolicProcessingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "affectsMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "increasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesMolecularModificationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)", - "rdfs:label": "decreasesMolecularModificationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other", - "rdfs:label": "affectsSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other", - "rdfs:label": "increasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSynthesisOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other", - "rdfs:label": "decreasesSynthesisOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest", - "rdfs:label": "affectsDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest", - "rdfs:label": "increasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesDegradationOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest", - "rdfs:label": "decreasesDegradationOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "affectsMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:increasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "increasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:decreasesMutationRateOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest", - "rdfs:label": "decreasesMutationRateOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GenomicEntity" - } - }, - { - "@id": "bts:affectsResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "affectsResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "increasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesResponseTo", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other", - "rdfs:label": "decreasesResponseTo", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA", - "rdfs:label": "affectsSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:increasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA", - "rdfs:label": "increasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:decreasesSplicingOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA", - "rdfs:label": "decreasesSplicingOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Transcript" - } - }, - { - "@id": "bts:affectsStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest", - "rdfs:label": "affectsStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest", - "rdfs:label": "increasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesStabilityOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest", - "rdfs:label": "decreasesStabilityOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "affectsTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "increasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesTransportOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest", - "rdfs:label": "decreasesTransportOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "affectsSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "increasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesSecretionOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ", - "rdfs:label": "decreasesSecretionOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:affectsUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "affectsUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:increasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "increasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:decreasesUptakeOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ", - "rdfs:label": "decreasesUptakeOf", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:regulates,ProcessToProcess", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,ProcessToProcess", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:regulates,EntityToEntity", - "@type": "rdf:Property", - "rdfs:comment": null, - "rdfs:label": "regulates,EntityToEntity", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasGeneProduct", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a transcribed and/or translated product generated from it", - "rdfs:label": "hasGeneProduct", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneProduct" - } - }, - { - "@id": "bts:inPathwayWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of in the same biological pathway", - "rdfs:label": "inPathwayWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inComplexWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex", - "rdfs:label": "inComplexWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:inCellPopulationWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between two genes or gene products that are expressed in the same cell type or population ", - "rdfs:label": "inCellPopulationWith", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:geneAssociatedWithCondition", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with", - "rdfs:label": "geneAssociatedWithCondition", - "schema:domainIncludes": { - "@id": "bts:Gene" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:treats", - "@type": "rdf:Property", - "rdfs:comment": "holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat", - "rdfs:label": "treats", - "schema:domainIncludes": { - "@id": "bts:Treatment" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:correlatedWith", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "correlatedWith", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:hasBiomarker", - "@type": "rdf:Property", - "rdfs:comment": "holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "hasBiomarker", - "schema:domainIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:MolecularEntity" - } - }, - { - "@id": "bts:biomarkerFor", - "@type": "rdf:Property", - "rdfs:comment": "holds between a measurable molecular entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.", - "rdfs:label": "biomarkerFor", - "schema:domainIncludes": { - "@id": "bts:MolecularEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:expressedIn", - "@type": "rdf:Property", - "rdfs:comment": "holds between a gene or gene product and an anatomical entity in which it is expressed", - "rdfs:label": "expressedIn", - "schema:domainIncludes": { - "@id": "bts:GeneOrGeneProduct" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:AnatomicalEntity" - } - }, - { - "@id": "bts:expresses", - "@type": "rdf:Property", - "rdfs:comment": "holds between an anatomical entity and gene or gene product that is expressed there", - "rdfs:label": "expresses", - "schema:domainIncludes": { - "@id": "bts:AnatomicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:GeneOrGeneProduct" - } - }, - { - "@id": "bts:hasPhenotype", - "@type": "rdf:Property", - "rdfs:comment": "holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). ", - "rdfs:label": "hasPhenotype", - "schema:domainIncludes": { - "@id": "bts:BiologicalEntity" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:DiseaseOrPhenotypicFeature" - } - }, - { - "@id": "bts:precedes", - "@type": "rdf:Property", - "rdfs:comment": "holds between two processes, where one completes before the other begins", - "rdfs:label": "precedes", - "schema:domainIncludes": { - "@id": "bts:Occurrent" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:Occurrent" - } - }, - { - "@id": "bts:subclassOf", - "@type": "rdf:Property", - "rdfs:comment": "holds between two classes where the domain class is a specialization of the range class", - "rdfs:label": "subclassOf", - "schema:domainIncludes": { - "@id": "bts:OntologyClass" - }, - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": { - "@id": "bts:OntologyClass" - } - }, - { - "@id": "bts:Assay", - "@type": "rdfs:Class", - "rdfs:comment": "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]", - "rdfs:label": "Assay", - "rdfs:subClassOf": [ - { - "@id": "schema:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Assay", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Device", - "@type": "rdfs:Class", - "rdfs:comment": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", - "rdfs:label": "Device", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Device", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Sequencing", - "@type": "rdfs:Class", - "rdfs:comment": "Module for next generation sequencing assays", - "rdfs:label": "Sequencing", - "rdfs:subClassOf": [ - { - "@id": "bts:Assay" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Component", - "@type": "rdfs:Class", - "rdfs:comment": "Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.", - "rdfs:label": "Component", - "rdfs:subClassOf": [ - { - "@id": "schema:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Component", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Patient", - "@type": "rdfs:Class", - "rdfs:comment": "HTAN patient", - "rdfs:label": "Patient", - "rdfs:subClassOf": [ - { - "@id": "bts:IndividualOrganism" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Patient", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:Demographics" - }, - { - "@id": "bts:FamilyHistory" - }, - { - "@id": "bts:Exposure" - }, - { - "@id": "bts:FollowUp" - }, - { - "@id": "bts:Diagnosis" - }, - { - "@id": "bts:Therapy" - }, - { - "@id": "bts:MolecularTest" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:HTANParticipantID" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:File", - "@type": "rdfs:Class", - "rdfs:comment": "A type of Information Content Entity specific to OS", - "rdfs:label": "File", - "rdfs:subClassOf": [ - { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "File", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Filename", - "@type": "rdfs:Class", - "rdfs:comment": "Name of a file", - "rdfs:label": "Filename", - "rdfs:subClassOf": [ - { - "@id": "schema:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Filename", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex search ^.+\\/\\S*$" - ] - }, - { - "@id": "bts:FileFormat", - "@type": "rdfs:Class", - "rdfs:comment": "Format of a file (e.g. txt, csv, fastq, bam, etc.)", - "rdfs:label": "FileFormat", - "rdfs:subClassOf": [ - { - "@id": "schema:Thing" - } - ], + "rdfs:comment": "Format of a file (e.g. txt, csv, fastq, bam, etc.)", + "rdfs:label": "FileFormat", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, @@ -2769,2864 +1295,1617 @@ "sms:validationRules": [] }, { - "@id": "bts:Checksum", + "@id": "bts:Hdf5", "@type": "rdfs:Class", - "rdfs:comment": "MD5 checksum of the BAM file", - "rdfs:label": "Checksum", + "rdfs:comment": "TBD", + "rdfs:label": "Hdf5", "rdfs:subClassOf": [ { - "@id": "bts:InformationContentEntity" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Checksum", - "sms:required": "sms:true", + "sms:displayName": "hdf5", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANDataFileID", + "@id": "bts:Bedgraph", "@type": "rdfs:Class", - "rdfs:comment": "Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANDataFileID", + "rdfs:comment": "TBD", + "rdfs:label": "Bedgraph", "rdfs:subClassOf": [ { - "@id": "bts:File" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "bedgraph", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANParticipantID", + "@id": "bts:Idx", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )", - "rdfs:label": "HTANParticipantID", + "rdfs:comment": "TBD", + "rdfs:label": "Idx", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Participant ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))$ warning" - ] + "sms:displayName": "idx", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANBiospecimenID", + "@id": "bts:Idat", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", - "rdfs:label": "HTANBiospecimenID", + "rdfs:comment": "TBD", + "rdfs:label": "Idat", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Biospecimen ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" - ] + "sms:displayName": "idat", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANParentID", + "@id": "bts:Bam", "@type": "rdfs:Class", - "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", - "rdfs:label": "HTANParentID", + "rdfs:comment": "TBD", + "rdfs:label": "Bam", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent ID", - "sms:required": "sms:true", + "sms:displayName": "bam", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HTANParentBiospecimenID", + "@id": "bts:Bai", "@type": "rdfs:Class", - "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", - "rdfs:label": "HTANParentBiospecimenID", + "rdfs:comment": "TBD", + "rdfs:label": "Bai", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Parent Biospecimen ID", - 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String", - "rdfs:label": "Slide-seqWorkflowType", + "rdfs:comment": "TBD", + "rdfs:label": "Pkc", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:FileFormat" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Workflow Type", - "sms:required": "sms:true", + "sms:displayName": "pkc", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqWorkflowParameterDescription", + "@id": "bts:Checksum", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the Slide-seq workflow. String", - "rdfs:label": "Slide-seqWorkflowParameterDescription", + "rdfs:comment": "MD5 checksum of the BAM file", + "rdfs:label": "Checksum", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:InformationContentEntity" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Slide-seq Workflow Parameter Description", + "sms:displayName": "Checksum", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Slide-seqBeadFileType", + "@id": "bts:HTANDataFileID", "@type": "rdfs:Class", - "rdfs:comment": "The type of Level 3 file submitted as part of the Slide-seq workflow.", - "rdfs:label": "Slide-seqBeadFileType", + "rdfs:comment": "Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)", + "rdfs:label": "HTANDataFileID", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:File" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MatrixFeatures" - }, - { - "@id": "bts:MatrixBarcodes" - }, - { - "@id": "bts:AllBeadLocations" - }, - { - "@id": "bts:AllBeadBarcodes" - }, - { - "@id": "bts:MatchedBeadBarcodes" - }, - { - "@id": "bts:MatchedBeadLocations" - }, + "sms:displayName": "HTAN Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" + ] + }, + { + "@id": "bts:HTANBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)", + "rdfs:label": "HTANBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:Biospecimen" } ], - "sms:displayName": "Slide-seq Bead File Type", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Biospecimen ID", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\\d*|0000))_([0-9]\\d*|0000)$ warning" + ] }, { - "@id": "bts:BulkRNA-seqLevel1", + "@id": "bts:Biospecimen", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq [EFO_0003738]", - "rdfs:label": "BulkRNA-seqLevel1", + "rdfs:comment": "HTAN biological entity; this can be tissue, blood, analyte and subsamples of those", + "rdfs:label": "Biospecimen", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biosample" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 1", + "sms:displayName": "Biospecimen", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -5634,188 +2913,191 @@ "@id": "bts:Component" }, { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentBiospecimenID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:LibraryLayout" - }, - { - "@id": "bts:ReadIndicator" - }, - { - "@id": "bts:NucleicAcidSource" - }, - { - "@id": "bts:Micro-regionSeqPlatform" - }, - { - "@id": "bts:ROITag" - }, - { - "@id": "bts:SequencingPlatform" - }, - { - "@id": "bts:SequencingBatchID" - }, - { - "@id": "bts:ReadLength" - }, - { - "@id": "bts:LibrarySelectionMethod" - }, - { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:HTANBiospecimenID" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:SourceHTANBiospecimenID" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:HTANParentID" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:SpikeIn" + "@id": "bts:CollectionDaysfromIndex" }, { - "@id": "bts:AdapterName" + "@id": "bts:AdjacentBiospecimenIDs" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:BiospecimenType" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:AcquisitionMethodType" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:FixativeType" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:StorageMethod" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:ProcessingDaysfromIndex" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:SiteDataSource" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:CollectionMedia" }, { - "@id": "bts:LaneNumber" + "@id": "bts:MountingMedium" }, { - "@id": "bts:LibraryStrand" + "@id": "bts:ProcessingLocation" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:HistologyAssessmentBy" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:HistologyAssessmentMedium" }, { - "@id": "bts:TargetDepth" + "@id": "bts:PreinvasiveMorphology" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:TumorInfiltratingLymphocytes" }, { - "@id": "bts:TranscriptIntegrityNumber" + "@id": "bts:DegreeofDysplasia" }, { - "@id": "bts:RIN" + "@id": "bts:DysplasiaFraction" }, { - "@id": "bts:DV200" + "@id": "bts:NumberProliferatingCells" }, { - "@id": "bts:AdapterContent" + "@id": "bts:PercentEosinophilInfiltration" }, { - "@id": "bts:BasicStatistics" + "@id": "bts:PercentGranulocyteInfiltration" }, { - "@id": "bts:Encoding" + "@id": "bts:PercentInflamInfiltration" }, { - "@id": "bts:KmerContent" + "@id": "bts:PercentLymphocyteInfiltration" }, { - "@id": "bts:OverrepresentedSequences" + "@id": "bts:PercentMonocyteInfiltration" }, { - "@id": "bts:PerBaseNContent" + "@id": "bts:PercentNecrosis" }, { - "@id": "bts:PerBaseSequenceContent" + "@id": "bts:PercentNeutrophilInfiltration" }, { - "@id": "bts:PerBaseSequenceQuality" + "@id": "bts:PercentNormalCells" }, { - "@id": "bts:PerSequenceGCContent" + "@id": "bts:PercentStromalCells" }, { - "@id": "bts:PerSequenceQualityScore" + "@id": "bts:PercentTumorCells" }, { - "@id": "bts:PerTileSequenceQuality" + "@id": "bts:PercentTumorNuclei" }, { - "@id": "bts:PercentGCContent" + "@id": "bts:FiducialMarker" }, { - "@id": "bts:SequenceDuplicationLevels" + "@id": "bts:SlicingMethod" }, { - "@id": "bts:SequenceLengthDistribution" + "@id": "bts:LysisBuffer" }, { - "@id": "bts:TotalReads" - }, + "@id": "bts:MethodofNucleicAcidIsolation" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.", + "rdfs:label": "HTANParentID", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowType" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentBiospecimenID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated", + "rdfs:label": "HTANParentBiospecimenID", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowVersion" - }, + "@id": "bts:Biospecimen" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Biospecimen ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:HTANParentDataFileID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Data File Identifier indicating the file(s) from which these files were derived", + "rdfs:label": "HTANParentDataFileID", + "rdfs:subClassOf": [ { - "@id": "bts:QCWorkflowLink" + "@id": "bts:File" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTAN Parent Data File ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BulkRNA-seqLevel2", + "@id": "bts:ClinicalDataTier2", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq alignment protocol description", - "rdfs:label": "BulkRNA-seqLevel2", + "rdfs:comment": "Tier 2 Cancer Data", + "rdfs:label": "ClinicalDataTier2", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk RNA-seq Level 2", + "sms:displayName": "Clinical Data Tier 2", "sms:required": "sms:false", "sms:requiresComponent": [ { - "@id": "bts:BulkRNA-seqLevel1" + "@id": "bts:Patient" } ], "sms:requiresDependency": [ @@ -5823,2417 +3105,2370 @@ "@id": "bts:Component" }, { - "@id": "bts:Filename" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:FileFormat" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:AlignmentWorkflowUrl" + "@id": "bts:SentinelLymphNodeCount" }, { - "@id": "bts:AlignmentWorkflowType" + "@id": "bts:SentinelNodePositiveAssessmentCount" }, { - "@id": "bts:GenomicReference" + "@id": "bts:TumorExtranodalExtensionIndicator" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:SatelliteMetastasisPresentIndicator" }, { - "@id": "bts:IndexFileName" + "@id": "bts:OtherBiopsyResectionSite" }, { - "@id": "bts:AverageBaseQuality" + "@id": "bts:ExtentofTumorResection" }, { - "@id": "bts:AverageInsertSize" + "@id": "bts:PrecancerousConditionType" }, { - "@id": "bts:AverageReadLength" + "@id": "bts:PriorSitesofRadiation" }, { - "@id": "bts:Contamination" + "@id": "bts:Immunosuppression" }, { - "@id": "bts:ContaminationError" + "@id": "bts:ConcomitantMedicationReceivedType" }, { - "@id": "bts:MeanCoverage" + "@id": "bts:FamilyMemberVitalStatusIndicator" }, { - "@id": "bts:MSIWorkflowLink" + "@id": "bts:COVID19OccurrenceIndicator" }, { - "@id": "bts:MSIScore" + "@id": "bts:COVID19CurrentStatus" }, { - "@id": "bts:MSIStatus" + "@id": "bts:COVID19PositiveLabTestIndicator" }, { - "@id": "bts:PairsOnDiffCHR" + "@id": "bts:COVID19AntibodyTesting" }, { - "@id": "bts:TotalReads" + "@id": "bts:COVID19ComplicationsSeverity" }, { - "@id": "bts:TotalUniquelyMapped" + "@id": "bts:COVID19CancerTreatmentFollowup" }, { - "@id": "bts:TotalUnmappedreads" + "@id": "bts:Ecigvapeuse" }, { - "@id": "bts:ProportionReadsDuplicated" + "@id": "bts:Ecigvape30dayusenum" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:Ecigvapetimesperday" }, { - "@id": "bts:ProportionTargetsNoCoverage" + "@id": "bts:Typeofsmokeexposurecumulativeyears" }, { - "@id": "bts:ProportionBaseMismatch" + "@id": "bts:Chewingtobaccodailyusecount" }, { - "@id": "bts:ShortReads" + "@id": "bts:Secondhandsmokeexposureyears" }, { - "@id": "bts:Islowestlevel" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:BulkRNA-seqLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA-seq gene expression matrices", - "rdfs:label": "BulkRNA-seqLevel3", - "rdfs:subClassOf": [ - { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk RNA-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:KnownGeneticPredispositionMutation" + }, { - "@id": "bts:BulkRNA-seqLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:HereditaryCancerPredispositionSyndrome" + }, { - "@id": "bts:Component" + "@id": "bts:CancerAssociatedGeneMutations" }, { - "@id": "bts:Filename" + "@id": "bts:MutationalSignatures" }, { - "@id": "bts:FileFormat" + "@id": "bts:MismatchRepairSystemStatus" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:LabTestsforMMRStatus" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:ModeofCancerDetection" }, { - "@id": "bts:PseudoAlignmentUsed" + "@id": "bts:EducationLevel" }, { - "@id": "bts:DataCategory" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:ExpressionUnits" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:MatrixType" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:FusionGeneDetected" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:FusionGeneIdentity" + "@id": "bts:CancerIncidenceLocation" } ], "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel1", + "@id": "bts:TimepointLabel", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing raw files", - "rdfs:label": "BulkWESLevel1", + "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": [ { - "@id": "bts:Sequencing" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 1", + "sms:displayName": "Timepoint Label", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@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:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Start Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:StopDaysfromIndex", + "@type": "rdfs:Class", + "rdfs:comment": "Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'", + "rdfs:label": "StopDaysfromIndex", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stop Days from Index", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:SentinelLymphNodeCount", + "@type": "rdfs:Class", + "rdfs:comment": "Numeric count of sentinel lymph nodes.", + "rdfs:label": "SentinelLymphNodeCount", + "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Diagnosis" } ], - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Lymph Node Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SentinelNodePositiveAssessmentCount", + "@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:subClassOf": [ { - "@id": "bts:Component" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sentinel Node Positive Assessment Count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TumorExtranodalExtensionIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "The indicator to determine extranodal involvement or extent of the disease.", + "rdfs:label": "TumorExtranodalExtensionIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Filename" - }, + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:FileFormat" + "@id": "bts:Absent" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Indeterminate" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:NO" }, { - "@id": "bts:SequencingBatchID" + "@id": "bts:YES" }, { - "@id": "bts:LibraryLayout" + "@id": "bts:Nosourcedocumentation" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:Notapplicable" }, { - "@id": "bts:LibrarySelectionMethod" + "@id": "bts:Notsampledordissected" }, { - "@id": "bts:ReadLength" + "@id": "bts:Present" }, { - "@id": "bts:TargetCaptureKit" + "@id": "bts:Present-extensive" }, { - "@id": "bts:LibraryPreparationKitName" + "@id": "bts:Present-minimal" }, { - "@id": "bts:LibraryPreparationKitVendor" + "@id": "bts:UNKNOWN" }, { - "@id": "bts:LibraryPreparationKitVersion" + "@id": "bts:Unspecified" + } + ], + "sms:displayName": "Tumor Extranodal Extension Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SatelliteMetastasisPresentIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no indicator to ask if intransit metastases or satellite lesions are present.", + "rdfs:label": "SatelliteMetastasisPresentIndicator", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:No" }, { - "@id": "bts:AdapterName" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Satellite Metastasis Present Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@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 HTAN Clinical Data Tier 1)", + "rdfs:label": "OtherBiopsyResectionSite", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Other Biopsy Resection Site", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ExtentofTumorResection", + "@type": "rdfs:Class", + "rdfs:comment": "The degree to which the lesion has been cut out, or resected.", + "rdfs:label": "ExtentofTumorResection", + "rdfs:subClassOf": [ + { + "@id": "bts:Diagnosis" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GrossTotalResection" }, { - "@id": "bts:AdapterSequence" + "@id": "bts:OpenBiopsy" }, { - "@id": "bts:BaseCallerName" + "@id": "bts:SubtotalResection" }, { - "@id": "bts:BaseCallerVersion" + "@id": "bts:ExtensiveSubtotal" }, { - "@id": "bts:FlowCellBarcode" + "@id": "bts:Minor" }, { - "@id": "bts:FragmentMaximumLength" + "@id": "bts:Optimaldebulking" }, { - "@id": "bts:FragmentMeanLength" + "@id": "bts:Other" }, { - "@id": "bts:FragmentMinimumLength" + "@id": "bts:Partialdebulking" }, { - "@id": "bts:FragmentStandardDeviationLength" + "@id": "bts:Segmental" }, { - "@id": "bts:LaneNumber" + "@id": "bts:Suboptimal" }, { - "@id": "bts:MultiplexBarcode" + "@id": "bts:Suboptimaldebulking" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:NTR" }, { - "@id": "bts:SizeSelectionRange" + "@id": "bts:Unknown" }, { - "@id": "bts:TargetDepth" + "@id": "bts:NotReported" }, { - "@id": "bts:ToTrimAdapterSequence" + "@id": "bts:NotApplicable" } ], + "sms:displayName": "Extent of Tumor Resection", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkWESLevel2", + "@id": "bts:PrecancerousConditionType", "@type": "rdfs:Class", - "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", - "rdfs:label": "BulkWESLevel2", + "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).", + "rdfs:label": "PrecancerousConditionType", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bulk WES Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:BulkWESLevel1" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Filename" - }, - { - "@id": "bts:FileFormat" - }, - { - "@id": "bts:HTANParentDataFileID" - }, - { - "@id": "bts:HTANDataFileID" - }, - { - "@id": "bts:AlignmentWorkflowType" - }, - { - 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"@id": "bts:PixelsBigEndian" + "@id": "bts:Yes" }, { - "@id": "bts:PlaneCount" + "@id": "bts:No" }, { - "@id": "bts:SizeC" + "@id": "bts:Unknown" }, { - "@id": "bts:SizeT" + "@id": "bts:NotApplicable" }, { - "@id": "bts:SizeX" + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Occurrence Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CurrentStatus", + "@type": "rdfs:Class", + "rdfs:comment": "The patient's current COVID-19 status of sign or symptom events or interventions", + "rdfs:label": "COVID19CurrentStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Patientcurrentlyhassymptoms" }, { - "@id": "bts:SizeY" + "@id": "bts:Patienthadsymptomsbutnowisfullyrecovered" }, { - "@id": "bts:SizeZ" + "@id": "bts:PatientneverhadanysymptomsofCOVID-19" }, { - "@id": "bts:PixelType" + "@id": "bts:StatusunknownduetogeneralCOVID-19relatedtravelrestrictions" }, { - "@id": "bts:MERFISHPositionsFile" + "@id": "bts:Statusunknownduetolackofdisease/tumorassessmentduetoCOVID-19diagnosis" }, { - "@id": "bts:MERFISHCodebookFile" + "@id": "bts:Statusunknownduetootherreasons" } ], + "sms:displayName": "COVID19 Current Status", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHPositionsFile", + "@id": "bts:COVID19PositiveLabTestIndicator", "@type": "rdfs:Class", - "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", - "rdfs:label": "MERFISHPositionsFile", + "rdfs:comment": "The indicator that describes whether or not there was a COVID-19 positive test result.", + "rdfs:label": "COVID19PositiveLabTestIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Positions File", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Positive Lab Test Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MERFISHCodebookFile", + "@id": "bts:COVID19AntibodyTesting", "@type": "rdfs:Class", - "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", - "rdfs:label": "MERFISHCodebookFile", + "rdfs:comment": "Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.", + "rdfs:label": "COVID19AntibodyTesting", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MERFISH Codebook File", + "schema:rangeIncludes": [ + { + "@id": "bts:SARS-CoV-2IgMantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgGantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgG/IgMantibodypositive" + }, + { + "@id": "bts:SARS-CoV-2IgMantibodynegative" + }, + { + "@id": "bts:SARS-CoV-2IgGantibodynegative" + }, + { + "@id": "bts:SARS-CoV-2IgG/IgMantibodynegative" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotDone" + } + ], + "sms:displayName": "COVID19 Antibody Testing", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Segmentation", + "@id": "bts:COVID19ComplicationsSeverity", "@type": "rdfs:Class", - "rdfs:comment": "Object segmentations", - "rdfs:label": "ImagingLevel3Segmentation", + "rdfs:comment": "Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.", + "rdfs:label": "COVID19ComplicationsSeverity", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Segmentation", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "schema:rangeIncludes": [ { - "@id": "bts:ImagingLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Cardiaccomplications" + }, { - "@id": "bts:Component" + "@id": "bts:Pulmonarycomplications" }, { - "@id": "bts:Filename" + "@id": "bts:Systemiccomplications" }, { - "@id": "bts:FileFormat" + "@id": "bts:Other" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:NotApplicable" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "COVID19 Complications Severity", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:COVID19CancerTreatmentFollowup", + "@type": "rdfs:Class", + "rdfs:comment": "Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder", + "rdfs:label": "COVID19CancerTreatmentFollowup", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:No" }, { - "@id": "bts:Parameterfile" + "@id": "bts:Unknown" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "COVID19 Cancer Treatment Followup", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvapeuse", + "@type": "rdfs:Class", + "rdfs:comment": "Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)", + "rdfs:label": "Ecigvapeuse", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Current" }, { - "@id": "bts:CommitSHA" + "@id": "bts:Former" }, { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Never" }, { - "@id": "bts:NumberofObjects" + "@id": "bts:Unknown" } ], + "sms:displayName": "Ecig vape use", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImagingLevel3Image", + "@id": "bts:Ecigvape30dayusenum", "@type": "rdfs:Class", - "rdfs:comment": "Quality controlled imaging data", - "rdfs:label": "ImagingLevel3Image", + "rdfs:comment": "Number of days e-cigarettes or vaping device was used in the last 30 days", + "rdfs:label": "Ecigvape30dayusenum", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Imaging Level 3 Image", + "sms:displayName": "Ecig vape 30 day use num", "sms:required": "sms:false", - "sms:requiresComponent": [ + "sms:validationRules": [] + }, + { + "@id": "bts:Ecigvapetimesperday", + "@type": "rdfs:Class", + "rdfs:comment": "e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)", + "rdfs:label": "Ecigvapetimesperday", + "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel3Channels" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ecig vape times per day", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Typeofsmokeexposurecumulativeyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's specific type of smoke exposure", + "rdfs:label": "Typeofsmokeexposurecumulativeyears", + "rdfs:subClassOf": [ { - "@id": "bts:ImagingLevel2" + "@id": "bts:Exposure" } ], - "sms:requiresDependency": [ + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Type of smoke exposure cumulative years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Chewingtobaccodailyusecount", + "@type": "rdfs:Class", + "rdfs:comment": "The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.", + "rdfs:label": "Chewingtobaccodailyusecount", + "rdfs:subClassOf": [ { - "@id": "bts:Component" + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Chewing tobacco daily use count", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Secondhandsmokeexposureyears", + "@type": "rdfs:Class", + "rdfs:comment": "The number of cumulative years of the patient's exposure to second-hand cigarette smoke", + "rdfs:label": "Secondhandsmokeexposureyears", + "rdfs:subClassOf": [ + { + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Second hand smoke exposure years", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KnownGeneticPredispositionMutation", + "@type": "rdfs:Class", + "rdfs:comment": "A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.", + "rdfs:label": "KnownGeneticPredispositionMutation", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" }, { - "@id": "bts:Filename" + "@id": "bts:No" }, { - "@id": "bts:FileFormat" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Known Genetic Predisposition Mutation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HereditaryCancerPredispositionSyndrome", + "@type": "rdfs:Class", + "rdfs:comment": "History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.", + "rdfs:label": "HereditaryCancerPredispositionSyndrome", + "rdfs:subClassOf": [ + { + "@id": "bts:FamilyHistory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Alpha-1antitrypsin" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Attenuatedfamilialadenomatouspolyposis" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:BAP1mutantdisease" }, { - "@id": "bts:HTANParentChannelMetadataID" + "@id": "bts:Beckwith-Wiedemann" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Biliarydisorder" }, { - "@id": "bts:ImagingAssayType" + "@id": "bts:Birt-Hogg-Dubesyndrome" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Carneycomplex" }, { - "@id": "bts:SoftwareandVersion" + "@id": "bts:Cirrhosisunknownetiology" }, { - "@id": "bts:Microscope" + "@id": "bts:Constitutionalmismatchrepairdeficiency" }, { - "@id": "bts:Objective" + "@id": "bts:Familialadenomatouspolyposis" }, { - "@id": "bts:NominalMagnification" + "@id": "bts:Familialgastrointestinalstromaltumor" }, { - "@id": "bts:LensNA" + "@id": "bts:Familialpancreaticcancer" }, { - "@id": "bts:WorkingDistance" + "@id": "bts:Familialprostatecancer" }, { - "@id": "bts:Immersion" + "@id": "bts:Familialrenalcancer" }, { - "@id": "bts:Pyramid" + "@id": "bts:Fanconianemia" }, { - "@id": "bts:Zstack" + "@id": "bts:GlycogenStorageDisease" }, { - "@id": "bts:Tseries" + "@id": "bts:Gorlinsyndrome" }, { - "@id": "bts:PassedQC" + "@id": "bts:Hereditarybreast–ovariancancersyndrome" }, { - "@id": "bts:Comment" + "@id": "bts:Hereditarydiffusegastriccancer" }, { - "@id": "bts:FOVnumber" + "@id": "bts:Hereditaryleiomyoma-renalcellcarcinoma" }, { - "@id": "bts:FOVX" + "@id": "bts:Hereditarymelanoma" }, { - "@id": "bts:FOVY" + "@id": "bts:Hereditarymixedpolyposissyndrome" }, { - "@id": "bts:FrameAveraging" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", - "rdfs:subClassOf": [ + "@id": "bts:HereditarypapillaryRCC" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:Hereditarypapillaryrenalcellcarcinoma" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Hereditaryparaganglioma–pheochromocytomasyndrome" + }, { - "@id": "bts:Component" + "@id": "bts:Hereditaryrenaloncocytoma" }, { - "@id": "bts:Filename" + "@id": "bts:Hereditaryretinoblastoma" }, { - "@id": "bts:RunID" + "@id": "bts:Juvenilepolyposissyndrome" }, { - "@id": "bts:FileFormat" + "@id": "bts:Li-Fraumenisyndrome" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Lynchsyndrome" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Melanoma–astrocytomasyndrome" }, { - "@id": "bts:ReadIndicator" + "@id": "bts:MultipleendocrineneoplasiatypeI" }, { - "@id": "bts:SpatialRead1" + "@id": "bts:MultipleendocrineneoplasiatypeII" }, { - "@id": "bts:SpatialRead2" + "@id": "bts:MUTYH-associatedpolyposis" }, { - "@id": "bts:SpatialLibraryConstructionMethod" + "@id": "bts:Nevoidbasalcellcarcinomasyndrome" }, { - "@id": "bts:LibraryPreparationDaysfromIndex" + "@id": "bts:NotApplicable" }, { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + "@id": "bts:NotReported" }, { - "@id": "bts:EndBias" + "@id": "bts:Peutz–Jegherssyndrome" }, { - "@id": "bts:ReverseTranscriptionPrimer" + "@id": "bts:Cowdensyndrome" }, { - "@id": "bts:SequencingPlatform" + "@id": "bts:RhabdoidtumorpredispositionsyndrometypeI" }, { - "@id": "bts:CaptureArea" + "@id": "bts:RhabdoidtumorpredispositionsyndrometypeII" }, { - "@id": "bts:ProtocolLink" + "@id": "bts:Rubinstein-Taybisyndrome" }, { - "@id": "bts:SlideVersion" + "@id": "bts:SDHassociatedrenalcancer" }, { - "@id": "bts:SlideID" + "@id": "bts:Serratedpolyposissyndrome" }, { - "@id": "bts:ImageRe-orientation" + "@id": "bts:Tuberoussclerosiscomplex" }, { - "@id": "bts:PermeabilizationTime" + "@id": "bts:Turcotsyndrome" }, { - "@id": "bts:RIN" + "@id": "bts:Tyrosinemia" }, { - "@id": "bts:DV200" + "@id": "bts:Unknown" + }, + { + "@id": "bts:VonHippel-LindauSyndrome" } ], + "sms:displayName": "Hereditary Cancer Predisposition Syndrome", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", + "@id": "bts:CancerAssociatedGeneMutations", "@type": "rdfs:Class", - "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", - 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"@id": "bts:UMITag" + "@id": "bts:BAP1mutation" }, { - "@id": "bts:WhitelistSpatialBarcodeFileLink" + "@id": "bts:BMPR1Amutation" }, { - "@id": "bts:SpatialBarcodeTag" + "@id": "bts:BLMmutation" }, { - "@id": "bts:AppliedHardTrimming" + "@id": "bts:BRCA1mutation" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:BRCA1and2mutation" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:BRCA2mutation" }, { - "@id": "bts:GenomicReference" + "@id": "bts:BRAFmutation" }, { - "@id": "bts:GenomicReferenceURL" + "@id": "bts:CDH1mutation" }, { - "@id": "bts:GenomeAnnotationURL" + "@id": "bts:CDKN2Amutation" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:CDKN2Aandp14ARFmutation" }, { - "@id": "bts:RunID" + "@id": "bts:CHKmutation" }, { - "@id": "bts:CaptureArea" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "@type": "rdfs:Class", - "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", - "rdfs:subClassOf": [ - { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", - "sms:required": "sms:false", - "sms:requiresComponent": [ - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" + "@id": "bts:ETV6mutation" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" - } - ], - "sms:requiresDependency": [ - { - "@id": "bts:Component" + "@id": "bts:EGFRmutation" }, { - "@id": "bts:Filename" + "@id": "bts:FHmutation" }, { - "@id": "bts:FileFormat" + "@id": "bts:FLCNmutation" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:GREM1mutation" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:HOXB13mutation" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:H3K27Mmutation" }, { - "@id": "bts:RunID" + "@id": "bts:H3G34R/Vmutation" }, { - "@id": "bts:VisiumFileType" + "@id": "bts:IKZF1mutation" }, { - "@id": "bts:SlideID" + "@id": "bts:KITmutation" }, { - "@id": "bts:CaptureArea" + "@id": "bts:KRASmutation" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:MAXmutation" }, { - "@id": "bts:WorkflowLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", - "rdfs:subClassOf": [ + "@id": "bts:MEN1mutation" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:METmutation" + }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + "@id": "bts:MLH1mutation" }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" - } - ], - "sms:requiresDependency": [ + "@id": "bts:MSH2mutation" + }, { - "@id": "bts:Component" + "@id": "bts:MSH6mutation" }, { - "@id": "bts:Filename" + "@id": "bts:MUTYHmutation" }, { - "@id": "bts:FileFormat" + "@id": "bts:NF1mutation" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:NF2mutation" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:NotApplicable" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:NotReported" }, { - "@id": "bts:RunID" + "@id": "bts:P14ARFmutation" }, { - "@id": "bts:VisiumFileType" + "@id": "bts:PALB2mutation" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:PAX5mutation" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:PDGFRAmutation" }, { - "@id": "bts:CaptureArea" + "@id": "bts:PHOX2Bmutation" }, { - "@id": "bts:Spotsundertissue" + "@id": "bts:PMS2mutation" }, { - "@id": "bts:MeanReadsperSpatialSpot" + "@id": "bts:PolDmutation" }, { - "@id": "bts:MedianNumberGenesperSpatialSpot" + "@id": "bts:PolEmutation" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:POT1mutation" }, { - "@id": "bts:ProportionReadsMapped" + "@id": "bts:PRKAR1Amutation" }, { - "@id": "bts:ProportionReadsMappedtoTranscriptome" + "@id": "bts:PTCHmutation" }, { - "@id": "bts:MedianUMICountsperSpot" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel4", - "@type": "rdfs:Class", - "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 3.", - "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel4", - "rdfs:subClassOf": [ + "@id": "bts:PTENmutation" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 4", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:ROS1mutation" + }, { - "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3" - } - ], - "sms:requiresDependency": [ + "@id": "bts:RB1mutation" + }, { - "@id": "bts:Component" + "@id": "bts:RETmutation" }, { - "@id": "bts:Filename" + "@id": "bts:SDHAF2mutation" }, { - "@id": "bts:FileFormat" + "@id": "bts:SDHBmutation" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:SDHCmutation" }, { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:SDHDmutation" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:SETD2mutation" }, { - "@id": "bts:RunID" + "@id": "bts:SMAD4mutation" }, { - "@id": "bts:WorkflowVersion" + "@id": "bts:SMARCA4mutation" }, { - "@id": "bts:WorkflowLink" + "@id": "bts:SMARCB1mutation" }, { - "@id": "bts:VisiumWorkflowType" + "@id": "bts:STK11mutation" }, { - "@id": "bts:VisiumWorkflowParametersDescription" + "@id": "bts:TMEM127mutation" + }, + { + "@id": "bts:TP53mutation" + }, + { + "@id": "bts:TSC1mutation" + }, + { + "@id": "bts:TSC2mutation" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:VHLmutation" } ], + "sms:displayName": "Cancer Associated Gene Mutations", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VisiumFileType", + "@id": "bts:MutationalSignatures", "@type": "rdfs:Class", - "rdfs:comment": "The file type generated for the visium experiment.", - "rdfs:label": "VisiumFileType", + "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.", + "rdfs:label": "MutationalSignatures", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -8241,132 +5476,138 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Referencepng" + "@id": "bts:UVlightinducedmutations" }, { - "@id": "bts:Referencejpg" + "@id": "bts:AlkylatingAgents(Temozolomide)inducedmutations" }, { - "@id": "bts:Jsonscalefactors" + "@id": "bts:Tobaccouseassociatedmutations" }, { - "@id": "bts:Probedatasetcsv" + "@id": "bts:Ageofcancerdiagnosis" }, { - "@id": "bts:Qcresulthtml" + "@id": "bts:Transcriptionalstrandbias" }, { - "@id": "bts:Filteredmex" + "@id": "bts:Microsatelliteinstability(additionsanddeletions)" }, { - "@id": "bts:Unfilteredmex" + "@id": "bts:MethylatedCpGsequencesmutagenesis(deaminationof5-methyl-cytosine)" }, { - "@id": "bts:TissuePositions" + "@id": "bts:ActivationInducedDeaminases(AID)associatedmutations" }, { - "@id": "bts:Barcodes" + "@id": "bts:APOBECenzymesassociatedmutations" }, { - "@id": "bts:Features" + "@id": "bts:Alteredactivityoftheerror-pronepolymerasePOLε(POLE)" }, { - "@id": "bts:Fiducialimagepng" + "@id": "bts:Localizedsubstitutionhypermutation(kataegis)" }, { - "@id": "bts:Fiducialimagejpg" + "@id": "bts:DNAMMRDeficiency" }, { - "@id": "bts:Detectedimagepng" + "@id": "bts:Iggenehypermutation" }, { - "@id": "bts:Detectedjpg" + "@id": "bts:Signature1A" }, { - "@id": "bts:Highresimage" + "@id": "bts:Signature1B" }, { - "@id": "bts:Lowresimage" + "@id": "bts:Signature2" }, { - "@id": "bts:Jsonscalefactors" + "@id": "bts:Signature3" }, { - "@id": "bts:Probedatasetcsv" - } - ], - "sms:displayName": "Visium File Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:RunID", - "@type": "rdfs:Class", - "rdfs:comment": "A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.", - "rdfs:label": "RunID", - "rdfs:subClassOf": [ + "@id": "bts:Signature4" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Run ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CaptureArea", - "@type": "rdfs:Class", - "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", - "rdfs:label": "CaptureArea", - "rdfs:subClassOf": [ + "@id": "bts:Signature5" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Signature6" + }, { - "@id": "bts:A" + "@id": "bts:Signature7" }, { - "@id": "bts:B" + "@id": "bts:Signature8" }, { - "@id": "bts:C" + "@id": "bts:Signature9" }, { - "@id": "bts:D" + "@id": "bts:Signature10" }, { - "@id": "bts:A1" + "@id": "bts:Signature11" }, { - "@id": "bts:B1" + "@id": "bts:Signature12" }, { - "@id": "bts:C1" + "@id": "bts:Signature13" }, { - "@id": "bts:D1" + "@id": "bts:Signature14" + }, + { + "@id": "bts:Signature15" + }, + { + "@id": "bts:Signature16" + }, + { + "@id": "bts:Signature17" + }, + { + "@id": "bts:Signature18" + }, + { + "@id": "bts:Signature19" + }, + { + "@id": "bts:Signature20" + }, + { + "@id": "bts:Signature21" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Capture Area", + "sms:displayName": "Mutational Signatures", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlideVersion", + "@id": "bts:MismatchRepairSystemStatus", "@type": "rdfs:Class", - "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", - "rdfs:label": "SlideVersion", + "rdfs:comment": "The text that best describes the condition or state of MMR (mismatch repair system) in the patient", + "rdfs:label": "MismatchRepairSystemStatus", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -8374,47 +5615,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:V1" + "@id": "bts:MismatchrepairdeficiencyMMRD" }, { - "@id": "bts:V2" + "@id": "bts:MismatchrepairproficiencyMMPP" }, { - "@id": "bts:V3" + "@id": "bts:MicrosatelliteinstabilityhighMSIH" }, { - "@id": "bts:V4" - } - ], - "sms:displayName": "Slide Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SlideID", - "@type": "rdfs:Class", - "rdfs:comment": "The unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.", - "rdfs:label": "SlideID", - "rdfs:subClassOf": [ + "@id": "bts:MicrosatellitestableMSS" + }, { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Unknownorother" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide ID", + "sms:displayName": "Mismatch Repair System Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImageRe-orientation", + "@id": "bts:LabTestsforMMRStatus", "@type": "rdfs:Class", - "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", - "rdfs:label": "ImageRe-orientation", + "rdfs:comment": "Laboratory tests used to evaluate the status of mismatch repair pathways", + "rdfs:label": "LabTestsforMMRStatus", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { @@ -8422,109 +5649,39 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:TRUE" + "@id": "bts:IHCstainingformismatchrepairproteins" }, { - "@id": "bts:FALSE" - } - ], - "sms:displayName": "Image Re-orientation", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PermeabilizationTime", - "@type": "rdfs:Class", - "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", - "rdfs:label": "PermeabilizationTime", - "rdfs:subClassOf": [ + "@id": "bts:PCRtoevaluatemicrosatelliteinstability" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Permeabilization Time", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WhitelistSpatialBarcodeFileLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", - "rdfs:label": "WhitelistSpatialBarcodeFileLink", - "rdfs:subClassOf": [ + "@id": "bts:MLH1 promotermethylationanalysis" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Whitelist Spatial Barcode File Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeTag", - "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)", - "rdfs:label": "SpatialBarcodeTag", - "rdfs:subClassOf": [ + "@id": "bts:BRAF sequencing" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode Tag", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeOffset", - "@type": "rdfs:Class", - "rdfs:comment": "Offset in sequence for spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeOffset", - "rdfs:subClassOf": [ + "@id": "bts:Other" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode Offset", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeLength", - "@type": "rdfs:Class", - "rdfs:comment": "Length of spot barcode read (in bp): number", - "rdfs:label": "SpatialBarcodeLength", - "rdfs:subClassOf": [ + "@id": "bts:NotApplicable" + }, { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode Length", - "sms:required": "sms:true", + "sms:displayName": "Lab Tests for MMR Status", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpatialRead1", + "@id": "bts:ModeofCancerDetection", "@type": "rdfs:Class", - "rdfs:comment": "Read 1 content description", - "rdfs:label": "SpatialRead1", + "rdfs:comment": "Text term used to describe the mode of cancer detection, like standard of care screening or random detection", + "rdfs:label": "ModeofCancerDetection", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -8532,24 +5689,33 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:StandardofCareScreening" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:ClinicalExaminationofunrelatedcancersymptoms" + }, + { + "@id": "bts:Incidentaloma" + }, + { + "@id": "bts:IntervalCancer" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Spatial Read1", - "sms:required": "sms:true", + "sms:displayName": "Mode of Cancer Detection", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpatialRead2", + "@id": "bts:EducationLevel", "@type": "rdfs:Class", - "rdfs:comment": "Read 2 content description", - "rdfs:label": "SpatialRead2", + "rdfs:comment": "Highest level of education that the patient completed (direct patient-derived information)", + "rdfs:label": "EducationLevel", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { @@ -8557,24 +5723,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CDNA" + "@id": "bts:Bachelor'sdegree" }, { - "@id": "bts:SpatialBarcodeandUMI" + "@id": "bts:Doctoraldegreeorprofessionaldegree" + }, + { + "@id": "bts:Gradeschool" + }, + { + "@id": "bts:Graduateorprofessionaldegree" + }, + { + "@id": "bts:Highschoolgraduate(includingequivalency)" + }, + { + "@id": "bts:Master'sdegree" + }, + { + "@id": "bts:Noformaleducation" + }, + { + "@id": "bts:Nothighschoolgraduate" + }, + { + "@id": "bts:Somecollegeorassociatedegree" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Spatial Read2", - "sms:required": "sms:true", + "sms:displayName": "Education Level", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SpatialLibraryConstructionMethod", + "@id": "bts:CountryofBirth", "@type": "rdfs:Class", - "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]", - "rdfs:label": "SpatialLibraryConstructionMethod", + "rdfs:comment": "Country where the patient was born.", + "rdfs:label": "CountryofBirth", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { @@ -8582,3645 +5772,2752 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Smart-seq2" + "@id": "bts:Afghanistan" }, { - "@id": "bts:Smart-SeqV4" + "@id": "bts:Albania" }, { - "@id": "bts:10xV1.0" + "@id": "bts:Algeria" }, { - "@id": "bts:10xV1.1" + "@id": "bts:Andorra" }, { - "@id": "bts:10xV2" + "@id": "bts:Angola" }, { - "@id": "bts:10xV3" + "@id": "bts:Anguilla" }, { - "@id": "bts:10xV3.1" + "@id": "bts:AntiguaandBarbuda" }, { - "@id": "bts:Drop-seq" + "@id": "bts:Argentina" }, { - "@id": "bts:InDropsV2" + "@id": "bts:Armenia" }, { - "@id": "bts:InDropsV3" + "@id": "bts:Aruba" }, { - "@id": "bts:TruDrop" + "@id": "bts:Australia" }, { - "@id": "bts:NexteraXT" - } - ], - "sms:displayName": "Spatial Library Construction Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpatialBarcodeandUMI", - "@type": "rdfs:Class", - "rdfs:comment": "Spot and transcript identifiers", - "rdfs:label": "SpatialBarcodeandUMI", - "rdfs:subClassOf": [ + "@id": "bts:Austria" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spatial Barcode and UMI", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:Azerbaijan" + }, { - "@id": "bts:SpatialBarcodeOffset" + "@id": "bts:Bahamas" }, { - "@id": "bts:SpatialBarcodeLength" + "@id": "bts:Bahrain" }, { - "@id": "bts:UMIBarcodeOffset" + "@id": "bts:Bangladesh" }, { - "@id": "bts:UMIBarcodeLength" - } - ], - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MeanReadsperSpatialSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.", - "rdfs:label": "MeanReadsperSpatialSpot", - "rdfs:subClassOf": [ + "@id": "bts:Barbados" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Reads per Spatial Spot", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:VisiumWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the visium data set.", - "rdfs:label": "VisiumWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Belarus" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Visium Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:VisiumWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow..", - "rdfs:label": "VisiumWorkflowParametersDescription", - "rdfs:subClassOf": [ + "@id": "bts:Belgium" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Visium Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Spotsundertissue", - "@type": "rdfs:Class", - "rdfs:comment": "The number of barcodes associated with a spot under tissue.", - "rdfs:label": "Spotsundertissue", - "rdfs:subClassOf": [ + "@id": "bts:Belize" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spots under tissue", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:MedianUMICountsperSpot", - "@type": "rdfs:Class", - "rdfs:comment": "The median number of UMI counts per tissue covered spot.", - "rdfs:label": "MedianUMICountsperSpot", - "rdfs:subClassOf": [ + "@id": "bts:Benin" + }, { - "@id": "bts:SpatialTranscriptomics" - } - ], - "schema:isPartOf": { - 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"bts:Tanzania" + }, + { + "@id": "bts:Thailand" + }, + { + "@id": "bts:Timor-Leste" + }, + { + "@id": "bts:Togo" + }, + { + "@id": "bts:Tokelau" + }, + { + "@id": "bts:Tonga" + }, + { + "@id": "bts:TrinidadandTobago" + }, + { + "@id": "bts:Tunisia" + }, + { + "@id": "bts:Turkey" + }, + { + "@id": "bts:Turkmenistan" + }, + { + "@id": "bts:Tuvalu" + }, + { + "@id": "bts:Uganda" + }, + { + "@id": "bts:Ukraine" + }, + { + "@id": "bts:UnitedArabEmirates" + }, + { + "@id": "bts:UnitedKingdom" + }, + { + "@id": "bts:UnitedStates" + }, + { + "@id": "bts:Uruguay" + }, + { + "@id": "bts:Uzbekistan" + }, + { + "@id": "bts:Vanuatu" + }, + { + "@id": "bts:Venezuela" + }, + { + "@id": "bts:Vietnam" + }, + { + "@id": "bts:VirginIslandsBritish" + }, + { + "@id": "bts:VirginIslandsU.S." + }, + { + "@id": "bts:WallisandFutuna" + }, + { + "@id": "bts:WesternSahara" + }, + { + "@id": "bts:Yemen" + }, + { + "@id": "bts:Zambia" + }, + { + "@id": "bts:Zimbabwe" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "GeoMx DSP Unique Probe Count", + "sms:displayName": "Country of Birth", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPUniqueTargetCount", + "@id": "bts:MedicallyUnderservedArea", "@type": "rdfs:Class", - "rdfs:comment": "Total number of unique genes reported.", - "rdfs:label": "GeoMxDSPUniqueTargetCount", + "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", + "rdfs:label": "MedicallyUnderservedArea", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Unique Target Count", + "schema:rangeIncludes": [ + { + "@id": "bts:MedicallyUnderservedArea-Yes" + }, + { + "@id": "bts:MedicallyUnderservedArea-No" + }, + { + "@id": "bts:MedicallyUnderservedArea-Unknown" + } + ], + "sms:displayName": "Medically Underserved Area", "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] + "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowType", + "@id": "bts:RuralvsUrban", "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze the GeoMx DSP data set.", - "rdfs:label": "GeoMxDSPWorkflowType", + "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", + "rdfs:label": "RuralvsUrban", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Type", + "schema:rangeIncludes": [ + { + "@id": "bts:UrbanPopulation(population>50000)" + }, + { + "@id": "bts:UrbanCluster(population2500-50000)" + }, + { + "@id": "bts:RuralPopulation(population<2500)" + } + ], + "sms:displayName": "Rural vs Urban", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowParameterDescription", + "@id": "bts:CancerIncidence", "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the GeoMx DSP workflow.", - "rdfs:label": "GeoMxDSPWorkflowParameterDescription", + "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", + "rdfs:label": "CancerIncidence", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Parameter Description", + "sms:displayName": "Cancer Incidence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GeoMxDSPWorkflowLink", + "@id": "bts:CancerIncidenceLocation", "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "GeoMxDSPWorkflowLink", + "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", + "rdfs:label": "CancerIncidenceLocation", "rdfs:subClassOf": [ { - "@id": "bts:SpatialTranscriptomics" + "@id": "bts:ClinicalTier2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GeoMx DSP Workflow Link", + "sms:displayName": "Cancer Incidence Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "@id": "bts:SRRSClinicalDataTier2", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ", - "rdfs:label": "NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata", + "rdfs:comment": "Cancer related clinical data specific to SRRS", + "rdfs:label": "SRRSClinicalDataTier2", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI RCC Segment Annotation Metadata", + "sms:displayName": "SRRS Clinical Data Tier 2", "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], "sms:requiresDependency": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Component" }, { - "@id": "bts:Scanname" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:ROIname" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Segmentname" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:EducationLevel" }, { - "@id": "bts:Tags" + "@id": "bts:CountryofBirth" }, { - "@id": "bts:QCstatus" + "@id": "bts:MedicallyUnderservedArea" }, { - "@id": "bts:ScanHeight" + "@id": "bts:RuralvsUrban" }, { - "@id": "bts:ScanWidth" + "@id": "bts:CancerIncidence" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:CancerIncidenceLocation" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:Ethnicity" }, { - "@id": "bts:BindingDensity" + "@id": "bts:Gender" }, { - "@id": "bts:Positivenormfactor" + "@id": "bts:Race" }, { - "@id": "bts:Surfacearea" + "@id": "bts:VitalStatus" }, { - "@id": "bts:Nucleicount" + "@id": "bts:AgeatDiagnosis" }, { - "@id": "bts:TissueStain" + "@id": "bts:DaystoLastFollowup" + }, + { + "@id": "bts:DaystoLastKnownDiseaseStatus" + }, + { + "@id": "bts:DaystoRecurrence" + }, + { + "@id": "bts:LastKnownDiseaseStatus" + }, + { + "@id": "bts:Morphology" + }, + { + "@id": "bts:PrimaryDiagnosis" + }, + { + "@id": "bts:ProgressionorRecurrence" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:TissueorOrganofOrigin" + }, + { + "@id": "bts:NCIAtlasCancerSite" + }, + { + "@id": "bts:TumorGrade" + }, + { + "@id": "bts:PackYearsSmoked" + }, + { + "@id": "bts:YearsSmoked" + }, + { + "@id": "bts:DaystoFollowUp" + }, + { + "@id": "bts:GeneSymbol" + }, + { + "@id": "bts:MolecularAnalysisMethod" + }, + { + "@id": "bts:TestResult" + }, + { + "@id": "bts:TreatmentType" + }, + { + "@id": "bts:TumorLargestDimensionDiameter" } ], "sms:validationRules": [] }, { - "@id": "bts:Scanname", + "@id": "bts:Ethnicity", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx Scan name (as appears in Segment Summary)", - "rdfs:label": "Scanname", + "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.", + "rdfs:label": "Ethnicity", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIname", - "@type": "rdfs:Class", - "rdfs:comment": "ROI name (application generated)", - "rdfs:label": "ROIname", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Hispanicorlatino" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Nothispanicorlatino" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI name", + "sms:displayName": "Ethnicity", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Segmentname", + "@id": "bts:Gender", "@type": "rdfs:Class", - "rdfs:comment": "Name given to segment at time of generation", - "rdfs:label": "Segmentname", + "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.]", + "rdfs:label": "Gender", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Segment name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Tags", - "@type": "rdfs:Class", - "rdfs:comment": "Unique descriptor of a variable group (ie. MAPK+)", - "rdfs:label": "Tags", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Female" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Male" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unspecified" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tags", + "sms:displayName": "Gender", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ROIXCoordinate", + "@id": "bts:Race", "@type": "rdfs:Class", - "rdfs:comment": "X location within the image", - "rdfs:label": "ROIXCoordinate", + "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.", + "rdfs:label": "Race", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" - }, - { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ROI X Coordinate", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ROIYCoordinate", - "@type": "rdfs:Class", - "rdfs:comment": "Y location within the image", - "rdfs:label": "ROIYCoordinate", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:White" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Americanindianoralaskanative" + }, + { + "@id": "bts:Blackorafricanamerican" + }, + { + "@id": "bts:Asian" + }, + { + "@id": "bts:Nativehawaiianorotherpacificislander" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:Notallowedtocollect" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ROI Y Coordinate", + "sms:displayName": "Race", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:QCstatus", + "@id": "bts:VitalStatus", "@type": "rdfs:Class", - "rdfs:comment": "ROI quality control flag as reported by the application", - "rdfs:label": "QCstatus", + "rdfs:comment": "The survival state of the person registered on the protocol.", + "rdfs:label": "VitalStatus", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "QC status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ScanHeight", - "@type": "rdfs:Class", - "rdfs:comment": "Height of the scan for GeoMx Analysis", - "rdfs:label": "ScanHeight", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Alive" + }, + { + "@id": "bts:Dead" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Scan Height", + "sms:displayName": "Vital Status", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanWidth", + "@id": "bts:AgeatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Width of the scan for GeoMx Analysis", - "rdfs:label": "ScanWidth", + "rdfs:comment": "Age at the time of diagnosis expressed in number of days since birth.", + "rdfs:label": "AgeatDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Width", + "sms:displayName": "Age at Diagnosis", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:ScanOffsetX", + "@id": "bts:DaystoLastFollowup", "@type": "rdfs:Class", - "rdfs:comment": "Offset X of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetX", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastFollowup", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset X", + "sms:displayName": "Days to Last Follow up", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:ScanOffsetY", + "@id": "bts:DaystoLastKnownDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "Offset Y of the scan for GeoMx Analysis", - "rdfs:label": "ScanOffsetY", + "rdfs:comment": "Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoLastKnownDiseaseStatus", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Scan Offset Y", + "sms:displayName": "Days to Last Known Disease Status", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:BindingDensity", + "@id": "bts:DaystoRecurrence", "@type": "rdfs:Class", - "rdfs:comment": "The binding density as reported by the application", - "rdfs:label": "BindingDensity", + "rdfs:comment": "Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoRecurrence", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Binding Density", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Days to Recurrence", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:Positivenormfactor", + "@id": "bts:LastKnownDiseaseStatus", "@type": "rdfs:Class", - "rdfs:comment": "The Positive Control Normalization factor calculated using pos-hyb controls", - "rdfs:label": "Positivenormfactor", + "rdfs:comment": "Text term that describes the last known state or condition of an individual's neoplasm.", + "rdfs:label": "LastKnownDiseaseStatus", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Positive norm factor", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Surfacearea", - "@type": "rdfs:Class", - "rdfs:comment": "Surface area of the ROI in square microns (µm2)", - "rdfs:label": "Surfacearea", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Distantmetrecurrence/progression" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Surface area", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Nucleicount", - "@type": "rdfs:Class", - "rdfs:comment": "Number of nuclei detected in the segment (if applicable)", - "rdfs:label": "Nucleicount", - "rdfs:subClassOf": [ + "@id": "bts:Loco-regionalrecurrence/progression" + }, { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Biochemicalevidenceofdiseasewithoutstructuralcorrelate" }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + "@id": "bts:Tumorfree" + }, + { + "@id": "bts:Unknowntumorstatus" + }, + { + "@id": "bts:Withtumor" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotAllowedToCollect" + }, + { + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei count", + "sms:displayName": "Last Known Disease Status", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TissueStain", + "@id": "bts:Morphology", "@type": "rdfs:Class", - "rdfs:comment": "e.g. CD45 or PanCK (if masking was performed)", - "rdfs:label": "TissueStain", + "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", + "rdfs:label": "Morphology", "rdfs:subClassOf": [ { - "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tissue Stain", - "sms:required": "sms:false", + "sms:displayName": "Morphology", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "@id": "bts:PrimaryDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. ", - "rdfs:label": "NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata", + "rdfs:comment": "Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).", + "rdfs:label": "PrimaryDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Assay" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:HTANParentBiospecimenID" + "@id": "bts:Acinarcellcarcinoma" }, { - "@id": "bts:Scanname" + "@id": "bts:Acutebasophilicleukaemia" }, { - "@id": "bts:Slidename" + "@id": "bts:AcuteleukemiaBurkitttype" }, { - "@id": "bts:ROIname" + "@id": "bts:AcuteleukemiaNOS" }, { - "@id": "bts:Segmentname" + "@id": "bts:Acutelymphaticleukemia" }, { - "@id": "bts:ROIXCoordinate" + "@id": "bts:Acutelymphoblasticleukemia-lymphomaNOS" }, { - "@id": "bts:ROIYCoordinate" + "@id": "bts:AcutelymphoblasticleukemiamatureB-celltype" }, { - "@id": "bts:Tags" + "@id": "bts:AcutelymphoblasticleukemiaNOS" }, { - "@id": "bts:ScanHeight" + "@id": "bts:Acutelymphoblasticleukemiaprecursorcelltype" }, { - "@id": "bts:ScanWidth" + "@id": "bts:Acutelymphocyticleukemia" }, { - "@id": "bts:ScanOffsetX" + "@id": "bts:Acutelymphoidleukemia" }, { - "@id": "bts:ScanOffsetY" + "@id": "bts:Acutemyeloidleukemiaminimaldifferentiation" }, { - "@id": "bts:Surfacearea" + "@id": "bts:AcutemyeloidleukemiaMLL" }, { - "@id": "bts:Nucleicount" + "@id": "bts:AcutemyeloidleukemiaNOS" }, { - "@id": "bts:SequencingSaturation" + "@id": "bts:Acutemyelomonocyticleukemia" }, { - "@id": "bts:MapQ30" + "@id": "bts:AcutepromyelocyticleukemiaNOS" }, { - "@id": "bts:Rawreads" + "@id": "bts:Adenocarcinoidtumor" }, { - "@id": "bts:Stitchedreads" + "@id": "bts:Adenocarcinomacombinedwithothertypesofcarcinoma" }, { - "@id": "bts:Alignedreads" + "@id": "bts:AdenocarcinomainapolypNOS" }, { - "@id": "bts:Deduplicatedreads" + "@id": "bts:Adenocarcinomainadenomatouspolyp" }, { - "@id": "bts:InSituNegativemedian" + "@id": "bts:Adenocarcinomainpolypoidadenoma" }, { - "@id": "bts:Biologicalprobemedian" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Slidename", - "@type": "rdfs:Class", - "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", - "rdfs:label": "Slidename", - "rdfs:subClassOf": [ + "@id": "bts:AdenocarcinomainsituinapolypNOS" + }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Slide name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Rawreads", - "@type": "rdfs:Class", - "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. 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A measure of signal to background for each segment", - "rdfs:label": "Biologicalprobemedian", - "rdfs:subClassOf": [ + "@id": "bts:Adenocarcinomainsituinadenomatouspolyp" + }, { - "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Biological probe median", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HI-C-seqLevel1", - "@type": "rdfs:Class", - "rdfs:comment": "Unaligned sequence data", - "rdfs:label": "HI-C-seqLevel1", - "rdfs:subClassOf": [ + "@id": "bts:Adenocarcinomainsituintubularadenoma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HI-C-seq Level 1", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:Adenocarcinomainsitumucinous" + }, { - "@id": "bts:Biospecimen" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Adenocarcinomainsitunon-mucinous" + }, { - 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"@id": "bts:LigationCondition" + "@id": "bts:AdultT-celllymphoma/leukemia" }, { - "@id": "bts:BiotinEnrichment" + "@id": "bts:Astrocytomaanaplastic" }, { - "@id": "bts:DNAInputAmount" + "@id": "bts:Astrocytomalowgrade" }, { - "@id": "bts:TotalReads" + "@id": "bts:AstrocytomaNOS" }, { - "@id": "bts:ProtocolLink" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HI-C-seqLevel2", - "@type": "rdfs:Class", - "rdfs:comment": "Aligned read pairs, contact matrix", - "rdfs:label": "HI-C-seqLevel2", - "rdfs:subClassOf": [ + "@id": "bts:BcelllymphomaNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HI-C-seq Level 2", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:Blymphoblasticleukemia/lymphomawithhyperdiploidy" + }, { - "@id": "bts:HI-C-seqLevel1" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Blymphoblasticleukemia/lymphomawithhypodiploidy(HypodiploidALL)" + }, { - "@id": "bts:Component" + "@id": "bts:Blymphoblasticleukemia/lymphomaNOS" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:B-ALL" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:B-celllymphocyticleukemia/smalllymphocyticlymphoma" }, { - "@id": "bts:Filename" + "@id": "bts:Basalcelladenocarcinoma" }, { - "@id": "bts:FileFormat" + "@id": "bts:Basalcelladenoma" }, { - "@id": "bts:GenomicReference" + "@id": "bts:BasalcellcarcinomaNOS" }, { - "@id": "bts:AlignedReadLength" + "@id": "bts:Basalcellepithelioma" }, { - "@id": "bts:Tool" + "@id": "bts:Basalcelltumor" }, { - "@id": "bts:Resolution" + "@id": "bts:Basophiladenocarcinoma" }, { - "@id": "bts:NormalizationMethod" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:HI-C-seqLevel3", - "@type": "rdfs:Class", - "rdfs:comment": "Summary data for the HI-C-seq assay.", - "rdfs:label": "HI-C-seqLevel3", - "rdfs:subClassOf": [ + "@id": "bts:Basophiladenoma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "HI-C-seq Level 3", - "sms:required": "sms:false", - "sms:requiresComponent": [ + "@id": "bts:Basophilcarcinoma" + }, { - "@id": "bts:HI-C-seqLevel2" - } - ], - "sms:requiresDependency": [ + "@id": "bts:Bileductadenocarcinoma" + }, { - "@id": "bts:Component" + "@id": "bts:Bileductadenoma" }, { - "@id": "bts:HTANParentDataFileID" + "@id": "bts:Bileductcarcinoma" }, { - "@id": "bts:HTANDataFileID" + "@id": "bts:Bileductcystadenocarcinoma" }, { - "@id": "bts:Filename" + "@id": "bts:Bileductcystadenoma" }, { - "@id": "bts:FileFormat" + "@id": "bts:Bronchialadenomacarcinoid" }, { - "@id": "bts:GenomicReference" + "@id": "bts:Bronchialadenomacylindroid" }, { - "@id": "bts:StripeCalling" + "@id": "bts:BronchialadenomaNOS" }, { - "@id": "bts:LoopWindow" + "@id": "bts:Bronchial-associatedlymphoidtissuelymphoma" }, { - "@id": "bts:StripeWindow" + "@id": "bts:Bronchio-alveolarcarcinomamixedmucinousandnon-mucinous" }, { - "@id": "bts:LoopCalling" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CrosslinkingCondtion", - "@type": "rdfs:Class", - "rdfs:comment": "Detailed condition for DNA crosslinking", - "rdfs:label": "CrosslinkingCondtion", - "rdfs:subClassOf": [ + "@id": "bts:Bronchio-alveolarcarcinomamucinous" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Crosslinking Condtion", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DNADigestionCondition", - "@type": "rdfs:Class", - "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", - "rdfs:label": "DNADigestionCondition", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolaradenocarcinoma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DNA Digestion Condition", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleiPermeabilizationMethod", - "@type": "rdfs:Class", - "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", - "rdfs:label": "NucleiPermeabilizationMethod", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolarcarcinoma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nuclei Permeabilization Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LigationCondition", - "@type": "rdfs:Class", - "rdfs:comment": "Name of ligase and condition for proximity ligation", - "rdfs:label": "LigationCondition", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolo-alveolaradenocarcinomaNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ligation Condition", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:BiotinEnrichment", - "@type": "rdfs:Class", - "rdfs:comment": "Whether biotin is used for enriching ligation product", - "rdfs:label": "BiotinEnrichment", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracell" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bronchiolo-alveolarcarcinomaClaracellandgobletcelltype" + }, { - "@id": "bts:Yes" + "@id": "bts:Bronchiolo-alveolarcarcinomagobletcelltype" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Biotin Enrichment", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DNAInputAmount", - "@type": "rdfs:Class", - "rdfs:comment": "Amount of DNA for library construction, in nanograms.", - "rdfs:label": "DNAInputAmount", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolo-alveolarcarcinomaindeterminatetype" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DNA Input Amount", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:Resolution", - "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", - "rdfs:label": "Resolution", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolo-alveolarcarcinomanon-mucinous" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Resolution", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StripeCalling", - "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying architectural stripe-forming, interaction hotspots.", - "rdfs:label": "StripeCalling", - "rdfs:subClassOf": [ + "@id": "bts:Bronchiolo-alveolarcarcinomaNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Burkittcellleukemia" + }, { - "@id": "bts:MACS2" + "@id": "bts:BurkittlymphomaNOS(Includesallvariants)" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Stripe Calling", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LoopWindow", - "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant dot interactions (loops)", - "rdfs:label": "LoopWindow", - "rdfs:subClassOf": [ + "@id": "bts:Burkitttumor" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loop Window", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:StripeWindow", - "@type": "rdfs:Class", - "rdfs:comment": "Binning size used for calling significant architectural stripes. Can be an integer or int/int, indicating bin size and sliding window size if different.", - "rdfs:label": "StripeWindow", - "rdfs:subClassOf": [ + "@id": "bts:Burkitt-likelymphoma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:C-ALL" + }, { - "@id": "bts:HiCCUPS" + "@id": "bts:Cancer" }, { - "@id": "bts:Cooltools" + "@id": "bts:Capillaryhemangioma" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Stripe Window", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LoopCalling", - "@type": "rdfs:Class", - "rdfs:comment": "Tool used for identifying loop interactions", - "rdfs:label": "LoopCalling", - "rdfs:subClassOf": [ + "@id": "bts:Capillarylymphangioma" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Loop Calling", - "sms:required": "sms:true", - "sms:validationRules": [] - 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"@id": "bts:Po" + "@id": "bts:PrecursorcelllymphoblasticleukemiaNOS" }, { - "@id": "bts:At" + "@id": "bts:PrecursorT-celllymphoblasticleukemia" }, { - "@id": "bts:Rn" + "@id": "bts:PrecursorT-celllymphoblasticlymphoma" }, { - "@id": "bts:Fr" + "@id": "bts:Preleukemia" }, { - "@id": "bts:Ra" + "@id": "bts:Preleukemicsyndrome" }, { - "@id": "bts:Ac" + "@id": "bts:Primaryamyloidosis" }, { - "@id": "bts:Th" + "@id": "bts:Pro-BALL" }, { - "@id": "bts:Pa" + "@id": "bts:Pro-TALL" }, { - "@id": "bts:U" + "@id": "bts:ProstaticintraepithelialneoplasiagradeIII" }, { - "@id": "bts:Np" + "@id": "bts:Pulmonaryadenomatosis" }, { - "@id": "bts:Pu" + "@id": "bts:Pulmonaryarteryintimalsarcoma" }, { - "@id": "bts:Am" + "@id": "bts:Pulmonaryblastoma" }, { - "@id": "bts:Bk" + "@id": "bts:Renalcarcinomacollectingducttype" }, { - "@id": "bts:Cf" + "@id": "bts:Renalcelladenocarcinoma" }, { - "@id": "bts:Es" + "@id": "bts:Renalcellcarcinomachromophobetype" }, { - "@id": "bts:Fm" + "@id": "bts:RenalcellcarcinomaNOS" }, { - 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"sms:validationRules": [] - }, - { - "@id": "bts:OligoBarcodeLowerStrand", - "@type": "rdfs:Class", - "rdfs:comment": "Oligo Barcode - Lower Strand", - "rdfs:label": "OligoBarcodeLowerStrand", - "rdfs:subClassOf": [ + "@id": "bts:High-gradeserouscarcinoma" + }, { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Oligo Barcode Lower Strand", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Dilution", - "@type": "rdfs:Class", - "rdfs:comment": "Dilution (eg 1:1000)", - "rdfs:label": "Dilution", - "rdfs:subClassOf": [ + "@id": "bts:Skinappendagecarcinoma" + }, { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Dilution", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Concentration", - "@type": "rdfs:Class", - "rdfs:comment": "Concentration (eg 10ug/mL)", - "rdfs:label": "Concentration", - "rdfs:subClassOf": [ + "@id": "bts:SmallcellcarcinomaNOS" + }, { - "@id": "bts:ImagingLevel3Channels" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Concentration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingAssayType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of imaging assay", - "rdfs:label": "ImagingAssayType", - "rdfs:subClassOf": [ + "@id": "bts:Smallcellneuroendocrinecarcinoma" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Smallcellosteosarcoma" + }, { - "@id": "bts:H&E" + "@id": "bts:Smallcellsarcoma" }, { - "@id": "bts:CyCIF" + "@id": "bts:Smallcongenitalnevus" }, { - "@id": "bts:T-CyCIF" + "@id": "bts:SpindlecellcarcinomaNOS" }, { - "@id": "bts:IHC" + "@id": "bts:SpindlecellmelanomaNOS" }, { - "@id": "bts:MIHC" + "@id": "bts:SplenicB-celllymphoma/leukemiaunclassifiable" }, { - "@id": "bts:MxIF" + "@id": "bts:SplenicdiffuseredpulpsmallB-celllymphoma" }, { - "@id": "bts:SABER" + "@id": "bts:Spleniclymphomawithvillouslymphocytes" }, { - "@id": "bts:IMC" + "@id": "bts:SplenicmarginalzoneB-celllymphoma" }, { - "@id": "bts:CODEX" + "@id": "bts:SplenicmarginalzonelymphomaNOS" }, { - "@id": "bts:GeoMX-DSP" + "@id": "bts:SquamouscellcarcinomainsituNOS" }, { - "@id": "bts:MIBI" + "@id": "bts:Squamouscellcarcinomaadenoid" }, { - "@id": "bts:MERFISH" + "@id": "bts:Squamouscellcarcinomaclearcelltype" }, { - "@id": "bts:ExSeq" + "@id": "bts:SquamouscellcarcinomaNOS" }, { - "@id": "bts:RareCyteOrion" + "@id": "bts:Tlymphoblasticleukemia/lymphoma" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Imaging Assay Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ChannelMetadataFilename", - "@type": "rdfs:Class", - "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", - "rdfs:label": "ChannelMetadataFilename", - "rdfs:subClassOf": [ + "@id": "bts:T-celllargegranularlymphocyticleukemia" + }, { - "@id": "bts:ImagingLevel2" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Channel Metadata Filename", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Microscope", - "@type": "rdfs:Class", - "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", - "rdfs:label": "Microscope", - "rdfs:subClassOf": [ + "@id": "bts:T-celllargegranularlymphocytosis" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Microscope", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Objective", - "@type": "rdfs:Class", - "rdfs:comment": "Objective", - "rdfs:label": "Objective", - "rdfs:subClassOf": [ + "@id": "bts:T-celllymphomaNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Objective", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NominalMagnification", - "@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:subClassOf": [ + "@id": "bts:TeratomamalignantNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "NominalMagnification", - "sms:required": "sms:true", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:LensNA", - "@type": "rdfs:Class", - "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", - "rdfs:label": "LensNA", - "rdfs:subClassOf": [ + "@id": "bts:TeratomaNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "LensNA", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@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": [ + "@id": "bts:Therapyrelatedmyeloidneoplasm" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "WorkingDistance", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Transitionalcarcinoma" + }, { - "@id": "bts:WorkingDistanceUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:WorkingDistanceUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "WorkingDistanceUnit", - "rdfs:subClassOf": [ + "@id": "bts:Transitionalcellcarcinoma" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Transitionalcellcarcinomainsitu" + }, { - "@id": "bts:Cm" + "@id": "bts:Tubularadenocarcinoma" }, { - "@id": "bts:Mm" + "@id": "bts:TubularadenomaNOS" }, { - "@id": "bts:Μm" + "@id": "bts:Tubularandroblastomawithlipidstorage" }, { - "@id": "bts:Nm" + "@id": "bts:TubularandroblastomaNOS" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "WorkingDistanceUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Immersion", - "@type": "rdfs:Class", - "rdfs:comment": "Immersion medium", - "rdfs:label": "Immersion", - "rdfs:subClassOf": [ + "@id": "bts:Tubularcarcinoid" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Tubularcarcinoma" + }, { - "@id": "bts:Air" + "@id": "bts:Tubulo-papillaryadenoma" }, { - "@id": "bts:Oil" + "@id": "bts:Tubulocysticrenalcellcarcinoma" }, { - "@id": "bts:Water" + "@id": "bts:Tubulolobularcarcinoma" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Immersion", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Pyramid", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain pyramid of images", - "rdfs:label": "Pyramid", - "rdfs:subClassOf": [ + "@id": "bts:Tubulopapillaryadenocarcinoma" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TubulovillousadenomaNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:Tumorcellsbenign" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Pyramid", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Zstack", - "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a Z-stack of images", - "rdfs:label": "Zstack", - "rdfs:subClassOf": [ + "@id": "bts:Tumorcellsmalignant" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:TumorcellsNOS" + }, { - "@id": "bts:Yes" + "@id": "bts:Tumorcellsuncertainwhetherbenignormalignant" }, { - "@id": "bts:No" + "@id": "bts:Tumorembolus" + }, + { + "@id": "bts:Tumorbenign" + }, + { + "@id": "bts:TumormalignantNOS" + }, + { + "@id": "bts:Tumormetastatic" + }, + { + "@id": "bts:TumorNOS" + }, + { + "@id": "bts:Tumorsecondary" + }, + { + "@id": "bts:Tumorletbenign" + }, + { + "@id": "bts:Typicalcarcinoid" + }, + { + "@id": "bts:Unclassifiedtumorbenign" + }, + { + "@id": "bts:Unclassifiedtumorborderlinemalignancy" + }, + { + "@id": "bts:Unclassifiedtumormalignant" + }, + { + "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" + }, + { + "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" + }, + { + "@id": "bts:Undifferentiatedepithelioidsarcoma" + }, + { + "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" + }, + { + "@id": "bts:Undifferentiatedleukaemia" + }, + { + "@id": "bts:Undifferentiatedpleomorphicsarcoma" + }, + { + "@id": "bts:Undifferentiatedroundcellsarcoma" + }, + { + "@id": "bts:Undifferentiatedsarcoma" + }, + { + "@id": "bts:Undifferentiatedspindlecellsarcoma" + }, + { + "@id": "bts:Undifferentiateduterinesarcoma" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Zstack", + "sms:displayName": "Primary Diagnosis", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Tseries", + "@id": "bts:ProgressionorRecurrence", "@type": "rdfs:Class", - "rdfs:comment": "Does data file contain a time-series of images", - "rdfs:label": "Tseries", + "rdfs:comment": "Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.", + "rdfs:label": "ProgressionorRecurrence", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -12228,24 +8525,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Yes-ProgressionorRecurrence" }, { "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Tseries", + "sms:displayName": "Progression or Recurrence", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PassedQC", + "@id": "bts:SiteofResectionorBiopsy", "@type": "rdfs:Class", - "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", - "rdfs:label": "PassedQC", + "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy 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": "SiteofResectionorBiopsy", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -12253,2448 +8556,1017 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:No-ChannelsQC" - } - ], - "sms:displayName": "Passed QC", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:No-ChannelsQC", - "@type": "rdfs:Class", - "rdfs:comment": "Not all channels passed QC", - "rdfs:label": "No-ChannelsQC", - "rdfs:subClassOf": [ + "@id": "bts:Abdominalesophagus" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "No - Channels QC", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:AccessorysinusNOS" + }, { - "@id": "bts:Comment" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:Comment", - "@type": "rdfs:Class", - "rdfs:comment": "Free text field (generally for QC comment)", - "rdfs:label": "Comment", - "rdfs:subClassOf": [ + "@id": "bts:Acousticnerve" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Comment", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVnumber", - "@type": "rdfs:Class", - "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", - "rdfs:label": "FOVnumber", - "rdfs:subClassOf": [ + "@id": "bts:AdrenalglandNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOV number", - "sms:required": "sms:false", - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVX", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension. Floating point", - "rdfs:label": "FOVX", - "rdfs:subClassOf": [ + "@id": "bts:AmpullaofVater" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVX", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Analcanal" + }, { - "@id": "bts:FOVXUnit" - } - ], - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVXUnit", - "rdfs:subClassOf": [ + "@id": "bts:Anterior2/3oftongueNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Anteriorfloorofmouth" + }, { - "@id": "bts:Cm" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:Mm" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:Μm" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:Nm" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVXUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FOVY", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension. Floating point value", - "rdfs:label": "FOVY", - "rdfs:subClassOf": [ + "@id": "bts:AnusNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "FOVY", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Aorticbodyandotherparaganglia" + }, { - "@id": "bts:FOVYUnit" - } - ], - "sms:validationRules": [ - "num" - ] - }, - { - "@id": "bts:FOVYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "FOVYUnit", - "rdfs:subClassOf": [ + "@id": "bts:Appendix" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ascendingcolon" + }, { - "@id": "bts:Cm" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:Mm" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:Μm" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:Nm" + "@id": "bts:Bladderneck" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "FOVYUnit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@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:BladderNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Frame Averaging", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImageID", - "@type": "rdfs:Class", - "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", - "rdfs:label": "ImageID", - "rdfs:subClassOf": [ + "@id": "bts:Blood" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Image ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:DimensionOrder", - "@type": "rdfs:Class", - "rdfs:comment": "The order in which the individual planes of data are interleaved.", - "rdfs:label": "DimensionOrder", - "rdfs:subClassOf": [ + "@id": "bts:Bodyofpancreas" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Bodyofpenis" + }, { - "@id": "bts:XYZCT" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:XYZTC" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:XYCTZ" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:XYCZT" + "@id": "bts:BoneNOS" }, { - "@id": "bts:XYTZC" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:ZYX" - } - ], - "sms:displayName": "DimensionOrder", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@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:Borderoftongue" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeX", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:Brainstem" + }, { - "@id": "bts:PhysicalSizeXUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeXUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeXUnit", - "rdfs:subClassOf": [ + "@id": "bts:BrainNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Branchialcleft" + }, { - "@id": "bts:Cm" + "@id": "bts:BreastNOS" }, { - "@id": "bts:Mm" + "@id": "bts:Broadligament" }, { - "@id": "bts:Μm" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:Nm" + "@id": "bts:Carotidbody" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeXUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeY", - "@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:subClassOf": [ + "@id": "bts:Caudaequina" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeY", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:Cecum" + }, { - "@id": "bts:PhysicalSizeYUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeYUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeYUnit", - "rdfs:subClassOf": [ + "@id": "bts:Centralportionofbreast" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CerebellumNOS" + }, { - "@id": "bts:Cm" + "@id": "bts:Cerebralmeninges" }, { - "@id": "bts:Mm" + "@id": "bts:Cerebrum" }, { - "@id": "bts:Μm" + "@id": "bts:Cervicalesophagus" }, { - "@id": "bts:Nm" + "@id": "bts:Cervixuteri" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeYUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeZ", - "@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:subClassOf": [ + "@id": "bts:Choroid" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PhysicalSizeZ", - "sms:required": "sms:true", - "sms:requiresDependency": [ + "@id": "bts:Ciliarybody" + }, { - "@id": "bts:PhysicalSizeZUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:PhysicalSizeZUnit", - "@type": "rdfs:Class", - "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", - "rdfs:label": "PhysicalSizeZUnit", - "rdfs:subClassOf": [ + "@id": "bts:Cloacogeniczone" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ColonNOS" + }, { - "@id": "bts:Cm" + "@id": "bts:Commissureoflip" }, { - "@id": "bts:Mm" + "@id": "bts:Conjunctiva" }, { - "@id": "bts:Μm" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Nm" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:Å" - } - ], - "sms:displayName": "PhysicalSizeZUnit", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PixelsBigEndian", - "@type": "rdfs:Class", - "rdfs:comment": "Boolean (True/False)", - "rdfs:label": "PixelsBigEndian", - "rdfs:subClassOf": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + }, { - "@id": "bts:True" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:False" - } - ], - "sms:displayName": "Pixels BigEndian", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PlaneCount", - "@type": "rdfs:Class", - "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", - "rdfs:label": "PlaneCount", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "PlaneCount", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeC", - "@type": "rdfs:Class", - "rdfs:comment": "Number of channels. Integer >= 1", - "rdfs:label": "SizeC", - "rdfs:subClassOf": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeC", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:SizeT", - "@type": "rdfs:Class", - "rdfs:comment": "Number of time points. Integer >= 1", - "rdfs:label": "SizeT", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeT", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:SizeX", - "@type": "rdfs:Class", - "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeX", - "rdfs:subClassOf": [ + "@id": "bts:CorneaNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeX", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:SizeY", - "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeY", - "rdfs:subClassOf": [ + "@id": "bts:Corpusuteri" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeY", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:SizeZ", - "@type": "rdfs:Class", - "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", - "rdfs:label": "SizeZ", - "rdfs:subClassOf": [ + "@id": "bts:Cortexofadrenalgland" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "SizeZ", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:PixelType", - "@type": "rdfs:Class", - "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", - "rdfs:label": "PixelType", - "rdfs:subClassOf": [ + "@id": "bts:CranialnerveNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Craniopharyngealduct" + }, { - "@id": "bts:Int8" + "@id": "bts:Descendedtestis" }, { - "@id": "bts:Int16" + "@id": "bts:Descendingcolon" }, { - "@id": "bts:Int32" + "@id": "bts:Domeofbladder" }, { - "@id": "bts:Uint8" + "@id": "bts:DorsalsurfaceoftongueNOS" }, { - "@id": "bts:Uint16" + "@id": "bts:Duodenum" }, { - "@id": "bts:Uint32" + "@id": "bts:Endocervix" }, { - "@id": "bts:Float" + "@id": "bts:EndocrineglandNOS" }, { - "@id": "bts:Double" + "@id": "bts:Endometrium" }, { - "@id": "bts:Bit" - } - ], - "sms:displayName": "PixelType", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingSegmentationDataType", - "@type": "rdfs:Class", - "rdfs:comment": "Specifies how the segmentation is stored", - "rdfs:label": "ImagingSegmentationDataType", - "rdfs:subClassOf": [ + "@id": "bts:Epididymis" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EsophagusNOS" + }, { - "@id": "bts:Mask" + "@id": "bts:Ethmoidsinus" }, { - "@id": "bts:Outline" + "@id": "bts:Exocervix" }, { - "@id": "bts:Polygon" + "@id": "bts:Externalear" }, { - "@id": "bts:ProbabilityMap" + "@id": "bts:ExternallipNOS" }, { - "@id": "bts:Point" - } - ], - "sms:displayName": "Imaging Segmentation Data Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Parameterfile", - "@type": "rdfs:Class", - "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", - "rdfs:label": "Parameterfile", - "rdfs:subClassOf": [ + "@id": "bts:Externallowerlip" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Parameter file", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CommitSHA", - "@type": "rdfs:Class", - "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", - "rdfs:label": "CommitSHA", - "rdfs:subClassOf": [ + "@id": "bts:Externalupperlip" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Commit SHA", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingObjectClass", - "@type": "rdfs:Class", - "rdfs:comment": "Defines the structure that the mask delineates", - "rdfs:label": "ImagingObjectClass", - "rdfs:subClassOf": [ + "@id": "bts:Extrahepaticbileduct" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EyeNOS" + }, { - "@id": "bts:Nucleus" + "@id": "bts:Eyelid" }, { - "@id": "bts:Cytoplasm" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:Plasmamembrane" + "@id": "bts:FemalegenitaltractNOS" }, { - "@id": "bts:Wholecell" + "@id": "bts:FloorofmouthNOS" }, { - "@id": "bts:Spot" + "@id": "bts:Frontallobe" }, { - "@id": "bts:ImagingObjectClassOther" - } - ], - "sms:displayName": "Imaging Object Class", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] - }, - { - "@id": "bts:ImagingObjectClassOther", - "@type": "rdfs:Class", - "rdfs:comment": "Imaging Object Class Other", - "rdfs:label": "ImagingObjectClassOther", - "rdfs:subClassOf": [ + "@id": "bts:Frontalsinus" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Object Class Other", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Fundusofstomach" + }, { - "@id": "bts:ImagingObjectClassDescription" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:ImagingObjectClassDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Free text description of object class [string]", - "rdfs:label": "ImagingObjectClassDescription", - "rdfs:subClassOf": [ + "@id": "bts:Fundusuteri" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Imaging Object Class Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberofObjects", - "@type": "rdfs:Class", - "rdfs:comment": "The number of objects (eg cells) described", - "rdfs:label": "NumberofObjects", - "rdfs:subClassOf": [ + "@id": "bts:Gallbladder" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number of Objects", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:NumberofFeatures", - "@type": "rdfs:Class", - "rdfs:comment": "The number of features (eg channels) described", - "rdfs:label": "NumberofFeatures", - "rdfs:subClassOf": [ + "@id": "bts:Gastricantrum" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number of Features", - "sms:required": "sms:true", - "sms:validationRules": [ - "int" - ] - }, - { - "@id": "bts:ImagingSummaryStatistic", - "@type": "rdfs:Class", - "rdfs:comment": "Function used to summarize object/feature intensity", - "rdfs:label": "ImagingSummaryStatistic", - "rdfs:subClassOf": [ + "@id": "bts:GastrointestinaltractNOS" + }, { - "@id": "bts:Imaging" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Glanspenis" + }, { - "@id": "bts:Mean" + "@id": "bts:Glottis" }, { - "@id": "bts:Median" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:NotSpecified" - } - ], - "sms:displayName": "Imaging Summary Statistic", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NucleicAcidSource", - "@type": "rdfs:Class", - "rdfs:comment": "The source of the input nucleic molecule", - 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If not applicable please enter 'Not Applicable'", - "rdfs:label": "LibraryPreparationDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:PelvisNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Days from Index", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:SingleCellDissociationDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SingleCellDissociationDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:PenisNOS" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Single Cell Dissociation Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:SequencingLibraryConstructionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SequencingLibraryConstructionDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Library Construction Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:NucleicAcidCaptureDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'", - "rdfs:label": "NucleicAcidCaptureDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Nucleic Acid Capture Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:CryopreservedCellsinSample", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if library preparation was based on revived frozen cells.", - "rdfs:label": "CryopreservedCellsinSample", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + }, { - "@id": "bts:Yes" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Cryopreserved Cells in Sample", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:EndBias", - "@type": "rdfs:Class", - "rdfs:comment": "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript", - "rdfs:label": "EndBias", - "rdfs:subClassOf": [ + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" + }, { - "@id": "bts:3Prime" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:5Prime" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:FullLengthTranscript" - } - ], - "sms:displayName": "End Bias", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ReverseTranscriptionPrimer", - "@type": "rdfs:Class", - "rdfs:comment": "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA", - "rdfs:label": "ReverseTranscriptionPrimer", - "rdfs:subClassOf": [ + "@id": "bts:Pinealgland" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pituitarygland" + }, { - "@id": "bts:Oligo-dT" + "@id": "bts:Placenta" }, { - "@id": "bts:Poly-dT" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:Featurebarcoding" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:Random" - } - ], - "sms:displayName": "Reverse Transcription Primer", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Featurebarcoding", - "@type": "rdfs:Class", - "rdfs:comment": "A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc]", - "rdfs:label": "Featurebarcoding", - "rdfs:subClassOf": [ + "@id": "bts:Posteriormediastinum" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Feature barcoding", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Posteriorwallofbladder" + }, { - "@id": "bts:FeatureReferenceId" - } - ], - "sms:validationRules": [] - }, - { - "@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:Posteriorwallofhypopharynx" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Feature Reference Id", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SpikeIn", - "@type": "rdfs:Class", - "rdfs:comment": "A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix", - "rdfs:label": "SpikeIn", - "rdfs:subClassOf": [ + "@id": "bts:Posteriorwallofnasopharynx" + }, { - "@id": "bts:ScRNA-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Posteriorwalloforopharynx" + }, { - "@id": "bts:ERCC" + "@id": "bts:Prepuce" }, { - "@id": "bts:OtherSpikeIn" + "@id": "bts:Prostategland" }, { - "@id": "bts:NoSpikeIn" + "@id": "bts:Pylorus" }, { - "@id": "bts:PhiX" - } - ], - "sms:displayName": "Spike In", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ERCC", - "@type": "rdfs:Class", - "rdfs:comment": "The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization", - "rdfs:label": "ERCC", - "rdfs:subClassOf": [ + "@id": "bts:Pyriformsinus" + }, { - "@id": "bts:SpikeIn" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "ERCC", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Rectosigmoidjunction" + }, { - "@id": "bts:SpikeInConcentration" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SpikeInConcentration", - "@type": "rdfs:Class", - "rdfs:comment": "The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]", - "rdfs:label": "SpikeInConcentration", - "rdfs:subClassOf": [ + "@id": "bts:RectumNOS" + }, { - "@id": "bts:ERCC" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Spike In Concentration", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SequencingPlatform", - "@type": "rdfs:Class", - "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.", - "rdfs:label": "SequencingPlatform", - "rdfs:subClassOf": [ + "@id": "bts:Renalpelvis" + }, { - "@id": "bts:Device" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ReticuloendothelialsystemNOS" + }, { - "@id": "bts:IlluminaNextSeq500" + "@id": "bts:Retina" }, { - "@id": "bts:IlluminaNextSeq550" + "@id": "bts:Retromolararea" }, { - "@id": "bts:IlluminaNextSeq2500" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:IlluminaNovaSeq6000" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:Roundligament" }, { - "@id": "bts:454GSFLXTitanium" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:ABSOLiD4" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:ABSOLiD2" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:ABSOLiD3" + "@id": "bts:Sigmoidcolon" }, { - "@id": "bts:CompleteGenomics" + "@id": "bts:SkinoflipNOS" }, { - "@id": "bts:IlluminaHiSeqXTen" + "@id": "bts:Skinoflowerlimbandhip" }, { - "@id": "bts:IlluminaHiSeqXFive" + "@id": "bts:Skinofotherandunspecifiedpartsofface" }, { - "@id": "bts:IlluminaGenomeAnalyzerII" + "@id": "bts:Skinofscalpandneck" }, { - "@id": "bts:IlluminaGenomeAnalyzerIIx" + "@id": "bts:Skinoftrunk" }, { - "@id": "bts:IlluminaHiSeq2000" + "@id": "bts:Skinofupperlimbandshoulder" }, { - "@id": "bts:IlluminaHiSeq2500" + "@id": "bts:SkinNOS" }, { - "@id": "bts:IlluminaHiSeq4000" + "@id": "bts:SmallintestineNOS" }, { - "@id": "bts:IlluminaMiSeq" + "@id": "bts:SoftpalateNOS" }, { - "@id": "bts:IlluminaNextSeq" + "@id": "bts:Specifiedpartsofperitoneum" }, { - "@id": "bts:IonTorrentPGM" + "@id": "bts:Spermaticcord" }, { - "@id": "bts:IonTorrentProton" + "@id": "bts:Sphenoidsinus" }, { - "@id": "bts:IonTorrentS5" + "@id": "bts:Spinalcord" }, { - "@id": "bts:PacBioRS" + "@id": "bts:Spinalmeninges" }, { - "@id": "bts:NovaSeq6000" + "@id": "bts:Spleen" }, { - "@id": "bts:NovaSeqS4" + "@id": "bts:Splenicflexureofcolon" }, { - "@id": "bts:UltimaGenomicsUG100" + "@id": "bts:StomachNOS" }, { - "@id": "bts:OxfordNanoporeminION" + "@id": "bts:Subglottis" }, { - "@id": "bts:GridION" + "@id": "bts:Sublingualgland" }, { - "@id": "bts:PromethION" + "@id": "bts:Submandibulargland" }, { - "@id": "bts:PacBioSequel2" + "@id": "bts:Superiorwallofnasopharynx" }, { - "@id": "bts:Revio" + "@id": "bts:Supraglottis" }, { - "@id": "bts:Other" + "@id": "bts:Tailofpancreas" }, { - "@id": "bts:Unknown" + "@id": "bts:Temporallobe" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequencing Platform", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@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": [ + "@id": "bts:TestisNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Technical Replicate Group", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalNumberofInputCells", - "@type": "rdfs:Class", - "rdfs:comment": "Number of cells loaded/placed on plates", - "rdfs:label": "TotalNumberofInputCells", - "rdfs:subClassOf": [ + "@id": "bts:Thoracicesophagus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Number of Input Cells", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SequencingBatchID", - "@type": "rdfs:Class", - "rdfs:comment": "Links samples to a specific local sequencer run. Can be string or 'null'", - "rdfs:label": "SequencingBatchID", - "rdfs:subClassOf": [ + "@id": "bts:ThoraxNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Sequencing Batch ID", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SingleNucleusBuffer", - "@type": "rdfs:Class", - "rdfs:comment": "Nuclei isolation buffer", - "rdfs:label": "SingleNucleusBuffer", - "rdfs:subClassOf": [ + "@id": "bts:Thymus" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Thyroidgland" + }, { - "@id": "bts:NIB" + "@id": "bts:TongueNOS" }, { - "@id": "bts:10x" + "@id": "bts:TonsilNOS" }, { - "@id": "bts:Omni" + "@id": "bts:Tonsillarfossa" }, { - "@id": "bts:TST" - } - ], - "sms:displayName": "Single Nucleus Buffer", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TranspositionReaction", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the transposase, transposon sequences", - "rdfs:label": "TranspositionReaction", - "rdfs:subClassOf": [ + "@id": "bts:Tonsillarpillar" + }, { - "@id": "bts:ScATAC-seqLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Trachea" + }, { - "@id": "bts:Tn5" + "@id": "bts:Transversecolon" }, { - "@id": "bts:EZ-Tn5" + "@id": "bts:Trigoneofbladder" }, { - "@id": "bts:Tn5-059" + "@id": "bts:Undescendedtestis" }, { - "@id": "bts:NexteraTn5" + "@id": "bts:Unknownprimarysite" }, { - "@id": "bts:Diagenode-unloadedApex-Bio" + "@id": "bts:Uppergum" }, { - "@id": "bts:Diagenode-loadedApex-Bio" + "@id": "bts:UpperlimbNOS" }, { - "@id": "bts:In-House" - } - ], - "sms:displayName": "Transposition Reaction", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ReadLength", - "@type": "rdfs:Class", - "rdfs:comment": "The length of the sequencing reads. Can be integer, null", - "rdfs:label": "ReadLength", - "rdfs:subClassOf": [ + "@id": "bts:Upperlobelung" + }, { - "@id": "bts:Sequencing" + "@id": "bts:UpperrespiratorytractNOS" + }, + { + "@id": "bts:Upperthirdofesophagus" + }, + { + "@id": "bts:Upper-innerquadrantofbreast" + }, + { + "@id": "bts:Upper-outerquadrantofbreast" + }, + { + "@id": "bts:Urachus" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Uretericorifice" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:UrinarysystemNOS" + }, + { + "@id": "bts:Uterineadnexa" + }, + { + "@id": "bts:UterusNOS" + }, + { + "@id": "bts:Uvula" + }, + { + "@id": "bts:VaginaNOS" + }, + { + "@id": "bts:Vallecula" + }, + { + "@id": "bts:VentralsurfaceoftongueNOS" + }, + { + "@id": "bts:VentricleNOS" + }, + { + "@id": "bts:Vertebralcolumn" + }, + { + "@id": "bts:Vestibuleofmouth" + }, + { + "@id": "bts:VulvaNOS" + }, + { + "@id": "bts:Waldeyerring" + }, + { + "@id": "bts:BiliarytractNOS" + }, + { + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Read Length", + "sms:displayName": "Site of Resection or Biopsy", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TargetCaptureKit", + "@id": "bts:TissueorOrganofOrigin", "@type": "rdfs:Class", - "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", - "rdfs:label": "TargetCaptureKit", + "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": "TissueorOrganofOrigin", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -14702,1937 +9574,1102 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:NotApplicable" + "@id": "bts:AbdomenNOS" }, { - "@id": "bts:CustomTargetsFileProvided" + "@id": "bts:Abdominalesophagus" }, { - "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" + "@id": "bts:AccessorysinusNOS" }, { - "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" + "@id": "bts:Acousticnerve" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" + "@id": "bts:AdrenalglandNOS" }, { - "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" + "@id": "bts:AmpullaofVater" }, { - "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" + "@id": "bts:Analcanal" }, { - "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" + "@id": "bts:Anterior2/3oftongueNOS" }, { - "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" + "@id": "bts:Anteriorfloorofmouth" }, { - "@id": "bts:CustomMSKIMPACTPanel-341Genes" + "@id": "bts:Anteriormediastinum" }, { - "@id": "bts:CustomMSKIMPACTPanel-410Genes" + "@id": "bts:Anteriorsurfaceofepiglottis" }, { - "@id": "bts:CustomMSKIMPACTPanel-468Genes" + "@id": "bts:Anteriorwallofbladder" }, { - "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" + "@id": "bts:Anteriorwallofnasopharynx" }, { - "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" + "@id": "bts:AnusNOS" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" + "@id": "bts:Aorticbodyandotherparaganglia" }, { - "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" + "@id": "bts:Appendix" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" + "@id": "bts:Ascendingcolon" }, { - "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" + "@id": "bts:AutonomicnervoussystemNOS" }, { - "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" + "@id": "bts:Axillarytailofbreast" }, { - "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" + "@id": "bts:BaseoftongueNOS" }, { - "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" + "@id": "bts:Bladderneck" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" + "@id": "bts:BladderNOS" }, { - "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" + "@id": "bts:Blood" }, { - "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" + "@id": "bts:Bodyofpancreas" }, { - "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" + "@id": "bts:Bodyofpenis" }, { - "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" + "@id": "bts:Bodyofstomach" }, { - "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" + "@id": "bts:Bonemarrow" }, { - "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" + "@id": "bts:BoneoflimbNOS" }, { - "@id": "bts:FoundationMedicineT5aPanel-322Genes" + "@id": "bts:BoneNOS" }, { - "@id": "bts:FoundationMedicineT7Panel-429Genes" + "@id": "bts:Bonesofskullandfaceandassociatedjoints" }, { - "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" + "@id": "bts:Borderoftongue" }, { - "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" + "@id": "bts:Brainstem" }, { - "@id": "bts:NexteraDNAExome" + "@id": "bts:BrainNOS" }, { - "@id": "bts:NexteraRapidCaptureExomev1.2" + "@id": "bts:Branchialcleft" }, { - "@id": "bts:SeqCapEZHGSCVCRomev2.1" + "@id": "bts:BreastNOS" }, { - "@id": "bts:SeqCapEZHumanExomev2.0" + "@id": "bts:Broadligament" }, { - "@id": "bts:SeqCapEZHumanExomev3.0" + "@id": "bts:CardiaNOS" }, { - "@id": "bts:SureSelectHumanAllExonv3" + "@id": "bts:Carotidbody" }, { - "@id": "bts:SureSelectHumanAllExonv4" + "@id": "bts:Caudaequina" }, { - "@id": "bts:SureSelectHumanAllExonv5" + "@id": "bts:Cecum" }, { - "@id": "bts:SureSelectHumanAllExonv5+UTR" + "@id": "bts:Centralportionofbreast" }, { - "@id": "bts:TruSeqAmpliconCancerPanel" + "@id": "bts:CerebellumNOS" }, { - "@id": "bts:TruSeqExomeEnrichment-62Mb" + "@id": "bts:Cerebralmeninges" }, { - 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"@id": "bts:AffinityEnrichment" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" }, { - "@id": "bts:Poly-TEnrichment" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" }, { - "@id": "bts:Random" + "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" }, { - "@id": "bts:RRNADepletion" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" }, { - "@id": "bts:MiRNASizeFractionation" + "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "Library Selection Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitName", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Name", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVendor", - "@type": "rdfs:Class", - "rdfs:comment": "Vendor of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVendor", - "rdfs:subClassOf": [ + "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Vendor", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryPreparationKitVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of Library Preparation Kit. String", - "rdfs:label": "LibraryPreparationKitVersion", - "rdfs:subClassOf": [ + "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Library Preparation Kit Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the sequencing adapter. String", - "rdfs:label": "AdapterName", - "rdfs:subClassOf": [ + "@id": "bts:CorneaNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Base sequence of the sequencing adapter. String", - "rdfs:label": "AdapterSequence", - "rdfs:subClassOf": [ + "@id": "bts:Corpusuteri" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BaseCallerName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of the base caller. String", - "rdfs:label": "BaseCallerName", - "rdfs:subClassOf": [ + "@id": "bts:Cortexofadrenalgland" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Base Caller Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BaseCallerVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of the base caller. String", - "rdfs:label": "BaseCallerVersion", - "rdfs:subClassOf": [ + "@id": "bts:CranialnerveNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Base Caller Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FlowCellBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "Flow cell barcode. Wrong or missing information may affect analysis results. String", - "rdfs:label": "FlowCellBarcode", - "rdfs:subClassOf": [ + "@id": "bts:Craniopharyngealduct" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Flow Cell Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMaximumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMaximumLength", - "rdfs:subClassOf": [ + "@id": "bts:Descendedtestis" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Maximum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMeanLength", - "@type": "rdfs:Class", - "rdfs:comment": "Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentMeanLength", - "rdfs:subClassOf": [ + "@id": "bts:Descendingcolon" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Mean Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentMinimumLength", - "@type": "rdfs:Class", - "rdfs:comment": "Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer", - "rdfs:label": "FragmentMinimumLength", - "rdfs:subClassOf": [ + "@id": "bts:Domeofbladder" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Minimum Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FragmentStandardDeviationLength", - "@type": "rdfs:Class", - "rdfs:comment": "Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number", - "rdfs:label": "FragmentStandardDeviationLength", - "rdfs:subClassOf": [ + "@id": "bts:DorsalsurfaceoftongueNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fragment Standard Deviation Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LaneNumber", - "@type": "rdfs:Class", - "rdfs:comment": "The 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:Duodenum" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Lane Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:LibraryStrand", - "@type": "rdfs:Class", - "rdfs:comment": "Library stranded-ness.", - "rdfs:label": "LibraryStrand", - "rdfs:subClassOf": [ + "@id": "bts:Endocervix" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EndocrineglandNOS" + }, { - "@id": "bts:Unstranded" + "@id": "bts:Endometrium" }, { - "@id": "bts:FirstStranded" + "@id": "bts:Epididymis" }, { - "@id": "bts:SecondStranded" + "@id": "bts:EsophagusNOS" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Library Strand", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MultiplexBarcode", - "@type": "rdfs:Class", - "rdfs:comment": "The barcode/index sequence used. Wrong or missing information may affect analysis results. String", - "rdfs:label": "MultiplexBarcode", - "rdfs:subClassOf": [ + "@id": "bts:Ethmoidsinus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Multiplex Barcode", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SizeSelectionRange", - "@type": "rdfs:Class", - "rdfs:comment": "Range of size selection. String", - "rdfs:label": "SizeSelectionRange", - "rdfs:subClassOf": [ + "@id": "bts:Exocervix" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Size Selection Range", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TargetDepth", - "@type": "rdfs:Class", - "rdfs:comment": "The targeted read depth prior to sequencing. Integer", - "rdfs:label": "TargetDepth", - "rdfs:subClassOf": [ + "@id": "bts:Externalear" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Target Depth", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ToTrimAdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Does the user suggest adapter trimming?", - "rdfs:label": "ToTrimAdapterSequence", - "rdfs:subClassOf": [ + "@id": "bts:ExternallipNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Externallowerlip" + }, { - "@id": "bts:Yes-TrimAdapterSequence" + "@id": "bts:Externalupperlip" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "To Trim Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes-TrimAdapterSequence", - "@type": "rdfs:Class", - "rdfs:comment": "Trim adapter sequence", - "rdfs:label": "Yes-TrimAdapterSequence", - "rdfs:subClassOf": [ + "@id": "bts:Extrahepaticbileduct" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:EyeNOS" + }, { - "@id": "bts:AdapterTrimmerName" + "@id": "bts:Eyelid" }, { - "@id": "bts:AdapterTrimmerVersion" + "@id": "bts:Fallopiantube" }, { - "@id": "bts:AdapterTrimmerOptions" - } - ], - "sms:displayName": "Yes - Trim Adapter Sequence", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterTrimmerName", - "@type": "rdfs:Class", - "rdfs:comment": "Name of adapter trimmer", - "rdfs:label": "AdapterTrimmerName", - "rdfs:subClassOf": [ + "@id": "bts:FemalegenitaltractNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Trimmer Name", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterTrimmerVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Version of the adapter trimmer", - "rdfs:label": "AdapterTrimmerVersion", - "rdfs:subClassOf": [ + "@id": "bts:FloorofmouthNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Trimmer Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterTrimmerOptions", - "@type": "rdfs:Class", - "rdfs:comment": "Options used by adapter trimmer", - "rdfs:label": "AdapterTrimmerOptions", - "rdfs:subClassOf": [ + "@id": "bts:Frontallobe" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adapter Trimmer Options", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TranscriptIntegrityNumber", - "@type": "rdfs:Class", - "rdfs:comment": "Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number", - "rdfs:label": "TranscriptIntegrityNumber", - "rdfs:subClassOf": [ + "@id": "bts:Frontalsinus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Transcript Integrity Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RIN", - "@type": "rdfs:Class", - "rdfs:comment": "A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number", - "rdfs:label": "RIN", - "rdfs:subClassOf": [ + "@id": "bts:Fundusofstomach" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "RIN", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:DV200", - "@type": "rdfs:Class", - "rdfs:comment": "Represents the percentage of RNA fragments that are >200 nucleotides in size. Number", - "rdfs:label": "DV200", - "rdfs:subClassOf": [ + "@id": "bts:Fundusuteri" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DV200", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AdapterContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "AdapterContent", - "rdfs:subClassOf": [ + "@id": "bts:Gallbladder" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Gastricantrum" + }, { - "@id": "bts:FAIL" + "@id": "bts:GastrointestinaltractNOS" }, { - "@id": "bts:PASS" + "@id": "bts:Glanspenis" }, { - "@id": "bts:WARN" + "@id": "bts:Glottis" }, { - "@id": "bts:Unknown" + "@id": "bts:GreatercurvatureofstomachNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Adapter Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BasicStatistics", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "BasicStatistics", - "rdfs:subClassOf": [ + "@id": "bts:GumNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hardpalate" + }, { - "@id": "bts:FAIL" + "@id": "bts:Headofpancreas" }, { - "@id": "bts:PASS" + "@id": "bts:HeadfaceorneckNOS" }, { - "@id": "bts:WARN" + "@id": "bts:Heart" }, { - "@id": "bts:Unknown" + "@id": "bts:HematopoieticsystemNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Basic Statistics", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Encoding", - "@type": "rdfs:Class", - "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", - "rdfs:label": "Encoding", - "rdfs:subClassOf": [ + "@id": "bts:Hepaticflexureofcolon" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Encoding", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:KmerContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "KmerContent", - "rdfs:subClassOf": [ + "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HypopharynxNOS" + }, { - "@id": "bts:FAIL" + "@id": "bts:Ileum" }, { - "@id": "bts:PASS" + "@id": "bts:Ill-definedsiteswithinrespiratorysystem" }, { - "@id": "bts:WARN" + "@id": "bts:IntestinaltractNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Intra-abdominallymphnodes" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Kmer Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OverrepresentedSequences", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "OverrepresentedSequences", - "rdfs:subClassOf": [ + "@id": "bts:Intrahepaticbileduct" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Intrathoraciclymphnodes" + }, { - "@id": "bts:FAIL" + "@id": "bts:IsletsofLangerhans" }, { - "@id": "bts:PASS" + "@id": "bts:Isthmusuteri" }, { - "@id": "bts:WARN" + "@id": "bts:Jejunum" }, { - "@id": "bts:Unknown" + "@id": "bts:KidneyNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Overrepresented Sequences", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseNContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseNContent", - "rdfs:subClassOf": [ + "@id": "bts:Labiummajus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Labiumminus" + }, { - "@id": "bts:FAIL" + "@id": "bts:Lacrimalgland" }, { - "@id": "bts:PASS" + "@id": "bts:Laryngealcartilage" }, { - "@id": "bts:WARN" + "@id": "bts:LarynxNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Lateralfloorofmouth" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base N Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseSequenceContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceContent", - "rdfs:subClassOf": [ + "@id": "bts:Lateralwallofbladder" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lateralwallofnasopharynx" + }, { - "@id": "bts:FAIL" + "@id": "bts:Lateralwalloforopharynx" }, { - "@id": "bts:PASS" + "@id": "bts:LessercurvatureofstomachNOS" }, { - "@id": "bts:WARN" + "@id": "bts:Lingualtonsil" }, { - "@id": "bts:Unknown" + "@id": "bts:LipNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerBaseSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerBaseSequenceQuality", - "rdfs:subClassOf": [ + "@id": "bts:Liver" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + }, { - "@id": "bts:FAIL" + "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" }, { - "@id": "bts:PASS" + "@id": "bts:Lowergum" }, { - "@id": "bts:WARN" + "@id": "bts:LowerlimbNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Lowerlobelung" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Base Sequence Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceGCContent", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceGCContent", - "rdfs:subClassOf": [ + "@id": "bts:Lowerthirdofesophagus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lower-innerquadrantofbreast" + }, { - "@id": "bts:FAIL" + "@id": "bts:Lower-outerquadrantofbreast" }, { - "@id": "bts:PASS" + "@id": "bts:LungNOS" }, { - "@id": "bts:WARN" + "@id": "bts:LymphnodeNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Lymphnodesofaxillaorarm" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence GC Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerSequenceQualityScore", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerSequenceQualityScore", - "rdfs:subClassOf": [ + "@id": "bts:Lymphnodesofheadfaceandneck" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Lymphnodesofinguinalregionorleg" + }, { - "@id": "bts:FAIL" + "@id": "bts:Lymphnodesofmultipleregions" }, { - "@id": "bts:PASS" + "@id": "bts:Mainbronchus" }, { - "@id": "bts:WARN" + "@id": "bts:MajorsalivaryglandNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:MalegenitalorgansNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Sequence Quality Score", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerTileSequenceQuality", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "PerTileSequenceQuality", - "rdfs:subClassOf": [ + "@id": "bts:Mandible" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Maxillarysinus" + }, { - "@id": "bts:FAIL" + "@id": "bts:Meckeldiverticulum" }, { - "@id": "bts:PASS" + "@id": "bts:MediastinumNOS" }, { - "@id": "bts:WARN" + "@id": "bts:Medullaofadrenalgland" }, { - "@id": "bts:Unknown" + "@id": "bts:MeningesNOS" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Per Tile Sequence Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PercentGCContent", - "@type": "rdfs:Class", - "rdfs:comment": "The overall %GC of all bases in all sequences. Integer", - "rdfs:label": "PercentGCContent", - "rdfs:subClassOf": [ + "@id": "bts:Middleear" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Percent GC Content", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SequenceDuplicationLevels", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceDuplicationLevels", - "rdfs:subClassOf": [ + "@id": "bts:Middlelobelung" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Middlethirdofesophagus" + }, { - "@id": "bts:FAIL" + "@id": "bts:MouthNOS" }, { - "@id": "bts:PASS" + "@id": "bts:MucosaoflipNOS" }, { - "@id": "bts:WARN" + "@id": "bts:Mucosaoflowerlip" }, { - "@id": "bts:Unknown" + "@id": "bts:Mucosaofupperlip" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Duplication Levels", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SequenceLengthDistribution", - "@type": "rdfs:Class", - "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", - "rdfs:label": "SequenceLengthDistribution", - "rdfs:subClassOf": [ + "@id": "bts:Myometrium" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Nasalcavity" + }, { - "@id": "bts:FAIL" + "@id": "bts:NasopharynxNOS" }, { - "@id": "bts:PASS" + "@id": "bts:NervoussystemNOS" }, { - "@id": "bts:WARN" + "@id": "bts:Nipple" }, { - "@id": "bts:Unknown" + "@id": "bts:Occipitallobe" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sequence Length Distribution", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalReads", - "@type": "rdfs:Class", - "rdfs:comment": "Total number of reads per sample. Integer", - "rdfs:label": "TotalReads", - "rdfs:subClassOf": [ + "@id": "bts:Olfactorynerve" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:WhitelistCellBarcodeFileLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to file listing all possible cell barcodes. URL", - "rdfs:label": "WhitelistCellBarcodeFileLink", - "rdfs:subClassOf": [ + "@id": "bts:Opticnerve" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Whitelist Cell Barcode File Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CellBarcodeTag", - "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)", - "rdfs:label": "CellBarcodeTag", - "rdfs:subClassOf": [ + "@id": "bts:OrbitNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cell Barcode Tag", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:UMITag", - "@type": "rdfs:Class", - "rdfs:comment": "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)", - "rdfs:label": "UMITag", - "rdfs:subClassOf": [ + "@id": "bts:OropharynxNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "UMI Tag", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AppliedHardTrimming", - "@type": "rdfs:Class", - "rdfs:comment": "Was Hard Trimming applied", - "rdfs:label": "AppliedHardTrimming", - "rdfs:subClassOf": [ + "@id": "bts:Otherill-definedsites" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Otherspecifiedpartsoffemalegenitalorgans" + }, { - "@id": "bts:Yes-AppliedHardTrimming" + "@id": "bts:Otherspecifiedpartsofmalegenitalorgans" }, { - "@id": "bts:No" - } - ], - "sms:displayName": "Applied Hard Trimming", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes-AppliedHardTrimming", - "@type": "rdfs:Class", - "rdfs:comment": "Hard Trimming was applied", - "rdfs:label": "Yes-AppliedHardTrimming", - "rdfs:subClassOf": [ + "@id": "bts:Otherspecifiedpartsofpancreas" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Applied Hard Trimming", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Ovary" + }, { - "@id": "bts:AlignedReadLength" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AlignedReadLength", - "@type": "rdfs:Class", - "rdfs:comment": "Read length used for alignment if hard trimming was applied", - "rdfs:label": "AlignedReadLength", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofaccessorysinuses" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Aligned Read Length", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNAseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScRNAseqWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofbladder" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilage" + }, { - "@id": "bts:CellRanger" + "@id": "bts:Overlappinglesionofbonesjointsandarticularcartilageoflimbs" }, { - "@id": "bts:STARsolo" + "@id": "bts:Overlappinglesionofbrain" }, { - "@id": "bts:HCAOptimus" + "@id": "bts:Overlappinglesionofbrainandcentralnervoussystem" }, { - "@id": "bts:DropEST" + "@id": "bts:Overlappinglesionofbreast" }, { - "@id": "bts:SEQC" + "@id": "bts:Overlappinglesionofcervixuteri" }, { - "@id": "bts:Cufflinks" + "@id": "bts:Overlappinglesionofcolon" }, { - "@id": "bts:DEXSeq" + "@id": "bts:Overlappinglesionofconnectivesubcutaneousandothersofttissues" }, { - "@id": "bts:HTSeq-FPKM" + "@id": "bts:Overlappinglesionofcorpusuteri" }, { - "@id": "bts:Cellannotation" + "@id": "bts:Overlappinglesionofdigestivesystem" }, { - "@id": "bts:Differentiationtrajectoryanalysis" + "@id": "bts:Overlappinglesionofendocrineglandsandrelatedstructures" }, { - "@id": "bts:Other" - } - ], - "sms:displayName": "scRNAseq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:WorkflowVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Major version of the workflow (e.g. Cell Ranger v3.1)", - "rdfs:label": "WorkflowVersion", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofesophagus" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Workflow Version", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScRNAseqWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion", - "rdfs:label": "ScRNAseqWorkflowParametersDescription", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofeyeandadnexa" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scRNAseq Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "ScATACseqWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionoffemalegenitalorgans" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ScATACseqWorkflowParametersDescription", - "@type": "rdfs:Class", - "rdfs:comment": "Parameters used to run the scATAC-seq workflow.", - "rdfs:label": "ScATACseqWorkflowParametersDescription", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionoffloorofmouth" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "scATACseq Workflow Parameters Description", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:WorkflowLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow or command. DockStore.org recommended. URL", - "rdfs:label": "WorkflowLink", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofheartmediastinumandpleura" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Workflow Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", - "rdfs:label": "QCWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofhypopharynx" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowVersion", - "@type": "rdfs:Class", - "rdfs:comment": "Major version for a workflow. String", - "rdfs:label": "QCWorkflowVersion", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofill-definedsites" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Version", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:QCWorkflowLink", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used. String", - "rdfs:label": "QCWorkflowLink", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionoflarynx" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "QC Workflow Link", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:GermlineVariantsWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document, e.g. Github, DockStore.org recommended", - "rdfs:label": "GermlineVariantsWorkflowURL", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionoflip" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Germline Variants Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:GermlineVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set", - "rdfs:label": "GermlineVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofliporalcavityandpharynx" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Overlappinglesionoflung" + }, { - "@id": "bts:GATK4" + "@id": "bts:Overlappinglesionofmajorsalivaryglands" }, { - "@id": "bts:OtherGermlineVariantsWorkflowType" + "@id": "bts:Overlappinglesionofmalegenitalorgans" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Germline Variants Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherGermlineVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Other Germline Variants Workflow Type", - "rdfs:label": "OtherGermlineVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofnasopharynx" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Germline Variants Workflow Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Overlappinglesionofotherandunspecifiedpartsofmouth" + }, { - "@id": "bts:CustomGermlineVariantsWorkflowType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CustomGermlineVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Specify the name of a custom alignment workflow", - "rdfs:label": "CustomGermlineVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofpalate" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Custom Germline Variants Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SomaticVariantsWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowURL", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofpancreas" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Somatic Variants Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SomaticVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "SomaticVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofpenis" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Overlappinglesionofperipheralnervesandautonomicnervoussystem" + }, { - "@id": "bts:CaVEMan" + "@id": "bts:Overlappinglesionofrectumanusandanalcanal" }, { - "@id": "bts:GATK4" + "@id": "bts:Overlappinglesionofrespiratorysystemandintrathoracicorgans" }, { - "@id": "bts:MuTect2" + "@id": "bts:Overlappinglesionofretroperitoneumandperitoneum" }, { - "@id": "bts:MuSE" + "@id": "bts:Overlappinglesionofskin" }, { - "@id": "bts:MuTect2" + "@id": "bts:Overlappinglesionofsmallintestine" }, { - "@id": "bts:Pindel" + "@id": "bts:Overlappinglesionofstomach" }, { - "@id": "bts:SomaticSniper" + "@id": "bts:Overlappinglesionoftongue" }, { - "@id": "bts:VarScan2" + "@id": "bts:Overlappinglesionoftonsil" }, { - "@id": "bts:OtherSomaticVariantsWorkflowType" + "@id": "bts:Overlappinglesionofurinaryorgans" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Somatic Variants Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherSomaticVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Other Somatic Variants Workflow Type", - "rdfs:label": "OtherSomaticVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Overlappinglesionofvulva" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Somatic Variants Workflow Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Overlappinglesionsoforopharynx" + }, { - "@id": "bts:CustomSomaticVariantsWorkflowType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CustomSomaticVariantsWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Specify the name of a custom workflow name", - "rdfs:label": "CustomSomaticVariantsWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:PalateNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Custom Somatic Variants Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SomaticVariantsSampleType", - "@type": "rdfs:Class", - "rdfs:comment": "Is the sample case or control in somatic variant analysis", - "rdfs:label": "SomaticVariantsSampleType", - "rdfs:subClassOf": [ + "@id": "bts:PancreasNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Pancreaticduct" + }, { - "@id": "bts:CaseSample" + "@id": "bts:Parametrium" }, { - "@id": "bts:ControlSample" + "@id": "bts:Paraspinal" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Somatic Variants Sample Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StructuralVariantWorkflowURL", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow document. DockStore.org recommended. URL", - "rdfs:label": "StructuralVariantWorkflowURL", - "rdfs:subClassOf": [ + "@id": "bts:Parathyroidgland" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Structural Variant Workflow URL", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:StructuralVariantWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "StructuralVariantWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Paraurethralgland" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Parietallobe" + }, { - "@id": "bts:BRASS" + "@id": "bts:Parotidgland" }, { - "@id": "bts:GATK4" + "@id": "bts:Pelvicbonessacrumcoccyxandassociatedjoints" }, { - "@id": "bts:CNV" + "@id": "bts:Pelviclymphnodes" }, { - "@id": "bts:CNVkit" + "@id": "bts:PelvisNOS" }, { - "@id": "bts:OtherStructuralVariantWorkflowType" + "@id": "bts:PenisNOS" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Structural Variant Workflow Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherStructuralVariantWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Other Structural Variant Workflow Type", - "rdfs:label": "OtherStructuralVariantWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofabdomen" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Structural Variant Workflow Type", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofheadfaceandneck" + }, { - "@id": "bts:CustomStructuralVariantWorkflowType" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CustomStructuralVariantWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Specify the name of a custom workflow name", - "rdfs:label": "CustomStructuralVariantWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemoflowerlimbandhip" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Custom Structural Variant Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowUrl", - "@type": "rdfs:Class", - "rdfs:comment": "Link to workflow used for read alignment. DockStore.org recommended. String", - "rdfs:label": "AlignmentWorkflowUrl", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofpelvis" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alignment Workflow Url", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlignmentWorkflowType", - "@type": "rdfs:Class", - "rdfs:comment": "Generic name for the workflow used to analyze a data set.", - "rdfs:label": "AlignmentWorkflowType", - "rdfs:subClassOf": [ + "@id": "bts:Peripheralnervesandautonomicnervoussystemofthorax" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PeripheralnervesandautonomicnervoussystemoftrunkNOS" + }, { - "@id": "bts:BWA" + "@id": "bts:Peripheralnervesandautonomicnervoussystemofupperlimbandshoulder" }, { - "@id": "bts:BWAwithBQSR" + "@id": "bts:PeritoneumNOS" }, { - "@id": "bts:BWA-aln" + "@id": "bts:PharynxNOS" }, { - "@id": "bts:BWA-mem" + "@id": "bts:Pinealgland" }, { - "@id": "bts:BWAwithMarkDuplicatesandBQSR" + "@id": "bts:Pituitarygland" }, { - "@id": "bts:STAR2-Pass" + "@id": "bts:Placenta" }, { - "@id": "bts:STAR2-PassChimeric" + "@id": "bts:PleuraNOS" }, { - "@id": "bts:STAR2-PassGenome" + "@id": "bts:Postcricoidregion" }, { - "@id": "bts:STAR2-PassTranscriptome" + "@id": "bts:Posteriormediastinum" }, { - "@id": "bts:Bowtie" + "@id": "bts:Posteriorwallofbladder" }, { - "@id": "bts:Bismark" + "@id": "bts:Posteriorwallofhypopharynx" }, { - "@id": "bts:GSNAP" + "@id": "bts:Posteriorwallofnasopharynx" }, { - "@id": "bts:BSMAP" + "@id": "bts:Posteriorwalloforopharynx" }, { - "@id": "bts:BSmooth" + "@id": "bts:Prepuce" }, { - "@id": "bts:BS-Seeker2" + "@id": "bts:Prostategland" }, { - "@id": "bts:BS-Seeker" + "@id": "bts:Pylorus" }, { - "@id": "bts:RMAP" + "@id": "bts:Pyriformsinus" }, { - "@id": "bts:MethylCoder" + "@id": "bts:Rectosigmoidjunction" }, { - "@id": "bts:BRAT-BW" + "@id": "bts:RectumNOS" }, { - "@id": "bts:Pash" + "@id": "bts:Renalpelvis" }, { - "@id": "bts:Segemehl" + "@id": "bts:ReticuloendothelialsystemNOS" }, { - "@id": "bts:Bisulfighter" + "@id": "bts:Retina" }, { - "@id": "bts:BatMeth" + "@id": "bts:Retromolararea" }, { - "@id": "bts:LAST" + "@id": "bts:Retroperitoneum" }, { - "@id": "bts:ERNE-BS5" + "@id": "bts:Ribsternumclavicleandassociatedjoints" }, { - "@id": "bts:B-SOLANA" + "@id": "bts:Roundligament" }, { - "@id": "bts:SOCS-B" + "@id": "bts:ScrotumNOS" }, { - "@id": "bts:BWA-meth" + "@id": "bts:Shortbonesoflowerlimbandassociatedjoints" }, { - "@id": "bts:OtherAlignmentWorkflow" + "@id": "bts:Shortbonesofupperlimbandassociatedjoints" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Alignment Workflow Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherAlignmentWorkflow", - "@type": "rdfs:Class", - "rdfs:comment": "Other Alignment Workflow", - "rdfs:label": "OtherAlignmentWorkflow", - "rdfs:subClassOf": [ + "@id": "bts:Sigmoidcolon" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Alignment Workflow", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:SkinoflipNOS" + }, { - "@id": "bts:CustomAlignmentWorkflow" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:CustomAlignmentWorkflow", - "@type": "rdfs:Class", - "rdfs:comment": "Specify the name of a custom alignment workflow", - "rdfs:label": "CustomAlignmentWorkflow", - "rdfs:subClassOf": [ + "@id": "bts:Skinoflowerlimbandhip" + }, { - "@id": "bts:Sequencing" + "@id": "bts:Skinofotherandunspecifiedpartsofface" + }, + { + "@id": "bts:Skinofscalpandneck" + }, + { + "@id": "bts:Skinoftrunk" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:SmallintestineNOS" + }, + { + "@id": "bts:SoftpalateNOS" + }, + { + "@id": "bts:Specifiedpartsofperitoneum" + }, + { + "@id": "bts:Spermaticcord" + }, + { + "@id": "bts:Sphenoidsinus" + }, + { + "@id": "bts:Spinalcord" + }, + { + "@id": "bts:Spinalmeninges" + }, + { + "@id": "bts:Spleen" + }, + { + "@id": "bts:Splenicflexureofcolon" + }, + { + "@id": "bts:StomachNOS" + }, + { + "@id": "bts:Subglottis" + }, + { + "@id": "bts:Sublingualgland" + }, + { + "@id": "bts:Submandibulargland" + }, + { + "@id": "bts:Superiorwallofnasopharynx" + }, + { + "@id": "bts:Supraglottis" + }, + { + "@id": "bts:Tailofpancreas" + }, + { + "@id": "bts:Temporallobe" + }, + { + "@id": "bts:TestisNOS" + }, + { + "@id": "bts:Thoracicesophagus" + }, + { + "@id": "bts:ThoraxNOS" + }, + { + "@id": "bts:Thymus" + }, + { + "@id": "bts:Thyroidgland" + }, + { + "@id": "bts:TongueNOS" + }, + { + "@id": "bts:TonsilNOS" + }, + { + "@id": "bts:Tonsillarfossa" + }, + { + "@id": "bts:Tonsillarpillar" + }, + { + "@id": "bts:Trachea" + }, + { + "@id": "bts:Transversecolon" + }, + { + "@id": "bts:Trigoneofbladder" + }, + { + "@id": "bts:Undescendedtestis" + }, + { + "@id": "bts:Unknownprimarysite" + }, + { + "@id": "bts:Uppergum" + }, + { + "@id": "bts:UpperlimbNOS" + }, + { + "@id": "bts:Upperlobelung" + }, + { + "@id": "bts:UpperrespiratorytractNOS" + }, + { + "@id": "bts:Upperthirdofesophagus" + }, + { + "@id": "bts:Upper-innerquadrantofbreast" + }, + { + "@id": "bts:Upper-outerquadrantofbreast" + }, + { + "@id": "bts:Urachus" + }, + { + "@id": "bts:Ureter" + }, + { + "@id": "bts:Uretericorifice" + }, + { + "@id": "bts:Urethra" + }, + { + "@id": "bts:UrinarysystemNOS" + }, + { + "@id": "bts:Uterineadnexa" + }, + { + "@id": "bts:UterusNOS" + }, + { + "@id": "bts:Uvula" + }, + { + "@id": "bts:VaginaNOS" + }, + { + "@id": "bts:Vallecula" + }, + { + "@id": "bts:VentralsurfaceoftongueNOS" + }, + { + "@id": "bts:VentricleNOS" + }, + { + "@id": "bts:Vertebralcolumn" + }, + { + "@id": "bts:Vestibuleofmouth" + }, + { + "@id": "bts:VulvaNOS" + }, + { + "@id": "bts:Waldeyerring" + }, + { + "@id": "bts:BiliarytractNOS" + }, + { + "@id": "bts:Cheekmucosa" + }, + { + "@id": "bts:Clitoris" + }, + { + "@id": "bts:Overlappinglesionofbiliarytract" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Custom Alignment Workflow", + "sms:displayName": "Tissue or Organ of Origin", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MSIWorkflowLink", + "@id": "bts:NCIAtlasCancerSite", "@type": "rdfs:Class", - "rdfs:comment": "Link to method workflow (or command) used in estimating the MSI. URL", - "rdfs:label": "MSIWorkflowLink", + "rdfs:comment": "The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017", + "rdfs:label": "NCIAtlasCancerSite", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MSI Workflow Link", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MSIScore", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number", - "rdfs:label": "MSIScore", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:Bladder" + }, + { + "@id": "bts:BrainAndOtherNervousSystem" + }, + { + "@id": "bts:FemaleBreast" + }, + { + "@id": "bts:InsituFemaleBreast" + }, + { + "@id": "bts:CervixUteri" + }, + { + "@id": "bts:LessThanAge" + }, + { + "@id": "bts:MalignantChildhoodNeoplasm" + }, + { + "@id": "bts:ColonAndRectum" + }, + { + "@id": "bts:Esophagus" + }, + { + "@id": "bts:KidneyAndRenalPelvis" + }, + { + "@id": "bts:Leukemia" + }, + { + "@id": "bts:LiverAndBileDuct" + }, + { + "@id": "bts:LungAndBronchus" + }, + { + "@id": "bts:CutaneousMelanoma" + }, + { + "@id": "bts:Non-Hodgkin'sLymphoma" + }, + { + "@id": "bts:OralCavityAndPharynx" + }, + { + "@id": "bts:Ovary" + }, + { + "@id": "bts:Pancreas" + }, + { + "@id": "bts:ProstateGland" + }, + { + "@id": "bts:Stomach" + }, + { + "@id": "bts:ThyroidGland" + }, + { + "@id": "bts:Uterus" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "MSI Score", + "sms:displayName": "NCI Atlas Cancer Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSIStatus", + "@id": "bts:TumorGrade", "@type": "rdfs:Class", - "rdfs:comment": "MSIsensor determination of either microsatellite stability or instability.", - "rdfs:label": "MSIStatus", + "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", + "rdfs:label": "TumorGrade", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Diagnosis" } ], "schema:isPartOf": { @@ -16640,387 +10677,270 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MSI" + "@id": "bts:G1" }, { - "@id": "bts:MSI-low" + "@id": "bts:G2" }, { - "@id": "bts:MSI-high" + "@id": "bts:G3" }, { - "@id": "bts:MSS" + "@id": "bts:G4" + }, + { + "@id": "bts:GX" + }, + { + "@id": "bts:GB" + }, + { + "@id": "bts:HighGrade" + }, + { + "@id": "bts:IntermediateGrade" + }, + { + "@id": "bts:LowGrade" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" } ], - "sms:displayName": "MSI Status", + "sms:displayName": "Tumor Grade", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GenomicReference", + "@id": "bts:PackYearsSmoked", "@type": "rdfs:Class", - "rdfs:comment": "Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)", - "rdfs:label": "GenomicReference", + "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": [ { - "@id": "bts:Sequencing" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference", + "sms:displayName": "Pack Years Smoked", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GenomicReferenceURL", + "@id": "bts:YearsSmoked", "@type": "rdfs:Class", - "rdfs:comment": "Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)", - "rdfs:label": "GenomicReferenceURL", + "rdfs:comment": "Numeric value (or unknown) to represent the number of years a person has been smoking.", + "rdfs:label": "YearsSmoked", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genomic Reference URL", + "sms:displayName": "Years Smoked", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GenomeAnnotationURL", + "@id": "bts:DaystoFollowUp", "@type": "rdfs:Class", - "rdfs:comment": "Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)", - "rdfs:label": "GenomeAnnotationURL", + "rdfs:comment": "Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoFollowUp", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:FollowUp" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genome Annotation URL", + "sms:displayName": "Days to Follow Up", "sms:required": "sms:true", - "sms:validationRules": [] + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:IndexFileName", + "@id": "bts:GeneSymbol", "@type": "rdfs:Class", - "rdfs:comment": "The name (or part of a name) of a file (of any type). String", - "rdfs:label": "IndexFileName", + "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": [ { - "@id": "bts:Sequencing" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Index File Name", + "sms:displayName": "Gene Symbol", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageBaseQuality", + "@id": "bts:MolecularAnalysisMethod", "@type": "rdfs:Class", - "rdfs:comment": "Average base quality collected from samtools. Number", - "rdfs:label": "AverageBaseQuality", + "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": "MolecularAnalysisMethod", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Base Quality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AverageInsertSize", - "@type": "rdfs:Class", - "rdfs:comment": "Average insert size collected from samtools. Integer", - "rdfs:label": "AverageInsertSize", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" + "@id": "bts:ComparativeGenomicHybridization" + }, + { + "@id": "bts:CytogeneticsNOS" + }, + { + "@id": "bts:FISH" + }, + { + "@id": "bts:FlowCytometry" + }, + { + "@id": "bts:IHC" + }, + { + "@id": "bts:ISH" + }, + { + "@id": "bts:Karyotype" + }, + { + "@id": "bts:Microarray" + }, + { + "@id": "bts:MicrosatelliteAnalysis" + }, + { + "@id": "bts:NuclearStaining" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:RNASequencing" + }, + { + "@id": "bts:RT-PCR" + }, + { + "@id": "bts:SequencingNOS" + }, + { + "@id": "bts:SouthernBlotting" + }, + { + "@id": "bts:TargetedSequencing" + }, + { + "@id": "bts:WGS" + }, + { + "@id": "bts:WXS" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Average Insert Size", - "sms:required": "sms:false", + "sms:displayName": "Molecular Analysis Method", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AverageReadLength", + "@id": "bts:TestResult", "@type": "rdfs:Class", - "rdfs:comment": "Average read length collected from samtools. Integer", - "rdfs:label": "AverageReadLength", + "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.", + "rdfs:label": "TestResult", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" + "@id": "bts:MolecularTest" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Average Read Length", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Contamination", - "@type": "rdfs:Class", - "rdfs:comment": "Fraction of reads coming from cross-sample contamination collected from GATK4. Number", - "rdfs:label": "Contamination", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Contamination", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ContaminationError", - "@type": "rdfs:Class", - "rdfs:comment": "Estimation error of cross-sample contamination collected from GATK4. Number", - "rdfs:label": "ContaminationError", - "rdfs:subClassOf": [ + "@id": "bts:AbnormalNOS" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Contamination Error", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MeanCoverage", - "@type": "rdfs:Class", - "rdfs:comment": "Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number", - "rdfs:label": "MeanCoverage", - "rdfs:subClassOf": [ + "@id": "bts:CopyNumberReported" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mean Coverage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PairsOnDiffCHR", - "@type": "rdfs:Class", - "rdfs:comment": "Pairs on different chromosomes collected from samtools. Integer", - "rdfs:label": "PairsOnDiffCHR", - "rdfs:subClassOf": [ + "@id": "bts:Equivocal" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pairs On Diff CHR", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalUniquelyMapped", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that map to genome. Integer", - "rdfs:label": "TotalUniquelyMapped", - "rdfs:subClassOf": [ + "@id": "bts:High" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Uniquely Mapped", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalUnmappedreads", - "@type": "rdfs:Class", - "rdfs:comment": "Number of reads that did not map to genome. Integer", - "rdfs:label": "TotalUnmappedreads", - "rdfs:subClassOf": [ + "@id": "bts:Intermediate" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Unmapped reads", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionReadsDuplicated", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of duplicated reads collected from samtools. Number", - "rdfs:label": "ProportionReadsDuplicated", - "rdfs:subClassOf": [ + "@id": "bts:LossofExpression" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Reads Duplicated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionReadsMapped", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mapped reads collected from samtools. Number", - "rdfs:label": "ProportionReadsMapped", - "rdfs:subClassOf": [ + "@id": "bts:Low" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Reads Mapped", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionTargetsNoCoverage", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number", - "rdfs:label": "ProportionTargetsNoCoverage", - "rdfs:subClassOf": [ + "@id": "bts:Negative" + }, { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Proportion Targets No Coverage", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ProportionBaseMismatch", - "@type": "rdfs:Class", - "rdfs:comment": "Proportion of mismatched bases collected from samtools. 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NO PHI/PII INFORMATION IS ALLOWED.", - "rdfs:label": "TimepointLabel", - "rdfs:subClassOf": [ + "@id": "bts:Maincarina" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Timepoint Label", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'", - "rdfs:label": "CollectionDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:Left" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Collection Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:ProtocolLink", - "@type": "rdfs:Class", - "rdfs:comment": "Protocols.io ID or DOI link to a free/open protocol resource describing in detail 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": [ + "@id": "bts:Right" + }, { - "@id": "bts:InformationContentEntity" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Protocol Link", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AdjacentBiospecimenIDs", - "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...", - "rdfs:label": "AdjacentBiospecimenIDs", - "rdfs:subClassOf": [ + "@id": "bts:Unknown" + }, { - "@id": "bts:Biospecimen" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Adjacent Biospecimen IDs", + "sms:displayName": "Lung Tumor Location Anatomic Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MountingMedium", + "@id": "bts:LungTumorLobeBronchialLocation", "@type": "rdfs:Class", - "rdfs:comment": "The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media", - "rdfs:label": "MountingMedium", + "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", + "rdfs:label": "LungTumorLobeBronchialLocation", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -17703,25 +11437,19 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Aqueouswaterbased" - }, - { - "@id": "bts:Non-AqueousSolventbased" - }, - { - "@id": "bts:Xylene" + "@id": "bts:Upperlobe" }, { - "@id": "bts:Toluene" + "@id": "bts:Middlelobe" }, { - "@id": "bts:AntifadewithDAPI" + "@id": "bts:Lowerlobe" }, { - "@id": "bts:AntifadewithoutDAPI" + "@id": "bts:Stump" }, { - "@id": "bts:PBS" + "@id": "bts:Bronchus" }, { "@id": "bts:Unknown" @@ -17730,18 +11458,18 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Mounting Medium", + "sms:displayName": "Lung Tumor Lobe Bronchial Location", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AnalyteType", + "@id": "bts:CurrentLungCancerSymptoms", "@type": "rdfs:Class", - "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", - "rdfs:label": "AnalyteType", + "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", + "rdfs:label": "CurrentLungCancerSymptoms", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -17749,181 +11477,114 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CfDNAAnalyte" - }, - { - "@id": "bts:DNAAnalyte" + "@id": "bts:Asbestosis" }, { - "@id": "bts:RNAAnalyte" + "@id": "bts:Productivecough" }, { - "@id": "bts:TotalRNAAnalyte" + "@id": "bts:Non-productivecough" }, { - "@id": "bts:TissueBlockAnalyte" + "@id": "bts:Wheezing" }, { - "@id": "bts:TissueSectionAnalyte" + "@id": "bts:Rhonci" }, { - "@id": "bts:PBMCsorPlasmaorSerumAnalyte" + "@id": "bts:Crackles" }, { - "@id": "bts:CDNALibrariesAnalyte" + "@id": "bts:Hemoptysis" }, { - "@id": "bts:PBMCs" + "@id": "bts:Dyspnea" }, { - "@id": "bts:Plasma" + "@id": "bts:Unexplainedweightloss" }, { - "@id": "bts:SerumAnalyte" + "@id": "bts:Unexplainedlossofenergy/fatigue" }, { - "@id": "bts:Lipid" + "@id": "bts:Chestpainordiscomfort" }, { - "@id": "bts:Protein" + "@id": "bts:Dysphagia" }, { - "@id": "bts:Metabolite" - } - ], - "sms:displayName": "Analyte Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "Records the method of acquisition or source for the specimen under consideration.", - "rdfs:label": "AcquisitionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Autopsy" + "@id": "bts:Pneumonia" }, { - "@id": "bts:Biopsy" + "@id": "bts:Hoarseness/laryngitis/vocalcordinflammation" }, { - "@id": "bts:FineNeedleAspirate" + "@id": "bts:Airentrydecreased/fair/poor/diminished" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:Fair/pooraeration" }, { - "@id": "bts:PunchBiopsy" + "@id": "bts:Shallowinspiration" }, { - "@id": "bts:ShaveBiopsy" + "@id": "bts:Breathsoundscoarse/diminished" }, { - "@id": "bts:Excision" + "@id": "bts:Dullnesstopercussion" }, { - "@id": "bts:Re-excision" + "@id": "bts:Abnormalbreathsounds" }, { - "@id": "bts:SentinelNodeBiopsy" + "@id": "bts:Clearlungstoauscultationorpercussion" }, { - "@id": "bts:Lymphadenectomy-RegionalNodes" + "@id": "bts:Unlabored/normalbreathing" }, { - "@id": "bts:OtherAcquisitionMethod" + "@id": "bts:Coldsymptoms/flu/sinus/nasalcongestion" }, { - "@id": "bts:Noninducedsputum" + "@id": "bts:Sinuspain/infection" }, { - "@id": "bts:Inducedsputum" + "@id": "bts:Fingerclubbing" }, { - "@id": "bts:BAL(bronchialalveolarlavage)" + "@id": "bts:Noevidenceoflungcancerrecurrence" }, { - "@id": "bts:Cytobrush" + "@id": "bts:PatientisNED" }, { - "@id": "bts:Blooddraw" + "@id": "bts:Oxygensupplemental-portableO2atnightorcontinuous" }, { - "@id": "bts:Fluidcollection" + "@id": "bts:Prolongedexpiration-long/forcedexpiratoryphase" }, { - "@id": "bts:Forcepsbiopsy" + "@id": "bts:Other" }, { - "@id": "bts:Coreneedlebiopsy" + "@id": "bts:Unknown" }, { - "@id": "bts:Endoscopicbiopsy" - }, - { - "@id": "bts:Notspecified" - } - ], - "sms:displayName": "Acquisition Method Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:OtherAcquisitionMethod", - "@type": "rdfs:Class", - "rdfs:comment": "A custom acquisition method", - "rdfs:label": "OtherAcquisitionMethod", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Other Acquisition Method", + "sms:displayName": "Current Lung Cancer Symptoms", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AcquisitionMethodOtherSpecify" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:AcquisitionMethodOtherSpecify", - "@type": "rdfs:Class", - "rdfs:comment": "A custom acquisition method [Text - max length 100 characters]", - "rdfs:label": "AcquisitionMethodOtherSpecify", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Acquisition Method Other Specify", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PreservationMethod", + "@id": "bts:LungTopography", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the method used to preserve the sample.", - "rdfs:label": "PreservationMethod", + "rdfs:comment": "Lung PCA specific topography (not covered in previous tiers)", + "rdfs:label": "LungTopography", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -17931,468 +11592,279 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Cryopreserved" + "@id": "bts:MC-Carinabetweenrightandleftlungs(maincarina)" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-deadtissue" + "@id": "bts:TR-Trachea(airwaywallbetweentracheo-esophagealbifurcationandmaincarina)" }, { - "@id": "bts:Cryopreservationindryice-deadtissue" + "@id": "bts:CarinaNOS(Carinanototherwisespecified)" }, { - "@id": "bts:Cryopreservationinliquidnitrogen-livecells" + "@id": "bts:LUDB-Carinabetweenthelingulaandupperdivisionleftupperlobe" }, { - "@id": "bts:Formalinfixedparaffinembedded-FFPE" + "@id": "bts:CarinabetweenLUDBorificeandlingulaorifice" }, { - "@id": "bts:Formalinfixed-unbuffered" + "@id": "bts:LUDB-orificeairwaywallbetweenLUDBandLB3(LB1+2carinae)" }, { - "@id": "bts:Formalinfixed-buffered" + "@id": "bts:LingulaorificeairwaywallbetweenLUDBandLB4/5carinae" }, { - "@id": "bts:Fresh" + "@id": "bts:RMB-Rightmainstembronchus(airwaywallbetweenMC&RULcarina)" }, { - "@id": "bts:FreshdissociatedandsinglecellsortedintoplatesinNP40buffer" + "@id": "bts:LMB-Leftmainstembronchus(airwaywallbetweenMC&LULcarina)" }, { - "@id": "bts:OCT" + "@id": "bts:RLNOS(Rightlungnototherwisespecified)" }, { - "@id": "bts:SnapFrozen" + "@id": "bts:RB1/2-Carinabetweenapicalandposteriorsegmentsrightupperlobe(CarinabetweenRB1orificeandRB2orifice)" }, { - "@id": "bts:Frozen" + "@id": "bts:RB6A/B-CarinabetweenapicalandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:Negative80DegC" + "@id": "bts:RB6A/C-CarinabetweenapicalandmedialsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:RB6B/C-CarinabetweenmedialandlateralsubsegmentssuperiorsegmentRLL" }, { - "@id": "bts:Freshdissociated" + "@id": "bts:RB7A/B-CarinabetweenmedialandlateralsubsegmentsmedialbasalsegmentRLL" }, { - "@id": "bts:Freshdissociatedandsinglecellsorted" + "@id": "bts:RB8/9-CarinabetweenanteriorandlateralsegmentsRLL(CarinabetweenRB8orificeandRB9orifice)" }, { - "@id": "bts:Freshdissociatedandsinglecellsortedintoplates" + "@id": "bts:RB8A/B-CarinabetweenmedialandlateralsubsegmentsanteriorsegmentRLL" }, { - "@id": "bts:Methacarnfixedparaffinembedded-MFPE" + "@id": "bts:RB9/10-CarinabetweenlateralandposteriorsegmentsRLL" }, { - "@id": "bts:Unknown" + "@id": "bts:RB9A/B-CarinabetweenmedialandlateralsubsegmentslateralsegmentRLL" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Preservation Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:FixativeType", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the type of fixative used to preserve a tissue specimen", - "rdfs:label": "FixativeType", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Acetone" + "@id": "bts:RB10A/B-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:Alcohol" + "@id": "bts:RB10A/C-CarinabetweenmedialandapicalsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:Formalin" + "@id": "bts:RB1A/B-CarinabetweenmedialandlateralsubsegmentsapicalsegmentRUL" }, { - "@id": "bts:Glutaraldehyde" + "@id": "bts:RB10B/C-CarinabetweenmedialandlateralsubsegmentsposteriorsegmentRLL" }, { - "@id": "bts:OCTmedia" + "@id": "bts:RB6-CarinaofsuperiorsegmentRLL(CarinabetweenRB6orificeandlowerportionofRLLorifice)" }, { - "@id": "bts:RNAlater" + "@id": "bts:RB6orificeAirwaywallbetweenRB6andRB6A/B/Ccarinae" }, { - "@id": "bts:Saline" + "@id": "bts:BronchusIntermediusBronchus(airwaywall)betweenrightupperandrightmiddlelobes" }, { - "@id": "bts:95%Ethanol" + "@id": "bts:RB1/3-CarinabetweenapicalandanteriorsegmentsRUL(CarinabetweenRB1orificeandRB3orifice)" }, { - "@id": "bts:Dimidoester" + "@id": "bts:RB2/3-CarinabetweenanteriorandposteriorsegmentsRUL(CarinabetweenRB2orificeandRB3orifice)" }, { - "@id": "bts:Carbodiimide" + "@id": "bts:RB2A/B-Carinabetweenthemedialandlateralsubsegmentsoftheposteriorsegment(RUL)" }, { - "@id": "bts:Dimethylacetamide" + "@id": "bts:RB3A/B-CarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentRUL" }, { - "@id": "bts:Para-benzoquinone" + "@id": "bts:RB4/5-Carinabetweenthelateralandmedialsegmentsrightmiddlelobe(CarinabetweenRB4orificeandRB5orifice)" }, { - "@id": "bts:PAXgenetissue" + "@id": "bts:RB4A/B-Carinabetweenthemedialandlateralsubsegmentsofthelateralsegmentoftherightmiddlelobe" }, { - "@id": "bts:TCLlysisbuffer" + "@id": "bts:RB5A/B-Carinabetweenthemedialandlateralsubsegmentsofthemedialsegmentoftherightmiddlelobe" }, { - "@id": "bts:NP40lysisbuffer" + "@id": "bts:RULCarinaebetweenRULorificeandbronchusintermedius" }, { - "@id": "bts:Methacarn" + "@id": "bts:RULorificeAirwaywallbetweenRULandRB1/RB2/RB3" }, { - "@id": "bts:Cryo-store" + "@id": "bts:RB1orificeApicalsegment-rightupperlobe(airwaywallbetweenRB1andRB1A/Bcarinae)" }, { - "@id": "bts:Carnoy'sFixative" + "@id": "bts:RB2orificePosteriorsegment-rightupperlobe(airwaywallbetweenRB2andRB2A/Bcarinae)" }, { - "@id": "bts:Polaxamer" + "@id": "bts:RB3orificeAnteriorsegment-rightupperlobe(airwaywallbetweenRB3andRB3A/Bcarinae)" }, { - "@id": "bts:Other" + "@id": "bts:RML-CarinabetweenRMLorificeandRLLorifice" }, { - "@id": "bts:None" + "@id": "bts:RMLorificeAirwaywallbetweenRMLandRB4/5" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Fixative Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@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": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Fixation Duration", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@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:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Ischemic Time", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:IschemicTemperature", - "@type": "rdfs:Class", - "rdfs:comment": "Specify whether specimen experienced warm or cold ischemia.", - "rdfs:label": "IschemicTemperature", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:WarmIschemia" + "@id": "bts:RB4orificeLateralsegmentrightmiddlelobe(airwaywallbetweenRB4andRB4A/Bcarinae)" }, { - "@id": "bts:ColdIschemia" + "@id": "bts:RB5orificeMedialsegmentrightmiddlelobe(airwaywallbetweenRB5andRB5A/Bcarinae)" }, { - "@id": "bts:Ambientair" + "@id": "bts:RLLorificeAirwaywallbetweenRMLandRB6-10carinae" }, { - "@id": "bts:4Cwetice" + "@id": "bts:RB7Medialbasalsegmentrightlowerlobe(CarinaatRB7orificetakeofffromRLLorifice)" }, { - "@id": "bts:Negative-20C" + "@id": "bts:RB7orificeAirwaywallbetweenRB7andRB7A/Bcarinae" }, { - "@id": "bts:DryIce" + "@id": "bts:RB8orificeAnteriorsegmentrightlowerlobe(airwaywallbetweenRB8andRB8A/Bcarinae)" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:RB9orificeLateralsegmentrightlowerlobe(airwaywallbetweenRB9andRB9A/Bcarinae)" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Ischemic Temperature", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CollectionMedia", - "@type": "rdfs:Class", - "rdfs:comment": "Material Specimen is collected into post procedure", - "rdfs:label": "CollectionMedia", - "rdfs:subClassOf": [ - { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:RB10Posteriorsegmentrightlowerlobe(CarinaatRB10orificetakeofffromRLLorifice)" + }, { - "@id": "bts:DMEM" + "@id": "bts:RB10orificeAirwaywallbetweenRB10andRB10A/Bcarinae" }, { - "@id": "bts:DMEM+Serum" + "@id": "bts:LLNOS(Leftlungnototherwisespecified)" }, { - "@id": "bts:RPMI" + "@id": "bts:LB1/2Carinabetweenapicalandposteriorsegmentleftupperlobe(CarinabetweenLB1orificeandLB2orifice)" }, { - "@id": "bts:RPMI+Serum" + "@id": "bts:LB4/5Carinabetweensuperiorandinferiorsegmentlingula(CarinabetweenLB4orificeandLB5orifice)" }, { - "@id": "bts:PBS" + "@id": "bts:LB4A/BCarinabetweenmedialandlateralsubsegmentssuperiorsegmentlingula" }, { - "@id": "bts:PBS+Serum" + "@id": "bts:LB5A/BCarinabetweenthemedialandlateralsubsegmentsinferiorsegmentlingula" }, { - "@id": "bts:None" - } - ], - "sms:displayName": "Collection Media", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SpecimenLaterality", - "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the specimen was obtained.", - "rdfs:label": "SpecimenLaterality", - "rdfs:subClassOf": [ + "@id": "bts:LB6A/BCarinabetweenthesuperiorandlateralsubsegmentssuperiorsegmentLLL" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LB6A/CCarinabetweenthesuperiorandmedialsubsegmentsofsuperiorsegmentLLL" + }, { - "@id": "bts:Bilateral" + "@id": "bts:LB6B/CCarinabetweenthemedialandlateralsubsegmentsofthesuperiorsegmentLLL" }, { - "@id": "bts:Left" + "@id": "bts:LB8/9CarinabetweentheanteriorandlateralsegmentsLLL(CarinabetweenLB8orificeandLB9orifice)" }, { - "@id": "bts:Right" + "@id": "bts:LB8A/BCarinabetweenthemedialandlateralsubsegmentsoftheanteriorsegmentLLL" }, { - "@id": "bts:Unknown" + "@id": "bts:LB9/10CarinabetweenthelateralandposteriorsegmentsLLL(CarinabetweenLB9orificeandLB10orifice)" }, { - "@id": "bts:NotReported" + "@id": "bts:LB9A/BCarinabetweenthemedialandlateralsubsegmentsofthelateralsegmentLLL" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Specimen Laterality", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:PortionWeight", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the sample portion weight, measured in milligrams.", - "rdfs:label": "PortionWeight", - "rdfs:subClassOf": [ + "@id": "bts:LB1A/BCarinabetweenthelateralandmedialsubsegmentsoftheapicalsegmentoftheLUL" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Portion Weight", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TotalVolume", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value for the total amount of sample or specimen", - "rdfs:label": "TotalVolume", - "rdfs:subClassOf": [ + "@id": "bts:LB10A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Total Volume", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "@id": "bts:LB10A/CCarinabetweentheapicalandmedialsegmentsoftheposteriorsegmentoftheLLL" + }, { - "@id": "bts:TotalVolumeUnit" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:TotalVolumeUnit", - "@type": "rdfs:Class", - "rdfs:comment": "Unit of measurement used for the total amount of sample or specimen", - "rdfs:label": "TotalVolumeUnit", - "rdfs:subClassOf": [ + "@id": "bts:LB10B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentoftheLLL" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LB1+2orificeTheapico-posteriorsegmentoftheleftupperlobe(airwaywallbetweenLB1+2/3carinaandLB1orLB2)" + }, { - "@id": "bts:ML" + "@id": "bts:LB6Thesuperiorsegmentoftheleftlowerlobe(CarinabetweenLB6orificeandlowerportionofLLLorifice)" }, { - "@id": "bts:Cubicmillimeter" + "@id": "bts:LB6orificeAirwaywallbetweenLB6andLB6A/Bcarinae" }, { - "@id": "bts:Squarecentimeter" - } - ], - "sms:displayName": "Total Volume Unit", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorTissueType", - "@type": "rdfs:Class", - "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": "TumorTissueType", - "rdfs:subClassOf": [ + "@id": "bts:LB1A/CCarinabetweentheapicalandlateralsubsegmentsoftheapicalsegmentleftupperlobe" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LB1B/CCarinabetweenthemedialandlateralsubsegmentsoftheapicalsegmentoftheleftupperlobe" + }, { - "@id": "bts:AdditionalPrimary" + "@id": "bts:LB2A/BCarinabetweentheapicalandlateralsubsegmentsoftheposteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:Localrecurrence" + "@id": "bts:LB2A/CCarinabetweentheapicalandmedialsubsegmentsoftheposteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:Metastatic" + "@id": "bts:LB2B/CCarinabetweenthemedialandlateralsubsegmentsoftheposteriorsegmentleftupperlobe" }, { - "@id": "bts:Premalignant" + "@id": "bts:LB1+2/3Carinabetweentheapico-posteriorandanteriorsegmentsoftheleftupperlobe(CarinabetweenLB1+2orificeandLB3orifice)" }, { - "@id": "bts:Primary" + "@id": "bts:LB3A/BCarinabetweentheapicalandlateralsubsegmentsoftheanteriorsegmentoftheleftupperlobe" }, { - "@id": "bts:Recurrent" + "@id": "bts:LULCarinabetweentheLULorificeandLLLorifice(airways)" }, { - "@id": "bts:Normal" + "@id": "bts:LULorificeAirwaywallbetweenLULandLUDB" }, { - "@id": "bts:Normaladjacent" + "@id": "bts:LB3orificeAnteriorsegmentleftupperlobe(airwaywallbetweenLB3andLB3A/Bcarinae)" }, { - "@id": "bts:Normaldistant" + "@id": "bts:LB4orificeSuperiorsegmentlingula(airwaywallbetweenLB4andLB4A/Bcarinae)" }, { - "@id": "bts:Posttherapy" + "@id": "bts:LB5orificeInferiorsegmentlingula(airwaywallbetweenLB5andLB5A/Bcarinae)" }, { - "@id": "bts:Posttherapyneoadjuvant" + "@id": "bts:LLLorificeAirwaywallbetweenLULcarinaandLB6-10carinae" }, { - "@id": "bts:Posttherapyadjuvant" + "@id": "bts:LB9orificeLateralsegmentleftlowerlobe(airwaywallbetweenLB9andLB9A/Bcarinae)" }, { - "@id": "bts:NotOtherwiseSpecified" + "@id": "bts:LB8orificeAnteriorsegmentleftlowerlobe(airwaywallbetweenLB8andLB8A/Bcarinae)" }, { - "@id": "bts:Premalignant-insitu" + "@id": "bts:LB10orificePosteriorsegmentleftlowerlobe(airwaywallbetweenLB10andLB10A/Bcarinae)" }, { - "@id": "bts:Atypia-hyperplasia" + "@id": "bts:Other" }, { - "@id": "bts:Notanalyzed" - } - ], - "sms:displayName": "Tumor Tissue Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:HistologicMorphologyCode", - "@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:subClassOf": [ + "@id": "bts:Unknown" + }, { - "@id": "bts:Biospecimen" + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Histologic Morphology Code", - "sms:required": "sms:true", + "sms:displayName": "Lung Topography", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PreinvasiveMorphology", + "@id": "bts:LungCancerHarboringGenomicAberrations", "@type": "rdfs:Class", - "rdfs:comment": "Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN", - "rdfs:label": "PreinvasiveMorphology", + "rdfs:comment": "Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)", + "rdfs:label": "LungCancerHarboringGenomicAberrations", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:LungCancerTier3" } ], "schema:isPartOf": { @@ -18400,273 +11872,237 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Melanocytichyperplasia" + "@id": "bts:G12AKRASmutation" }, { - "@id": "bts:Atypicalmelanocyticproliferation" + "@id": "bts:G12CKRASmutation" }, { - "@id": "bts:Melanomainsitu-superficialspreading" + "@id": "bts:G12DKRASmutation" }, { - "@id": "bts:Melanomainsitu-lentigomalignatype" + "@id": "bts:G12RKRASmutation" }, { - "@id": "bts:Melanomainsitu-acral-lentiginous" + "@id": "bts:G12SKRASmutation" }, { - "@id": "bts:Melanomainsitu-arisinginagiantcongenitalnevus" + "@id": "bts:G12VKRASmutation" }, { - "@id": "bts:Persistentmelanomainsitu" + "@id": "bts:G13DKRASmutation" }, { - "@id": "bts:Melanomainsitu-nototherwiseclassified" + "@id": "bts:G13RKRASmutation" }, { - "@id": "bts:Scar-noresidualmelanoma" + "@id": "bts:G13CKRASmutation" }, { - "@id": "bts:Invasivemelanoma-superficialspreading" + "@id": "bts:G13AKRASmutation" }, { - "@id": "bts:Invasivemelanoma-nodulartype" + "@id": "bts:G13VKRASmutation" }, { - "@id": "bts:Invasivemelanoma-lentigomaligna" + "@id": "bts:Q61LKRASmutation" }, { - "@id": "bts:Invasivemelanoma-acrallentiginous" + "@id": "bts:Q61HKRASmutation" }, { - "@id": "bts:Invasivemelanoma-desmoplastic" + "@id": "bts:A146TKRASmutation" }, { - "@id": "bts:Invasivemelanoma-nevoid" + "@id": "bts:G719XEGFRmutation" }, { - "@id": "bts:Invasivemelanoma-other" + "@id": "bts:T790MEGFRmutation" }, { - "@id": "bts:NormalWDA" + "@id": "bts:C797SEGFRmutation" }, { - "@id": "bts:Reservecellhyperplasia" + "@id": "bts:L858REGFRmutation" }, { - "@id": "bts:Squamousmetaplasia-mature" + "@id": "bts:L861QEGFRmutation" }, { - "@id": "bts:Squamousmetaplasia-immature" + "@id": "bts:Exon19deletion" }, { - "@id": "bts:Milddysplasia" + "@id": "bts:Exon20insertion" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:EML4-ALKtranslocation-variant1" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:EML4-ALKtranslocation-variant2" }, { - "@id": "bts:SquamousCarcinomainsitu" + "@id": "bts:EML4-ALKtranslocation-variant3" }, { - "@id": "bts:Atypicaladenomatoushyperplasia" + "@id": "bts:EML4-ALKtranslocation-variant4" }, { - "@id": "bts:Adenocarcinomainsitu-nonmucinous" + "@id": "bts:EML4-ALKtranslocation-variant5" }, { - "@id": "bts:Adenocarcinomainsitu-mucinous" + "@id": "bts:V600EBRAFmutation" }, { - "@id": "bts:BenigntumorNOS" + "@id": "bts:V600DBRAFmutation" }, { - "@id": "bts:Hamartoma" + "@id": "bts:V600KBRAFmutation" }, { - "@id": "bts:CarcinomaNOS" + "@id": "bts:V600RBRAFmutation" }, { - "@id": "bts:Nodiagnosispossible" - } - ], - "sms:displayName": "Preinvasive Morphology", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SlideChargeType", - "@type": "rdfs:Class", - "rdfs:comment": "A description of the charge on the glass slide.", - "rdfs:label": "SlideChargeType", - "rdfs:subClassOf": [ + "@id": "bts:K601EBRAFmutation" + }, { - "@id": "bts:Biospecimen" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:D963spliceMETmutation" + }, { - "@id": "bts:Uncharged" + "@id": "bts:D1010NMETmutation" }, { - "@id": "bts:Charged" + "@id": "bts:D1010spliceMETmutation" }, { - "@id": "bts:Coverslip" + "@id": "bts:Intron13mutation" }, { - "@id": "bts:Notapplicable" + "@id": "bts:Intron14mutation" + }, + { + "@id": "bts:Exon14mutation" + }, + { + "@id": "bts:Exon14deletion" }, { "@id": "bts:Other" - } - ], - "sms:displayName": "Slide Charge Type", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:SectionThicknessValue", - "@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:subClassOf": [ + }, { - "@id": "bts:Biospecimen" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Section Thickness Value", - "sms:required": "sms:true", + "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SectioningDaysfromIndex", + "@id": "bts:ColorectalCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable'", - "rdfs:label": "SectioningDaysfromIndex", + "rdfs:comment": "Colorectal cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ColorectalCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sectioning Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:StorageMethod", - "@type": "rdfs:Class", - "rdfs:comment": "The method by which a biomaterial was stored after preservation or before another protocol was used.", - "rdfs:label": "StorageMethod", - "rdfs:subClassOf": [ + "sms:displayName": "Colorectal Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Ambienttemperature" + "@id": "bts:Component" }, { - "@id": "bts:Cutslide" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Fresh" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Frozenat-70C" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Frozenat-80C" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Frozenat-150C" + "@id": "bts:ColorectalCancerDetectionMethodType" }, { - "@id": "bts:Frozeninliquidnitrogen" + "@id": "bts:HistoryofPriorColonPolyps" }, { - "@id": "bts:Frozeninvaporphase" + "@id": "bts:FamilyColonCancerHistoryIndicator" }, { - "@id": "bts:Paraffinblock" + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis" }, { - "@id": "bts:RNAlaterat4C" + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer" }, { - "@id": "bts:RNAlaterat25C" + "@id": "bts:ImmediateFamilyHistoryOvarianCancer" }, { - "@id": "bts:RNAlaterat-20C" + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory" }, { - "@id": "bts:Refrigeratedat4degrees" + "@id": "bts:PatientColonoscopyPerformedIndicator" }, { - "@id": "bts:Refrigeratedvacuumchamber" + "@id": "bts:ColorectalCancerTumorBorderConfiguration" }, { - "@id": "bts:4Cinvacuumchamber" + "@id": "bts:MLH1PromoterMethylationStatus" }, { - "@id": "bts:Desiccantat4C" + "@id": "bts:ColorectalCancerKRASIndicator" }, { - "@id": "bts:NotApplicable" + "@id": "bts:ColonPolypOccurenceIndicator" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Storage Method", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:ProcessingDaysfromIndex", - "@type": "rdfs:Class", - "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'", - "rdfs:label": "ProcessingDaysfromIndex", - "rdfs:subClassOf": [ + "@id": "bts:FamilyHistoryColorectalPolyp" + }, { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalPolypNewIndicator" + }, + { + "@id": "bts:ColorectalPolypShape" + }, + { + "@id": "bts:SizeofPolypRemoved" + }, + { + "@id": "bts:ColorectalPolypCount" + }, + { + "@id": "bts:ColorectalPolypType" + }, + { + "@id": "bts:ColorectalPolypAdenomaType" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Processing Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:ShippingConditionType", + "@id": "bts:ColorectalCancerDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Text descriptor of the shipping environment of a biospecimen.", - "rdfs:label": "ShippingConditionType", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", + "rdfs:label": "ColorectalCancerDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -18674,76 +12110,104 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AmbientPack" + "@id": "bts:Fecaloccultbloodtest" }, { - "@id": "bts:ColdPack" + "@id": "bts:Sigmoidoscopy" }, { - "@id": "bts:DryIce" + "@id": "bts:Colonoscopy" }, { - "@id": "bts:IcePack" + "@id": "bts:Virtualcolonoscopy" }, { - "@id": "bts:LiquidNitrogen" + "@id": "bts:DNAstooltest" }, { - "@id": "bts:SpecimenatRoomTemperature" + "@id": "bts:Other" }, { - "@id": "bts:OtherShippingEnvironment" + "@id": "bts:Unknown" }, { - "@id": "bts:NotShipped" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Shipping Condition Type", - "sms:required": "sms:true", + "sms:displayName": "Colorectal Cancer Detection Method Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SiteDataSource", + "@id": "bts:HistoryofPriorColonPolyps", "@type": "rdfs:Class", - "rdfs:comment": "Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.", - "rdfs:label": "SiteDataSource", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "HistoryofPriorColonPolyps", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Site Data Source", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "History of Prior Colon Polyps", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProcessingLocation", + "@id": "bts:FamilyColonCancerHistoryIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.", - "rdfs:label": "ProcessingLocation", + "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", + "rdfs:label": "FamilyColonCancerHistoryIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Processing Location", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Family Colon Cancer History Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentBy", + "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "Text term describing who (in what role) made the histological assessments of the sample", - "rdfs:label": "HistologyAssessmentBy", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -18751,30 +12215,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Pathologist" + "@id": "bts:Yes" }, { - "@id": "bts:ResearchScientist" + "@id": "bts:No" }, { - "@id": "bts:Other" + "@id": "bts:NotApplicable" }, { "@id": "bts:Unknown" } ], - "sms:displayName": "Histology Assessment By", + "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistologyAssessmentMedium", + "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", "@type": "rdfs:Class", - "rdfs:comment": "The method of assessment used to characterize histology", - "rdfs:label": "HistologyAssessmentMedium", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -18782,47 +12246,61 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Digital" + "@id": "bts:Beforeage50" }, { - "@id": "bts:Microscopy" + "@id": "bts:Notbeforeage50" }, { - "@id": "bts:Other" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Histology Assessment Medium", + "sms:displayName": "Immediate Family History Endometrial Cancer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorInfiltratingLymphocytes", + "@id": "bts:ImmediateFamilyHistoryOvarianCancer", "@type": "rdfs:Class", - "rdfs:comment": "Measure of Tumor-Infiltrating Lymphocytes [Number]", - "rdfs:label": "TumorInfiltratingLymphocytes", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Tumor Infiltrating Lymphocytes", + "schema:rangeIncludes": [ + { + "@id": "bts:Beforeage50" + }, + { + "@id": "bts:Notbeforeage50" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Immediate Family History Ovarian Cancer", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DegreeofDysplasia", + "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", "@type": "rdfs:Class", - "rdfs:comment": "Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.", - "rdfs:label": "DegreeofDysplasia", + "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", + "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { @@ -18830,297 +12308,539 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Normalorbasalcellhyperplasiaormetaplasia" - }, - { - "@id": "bts:Milddysplasia" + "@id": "bts:Yes-Crohn'sdisease" }, { - "@id": "bts:Moderatedysplasia" + "@id": "bts:Yes-Ulcerativecolitis" }, { - "@id": "bts:Severedysplasia" + "@id": "bts:No" }, { - "@id": "bts:CarcinomainSitu" + "@id": "bts:Unknown" }, { - "@id": "bts:Unknown" + "@id": "bts:NotApplicable" } ], - "sms:displayName": "Degree of Dysplasia", + "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DysplasiaFraction", + "@id": "bts:PatientColonoscopyPerformedIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]", - "rdfs:label": "DysplasiaFraction", + "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", + "rdfs:label": "PatientColonoscopyPerformedIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dysplasia Fraction", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NumberProliferatingCells", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).", - "rdfs:label": "NumberProliferatingCells", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:NotApplicable" + }, + { + "@id": "bts:Unknown" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Number Proliferating Cells", + "sms:displayName": "Patient Colonoscopy Performed Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentEosinophilInfiltration", + "@id": "bts:ColorectalCancerTumorBorderConfiguration", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.", - "rdfs:label": "PercentEosinophilInfiltration", + "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", + "rdfs:label": "ColorectalCancerTumorBorderConfiguration", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Eosinophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:Infiltrating" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Pushing" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Cancer Tumor Border Configuration", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentGranulocyteInfiltration", + "@id": "bts:MLH1PromoterMethylationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.", - "rdfs:label": "PercentGranulocyteInfiltration", + "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", + "rdfs:label": "MLH1PromoterMethylationStatus", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Granulocyte Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Indeterminate" + }, + { + "@id": "bts:NotAssessed" + }, + { + "@id": "bts:Present" + } + ], + "sms:displayName": "MLH1 Promoter Methylation Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentInflamInfiltration", + "@id": "bts:ColorectalCancerKRASIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.", - "rdfs:label": "PercentInflamInfiltration", + "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", + "rdfs:label": "ColorectalCancerKRASIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Inflam Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Cancer KRAS Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentLymphocyteInfiltration", + "@id": "bts:ColonPolypOccurenceIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.", - "rdfs:label": "PercentLymphocyteInfiltration", + "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", + "rdfs:label": "ColonPolypOccurenceIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Lymphocyte Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colon Polyp Occurence Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentMonocyteInfiltration", + "@id": "bts:FamilyHistoryColorectalPolyp", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.", - "rdfs:label": "PercentMonocyteInfiltration", + "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", + "rdfs:label": "FamilyHistoryColorectalPolyp", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Monocyte Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Family History Colorectal Polyp", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNecrosis", + "@id": "bts:ColorectalPolypNewIndicator", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNecrosis", + "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", + "rdfs:label": "ColorectalPolypNewIndicator", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Necrosis", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp New Indicator", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNeutrophilInfiltration", + "@id": "bts:ColorectalPolypShape", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.", - "rdfs:label": "PercentNeutrophilInfiltration", + "rdfs:comment": "Shape of polyp identified in the participant", + "rdfs:label": "ColorectalPolypShape", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Neutrophil Infiltration", + "schema:rangeIncludes": [ + { + "@id": "bts:Pedunculated" + }, + { + "@id": "bts:Sessile" + }, + { + "@id": "bts:Flat" + }, + { + "@id": "bts:Notstated" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp Shape", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentNormalCells", + "@id": "bts:SizeofPolypRemoved", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.", - "rdfs:label": "PercentNormalCells", + "rdfs:comment": "Size of the polyp removed in cm", + "rdfs:label": "SizeofPolypRemoved", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Normal Cells", + "sms:displayName": "Size of Polyp Removed", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentStromalCells", + "@id": "bts:ColorectalPolypCount", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.", - "rdfs:label": "PercentStromalCells", + "rdfs:comment": "The total number of polyps detected", + "rdfs:label": "ColorectalPolypCount", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Stromal Cells", + "sms:displayName": "Colorectal Polyp Count", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorCells", + "@id": "bts:ColorectalPolypType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the percentage of infiltration by tumor cells in a sample.", - "rdfs:label": "PercentTumorCells", + "rdfs:comment": "Type of polyp found in the participant", + "rdfs:label": "ColorectalPolypType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Cells", + "schema:rangeIncludes": [ + { + "@id": "bts:Adenoma" + }, + { + "@id": "bts:Hyperplastic" + }, + { + "@id": "bts:Mixed" + }, + { + "@id": "bts:Papillomatous" + }, + { + "@id": "bts:Normal" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Colorectal Polyp Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorNuclei", + "@id": "bts:ColorectalPolypAdenomaType", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.", - "rdfs:label": "PercentTumorNuclei", + "rdfs:comment": "Type of adenoma associated with the polyp", + "rdfs:label": "ColorectalPolypAdenomaType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:ColorectalCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Nuclei", + "schema:rangeIncludes": [ + { + "@id": "bts:Tubular" + }, + { + "@id": "bts:Villous" + }, + { + "@id": "bts:Tubulovillous" + }, + { + "@id": "bts:Sessileserrated" + }, + { + "@id": "bts:Traditionalserrated" + }, + { + "@id": "bts:Serratednotspecified" + }, + { + "@id": "bts:Notstated" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Colorectal Polyp Adenoma Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FiducialMarker", + "@id": "bts:BreastCancerTier3", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.", - "rdfs:label": "FiducialMarker", + "rdfs:comment": "Breast cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "BreastCancerTier3", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Breast Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:NuclearStain-DAPI" + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:FluorescentBeads" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:GridSlides-Hemocytometer" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:AdhesiveMarkers" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Other" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:Unknown" + "@id": "bts:BreastCarcinomaDetectionMethodType" }, { - "@id": "bts:NotReported" + "@id": "bts:BreastCarcinomaHistologyCategory" + }, + { + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory" + }, + { + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + }, + { + "@id": "bts:BreastBiopsyProcedureFindingType" + }, + { + "@id": "bts:BreastQuadrantSite" + }, + { + "@id": "bts:BreastCancerAssessmentTests" + }, + { + "@id": "bts:BreastCancerGenomicTestPerformed" + }, + { + "@id": "bts:MammaprintRiskGroup" + }, + { + "@id": "bts:OncotypeRiskGroup" + }, + { + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus" + }, + { + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus" + }, + { + "@id": "bts:BreastCancerAllredEstrogenReceptorScore" + }, + { + "@id": "bts:PriorInvasiveBreastDisease" + }, + { + "@id": "bts:BreastCarcinomaERStatusPercentageValue" + }, + { + "@id": "bts:BreastCarcinomaPRStatusPercentageValue" + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal" + }, + { + "@id": "bts:BreastCarcinomaCentromere17CopyNumber" + }, + { + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal" + }, + { + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio" + }, + { + "@id": "bts:BreastCarcinomaSurgicalProcedureName" + }, + { + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis" + }, + { + "@id": "bts:BreastCarcinomaHER2Status" + }, + { + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator" + }, + { + "@id": "bts:BreastCarcinomaERStainingIntensity" + }, + { + "@id": "bts:BreastCarcinomaPRStainingIntensity" + }, + { + "@id": "bts:OncotypeScore" + }, + { + "@id": "bts:BreastImagingPerformedType" + }, + { + "@id": "bts:MultifocalBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:MulticentricBreastCarcinomaPresentIndicator" + }, + { + "@id": "bts:BIRADSMammographyBreastDensityCategory" } ], - "sms:displayName": "Fiducial Marker", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SlicingMethod", + "@id": "bts:BreastCarcinomaDetectionMethodType", "@type": "rdfs:Class", - "rdfs:comment": "Imaging specific: the method by which the tissue was sliced.", - "rdfs:label": "SlicingMethod", + "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", + "rdfs:label": "BreastCarcinomaDetectionMethodType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19128,132 +12848,245 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Vibratome" + "@id": "bts:ClinicalExam" }, { - "@id": "bts:Cryosectioning" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:Tissuemolds" + "@id": "bts:NippleDischarge" }, { - "@id": "bts:Slidingmicrotome" + "@id": "bts:Other" }, { - "@id": "bts:Sectioning" + "@id": "bts:ScreeningMammography" }, { - "@id": "bts:Other" + "@id": "bts:ScreeningMRI" }, { - "@id": "bts:Unknown" + "@id": "bts:Selfexam" }, { - "@id": "bts:NotReported" + "@id": "bts:Unknown" } ], - "sms:displayName": "Slicing Method", + "sms:displayName": "Breast Carcinoma Detection Method Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LysisBuffer", + "@id": "bts:BreastCarcinomaHistologyCategory", "@type": "rdfs:Class", - "rdfs:comment": "scRNA-seq specific: Type of lysis buffer used", - "rdfs:label": "LysisBuffer", + "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", + "rdfs:label": "BreastCarcinomaHistologyCategory", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lysis Buffer", + "schema:rangeIncludes": [ + { + "@id": "bts:Infiltratingductalcarcinoma" + }, + { + "@id": "bts:Infiltratinglobularcarcinoma" + }, + { + "@id": "bts:InvasivemammarycarcinomaNOS" + }, + { + "@id": "bts:Invasivemixedductalandlobularcarcinoma" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Carcinoma Histology Category", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofNucleicAcidIsolation", + "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", "@type": "rdfs:Class", - "rdfs:comment": "Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]", - "rdfs:label": "MethodofNucleicAcidIsolation", + "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", + "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Method of Nucleic Acid Isolation", + "schema:rangeIncludes": [ + { + "@id": "bts:Alveolartype" + }, + { + "@id": "bts:Classicaltype" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Pleomorphictype" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenDimension1", + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", "@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": "The histologic subtype for the most common type of invasive breast carcinoma.", + "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen Dimension 1", - "sms:required": "sms:false", - "sms:requiresDependency": [ + "schema:rangeIncludes": [ { - "@id": "bts:DimensionsUnit" + "@id": "bts:Classicaltype" + }, + { + "@id": "bts:Invasivecarcinoma-typecannotbedetermined" + }, + { + "@id": "bts:Invasivecribriformcarcinoma" + }, + { + "@id": "bts:Invasivemicropapillarycarcinoma" + }, + { + "@id": "bts:Invasivepapillarycarcinoma" + }, + { + "@id": "bts:Invasivetubularcarcinoma" + }, + { + "@id": "bts:Medullarycarcinoma" + }, + { + "@id": "bts:Mucinouscarcinoma" + }, + { + "@id": "bts:Tubulolobularcarcinoma" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], + "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenDimension2", + "@id": "bts:BreastBiopsyProcedureFindingType", "@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": "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": "BreastBiopsyProcedureFindingType", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen Dimension 2", + "schema:rangeIncludes": [ + { + "@id": "bts:Atypicalhyperplasia" + }, + { + "@id": "bts:DCIS" + }, + { + "@id": "bts:LCIS" + }, + { + "@id": "bts:Cancer" + }, + { + "@id": "bts:Nocancer" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Breast Biopsy Procedure Finding Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BiospecimenDimension3", + "@id": "bts:BreastQuadrantSite", "@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": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", + "rdfs:label": "BreastQuadrantSite", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Biospecimen Dimension 3", + "schema:rangeIncludes": [ + { + "@id": "bts:Upperouterquadrant" + }, + { + "@id": "bts:Lowerouterquadrant" + }, + { + "@id": "bts:Upperinnerquadrant" + }, + { + "@id": "bts:Lowerinnerquadrant" + }, + { + "@id": "bts:Central" + }, + { + "@id": "bts:Nipple" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Breast Quadrant Site", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DimensionsUnit", + "@id": "bts:BreastCancerAssessmentTests", "@type": "rdfs:Class", - "rdfs:comment": "Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)", - "rdfs:label": "DimensionsUnit", + "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", + "rdfs:label": "BreastCancerAssessmentTests", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19261,79 +13094,147 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Mm" + "@id": "bts:EstrogenreceptorIHC" }, { - "@id": "bts:Cm" + "@id": "bts:ProgesteronereceptorIHC" + }, + { + "@id": "bts:HER2IHC" + }, + { + "@id": "bts:HER2FISH-CISH" + }, + { + "@id": "bts:HER2FISH" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Dimensions Unit", + "sms:displayName": "Breast Cancer Assessment Tests", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SectionNumberinSequence", + "@id": "bts:BreastCancerGenomicTestPerformed", "@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:comment": "Text term that represents the name of the genomic test performed for breast cancer.", + "rdfs:label": "BreastCancerGenomicTestPerformed", "rdfs:subClassOf": [ { - "@id": "bts:Biospecimen" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Section Number in Sequence", + "schema:rangeIncludes": [ + { + "@id": "bts:Oncotype" + }, + { + "@id": "bts:MammaPrint" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Notperformed" + } + ], + "sms:displayName": "Breast Cancer Genomic Test Performed", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:StartDaysfromIndex", + "@id": "bts:MammaprintRiskGroup", "@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": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", + "rdfs:label": "MammaprintRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Start Days from Index", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "schema:rangeIncludes": [ + { + "@id": "bts:Highrisk" + }, + { + "@id": "bts:Intermediaterisk" + }, + { + "@id": "bts:Lowrisk" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Mammaprint Risk Group", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:StopDaysfromIndex", + "@id": "bts:OncotypeRiskGroup", "@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": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", + "rdfs:label": "OncotypeRiskGroup", "rdfs:subClassOf": [ { - "@id": "bts:Patient" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Stop Days from Index", + "schema:rangeIncludes": [ + { + "@id": "bts:Highrisk" + }, + { + "@id": "bts:Intermediaterisk" + }, + { + "@id": "bts:Lowrisk" + }, + { + "@id": "bts:Datanotavailable" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Oncotype Risk Group", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:Ethnicity", + "@id": "bts:BreastCarcinomaEstrogenReceptorStatus", "@type": "rdfs:Class", - "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.", - "rdfs:label": "Ethnicity", + "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19341,33 +13242,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Hispanicorlatino" + "@id": "bts:Borderline" }, { - "@id": "bts:Nothispanicorlatino" + "@id": "bts:Equivocal" }, { - "@id": "bts:Unknown" + "@id": "bts:Indeterminate" }, { - "@id": "bts:NotReported" + "@id": "bts:Negative" }, { - "@id": "bts:Notallowedtocollect" + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:PerformedbutNotAvailable" + }, + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Ethnicity", - "sms:required": "sms:true", + "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Gender", + "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", "@type": "rdfs:Class", - "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.]", - "rdfs:label": "Gender", + "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19375,33 +13285,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Female" + "@id": "bts:Borderline" }, { - "@id": "bts:Male" + "@id": "bts:Equivocal" }, { - "@id": "bts:Unknown" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Unspecified" + "@id": "bts:Negative" }, { - "@id": "bts:NotReported" + "@id": "bts:NotPerformed" + }, + { + "@id": "bts:PerformedbutNotAvailable" + }, + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Gender", - "sms:required": "sms:true", + "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Race", + "@id": "bts:BreastCancerAllredEstrogenReceptorScore", "@type": "rdfs:Class", - "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.", - "rdfs:label": "Race", + "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", + "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19409,45 +13328,51 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:White" + "@id": "bts:0" }, { - "@id": "bts:Americanindianoralaskanative" + "@id": "bts:1" }, { - "@id": "bts:Blackorafricanamerican" + "@id": "bts:2" }, { - "@id": "bts:Asian" + "@id": "bts:3" }, { - "@id": "bts:Nativehawaiianorotherpacificislander" + "@id": "bts:4" }, { - "@id": "bts:Other" + "@id": "bts:5" }, { - "@id": "bts:Unknown" + "@id": "bts:6" }, { - "@id": "bts:NotReported" + "@id": "bts:7" }, { - "@id": "bts:Notallowedtocollect" + "@id": "bts:8" + }, + { + "@id": "bts:10" + }, + { + "@id": "bts:Unknown" } ], - "sms:displayName": "Race", - "sms:required": "sms:true", + "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VitalStatus", + "@id": "bts:PriorInvasiveBreastDisease", "@type": "rdfs:Class", - "rdfs:comment": "The survival state of the person registered on the protocol.", - "rdfs:label": "VitalStatus", + "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", + "rdfs:label": "PriorInvasiveBreastDisease", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19455,97 +13380,138 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Alive" + "@id": "bts:DCIS" }, { - "@id": "bts:Dead" + "@id": "bts:LCIS" + }, + { + "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" }, { - "@id": "bts:NotReported" + "@id": "bts:Datanotavailable" } ], - "sms:displayName": "Vital Status", - "sms:required": "sms:true", + "sms:displayName": "Prior Invasive Breast Disease", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Dead", + "@id": "bts:BreastCarcinomaERStatusPercentageValue", "@type": "rdfs:Class", - "rdfs:comment": "This indicates the participant is dead and defines further required metadata", - "rdfs:label": "Dead", + "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": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dead", + "sms:displayName": "Breast Carcinoma ER Status Percentage Value", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:YearofDeath" - }, + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaPRStatusPercentageValue", + "@type": "rdfs:Class", + "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": [ { - "@id": "bts:CauseofDeath" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@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:subClassOf": [ { - "@id": "bts:CauseofDeathSource" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@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:DaystoDeath" + "@id": "bts:BreastCancerTier3" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoBirth", + "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", "@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. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoBirth", + "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Birth", + "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] + "sms:validationRules": [] }, { - "@id": "bts:YearofDeath", + "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of the death of an individual.", - "rdfs:label": "YearofDeath", + "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year of Death", - "sms:required": "sms:true", + "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CountryofResidence", + "@id": "bts:BreastCarcinomaSurgicalProcedureName", "@type": "rdfs:Class", - "rdfs:comment": "Country of Residence at enrollment", - "rdfs:label": "CountryofResidence", + "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", + "rdfs:label": "BreastCarcinomaSurgicalProcedureName", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:BreastCancerTier3" } ], "schema:isPartOf": { @@ -19553,714 +13519,1273 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Afghanistan" + "@id": "bts:Lumpectomy" }, { - "@id": "bts:Albania" + "@id": "bts:Radicalmastectomy" }, { - "@id": "bts:Algeria" + "@id": "bts:Modifiedradicalmastectomy" }, { - "@id": "bts:Andorra" + "@id": "bts:Other" }, { - "@id": "bts:Angola" + "@id": "bts:Partialmastectomy" }, { - "@id": "bts:Anguilla" + "@id": "bts:Re-excision" }, { - "@id": "bts:AntiguaandBarbuda" + "@id": "bts:Simplemastectomy" }, { - "@id": "bts:Argentina" + "@id": "bts:Surgerynotperformed" }, { - "@id": "bts:Armenia" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma Surgical Procedure Name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", + "@type": "rdfs:Class", + "rdfs:comment": "HER2 ratio of the participant at diagnosis", + "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", + "rdfs:subClassOf": [ { - "@id": "bts:Aruba" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Breast Carcinoma HER2 Ratio Diagnosis", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaHER2Status", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaHER2Status", + "rdfs:subClassOf": [ { - "@id": "bts:Australia" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Austria" + "@id": "bts:Positive" }, { - "@id": "bts:Azerbaijan" + "@id": "bts:Negative" }, { - "@id": "bts:Bahamas" + "@id": "bts:Amplified" }, { - "@id": "bts:Bahrain" + "@id": "bts:Non-amplified" }, { - "@id": "bts:Bangladesh" + "@id": "bts:Equivocal" }, { - "@id": "bts:Barbados" + "@id": "bts:Indeterminate" }, { - "@id": "bts:Belarus" + "@id": "bts:NotPerformed" }, { - "@id": "bts:Belgium" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Breast Carcinoma HER2 Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", + "@type": "rdfs:Class", + "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", + "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", + "rdfs:subClassOf": [ { - "@id": "bts:Belize" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Benin" + "@id": "bts:Yes" }, { - "@id": "bts:Bermuda" + "@id": "bts:No" }, { - "@id": "bts:Bhutan" + "@id": "bts:Unknown" }, { - "@id": "bts:Bolivia" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BreastCarcinomaERStainingIntensity", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", + "rdfs:label": "BreastCarcinomaERStainingIntensity", + "rdfs:subClassOf": [ { - "@id": "bts:BosniaandHerzegovina" - }, + "@id": "bts:BreastCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Botswana" + "@id": "bts:Strong" }, { - 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"@id": "bts:Nicaragua" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Niger" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:Nigeria" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Niue" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:NorthKorea" + "@id": "bts:OvarianCancerHistologicSubtype" }, { - "@id": "bts:NorthMacedonia" + "@id": "bts:OvarianCancerSurgicalOutcome" }, { - "@id": "bts:NorthernMarianaIslands" + "@id": "bts:OvarianCancerPlatinumStatus" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianCancerHistologicSubtype", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to describe the histological subtype of ovarian cancer in the participant", + "rdfs:label": "OvarianCancerHistologicSubtype", + "rdfs:subClassOf": [ + { + "@id": "bts:OvarianCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:High-gradeserous" }, { - "@id": "bts:Norway" + "@id": "bts:Low-gradeserous" }, { - "@id": "bts:Oman" + "@id": "bts:High-gradeendometrioid" }, { - "@id": "bts:Pakistan" + "@id": "bts:Low-gradeendometrioid" }, { - "@id": "bts:Palau" + "@id": "bts:Clearcell" }, { - "@id": "bts:Panama" + "@id": "bts:Mucinous" }, { - "@id": "bts:PapuaNewGuinea" + "@id": "bts:Sex-cordstromal" }, { - "@id": "bts:Paraguay" + "@id": "bts:Germcell" }, { - "@id": "bts:Peru" + "@id": "bts:Other" }, { - "@id": "bts:Philippines" + "@id": "bts:Unknown" }, { - "@id": "bts:Poland" + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Ovarian Cancer Histologic Subtype", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianCancerSurgicalOutcome", + "@type": "rdfs:Class", + "rdfs:comment": "Text term that describes the kind of surgical treatment administered.", + "rdfs:label": "OvarianCancerSurgicalOutcome", + "rdfs:subClassOf": [ + { + "@id": "bts:OvarianCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:R0resection" }, { - "@id": "bts:Portugal" + "@id": "bts:Optimalcytoreduction" }, { - "@id": "bts:PuertoRico" + "@id": "bts:Sub-optimalcytoreduction" }, { - "@id": "bts:Qatar" + "@id": "bts:Other" }, { - "@id": "bts:Reunion" + "@id": "bts:Unknown" }, { - "@id": "bts:Romania" + "@id": "bts:Datanotavailable" + } + ], + "sms:displayName": "Ovarian Cancer Surgical Outcome", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OvarianCancerPlatinumStatus", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate the status of treatment with platinum in participant with ovarian cancer", + "rdfs:label": "OvarianCancerPlatinumStatus", + "rdfs:subClassOf": [ + { + "@id": "bts:OvarianCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Platinum-refractory" }, { - "@id": "bts:Russia" + "@id": "bts:Platinum-sensitive" }, { - "@id": "bts:Rwanda" + "@id": "bts:Platinum-resistant" }, { - "@id": "bts:SaintHelenaAscensionandTristandaCunha" + "@id": "bts:Datanotavailable" }, { - "@id": "bts:SaintKittsandNevis" + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Ovarian Cancer Platinum Status", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProstateCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Prostate cancer specific attributes in Clinical Data Tier 3", + "rdfs:label": "ProstateCancerTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Prostate Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:SaintLucia" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:SaintPierreandMiquelon" + "@id": "bts:TimepointLabel" }, { - "@id": "bts:SaintVincentandtheGrenadines" + "@id": "bts:StartDaysfromIndex" }, { - "@id": "bts:Samoa" + "@id": "bts:StopDaysfromIndex" }, { - "@id": "bts:SanMarino" + "@id": "bts:LocationExtentExtraprostaticExtension" }, { - "@id": "bts:SaoTomeandPrincipe" + "@id": "bts:LocationNaturePositiveMargins" }, { - "@id": "bts:SaudiArabia" + "@id": "bts:SeminalVesicleInvasion" }, { - "@id": "bts:Senegal" + "@id": "bts:ProstateCarcinomaHistologicType" }, { - "@id": "bts:Serbia" + "@id": "bts:ProstateCancerLocalExtent" }, { - "@id": "bts:Seychelles" + "@id": "bts:AdditonalFindingsUninvolvedProstate" }, { - "@id": "bts:SierraLeone" + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:LocationExtentExtraprostaticExtension", + "@type": "rdfs:Class", + "rdfs:comment": "Location and extent of extraprostatic extension", + "rdfs:label": "LocationExtentExtraprostaticExtension", + "rdfs:subClassOf": [ + { + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:LeftAnterior" }, { - "@id": "bts:Singapore" + "@id": "bts:LeftLateral" }, { - "@id": "bts:Slovakia" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:Slovenia" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:SolomonIslands" + "@id": "bts:LeftApex" }, { - "@id": "bts:Somalia" + "@id": "bts:LeftMid" }, { - "@id": "bts:SouthAfrica" + "@id": "bts:LeftBase" }, { - "@id": "bts:SouthKorea" + "@id": "bts:LeftFocal" }, { - "@id": "bts:SouthSudan" + "@id": "bts:LeftNon-focal(established)" }, { - "@id": "bts:Spain" + "@id": "bts:RightAnterior" }, { - "@id": "bts:SriLanka" + "@id": "bts:RightLateral" }, { - "@id": "bts:StateofPalestine" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:Sudan" + "@id": "bts:RightPosterior" }, { - "@id": "bts:Suriname" + "@id": "bts:RightApex" }, { - "@id": "bts:Svalbard&JanMayenIslands" + "@id": "bts:RightMid" }, { - "@id": "bts:Sweden" + "@id": "bts:RightBase" }, { - "@id": "bts:Switzerland" + "@id": "bts:RightFocal" }, { - "@id": "bts:Syria" + "@id": "bts:RightNon-focal(established)" }, { - "@id": "bts:Taiwan" + "@id": "bts:Unknown" }, { - "@id": "bts:Tajikistan" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Location Extent Extraprostatic Extension", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:LocationNaturePositiveMargins", + "@type": "rdfs:Class", + "rdfs:comment": "Location and nature of positive margins", + "rdfs:label": "LocationNaturePositiveMargins", + "rdfs:subClassOf": [ + { + "@id": "bts:ProstateCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:LeftAnterior" }, { - "@id": "bts:Tanzania" + "@id": "bts:LeftLateral" }, { - "@id": "bts:Thailand" + "@id": "bts:LeftPosterolateral" }, { - "@id": "bts:Timor-Leste" + "@id": "bts:LeftPosterior" }, { - "@id": "bts:Togo" + "@id": "bts:LeftApex" }, { - "@id": "bts:Tokelau" + "@id": "bts:LeftMid" }, { - "@id": "bts:Tonga" + "@id": "bts:LeftBase" }, { - "@id": "bts:TrinidadandTobago" + "@id": "bts:LeftFocal" }, { - "@id": "bts:Tunisia" + "@id": "bts:LeftExtensive" }, { - "@id": "bts:Turkey" + "@id": "bts:LeftPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:Turkmenistan" + "@id": "bts:LeftPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:Tuvalu" + "@id": "bts:LeftPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:Uganda" + "@id": "bts:RightAnterior" }, { - "@id": "bts:Ukraine" + "@id": "bts:RightLateral" }, { - "@id": "bts:UnitedArabEmirates" + "@id": "bts:RightPosterolateral" }, { - "@id": "bts:UnitedKingdom" + "@id": "bts:RightPosterior" }, { - "@id": "bts:UnitedStates" + "@id": "bts:RightApex" }, { - "@id": "bts:Uruguay" + "@id": "bts:RightMid" }, { - "@id": "bts:Uzbekistan" + "@id": "bts:RightBase" }, { - "@id": "bts:Vanuatu" + "@id": "bts:RightFocal" }, { - "@id": "bts:Venezuela" + "@id": "bts:RightExtensive" }, { - "@id": "bts:Vietnam" + "@id": "bts:RightPositiveinanareaofextraprostaticextension(EPE)" }, { - "@id": "bts:VirginIslandsBritish" + "@id": "bts:RightPositiveinanareaofintraprostaticincision(II)" }, { - "@id": "bts:VirginIslandsU.S." + "@id": "bts:RightPositivewhereitisdifficulttodistinguishEPEvsII" }, { - "@id": "bts:WallisandFutuna" + "@id": "bts:Bladderneck(blockPUM)" }, { - "@id": "bts:WesternSahara" + "@id": "bts:Vasdeferens" }, { - "@id": "bts:Yemen" + "@id": "bts:Apicalmargin(blockDUM)" }, { - "@id": "bts:Zambia" + "@id": "bts:Unknown" }, { - "@id": "bts:Zimbabwe" + "@id": "bts:NotReported" } ], - "sms:displayName": "Country of Residence", + "sms:displayName": "Location Nature Positive Margins", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AgeIsObfuscated", + "@id": "bts:SeminalVesicleInvasion", "@type": "rdfs:Class", - "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.", - "rdfs:label": "AgeIsObfuscated", + "rdfs:comment": "An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.", + "rdfs:label": "SeminalVesicleInvasion", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -20268,41 +14793,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:True" + "@id": "bts:None" }, { - "@id": "bts:False" - } - ], - "sms:displayName": "Age Is Obfuscated", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@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": [ + "@id": "bts:Left" + }, { - "@id": "bts:Demographics" + "@id": "bts:Right" + }, + { + "@id": "bts:Bothsides" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Year Of Birth", + "sms:displayName": "Seminal Vesicle Invasion", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CauseofDeath", + "@id": "bts:ProstateCarcinomaHistologicType", "@type": "rdfs:Class", - "rdfs:comment": "The cause of death", - "rdfs:label": "CauseofDeath", + "rdfs:comment": "The diagnostic subclassification of an invasive prostate carcinoma.", + "rdfs:label": "ProstateCarcinomaHistologicType", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -20310,54 +14830,48 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:CancerRelated" - }, - { - "@id": "bts:CardiovascularDisorderNOS" - }, - { - "@id": "bts:End-stageRenalDisease" + "@id": "bts:Prostaticadenocarcinoma(conventionalNOS)" }, { - "@id": "bts:Infection" + "@id": "bts:Prostaticductadenocarcinoma" }, { - "@id": "bts:NotCancerRelated" + "@id": "bts:Acinarprostatemucinous(colloid)adenocarcinoma" }, { - "@id": "bts:RenalDisorderNOS" + "@id": "bts:Acinarprostateadenocarcinoma-signet-ringvariant" }, { - "@id": "bts:SpinalMuscularAtrophy" + "@id": "bts:Prostaticadenosquamouscarcinoma" }, { - "@id": "bts:SurgicalComplications" + "@id": "bts:Acinarprostatemucinousadenocarcinoma" }, { - "@id": "bts:Toxicity" + "@id": "bts:Prostaticsmallcellcarcinoma" }, { - "@id": "bts:NotReported" + "@id": "bts:Acinarprostateadenocarcinoma-sarcomatoidvariant" }, { - "@id": "bts:Unknown" + "@id": "bts:UndifferentiatedcarcinomaNOS" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Other" } ], - "sms:displayName": "Cause of Death", - "sms:required": "sms:true", + "sms:displayName": "Prostate Carcinoma Histologic Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CauseofDeathSource", + "@id": "bts:ProstateCancerLocalExtent", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the source used to determine the patient's cause of death.", - "rdfs:label": "CauseofDeathSource", + "rdfs:comment": "The response used to categorize the local extent of disease for prostate cancer.", + "rdfs:label": "ProstateCancerLocalExtent", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -20365,16 +14879,10 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Autopsy" - }, - { - "@id": "bts:DeathCertificate" - }, - { - "@id": "bts:MedicalRecord" + "@id": "bts:OrganConfined" }, { - "@id": "bts:SocialSecurityDeathIndex" + "@id": "bts:Extraprostaticextension" }, { "@id": "bts:Unknown" @@ -20383,54 +14891,58 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Cause of Death Source", + "sms:displayName": "Prostate Cancer Local Extent", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DaystoDeath", + "@id": "bts:AdditonalFindingsUninvolvedProstate", "@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. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDeath", + "rdfs:comment": "Additional findings, uninvolved prostate", + "rdfs:label": "AdditonalFindingsUninvolvedProstate", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Death", - "sms:required": "sms:false", - "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" - ] - }, - { - "@id": "bts:OccupationDurationYears", - "@type": "rdfs:Class", - "rdfs:comment": "The number of years a patient worked in a specific occupation.", - "rdfs:label": "OccupationDurationYears", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ { - "@id": "bts:Demographics" + "@id": "bts:High-gradeprostaticintraepithelialneoplasia(PIN)" + }, + { + "@id": "bts:Inflammation" + }, + { + "@id": "bts:Benignprostatichyperplasia(BPH)" + }, + { + "@id": "bts:ProstaticIntraductaladenocarcinoma" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Occupation Duration Years", + "sms:displayName": "Additonal Findings Uninvolved Prostate", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PrematureAtBirth", + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", - "rdfs:label": "PrematureAtBirth", + "rdfs:comment": "Text term that describes various morphological and cytological subtypes in protate tumors.", + "rdfs:label": "ProstateCancerCytologicMorphologicSubtypes", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:ProstateCancerTier3" } ], "schema:isPartOf": { @@ -20438,10 +14950,22 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Prostaticbasalcellhyperplasia" }, { - "@id": "bts:No" + "@id": "bts:Prostaticclearcellcribiformhyperplasia" + }, + { + "@id": "bts:Prostaticatypicaladenomatoushyperplasia(adenosisorAAH)" + }, + { + "@id": "bts:Lowgradeprostaticintraepithelialneoplasia(PIN)/(PINI)" + }, + { + "@id": "bts:Highgradeprostaticintraepithelialneoplasia(HGPIN)/(PINII&PINIII)" + }, + { + "@id": "bts:Other" }, { "@id": "bts:Unknown" @@ -20450,84 +14974,991 @@ "@id": "bts:NotReported" } ], - "sms:displayName": "Premature At Birth", + "sms:displayName": "Prostate Cancer Cytologic Morphologic Subtypes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WeeksGestationatBirth", + "@id": "bts:SarcomaTier3", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", - "rdfs:label": "WeeksGestationatBirth", + "rdfs:comment": "Sarcoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "SarcomaTier3", "rdfs:subClassOf": [ { - "@id": "bts:Demographics" + "@id": "bts:Patient" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Weeks Gestation at Birth", + "sms:displayName": "Sarcoma Tier 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EducationLevel", - "@type": "rdfs:Class", - "rdfs:comment": "Highest level of education that the patient completed (direct patient-derived information)", - "rdfs:label": "EducationLevel", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Patient" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:SarcomaSubtype" + }, + { + "@id": "bts:SarcomaDiagnosisClassificationCategory" + }, + { + "@id": "bts:SarcomaTumorExtensionType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaSubtype", + "@type": "rdfs:Class", + "rdfs:comment": "The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.", + "rdfs:label": "SarcomaSubtype", + "rdfs:subClassOf": [ + { + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ { - "@id": "bts:Bachelor'sdegree" + "@id": "bts:Undifferentiatedpleomorphicsarcoma" }, { - "@id": "bts:Doctoraldegreeorprofessionaldegree" + "@id": "bts:Leiomyosarcoma(uterineorextra-uterine)" }, { - "@id": "bts:Gradeschool" + "@id": "bts:OtherSynovialSarcomaOrMalignantPeripheralNerveSheathTumorSarcoma" }, { - "@id": "bts:Graduateorprofessionaldegree" + "@id": "bts:GastrointestinalStromalTumor" }, { - "@id": "bts:Highschoolgraduate(includingequivalency)" + "@id": "bts:Liposarcoma" }, { - "@id": "bts:Master'sdegree" + "@id": "bts:Undifferentiatedpleomorphicsarcomaormalignantfibroushistiosarcoma" }, { - "@id": "bts:Noformaleducation" + "@id": "bts:Other" }, { - "@id": "bts:Nothighschoolgraduate" + "@id": "bts:Unknown" }, { - "@id": "bts:Somecollegeorassociatedegree" + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Subtype", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SarcomaDiagnosisClassificationCategory", + "@type": "rdfs:Class", + "rdfs:comment": "High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.", + "rdfs:label": "SarcomaDiagnosisClassificationCategory", + "rdfs:subClassOf": [ + { + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:BoneSarcoma" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:MusculoskeletalSarcoma" + }, + { + "@id": "bts:SoftTissueSarcoma" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Education Level", + "sms:displayName": "Sarcoma Diagnosis Classification Category", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CountryofBirth", + "@id": "bts:SarcomaTumorExtensionType", "@type": "rdfs:Class", - "rdfs:comment": "Country where the patient was born.", - "rdfs:label": "CountryofBirth", + "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", + "rdfs:label": "SarcomaTumorExtensionType", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:SarcomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Extraosseous" + }, + { + "@id": "bts:Intracranial" + }, + { + "@id": "bts:Lymphnodes" + }, + { + "@id": "bts:Parameningeal" + }, + { + "@id": "bts:Thoraciccavity" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sarcoma Tumor Extension Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticCancerTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Pancreatic cancer specific attributes in Clinical Tier Data 3", + "rdfs:label": "PancreaticCancerTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Pancreatic Cancer Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:PancreasPrecancerHistopathologicGrade" + }, + { + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" + }, + { + "@id": "bts:PancreaticDuctFinalPathologyType" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PancreasPrecancerHistopathologicGrade", + "@type": "rdfs:Class", + "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", + "rdfs:label": "PancreasPrecancerHistopathologicGrade", + "rdfs:subClassOf": [ + { + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:IPMN-Adenoma" + }, + { + "@id": "bts:IPMN-Borderline" + }, + { + "@id": "bts:IPMN-Carcinomainsitu" + }, + { + "@id": "bts:IPMN-Invasivecarcinoma" + }, + { + "@id": "bts:PanIN1" + }, + { + "@id": "bts:PanIN1A" + }, + { + "@id": "bts:PanIN1B" + }, + { + "@id": "bts:PanIN2" + }, + { + "@id": "bts:PanIN3" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreas Precancer Histopathologic Grade", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", + "@type": "rdfs:Class", + "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", + "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", + "rdfs:subClassOf": [ + { + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:GastricFoveolar" + }, + { + "@id": "bts:Intestinal" + }, + { + "@id": "bts:IntraductalTubopapillary" + }, + { + "@id": "bts:Pancreatobiliary" + }, + { + "@id": "bts:Oncocytic" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PancreaticDuctFinalPathologyType", + "@type": "rdfs:Class", + "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", + "rdfs:label": "PancreaticDuctFinalPathologyType", + "rdfs:subClassOf": [ + { + "@id": "bts:PancreaticCancerTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Side-Branch" + }, + { + "@id": "bts:MainDuct" + }, + { + "@id": "bts:Mixed" + }, + { + "@id": "bts:NotSpecified" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Pancreatic Duct Final Pathology Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaTier3", + "@type": "rdfs:Class", + "rdfs:comment": "Melanoma specific attributes in Clinical Data Tier 3", + "rdfs:label": "MelanomaTier3", + "rdfs:subClassOf": [ + { + "@id": "bts:Patient" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Melanoma Tier 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:Patient" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:TimepointLabel" + }, + { + "@id": "bts:StartDaysfromIndex" + }, + { + "@id": "bts:StopDaysfromIndex" + }, + { + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes" + }, + { + "@id": "bts:CutaneousMelanomaTumorRegressionRange" + }, + { + "@id": "bts:MelanomaSpecimenClarkLevelValue" + }, + { + "@id": "bts:CutaneousMelanomaSurgicalMargins" + }, + { + "@id": "bts:MelanomaLesionSize" + }, + { + "@id": "bts:HistoryofAtypicalNevi" + }, + { + "@id": "bts:FitzpatrickSkinTone" + }, + { + "@id": "bts:HistoryofChronicUVExposure" + }, + { + "@id": "bts:HistoryofBlisteringSunburn" + }, + { + "@id": "bts:HistoryofTanningBedUse" + }, + { + "@id": "bts:ImmediateFamilyHistoryMelanoma" + }, + { + "@id": "bts:MelanomaBiopsyResectionSites" + }, + { + "@id": "bts:CutaneousMelanomaUlceration" + }, + { + "@id": "bts:CutaneousMelanomaAdditionalFindings" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", + "@type": "rdfs:Class", + "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Brisk" + }, + { + "@id": "bts:Nonbrisk" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaTumorRegressionRange", + "@type": "rdfs:Class", + "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", + "rdfs:label": "CutaneousMelanomaTumorRegressionRange", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Presentinvolving75%ormore" + }, + { + "@id": "bts:Presentinvolvinglessthan75%" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaSpecimenClarkLevelValue", + "@type": "rdfs:Class", + "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", + "rdfs:label": "MelanomaSpecimenClarkLevelValue", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:I" + }, + { + "@id": "bts:II" + }, + { + "@id": "bts:III" + }, + { + "@id": "bts:IV" + }, + { + "@id": "bts:V" + }, + { + "@id": "bts:NoSourceDocumentation" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Melanoma Specimen Clark Level Value", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaSurgicalMargins", + "@type": "rdfs:Class", + "rdfs:comment": "Text term to indicate presence of tumor at resection margins", + "rdfs:label": "CutaneousMelanomaSurgicalMargins", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Positive" + }, + { + "@id": "bts:Negative" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cutaneous Melanoma Surgical Margins", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaLesionSize", + "@type": "rdfs:Class", + "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", + "rdfs:label": "MelanomaLesionSize", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Melanoma Lesion Size", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofAtypicalNevi", + "@type": "rdfs:Class", + "rdfs:comment": "Patient has a history of atypical nevi", + "rdfs:label": "HistoryofAtypicalNevi", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes(morethan50)" + }, + { + "@id": "bts:Yes(lessthan50)" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Atypical Nevi", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:FitzpatrickSkinTone", + "@type": "rdfs:Class", + "rdfs:comment": "The Fitzpatrick classification of skin phototype", + "rdfs:label": "FitzpatrickSkinTone", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:I" + }, + { + "@id": "bts:II" + }, + { + "@id": "bts:III" + }, + { + "@id": "bts:IV" + }, + { + "@id": "bts:V" + }, + { + "@id": "bts:VI" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Fitzpatrick Skin Tone", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofChronicUVExposure", + "@type": "rdfs:Class", + "rdfs:comment": "History of chronic UV exposure", + "rdfs:label": "HistoryofChronicUVExposure", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Outdooroccupational" + }, + { + "@id": "bts:Outdoorrecreational" + }, + { + "@id": "bts:Therapeutic" + }, + { + "@id": "bts:None" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Chronic UV Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofBlisteringSunburn", + "@type": "rdfs:Class", + "rdfs:comment": "Patient has history of blistering sunburn", + "rdfs:label": "HistoryofBlisteringSunburn", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Blistering Sunburn", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HistoryofTanningBedUse", + "@type": "rdfs:Class", + "rdfs:comment": "History of tanning bed use of the patient", + "rdfs:label": "HistoryofTanningBedUse", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Never" + }, + { + "@id": "bts:Lessthan10times" + }, + { + "@id": "bts:10-50times" + }, + { + "@id": "bts:50-100times" + }, + { + "@id": "bts:Morethan100times" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "History of Tanning Bed Use", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ImmediateFamilyHistoryMelanoma", + "@type": "rdfs:Class", + "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", + "rdfs:label": "ImmediateFamilyHistoryMelanoma", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Beforeage50" + }, + { + "@id": "bts:Notbeforeage50" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Immediate Family History Melanoma", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:MelanomaBiopsyResectionSites", + "@type": "rdfs:Class", + "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", + "rdfs:label": "MelanomaBiopsyResectionSites", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Skinofscalp" + }, + { + "@id": "bts:Skinofeyelid" + }, + { + "@id": "bts:Skinofnose" + }, + { + "@id": "bts:Skinoflip" + }, + { + "@id": "bts:Skinofear" + }, + { + "@id": "bts:Skinofneck" + }, + { + "@id": "bts:Skinofotherpartsofface" + }, + { + "@id": "bts:Skinofchest" + }, + { + "@id": "bts:Skinofback" + }, + { + "@id": "bts:Skinofabdomen" + }, + { + "@id": "bts:Skinoftrunk-other" + }, + { + "@id": "bts:Skinofbreast" + }, + { + "@id": "bts:Skinofupperlimbandshoulder" + }, + { + "@id": "bts:Skinofpalm" + }, + { + "@id": "bts:Skinoflowerlimbandhip" + }, + { + "@id": "bts:Skinofsole" + }, + { + "@id": "bts:Skinofpenis" + }, + { + "@id": "bts:Skinofscrotum" + }, + { + "@id": "bts:Skinofvulva" + }, + { + "@id": "bts:Skinother" + }, + { + "@id": "bts:SkinNOS" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Melanoma Biopsy Resection Sites", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaUlceration", + "@type": "rdfs:Class", + "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaUlceration", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:Absent" + }, + { + "@id": "bts:Present" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Cutaneous Melanoma Ulceration", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CutaneousMelanomaAdditionalFindings", + "@type": "rdfs:Class", + "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", + "rdfs:label": "CutaneousMelanomaAdditionalFindings", + "rdfs:subClassOf": [ + { + "@id": "bts:MelanomaTier3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:ActinicKeratosis" + }, + { + "@id": "bts:NevusRemnant" + }, + { + "@id": "bts:SolarElastosis" + }, + { + "@id": "bts:FibrosingRegression" + }, + { + "@id": "bts:NestingMelanoma" + }, + { + "@id": "bts:PagetoidSpread" + }, + { + "@id": "bts:VascularProliferation" + }, + { + "@id": "bts:Other" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Cutaneous Melanoma Additional Findings", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@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. If not applicable please enter 'Not Applicable'", + "rdfs:label": "DaystoBirth", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Days to Birth", + "sms:required": "sms:false", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] + }, + { + "@id": "bts:CountryofResidence", + "@type": "rdfs:Class", + "rdfs:comment": "Country of Residence at enrollment", + "rdfs:label": "CountryofResidence", + "rdfs:subClassOf": [ + { + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -21229,23 +16660,20 @@ }, { "@id": "bts:Zimbabwe" - }, - { - "@id": "bts:Unknown" } ], - "sms:displayName": "Country of Birth", + "sms:displayName": "Country of Residence", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedicallyUnderservedArea", + "@id": "bts:AgeIsObfuscated", "@type": "rdfs:Class", - "rdfs:comment": "Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select \"Query Data\". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select \"View Data\". Enter the name of the county (_______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is \"medically underserved area\" enter \"Yes\" as the value. If the county generates a \"No data available in table\" enter \"No\" as the value. A value of \"Unknown\" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.", - "rdfs:label": "MedicallyUnderservedArea", + "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.", + "rdfs:label": "AgeIsObfuscated", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Demographics" } ], "schema:isPartOf": { @@ -21253,100 +16681,106 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:MedicallyUnderservedArea-Yes" - }, - { - "@id": "bts:MedicallyUnderservedArea-No" + "@id": "bts:True" }, { - "@id": "bts:MedicallyUnderservedArea-Unknown" + "@id": "bts:False" } ], - "sms:displayName": "Medically Underserved Area", + "sms:displayName": "Age Is Obfuscated", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedicallyUnderservedArea-Yes", + "@id": "bts:YearOfBirth", "@type": "rdfs:Class", - "rdfs:comment": "Patient's zip code is in a medically underserved area", - "rdfs:label": "MedicallyUnderservedArea-Yes", + "rdfs:comment": "Numeric value to represent the calendar year in which an individual was born.", + "rdfs:label": "YearOfBirth", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Medically Underserved Area - Yes", + "sms:displayName": "Year Of Birth", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:MedicallyUnderservedScore" - } - ], "sms:validationRules": [] }, { - "@id": "bts:MedicallyUnderservedArea-No", + "@id": "bts:OccupationDurationYears", "@type": "rdfs:Class", - "rdfs:comment": "Patient's zip code is not in a medically underserved area", - "rdfs:label": "MedicallyUnderservedArea-No", + "rdfs:comment": "The number of years a patient worked in a specific occupation.", + "rdfs:label": "OccupationDurationYears", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Medically Underserved Area - No", + "sms:displayName": "Occupation Duration Years", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedicallyUnderservedArea-Unknown", + "@id": "bts:PrematureAtBirth", "@type": "rdfs:Class", - "rdfs:comment": "Insufficient data to look up the Medically Underserved Area value", - "rdfs:label": "MedicallyUnderservedArea-Unknown", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.", + "rdfs:label": "PrematureAtBirth", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Medically Underserved Area - Unknown", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Premature At Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MedicallyUnderservedScore", + "@id": "bts:WeeksGestationatBirth", "@type": "rdfs:Class", - "rdfs:comment": "Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.", - "rdfs:label": "MedicallyUnderservedScore", + "rdfs:comment": "Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.", + "rdfs:label": "WeeksGestationatBirth", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Demographics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Medically Underserved Score", + "sms:displayName": "Weeks Gestation at Birth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RuralvsUrban", + "@id": "bts:RelativewithCancerHistory", "@type": "rdfs:Class", - "rdfs:comment": "Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of \"Rural Population\"; if 2,500 - 50,000 enter a value of \"Urban Cluster\"; or if >50,000 enter \"Urban Population\"", - "rdfs:label": "RuralvsUrban", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", + "rdfs:label": "RelativewithCancerHistory", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:FamilyHistory" } ], "schema:isPartOf": { @@ -21354,61 +16788,86 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:UrbanPopulation(population>50000)" + "@id": "bts:Yes-CancerHistoryRelative" }, { - "@id": "bts:UrbanCluster(population2500-50000)" + "@id": "bts:None" }, { - "@id": "bts:RuralPopulation(population<2500)" + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" } ], - "sms:displayName": "Rural vs Urban", + "sms:displayName": "Relative with Cancer History", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CancerIncidence", + "@id": "bts:SmokingExposure", "@type": "rdfs:Class", - "rdfs:comment": "Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the \"primary_diagnosis\" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose \"Incidence\" from the Topic dropdown menu, state of interest from the Area menu, \"All Races\" from the Race menu, and the cancer type (\"Both Sexes\" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.", - "rdfs:label": "CancerIncidence", + "rdfs:comment": "Indicate if individual has smoking exposure", + "rdfs:label": "SmokingExposure", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cancer Incidence", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-SmokingExposure" + }, + { + "@id": "bts:No-SmokingExposure" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Smoking Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CancerIncidenceLocation", + "@id": "bts:AlcoholExposure", "@type": "rdfs:Class", - "rdfs:comment": "The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as \"County, State\" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website", - "rdfs:label": "CancerIncidenceLocation", + "rdfs:comment": "Indicate if individual has alcohol exposure", + "rdfs:label": "AlcoholExposure", "rdfs:subClassOf": [ { - "@id": "bts:ClinicalTier2" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Cancer Incidence Location", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes-AlcoholExposure" + }, + { + "@id": "bts:No-AlcoholExposure" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Alcohol Exposure", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:RelationshipGender", + "@id": "bts:AsbestosExposure", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the gender of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipGender", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", + "rdfs:label": "AsbestosExposure", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -21416,50 +16875,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Female" + "@id": "bts:Yes" }, { - "@id": "bts:Male" + "@id": "bts:No" }, { "@id": "bts:Unknown" }, - { - "@id": "bts:Unspecified" - }, { "@id": "bts:NotReported" } ], - "sms:displayName": "Relationship Gender", + "sms:displayName": "Asbestos Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipAgeatDiagnosis", + "@id": "bts:CoalDustExposure", "@type": "rdfs:Class", - "rdfs:comment": "The age (in years) when the patient's relative was first diagnosed.", - "rdfs:label": "RelationshipAgeatDiagnosis", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", + "rdfs:label": "CoalDustExposure", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Relationship Age at Diagnosis", + "schema:rangeIncludes": [ + { + "@id": "bts:Yes" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Coal Dust Exposure", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RelationshipPrimaryDiagnosis", + "@id": "bts:EnvironmentalTobaccoSmokeExposure", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", - "rdfs:label": "RelationshipPrimaryDiagnosis", + "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.", + "rdfs:label": "EnvironmentalTobaccoSmokeExposure", "rdfs:subClassOf": [ { - "@id": "bts:FamilyHistory" + "@id": "bts:Exposure" } ], "schema:isPartOf": { @@ -21467,1755 +16934,574 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AdrenalGlandCancer" + "@id": "bts:Yes" }, { - "@id": "bts:BasalCellCancer" + "@id": "bts:No" }, { - "@id": "bts:BileDuctCancer" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Environmental Tobacco Smoke Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RadonExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", + "rdfs:label": "RadonExposure", + "rdfs:subClassOf": [ { - "@id": "bts:BladderCancer" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:BloodCancer" + "@id": "bts:Yes" }, { - "@id": "bts:BoneCancer" + "@id": "bts:No" }, { - "@id": "bts:BrainCancer" + "@id": "bts:Unknown" }, { - "@id": "bts:BreastCancer" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Radon Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:RespirableCrystallineSilicaExposure", + "@type": "rdfs:Class", + "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", + "rdfs:label": "RespirableCrystallineSilicaExposure", + "rdfs:subClassOf": [ { - "@id": "bts:Cancer" - }, + "@id": "bts:Exposure" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CervicalCancer" + "@id": "bts:Yes" }, { - "@id": "bts:Chondrosarcoma" + "@id": "bts:No" }, { - "@id": "bts:CNSCancer" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Respirable Crystalline Silica Exposure", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdverseEvent", + "@type": "rdfs:Class", + "rdfs:comment": "Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.", + "rdfs:label": "AdverseEvent", + "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancer" - }, + "@id": "bts:FollowUp" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:EsophagealCancer" + "@id": "bts:AbdominalDistension" }, { - "@id": "bts:EwingSarcoma" + "@id": "bts:AbdominalInfection" }, { - "@id": "bts:GallbladderCancer" + "@id": "bts:AbdominalPain" }, { - "@id": "bts:GastricCancer" + "@id": "bts:AbdominalSoftTissueNecrosis" }, { - "@id": "bts:Glioblastoma" + "@id": "bts:AbducensNerveDisorder" }, { - "@id": "bts:GynecologicCancer" + "@id": "bts:AccessoryNerveDisorder" }, { - "@id": "bts:HeadandNeckCancer" + "@id": "bts:Acidosis" }, { - "@id": "bts:HematologicCancer" + "@id": "bts:AcousticNerveDisorderNOS" }, { - "@id": "bts:KaposiSarcoma" + "@id": "bts:ActivatedPartialThromboplastinTimeProlonged" }, { - "@id": "bts:KidneyCancer" + "@id": "bts:AcuteCoronarySyndrome" }, { - "@id": "bts:LaryngealCancer" + "@id": "bts:AcuteKidneyInjury" }, { - "@id": "bts:Leukemia" + "@id": "bts:AdrenalInsufficiency" }, { - "@id": "bts:LiverCancer" + "@id": "bts:AdultRespiratoryDistressSyndrome" }, { - "@id": "bts:LungCancer" + "@id": "bts:Agitation" }, { - "@id": "bts:LymphNodeCancer" + "@id": "bts:Akathisia" }, { - "@id": "bts:Lymphoma" + "@id": "bts:AlanineAminotransferaseIncreased" }, { - "@id": "bts:Melanoma" + "@id": "bts:AlcoholIntolerance" }, { - "@id": "bts:Mesothelioma" + "@id": "bts:AlkalinePhosphataseIncreased" }, { - "@id": "bts:MultipleMyeloma" + "@id": "bts:Alkalosis" }, { - "@id": "bts:Neuroblastoma" + "@id": "bts:AllergicReaction" }, { - "@id": "bts:Osteosarcoma" + "@id": "bts:AllergicRhinitis" }, { - "@id": "bts:OvarianCancer" + "@id": "bts:Alopecia" }, { - "@id": "bts:PancreasCancer" + "@id": "bts:Amnesia" }, { - "@id": "bts:ProstateCancer" + "@id": "bts:AnalFistula" }, { - "@id": "bts:RectalCancer" + "@id": "bts:AnalHemorrhage" }, { - "@id": "bts:Rhabdomyosarcoma" + "@id": "bts:AnalMucositis" }, { - "@id": "bts:Sarcoma" + "@id": "bts:AnalNecrosis" }, { - "@id": "bts:SkinCancer" + "@id": "bts:AnalPain" }, { - "@id": "bts:SpleenCancer" + "@id": "bts:AnalStenosis" }, { - "@id": "bts:TesticularCancer" + "@id": "bts:AnalUlcer" }, { - "@id": "bts:ThroatCancer" + "@id": "bts:Anaphylaxis" }, { - "@id": "bts:ThyroidCancer" + "@id": "bts:Anemia" }, { - "@id": "bts:TongueCancer" + "@id": "bts:AnkleFracture" }, { - "@id": "bts:TonsillarCancer" + "@id": "bts:AnorectalInfection" }, { - "@id": "bts:UterineCancer" + "@id": "bts:Anorexia" }, { - "@id": "bts:WilmsTumor" + "@id": "bts:Anorgasmia" }, { - "@id": "bts:Unknown" + "@id": "bts:Anxiety" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relationship Primary Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@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": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Relationship Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RelativewithCancerHistory", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.", - "rdfs:label": "RelativewithCancerHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-CancerHistoryRelative" + "@id": "bts:AorticInjury" }, { - "@id": "bts:None" + "@id": "bts:AorticValveDisease" }, { - "@id": "bts:Unknown" + "@id": "bts:Aphonia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Relative with Cancer History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@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": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Relatives with Cancer History Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes-CancerHistoryRelative", - "@type": "rdfs:Class", - "rdfs:comment": "Individual has a relative with cancer history", - "rdfs:label": "Yes-CancerHistoryRelative", - "rdfs:subClassOf": [ - { - "@id": "bts:FamilyHistory" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Cancer History Relative", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:RelativeswithCancerHistoryCount" + "@id": "bts:Apnea" }, { - "@id": "bts:RelationshipType" + "@id": "bts:Appendicitis" }, { - "@id": "bts:RelationshipPrimaryDiagnosis" + "@id": "bts:AppendicitisPerforated" }, { - "@id": "bts:RelationshipGender" + "@id": "bts:Arachnoiditis" }, { - "@id": "bts:RelationshipAgeatDiagnosis" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has smoking exposure", - "rdfs:label": "SmokingExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-SmokingExposure" + "@id": "bts:ArterialInjury" }, { - "@id": "bts:No-SmokingExposure" + "@id": "bts:ArteritisInfective" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoking Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes-SmokingExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Individual has been exposed to smoke; requires additional metadata", - "rdfs:label": "Yes-SmokingExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Smoking Exposure", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:YearsSmoked" + "@id": "bts:Arthralgia" }, { - "@id": "bts:PackYearsSmoked" + "@id": "bts:Arthritis" }, { - "@id": "bts:CigarettesperDay" + "@id": "bts:Ascites" }, { - "@id": "bts:SmokingFrequency" + "@id": "bts:AspartateAminotransferaseIncreased" }, { - "@id": "bts:TypeofSmokeExposure" + "@id": "bts:Aspiration" }, { - "@id": "bts:TimebetweenWakingandFirstSmoke" + "@id": "bts:Asystole" }, { - "@id": "bts:TobaccoSmokingOnsetYear" + "@id": "bts:Ataxia" }, { - "@id": "bts:TobaccoSmokingQuitYear" + "@id": "bts:Atelectasis" }, { - "@id": "bts:TobaccoSmokingStatus" + "@id": "bts:AtrialFibrillation" }, { - "@id": "bts:TypeofTobaccoUsed" + "@id": "bts:AtrialFlutter" }, { - "@id": "bts:SecondhandSmokeasChild" + "@id": "bts:AtrioventricularBlockComplete" }, { - "@id": "bts:SmokeExposureDuration" + "@id": "bts:AtrioventricularBlockFirstDegree" }, { - "@id": "bts:TobaccoUseperDay" + "@id": "bts:AutoimmuneDisorder" }, { - "@id": "bts:SmokelessTobaccoQuitAge" - } - ], - "sms:validationRules": [] - }, - { - "@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": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Pack Years Smoked", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@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:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Years Smoked", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Indicate if individual has alcohol exposure", - "rdfs:label": "AlcoholExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-AlcoholExposure" + "@id": "bts:AvascularNecrosis" }, { - "@id": "bts:No-AlcoholExposure" + "@id": "bts:Azoospermia" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Exposure", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:Yes-AlcoholExposure", - "@type": "rdfs:Class", - "rdfs:comment": "Individual has been exposed to alcohol", - "rdfs:label": "Yes-AlcoholExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Yes - Alcohol Exposure", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:AlcoholDaysPerWeek" + "@id": "bts:BackPain" }, { - "@id": "bts:AlcoholDrinksPerDay" + "@id": "bts:BileDuctStenosis" }, { - "@id": "bts:AlcoholHistory" + "@id": "bts:BiliaryAnastomoticLeak" }, { - "@id": "bts:AlcoholIntensity" + "@id": "bts:BiliaryFistula" }, { - "@id": "bts:AlcoholType" - } - ], - "sms:validationRules": [] - }, - { - "@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": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alcohol Days Per Week", - "sms:required": "sms:false", - "sms:validationRules": [ - "int" - ] - }, - { - "@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": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Alcohol Drinks Per Day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholHistory", - "@type": "rdfs:Class", - "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.", - "rdfs:label": "AlcoholHistory", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:BiliaryTractInfection" }, { - "@id": "bts:No" + "@id": "bts:BladderAnastomoticLeak" }, { - "@id": "bts:Unknown" + "@id": "bts:BladderInfection" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol History", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholIntensity", - "@type": "rdfs:Class", - "rdfs:comment": "Category to describe the patient's current level of alcohol use as self-reported by the patient.", - "rdfs:label": "AlcoholIntensity", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Drinker" + "@id": "bts:BladderPerforation" }, { - "@id": "bts:HeavyDrinker" + "@id": "bts:BladderSpasm" }, { - "@id": "bts:LifelongNon-Drinker" + "@id": "bts:Bloating" }, { - "@id": "bts:Non-Drinker" + "@id": "bts:BloodandLymphaticSystemDisordersOther" }, { - "@id": "bts:OccasionalDrinker" + "@id": "bts:BloodAntidiureticHormoneAbnormal" }, { - "@id": "bts:Unknown" + "@id": "bts:BloodBilirubinIncreased" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Intensity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AlcoholType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of alcohol use", - "rdfs:label": "AlcoholType", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beer" + "@id": "bts:BloodCorticotrophinDecreased" }, { - "@id": "bts:Liquor" + "@id": "bts:BloodGonadotrophinAbnormal" }, { - "@id": "bts:Other" + "@id": "bts:BloodProlactinAbnormal" }, { - "@id": "bts:Wine" + "@id": "bts:BlurredVision" }, { - "@id": "bts:Unknown" + "@id": "bts:BodyOdor" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Alcohol Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AsbestosExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.", - "rdfs:label": "AsbestosExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes" + "@id": "bts:BoneInfection" }, { - "@id": "bts:No" + "@id": "bts:BoneMarrowHypocellular" }, { - "@id": "bts:Unknown" + "@id": "bts:BonePain" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Asbestos Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CigarettesperDay", - "@type": "rdfs:Class", - "rdfs:comment": "The average number of cigarettes smoked per day.", - "rdfs:label": "CigarettesperDay", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Cigarettes per Day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CoalDustExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.", - "rdfs:label": "CoalDustExposure", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BrachialPlexopathy" + }, { - "@id": "bts:Yes" + "@id": "bts:BreastAtrophy" }, { - "@id": "bts:No" + "@id": "bts:BreastInfection" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Coal Dust Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:EnvironmentalTobaccoSmokeExposure", - "@type": "rdfs:Class", - "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.", - "rdfs:label": "EnvironmentalTobaccoSmokeExposure", - "rdfs:subClassOf": [ + "@id": "bts:BreastPain" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BronchialFistula" + }, { - "@id": "bts:Yes" + "@id": "bts:BronchialInfection" }, { - "@id": "bts:No" + "@id": "bts:BronchialObstruction" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Environmental Tobacco Smoke Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RadonExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the patient was exposed to radon.", - "rdfs:label": "RadonExposure", - "rdfs:subClassOf": [ + "@id": "bts:BronchialStricture" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:BronchopleuralFistula" + }, { - "@id": "bts:Yes" + "@id": "bts:BronchopulmonaryHemorrhage" }, { - "@id": "bts:No" + "@id": "bts:Bronchospasm" }, { - "@id": "bts:Unknown" + "@id": "bts:Bruising" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Radon Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:RespirableCrystallineSilicaExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.", - "rdfs:label": "RespirableCrystallineSilicaExposure", - "rdfs:subClassOf": [ + "@id": "bts:BullousDermatitis" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Burn" + }, { - "@id": "bts:Yes" + "@id": "bts:ButtockPain" }, { - "@id": "bts:No" + "@id": "bts:CapillaryLeakSyndrome" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Respirable Crystalline Silica Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokingFrequency", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", - "rdfs:label": "SmokingFrequency", - "rdfs:subClassOf": [ + "@id": "bts:CarbonMonoxideDiffusingCapacityDecreased" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CardiacArrest" + }, { - "@id": "bts:Everyday" + "@id": "bts:CardiacDisordersOther" }, { - "@id": "bts:Somedays" + "@id": "bts:CardiacTroponinIIncreased" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Smoking Frequency", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SecondhandSmokeasChild", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to indicate whether the patient was exposed to secondhand smoke as a child.", - "rdfs:label": "SecondhandSmokeasChild", - "rdfs:subClassOf": [ + "@id": "bts:CardiacTroponinTIncreased" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Cataract" + }, { - "@id": "bts:Yes" + "@id": "bts:CatheterRelatedInfection" }, { - "@id": "bts:No" + "@id": "bts:CD4LymphocytesDecreased" }, { - "@id": "bts:Unknown" + "@id": "bts:CecalHemorrhage" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Secondhand Smoke as Child", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokeExposureDuration", - "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the length of time the patient was exposed to an environmental factor.", - "rdfs:label": "SmokeExposureDuration", - "rdfs:subClassOf": [ + "@id": "bts:CecalInfection" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:CentralNervousSystemNecrosis" + }, { - "@id": "bts:SixWeeksorMore" + "@id": "bts:CerebrospinalFluidLeakage" }, { - "@id": "bts:Unknown" + "@id": "bts:CervicitisInfection" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Smoke Exposure Duration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TypeofSmokeExposure", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the patient's specific type of smoke exposure.", - "rdfs:label": "TypeofSmokeExposure", - "rdfs:subClassOf": [ + "@id": "bts:Cheilitis" + }, { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ChestPainCardiac" + }, { - "@id": "bts:Accidentalbuildingfiresmoke" + "@id": "bts:ChestWallPain" }, { - "@id": "bts:Accidentalgrassfiresmoke" + "@id": "bts:Chills" }, { - "@id": "bts:AccidentalfiresmokeNOS" + "@id": "bts:Cholecystitis" }, { - "@id": "bts:Accidentalforestfiresmoke" + "@id": "bts:CholesterolHigh" }, { - "@id": "bts:Accidentalvehiclefiresmoke" + "@id": "bts:ChronicKidneyDisease" }, { - "@id": "bts:Aircraftsmoke" + "@id": "bts:Chylothorax" }, { - "@id": "bts:Burningtreesmoke" + "@id": "bts:CognitiveDisturbance" }, { - "@id": "bts:CoalsmokeNOS" + "@id": "bts:Colitis" }, { - "@id": "bts:CookingrelatedsmokeNOS" + "@id": "bts:ColonicFistula" }, { - "@id": "bts:ElectroniccigarettesmokeNOS" + "@id": "bts:ColonicHemorrhage" }, { - "@id": "bts:Electricalfiresmoke" + "@id": "bts:ColonicObstruction" }, { - "@id": "bts:Environmentaltobaccosmoke" + "@id": "bts:ColonicPerforation" }, { - "@id": "bts:Factorysmokestacksmoke" + "@id": "bts:ColonicStenosis" }, { - "@id": "bts:Fieldburningsmoke" + "@id": "bts:ColonicUlcer" }, { - "@id": "bts:FiresmokeNOS" + "@id": "bts:ConcentrationImpairment" }, { - "@id": "bts:Furnaceorboilersmoke" + "@id": "bts:ConductionDisorder" }, { - "@id": "bts:Gasburningsmokepropane" + "@id": "bts:Confusion" }, { - "@id": "bts:Greasefiresmoke" + "@id": "bts:Congenital" }, { - "@id": "bts:Grillingsmoke" + "@id": "bts:FamilialandGeneticDisordersOther" }, { - "@id": "bts:Hashishsmoke" + "@id": "bts:Conjunctivitis" }, { - "@id": "bts:Indoorcoalburningstoveorfireplacesmoke" + "@id": "bts:ConjunctivitisInfective" }, { - "@id": "bts:IndoorstoveorfireplacesmokeNOS" + "@id": "bts:Constipation" }, { - "@id": "bts:Indoorwoodburningstoveorfireplacesmoke" + "@id": "bts:ConstrictivePericarditis" }, { - "@id": "bts:Machinesmoke" + "@id": "bts:CornealInfection" }, { - "@id": "bts:Marijuanasmoke" + "@id": "bts:CornealUlcer" }, { - "@id": "bts:NoSmokeExposure" + "@id": "bts:Cough" }, { - "@id": "bts:OilburningsmokeKerosene" + "@id": "bts:CPKIncreased" }, { - "@id": "bts:OilburningsmokeNOS" + "@id": "bts:CranialNerveInfection" }, { - "@id": "bts:Recreationalfiresmoke" + "@id": "bts:CreatinineIncreased" }, { - "@id": "bts:SmokeexposureNOS" + "@id": "bts:Cushingoid" }, { - "@id": "bts:Smokehousesmoke" + "@id": "bts:CystitisNoninfective" }, { - "@id": "bts:Tobaccosmokecigar" + "@id": "bts:CytokineReleaseSyndrome" }, { - "@id": "bts:Tobaccosmokecigarettes" + "@id": "bts:DeathNeonatal" }, { - "@id": "bts:Tobaccosmokepipe" + "@id": "bts:DeathNOS" }, { - "@id": "bts:Unknown" + "@id": "bts:Dehydration" }, { - "@id": "bts:Volcanicsmoke" + "@id": "bts:DelayedOrgasm" }, { - "@id": "bts:Wasteburningsmoke" + "@id": "bts:DelayedPuberty" }, { - "@id": "bts:Woodburningsmokefactory" + "@id": "bts:Delirium" }, { - "@id": "bts:WoodburningsmokeNOS" + "@id": "bts:Delusions" }, { - "@id": "bts:Workrelatedsmokeartificialsmokemachines" + "@id": "bts:DentalCaries" }, { - "@id": "bts:Workrelatedsmokefirefighting" + "@id": "bts:DepressedLevelofConsciousness" }, { - "@id": "bts:Workrelatedsmokefoundry" + "@id": "bts:Depression" }, { - "@id": "bts:Workrelatedsmokegenerators" + "@id": "bts:DermatitisRadiation" }, { - "@id": "bts:Workrelatedsmokemilitary" + "@id": "bts:DeviceRelatedInfection" }, { - "@id": "bts:WorkrelatedsmokeNOS" + "@id": "bts:Diarrhea" }, { - "@id": "bts:Workrelatedsmokepaintbaking" + "@id": "bts:DisseminatedIntravascularCoagulation" }, { - "@id": "bts:Workrelatedsmokeplasticsfactory" + "@id": "bts:Dizziness" }, { - "@id": "bts:Workrelatedsmokeplumbing" - }, - { - "@id": "bts:Workrelatedsmokesoldering/welding" - } - ], - "sms:displayName": "Type of Smoke Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:Marijuanasmoke", - "@type": "rdfs:Class", - "rdfs:comment": "Marijuana smoke exposure", - "rdfs:label": "Marijuanasmoke", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Marijuana smoke", - "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:MarijuanaUsePerWeek" - } - ], - "sms:validationRules": [] - }, - { - "@id": "bts:MarijuanaUsePerWeek", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the number of times the patient uses marijuana each day.", - "rdfs:label": "MarijuanaUsePerWeek", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Marijuana Use Per Week", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoUseperDay", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value that represents the number of times the patient uses tobacco each day.", - "rdfs:label": "TobaccoUseperDay", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tobacco Use per Day", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SmokelessTobaccoQuitAge", - "@type": "rdfs:Class", - "rdfs:comment": "Smokeless tobacco quit age", - "rdfs:label": "SmokelessTobaccoQuitAge", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Smokeless Tobacco Quit Age", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TimebetweenWakingandFirstSmoke", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.", - "rdfs:label": "TimebetweenWakingandFirstSmoke", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Within5Minutes" - }, - { - "@id": "bts:6-30Minutes" - }, - { - "@id": "bts:31-60Minutes" - }, - { - "@id": "bts:After60Minutes" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Time between Waking and First Smoke", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TobaccoSmokingOnsetYear", - "@type": "rdfs:Class", - "rdfs:comment": "The year in which the participant began smoking.", - "rdfs:label": "TobaccoSmokingOnsetYear", - "rdfs:subClassOf": [ - { - "@id": "bts:Exposure" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - 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Number", + "rdfs:label": "DV200", + "rdfs:subClassOf": [ { - "@id": "bts:Malignantlymphomanon-HodgkinNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DV200", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AdapterContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "AdapterContent", + "rdfs:subClassOf": [ { - "@id": "bts:MalignantlymphomaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MalignantlymphomasmallBlymphocyticNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:Malignantmelanomaincongenitalmelanocyticnevus" + "@id": "bts:PASS" }, { - "@id": "bts:Malignantmelanomaingiantpigmentednevus" + "@id": "bts:WARN" }, { - "@id": "bts:MalignantmelanomainHutchinsonmelanoticfreckle" + "@id": "bts:Unknown" }, { - "@id": "bts:Malignantmelanomainjunctionalnevus" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Adapter Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BasicStatistics", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "BasicStatistics", + "rdfs:subClassOf": [ { - "@id": "bts:Malignantmelanomainprecancerousmelanosis" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MalignantmelanomaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:Malignantmelanomaregressing" + "@id": "bts:PASS" }, { - "@id": "bts:Mammarycarcinomainsitu" + "@id": "bts:WARN" }, { - "@id": "bts:Medullaryadenocarcinoma" + "@id": "bts:Unknown" }, { - "@id": "bts:MedullarycarcinomaNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Basic Statistics", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Encoding", + "@type": "rdfs:Class", + "rdfs:comment": "Version of ASCII encoding of quality values found in the file. String", + "rdfs:label": "Encoding", + "rdfs:subClassOf": [ { - "@id": "bts:Medullaryosteosarcoma" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Encoding", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:KmerContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "KmerContent", + "rdfs:subClassOf": [ { - "@id": "bts:MedulloblastomaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Melanoameloblastoma" + "@id": "bts:FAIL" }, { - "@id": "bts:Melanocyticnevus" + "@id": "bts:PASS" }, { - "@id": "bts:Melanocytomaeyeball" + "@id": "bts:WARN" }, { - "@id": "bts:MelanocytomaNOS" + "@id": "bts:Unknown" }, { - "@id": "bts:Melanomainsitu" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Kmer Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:OverrepresentedSequences", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "OverrepresentedSequences", + "rdfs:subClassOf": [ { - "@id": "bts:Melanomamalignantofsoftparts" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MelanomaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:Melanoticmedulloblastoma" + "@id": "bts:PASS" }, { - "@id": "bts:MelanoticMPNST" + "@id": "bts:WARN" }, { - "@id": "bts:Melanoticneuroectodermaltumor" + "@id": "bts:Unknown" }, { - "@id": "bts:Melanoticneurofibroma" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Overrepresented Sequences", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseNContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseNContent", + "rdfs:subClassOf": [ { - "@id": "bts:Melanoticprogonoma" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MelanoticpsammomatousMPNST" + "@id": "bts:FAIL" }, { - "@id": "bts:Melanoticschwannoma" + "@id": "bts:PASS" }, { - "@id": "bts:Meningealmelanocytoma" + "@id": "bts:WARN" }, { - "@id": "bts:Meningealmelanoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Meningiomaanaplastic" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base N Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseSequenceContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceContent", + "rdfs:subClassOf": [ { - "@id": "bts:Meningiomamalignant" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MeningiomaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:MicropapillarycarcinomaNOS" + "@id": "bts:PASS" }, { - "@id": "bts:Mixedadenocarcinomaandepidermoidcarcinoma" + "@id": "bts:WARN" }, { - "@id": "bts:Mixedadenocarcinomaandsquamouscellcarcinoma" + "@id": "bts:Unknown" }, { - "@id": "bts:Mixedmedullary-follicularcarcinoma" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerBaseSequenceQuality", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerBaseSequenceQuality", + "rdfs:subClassOf": [ { - "@id": "bts:Mixedmedullary-papillarycarcinoma" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Mixedpancreaticendocrineandexocrinetumormalignant" + "@id": "bts:FAIL" }, { - "@id": "bts:Mixedpinealtumor" + "@id": "bts:PASS" }, { - "@id": "bts:Mixedsmallcellcarcinoma" + "@id": "bts:WARN" }, { - "@id": "bts:Mixedsquamouscellandglandularpapilloma" + "@id": "bts:Unknown" }, { - "@id": "bts:MixedtumormalignantNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Base Sequence Quality", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceGCContent", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceGCContent", + "rdfs:subClassOf": [ { - "@id": "bts:MixedtumorNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MonocyticleukemiaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:Mucosal-associatedlymphoidtissuelymphoma" + "@id": "bts:PASS" }, { - "@id": "bts:Mucousadenocarcinoma" + "@id": "bts:WARN" }, { - "@id": "bts:Multiplemyeloma" + "@id": "bts:Unknown" }, { - "@id": "bts:MyelocyticleukemiaNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence GC Content", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerSequenceQualityScore", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "PerSequenceQualityScore", + "rdfs:subClassOf": [ { - "@id": "bts:MyeloidleukemiaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:MyelomaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:Myoepithelioma" + "@id": "bts:PASS" }, { - "@id": "bts:Neoplasmbenign" + "@id": "bts:WARN" }, { - "@id": "bts:Neoplasmmalignant" + "@id": "bts:Unknown" }, { - "@id": "bts:Neoplasmmalignantuncertainwhetherprimaryormetastatic" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Per Sequence Quality Score", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:PerTileSequenceQuality", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. 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Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceDuplicationLevels", + "rdfs:subClassOf": [ { - "@id": "bts:NeuroepitheliomaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:NeurofibromaNOS" + "@id": "bts:FAIL" }, { - "@id": "bts:NeurofibromatosisNOS" + "@id": "bts:PASS" }, { - "@id": "bts:Neurofibrosarcoma" + "@id": "bts:WARN" }, { - "@id": "bts:Neurosarcoma" + "@id": "bts:Unknown" }, { - "@id": "bts:NevusNOS" - }, + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Sequence Duplication Levels", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:SequenceLengthDistribution", + "@type": "rdfs:Class", + "rdfs:comment": "State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.", + "rdfs:label": "SequenceLengthDistribution", + "rdfs:subClassOf": [ { - "@id": "bts:Non-HodgkinlymphomaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Non-invasivelowgradeserouscarcinoma" + "@id": "bts:FAIL" }, { - "@id": "bts:Non-lymphocyticleukemiaNOS" + "@id": "bts:PASS" }, { - "@id": "bts:Non-smallcellcarcinoma" + "@id": "bts:WARN" }, { - "@id": "bts:Nonpigmentednevus" + "@id": "bts:Unknown" }, { "@id": "bts:NotReported" - }, + } + ], + "sms:displayName": "Sequence Length Distribution", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:TotalReads", + "@type": "rdfs:Class", + "rdfs:comment": "Total number of reads per sample. Integer", + "rdfs:label": "TotalReads", + "rdfs:subClassOf": [ { - "@id": "bts:Oatcellcarcinoma" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Total Reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowType", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set. String", + "rdfs:label": "QCWorkflowType", + "rdfs:subClassOf": [ { - "@id": "bts:Osteoblastomamalignant" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Type", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Major version for a workflow. String", + "rdfs:label": "QCWorkflowVersion", + "rdfs:subClassOf": [ { - "@id": "bts:OsteoblastomaNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "QC Workflow Version", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:QCWorkflowLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to workflow used. 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}, - { - "@id": "bts:Unclassifiedtumormalignantuncertainwhetherprimaryormetastatic" - }, - { - "@id": "bts:Unclassifiedtumoruncertainwhetherbenignormalignant" - }, - { - "@id": "bts:Undifferentiatedepithelioidsarcoma" - }, - { - "@id": "bts:Undifferentiatedhigh-gradepleomorphicsarcoma" - }, - { - "@id": "bts:Undifferentiatedleukaemia" - }, - { - "@id": "bts:Undifferentiatedpleomorphicsarcoma" - }, - { - "@id": "bts:Undifferentiatedroundcellsarcoma" + "@id": "bts:RPKM" }, { - "@id": "bts:Undifferentiatedsarcoma" + "@id": "bts:FPKM" }, { - "@id": "bts:Undifferentiatedspindlecellsarcoma" + "@id": "bts:Counts" }, { - "@id": "bts:Undifferentiateduterinesarcoma" + "@id": "bts:Other" }, { - "@id": "bts:Unknown" + "@id": "bts:NA" } ], - "sms:displayName": "Primary Diagnosis", + "sms:displayName": "Expression Units", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PriorMalignancy", + "@id": "bts:FusionGeneDetected", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.", - "rdfs:label": "PriorMalignancy", + "rdfs:comment": "Was a fusion gene identified?", + "rdfs:label": "FusionGeneDetected", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -36950,33 +34018,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:Yes-FusionGeneDetected" }, { "@id": "bts:No" }, { "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - }, - { - "@id": "bts:NotAllowedToCollect" } ], - "sms:displayName": "Prior Malignancy", + "sms:displayName": "Fusion Gene Detected", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorTreatment", + "@id": "bts:FusionGeneIdentity", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.", - "rdfs:label": "PriorTreatment", + "rdfs:comment": "The gene symbols of fused genes.", + "rdfs:label": "FusionGeneIdentity", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -36984,2069 +34046,3467 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:EWS-FLI" }, { - "@id": "bts:No" + "@id": "bts:EWS-ERG" }, { - "@id": "bts:Unknown" + "@id": "bts:SYT-SSX1" }, { - "@id": "bts:NotReported" + "@id": "bts:SYT-SSX2" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:EWS-WT1" + }, + { + "@id": "bts:OtherFusionGene" } ], - "sms:displayName": "Prior Treatment", + "sms:displayName": "Fusion Gene Identity", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "list like" + ] }, { - "@id": "bts:SiteofResectionorBiopsy", + "@id": "bts:BulkWESLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the anatomic site of the resection or biopsy 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": "SiteofResectionorBiopsy", + "rdfs:comment": "Bulk Whole Exome Sequencing raw files", + "rdfs:label": "BulkWESLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AbdomenNOS" - }, - { - "@id": "bts:Abdominalesophagus" - }, - { - "@id": "bts:AccessorysinusNOS" - }, - { - "@id": "bts:Acousticnerve" - }, + "sms:displayName": "Bulk WES Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:AdrenalglandNOS" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:AmpullaofVater" + "@id": "bts:Component" }, { - "@id": "bts:Analcanal" + "@id": "bts:Filename" }, { - "@id": "bts:Anterior2/3oftongueNOS" + "@id": "bts:FileFormat" }, { - "@id": "bts:Anteriorfloorofmouth" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Anteriormediastinum" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Anteriorsurfaceofepiglottis" + "@id": "bts:SequencingBatchID" }, { - "@id": "bts:Anteriorwallofbladder" + "@id": "bts:LibraryLayout" }, { - "@id": "bts:Anteriorwallofnasopharynx" + "@id": "bts:ReadIndicator" }, { - "@id": "bts:AnusNOS" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:Aorticbodyandotherparaganglia" + "@id": "bts:ReadLength" }, { - "@id": "bts:Appendix" + "@id": "bts:TargetCaptureKit" }, { - "@id": "bts:Ascendingcolon" + "@id": "bts:LibraryPreparationKitName" }, { - "@id": "bts:AutonomicnervoussystemNOS" + "@id": "bts:LibraryPreparationKitVendor" }, { - "@id": "bts:Axillarytailofbreast" + "@id": "bts:LibraryPreparationKitVersion" }, { - "@id": "bts:BaseoftongueNOS" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Bladderneck" + "@id": "bts:AdapterName" }, { - "@id": "bts:BladderNOS" + "@id": "bts:AdapterSequence" }, { - "@id": "bts:Blood" + "@id": "bts:BaseCallerName" }, { - "@id": "bts:Bodyofpancreas" + "@id": "bts:BaseCallerVersion" }, { - "@id": "bts:Bodyofpenis" + "@id": "bts:FlowCellBarcode" }, { - "@id": "bts:Bodyofstomach" + "@id": "bts:FragmentMaximumLength" }, { - "@id": "bts:Bonemarrow" + "@id": "bts:FragmentMeanLength" }, { - "@id": "bts:BoneoflimbNOS" + "@id": "bts:FragmentMinimumLength" }, { - "@id": "bts:BoneNOS" + "@id": "bts:FragmentStandardDeviationLength" }, { - "@id": "bts:Bonesofskullandfaceandassociatedjoints" + "@id": "bts:LaneNumber" }, { - "@id": "bts:Borderoftongue" + "@id": "bts:MultiplexBarcode" }, { - "@id": "bts:Brainstem" + "@id": "bts:LibraryPreparationDaysfromIndex" }, { - "@id": "bts:BrainNOS" + "@id": "bts:SizeSelectionRange" }, { - "@id": "bts:Branchialcleft" + "@id": "bts:TargetDepth" }, { - "@id": "bts:BreastNOS" - }, + "@id": "bts:ToTrimAdapterSequence" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:TargetCaptureKit", + "@type": "rdfs:Class", + "rdfs:comment": "Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.", + "rdfs:label": "TargetCaptureKit", + "rdfs:subClassOf": [ { - "@id": "bts:Broadligament" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:CardiaNOS" + "@id": "bts:NotApplicable" }, { - "@id": "bts:Carotidbody" + "@id": "bts:CustomTargetsFileProvided" }, { - "@id": "bts:Caudaequina" + "@id": "bts:CustomAmpliSeqCancerHotspotGENIE-MDAAugmentedPanelv1-46Genes" }, { - "@id": "bts:Cecum" + "@id": "bts:CustomGENIE-DFCIOncoPanel-275Genes" }, { - "@id": "bts:Centralportionofbreast" + "@id": "bts:CustomGENIE-DFCIOncopanel-300Genes" }, { - "@id": "bts:CerebellumNOS" + "@id": "bts:CustomGENIE-DFCIOncopanel-447Genes" }, { - "@id": "bts:Cerebralmeninges" + "@id": "bts:CustomHaloPlexDLBCLPanel-370Genes" }, { - "@id": "bts:Cerebrum" + "@id": "bts:CustomIonAmpliSeqHotspotGENIE-MOSC3AugmentedPanel-74Genes" }, { - "@id": "bts:Cervicalesophagus" + "@id": "bts:CustomLargeConstructCaptureTARGET-OSPanel-8Genes" }, { - "@id": "bts:Cervixuteri" + "@id": "bts:CustomMSKIMPACTPanel-341Genes" }, { - "@id": "bts:Choroid" + "@id": "bts:CustomMSKIMPACTPanel-410Genes" }, { - "@id": "bts:Ciliarybody" + "@id": "bts:CustomMSKIMPACTPanel-468Genes" }, { - "@id": "bts:Cloacogeniczone" + "@id": "bts:CustomMyeloidGENIE-VICCPanel-37Genes" }, { - "@id": "bts:ColonNOS" + "@id": "bts:CustomPersonalisACEcpVAREPOP-APOLLOPanelv2" }, { - "@id": "bts:Commissureoflip" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-203Genes" }, { - "@id": "bts:Conjunctiva" + "@id": "bts:CustomPGDXSureSelectCancerSelectVAREPOP-APOLLOPanel-88Genes" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofabdomen" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv1" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofheadfaceandneck" + "@id": "bts:CustomSeqCapEZHGSCVCRomev2.1ERAugmentedv2" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesoflowerlimbandhip" + "@id": "bts:CustomSeqCapEZTARGET-OSPanel-7.0Mb" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofpelvis" + "@id": "bts:CustomSolidTumorGENIE-VICCPanel-34Genes" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofthorax" + "@id": "bts:CustomSureSelectCGCI-BLGSPPanel-4.6Mb" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesoftrunkNOS" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCKMT2DAndHotspotPanel-37.0Kb" }, { - "@id": "bts:Connectivesubcutaneousandothersofttissuesofupperlimbandshoulder" + "@id": "bts:CustomSureSelectCGCI-HTMCP-CCPanel-19.7Mb" }, { - "@id": "bts:ConnectivesubcutaneousandothersofttissuesNOS" + "@id": "bts:CustomSureSelectGENIE-UHNPanel-555Genes" }, { - "@id": "bts:CorneaNOS" + "@id": "bts:CustomSureSelectHumanAllExonv1.1Plus3Boosters" }, { - "@id": "bts:Corpusuteri" + "@id": "bts:CustomSureSelectTARGET-AMLNBLWTPanel-2.8Mb" }, { - "@id": "bts:Cortexofadrenalgland" + "@id": "bts:CustomTwistBroadExomev1.0-35.0Mb" }, { - "@id": "bts:CranialnerveNOS" + "@id": "bts:CustomTwistBroadPanCancerPanel-396Genes" }, { - "@id": "bts:Craniopharyngealduct" + "@id": "bts:FoundationMedicineT5aPanel-322Genes" }, { - "@id": "bts:Descendedtestis" + "@id": "bts:FoundationMedicineT7Panel-429Genes" }, { - "@id": "bts:Descendingcolon" + "@id": "bts:IonAmpliSeqCancerHotspotPanelv2" }, { - "@id": "bts:Domeofbladder" + "@id": "bts:IonAmpliSeqComprehensiveCancerPanel" }, { - "@id": "bts:DorsalsurfaceoftongueNOS" + "@id": "bts:NexteraDNAExome" }, { - "@id": "bts:Duodenum" + "@id": "bts:NexteraRapidCaptureExomev1.2" }, { - "@id": "bts:Endocervix" + "@id": "bts:SeqCapEZHGSCVCRomev2.1" }, { - "@id": "bts:EndocrineglandNOS" + "@id": "bts:SeqCapEZHumanExomev2.0" }, { - "@id": "bts:Endometrium" + "@id": "bts:SeqCapEZHumanExomev3.0" }, { - "@id": "bts:Epididymis" + "@id": "bts:SureSelectHumanAllExonv3" }, { - "@id": "bts:EsophagusNOS" + "@id": "bts:SureSelectHumanAllExonv4" }, { - "@id": "bts:Ethmoidsinus" + "@id": "bts:SureSelectHumanAllExonv5" }, { - "@id": "bts:Exocervix" + "@id": "bts:SureSelectHumanAllExonv5+UTR" }, { - "@id": "bts:Externalear" + "@id": "bts:TruSeqAmpliconCancerPanel" }, { - "@id": "bts:ExternallipNOS" + "@id": "bts:TruSeqExomeEnrichment-62Mb" }, { - "@id": "bts:Externallowerlip" + "@id": "bts:TruSeqRNAExome" }, { - "@id": "bts:Externalupperlip" + "@id": "bts:TruSightMyeloidSequencingPanel" }, { - "@id": "bts:Extrahepaticbileduct" + "@id": "bts:XGenExomeResearchPanelv1.0" }, { - "@id": "bts:EyeNOS" + "@id": "bts:XGenUniversalBlockingOligo–TSHT-i5-25rxn" }, { - "@id": "bts:Eyelid" + "@id": "bts:25rxnxGenUniversalBlockingOligo–TSHT-i7" }, { - "@id": "bts:Fallopiantube" + "@id": "bts:SureSelectHumanAllExonv6" }, { - "@id": "bts:FemalegenitaltractNOS" - }, + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Target Capture Kit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkWESLevel2", + "@type": "rdfs:Class", + "rdfs:comment": "Bulk Whole Exome Sequencing aligned files and QC", + "rdfs:label": "BulkWESLevel2", + "rdfs:subClassOf": [ { - "@id": "bts:FloorofmouthNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk WES Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Frontallobe" - }, + "@id": "bts:BulkWESLevel1" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Frontalsinus" + "@id": "bts:Component" }, { - "@id": "bts:Fundusofstomach" + "@id": "bts:Filename" }, { - "@id": "bts:Fundusuteri" + "@id": "bts:FileFormat" }, { - "@id": "bts:Gallbladder" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Gastricantrum" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:GastrointestinaltractNOS" + "@id": "bts:AlignmentWorkflowType" }, { - "@id": "bts:Glanspenis" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Glottis" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:GreatercurvatureofstomachNOS" + "@id": "bts:IndexFileName" }, { - "@id": "bts:GumNOS" + "@id": "bts:AverageBaseQuality" }, { - "@id": "bts:Hardpalate" + "@id": "bts:AverageInsertSize" }, { - "@id": "bts:Headofpancreas" + "@id": "bts:AverageReadLength" }, { - "@id": "bts:HeadfaceorneckNOS" + "@id": "bts:Contamination" }, { - "@id": "bts:Heart" + "@id": "bts:ContaminationError" }, { - "@id": "bts:HematopoieticsystemNOS" + "@id": "bts:MeanCoverage" }, { - "@id": "bts:Hepaticflexureofcolon" + "@id": "bts:AdapterContent" }, { - "@id": "bts:Hypopharyngealaspectofaryepiglotticfold" + "@id": "bts:BasicStatistics" }, { - "@id": "bts:HypopharynxNOS" + "@id": "bts:Encoding" }, { - "@id": "bts:Ileum" + "@id": "bts:OverrepresentedSequences" }, { - "@id": "bts:Ill-definedsiteswithinrespiratorysystem" + "@id": "bts:PerBaseNContent" }, { - "@id": "bts:IntestinaltractNOS" + "@id": "bts:PerBaseSequenceContent" }, { - "@id": "bts:Intra-abdominallymphnodes" + "@id": "bts:PerBaseSequenceQuality" }, { - "@id": "bts:Intrahepaticbileduct" + "@id": "bts:PerSequenceGCContent" }, { - "@id": "bts:Intrathoraciclymphnodes" + "@id": "bts:PerSequenceQualityScore" }, { - "@id": "bts:IsletsofLangerhans" + "@id": "bts:PerTileSequenceQuality" }, { - "@id": "bts:Isthmusuteri" + "@id": "bts:PercentGCContent" }, { - "@id": "bts:Jejunum" + "@id": "bts:SequenceDuplicationLevels" }, { - "@id": "bts:KidneyNOS" + "@id": "bts:SequenceLengthDistribution" }, { - "@id": "bts:Labiummajus" + "@id": "bts:QCWorkflowType" }, { - "@id": "bts:Labiumminus" + "@id": "bts:QCWorkflowVersion" }, { - "@id": "bts:Lacrimalgland" + "@id": "bts:QCWorkflowLink" }, { - "@id": "bts:Laryngealcartilage" + "@id": "bts:MSIWorkflowLink" }, { - "@id": "bts:LarynxNOS" + "@id": "bts:MSIScore" }, { - "@id": "bts:Lateralfloorofmouth" + "@id": "bts:MSIStatus" }, { - "@id": "bts:Lateralwallofbladder" + "@id": "bts:PairsOnDiffCHR" }, { - "@id": "bts:Lateralwallofnasopharynx" + "@id": "bts:TotalReads" }, { - "@id": "bts:Lateralwalloforopharynx" + "@id": "bts:TotalUniquelyMapped" }, { - "@id": "bts:LessercurvatureofstomachNOS" + "@id": "bts:TotalUnmappedreads" }, { - "@id": "bts:Lingualtonsil" + "@id": "bts:ProportionReadsDuplicated" }, { - "@id": "bts:LipNOS" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:Liver" + "@id": "bts:ProportionTargetsNoCoverage" }, { - "@id": "bts:Longbonesoflowerlimbandassociatedjoints" + "@id": "bts:ProportionBaseMismatch" }, { - "@id": "bts:Longbonesofupperlimbscapulaandassociatedjoints" + "@id": "bts:ShortReads" }, { - "@id": "bts:Lowergum" + "@id": "bts:ProportionCoverage10x" }, { - "@id": "bts:LowerlimbNOS" + "@id": "bts:ProportionCoverage30X" }, { - "@id": "bts:Lowerlobelung" - }, + "@id": "bts:Islowestlevel" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage10x", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage10x", + "rdfs:subClassOf": [ { - "@id": "bts:Lowerthirdofesophagus" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion Coverage 10x", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionCoverage30X", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.", + "rdfs:label": "ProportionCoverage30X", + "rdfs:subClassOf": [ { - 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"@id": "bts:SmallintestineNOS" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SoftpalateNOS" + "@id": "bts:HG19" }, { - "@id": "bts:Specifiedpartsofperitoneum" + "@id": "bts:HG38" }, { - "@id": "bts:Spermaticcord" - }, - { - "@id": "bts:Sphenoidsinus" - }, - { - "@id": "bts:Spinalcord" - }, - { - "@id": "bts:Spinalmeninges" - }, - { - "@id": "bts:Spleen" - }, - { - "@id": "bts:Splenicflexureofcolon" - }, - { - "@id": "bts:StomachNOS" - }, - { - "@id": "bts:Subglottis" - }, - { - "@id": "bts:Sublingualgland" - }, - { - "@id": "bts:Submandibulargland" - }, - { - "@id": "bts:Superiorwallofnasopharynx" - }, - { - "@id": "bts:Supraglottis" - }, - { - "@id": "bts:Tailofpancreas" - }, - { - "@id": "bts:Temporallobe" - }, - { - "@id": "bts:TestisNOS" - }, + "@id": "bts:T2TCHM13" + } + ], + "sms:displayName": "Bulk Methylation Genomic Reference", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DuplicateRemovalSoftware", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for remove duplicate reads", + "rdfs:label": "DuplicateRemovalSoftware", + "rdfs:subClassOf": [ { - "@id": "bts:Thoracicesophagus" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:ThoraxNOS" + "@id": "bts:Samtoolssort" }, { - "@id": "bts:Thymus" - }, + "@id": "bts:PicardMarkDuplicates" + } + ], + "sms:displayName": "Duplicate Removal Software", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ProportionofMinimumCpGCoverage10X", + "@type": "rdfs:Class", + "rdfs:comment": "Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.", + "rdfs:label": "ProportionofMinimumCpGCoverage10X", + "rdfs:subClassOf": [ { - "@id": "bts:Thyroidgland" - }, + "@id": "bts:BulkMethylation-seqLevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Proportion of Minimum CpG Coverage 10X", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:BulkMethylation-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.", + "rdfs:label": "BulkMethylation-seqLevel3", + "rdfs:subClassOf": [ { - "@id": "bts:TongueNOS" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Bulk Methylation-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:TonsilNOS" + "@id": "bts:BulkMethylation-seqLevel2" }, { - "@id": "bts:Tonsillarfossa" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Tonsillarpillar" + "@id": "bts:Component" }, { - "@id": "bts:Trachea" + "@id": "bts:Filename" }, { - "@id": "bts:Transversecolon" + "@id": "bts:FileFormat" }, { - "@id": "bts:Trigoneofbladder" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Undescendedtestis" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Unknownprimarysite" + "@id": "bts:DMCCallingTool" }, { - "@id": "bts:Uppergum" + "@id": "bts:DMCCallingWorkflowURL" }, { - "@id": "bts:UpperlimbNOS" + "@id": "bts:DMRCallingTool" }, { - "@id": "bts:Upperlobelung" + "@id": "bts:DMRCallingWorkflowURL" }, { - "@id": "bts:UpperrespiratorytractNOS" + "@id": "bts:PUC19methylationratio" }, { - "@id": "bts:Upperthirdofesophagus" + "@id": "bts:Lambdamethylationratio" }, { - "@id": "bts:Upper-innerquadrantofbreast" + "@id": "bts:DMCdatafileformat" }, { - "@id": "bts:Upper-outerquadrantofbreast" - }, + "@id": "bts:DMRdatafileFormat" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:DMCCallingTool", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMCCallingTool", + "rdfs:subClassOf": [ { - "@id": "bts:Urachus" - }, + "@id": "bts:BulkMethylation-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Ureter" + "@id": "bts:MethylKit" }, { - "@id": "bts:Uretericorifice" + "@id": "bts:BSmooth" }, { - "@id": "bts:Urethra" + "@id": "bts:BiSeq" }, { - "@id": "bts:UrinarysystemNOS" + "@id": "bts:MethylSig" }, { - "@id": "bts:Uterineadnexa" + "@id": "bts:DSS" }, { - "@id": "bts:UterusNOS" + "@id": "bts:MOABS" }, { - "@id": "bts:Uvula" + "@id": "bts:DSS-single" }, { - "@id": "bts:VaginaNOS" + "@id": "bts:Metilene" }, { - "@id": "bts:Vallecula" + "@id": "bts:MACAU" }, { - "@id": "bts:VentralsurfaceoftongueNOS" - }, + "@id": "bts:MethylDackel" + } + ], + "sms:displayName": "DMC Calling Tool", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DMCCallingWorkflowURL", + "@type": "rdfs:Class", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMCCallingWorkflowURL", + "rdfs:subClassOf": [ { - "@id": "bts:VentricleNOS" - }, + "@id": "bts:BulkMethylation-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DMC Calling Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [ + "url" + ] + }, + { + "@id": "bts:DMRCallingTool", + "@type": "rdfs:Class", + "rdfs:comment": "Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)", + "rdfs:label": "DMRCallingTool", + "rdfs:subClassOf": [ { - "@id": "bts:Vertebralcolumn" - }, + "@id": "bts:BulkMethylation-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Vestibuleofmouth" + "@id": "bts:MethylKit" }, { - "@id": "bts:VulvaNOS" + "@id": "bts:BSmooth" }, { - "@id": "bts:Waldeyerring" + "@id": "bts:BiSeq" }, { - "@id": "bts:BiliarytractNOS" + "@id": "bts:MethylSig" }, { - "@id": "bts:Cheekmucosa" + "@id": "bts:DSS" }, { - "@id": "bts:Clitoris" + "@id": "bts:MOABS" }, { - "@id": "bts:Overlappinglesionofbiliarytract" + "@id": "bts:DSS-single" }, { - "@id": "bts:Unknown" + "@id": "bts:Metilene" }, { - "@id": "bts:NotReported" + "@id": "bts:MACAU" } ], - "sms:displayName": "Tissue or Organ of Origin", + "sms:displayName": "DMR Calling Tool", "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:TumorGrade", + "@id": "bts:DMRCallingWorkflowURL", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.", - "rdfs:label": "TumorGrade", + "rdfs:comment": "Generic name for the workflow used to analyze a data set", + "rdfs:label": "DMRCallingWorkflowURL", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -39054,54 +37514,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:G1" - }, - { - "@id": "bts:G2" - }, - { - "@id": "bts:G3" - }, - { - "@id": "bts:G4" - }, - { - "@id": "bts:GX" - }, - { - "@id": "bts:GB" - }, - { - "@id": "bts:HighGrade" - }, - { - "@id": "bts:IntermediateGrade" - }, - { - "@id": "bts:LowGrade" + "@id": "bts:Github" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:Synapse" + } + ], + "sms:displayName": "DMR Calling Workflow URL", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PUC19methylationratio", + "@type": "rdfs:Class", + "rdfs:comment": "Methylation ratio of mostly methylated pUC19 control, as a percentage", + "rdfs:label": "PUC19methylationratio", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" - }, + "@id": "bts:BulkMethylation-seqLevel3" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "pUC19 methylation ratio", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Lambdamethylationratio", + "@type": "rdfs:Class", + "rdfs:comment": "Methylation ratio of mostly unmethylated lambda control, as a percentage", + "rdfs:label": "Lambdamethylationratio", + "rdfs:subClassOf": [ { - "@id": "bts:NotApplicable" + "@id": "bts:BulkMethylation-seqLevel3" } ], - "sms:displayName": "Tumor Grade", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Lambda methylation ratio", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalM", + "@id": "bts:DMCdatafileformat", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalM", + "rdfs:comment": "Format of the data files", + "rdfs:label": "DMCdatafileformat", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -39109,45 +37573,24 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:M0" - }, - { - "@id": "bts:M1" - }, - { - "@id": "bts:M1a" - }, - { - "@id": "bts:M1b" - }, - { - "@id": "bts:M1c" - }, - { - "@id": "bts:MX" - }, - { - "@id": "bts:CM0(i+)" - }, - { - "@id": "bts:Unknown" + "@id": "bts:BED" }, { - "@id": "bts:NotReported" + "@id": "bts:BedGraph" } ], - "sms:displayName": "AJCC Clinical M", - "sms:required": "sms:false", + "sms:displayName": "DMC data file format", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalN", + "@id": "bts:DMRdatafileFormat", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalN", + "rdfs:comment": "Format of the data files.", + "rdfs:label": "DMRdatafileFormat", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:BulkMethylation-seqLevel3" } ], "schema:isPartOf": { @@ -39155,96 +37598,84 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:N0" - }, - { - "@id": "bts:N0(i+)" - }, - { - "@id": "bts:N0(i-)" - }, - { - "@id": "bts:N0(mol+)" - }, - { - "@id": "bts:N0(mol-)" - }, - { - "@id": "bts:N1" - }, - { - "@id": "bts:N1a" - }, - { - "@id": "bts:N1b" - }, - { - "@id": "bts:N1bI" - }, - { - "@id": "bts:N1bII" - }, - { - "@id": "bts:N1bIII" + "@id": "bts:BED" }, { - "@id": "bts:N1bIV" - }, + "@id": "bts:BedGraph" + } + ], + "sms:displayName": "DMR data file Format", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Raw imaging data", + "rdfs:label": "ImagingLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:N1c" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Imaging Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:N1mi" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:N2" + "@id": "bts:Component" }, { - "@id": "bts:N2a" + "@id": "bts:Filename" }, { - "@id": "bts:N2b" + "@id": "bts:FileFormat" }, { - "@id": "bts:N2c" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:N3" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:N3a" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:N3b" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:N3c" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:N4" + "@id": "bts:CommitSHA" }, { - "@id": "bts:NX" + "@id": "bts:Pre-processingCompleted" }, { - "@id": "bts:Unknown" + "@id": "bts:Pre-processingRequired" }, { - "@id": "bts:NotReported" + "@id": "bts:Comment" } ], - "sms:displayName": "AJCC Clinical N", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalStage", + "@id": "bts:ImagingAssayType", "@type": "rdfs:Class", - "rdfs:comment": "Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.", - "rdfs:label": "AJCCClinicalStage", + "rdfs:comment": "Type of imaging assay", + "rdfs:label": "ImagingAssayType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39252,387 +37683,576 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Stage0" - }, - { - "@id": "bts:Stage0a" + "@id": "bts:H&E" }, { - "@id": "bts:Stage0is" + "@id": "bts:CyCIF" }, { - "@id": "bts:StageI" + "@id": "bts:T-CyCIF" }, { - "@id": "bts:StageIA" + "@id": "bts:IHC" }, { - "@id": "bts:StageIA1" + "@id": "bts:MIHC" }, { - "@id": "bts:StageIA2" + "@id": "bts:MxIF" }, { - "@id": "bts:StageIB" + "@id": "bts:SABER" }, { - "@id": "bts:StageIB1" + "@id": "bts:IMC" }, { - "@id": "bts:StageIB2" + "@id": "bts:CODEX" }, { - "@id": "bts:StageIC" + "@id": "bts:GeoMX-DSP" }, { - "@id": "bts:StageII" + "@id": "bts:MIBI" }, { - "@id": "bts:StageIIA" + "@id": "bts:MERFISH" }, { - "@id": "bts:StageIIA1" + "@id": "bts:ExSeq" }, { - "@id": "bts:StageIIA2" + "@id": "bts:RareCyteOrion" }, { - "@id": "bts:StageIIB" - }, + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Imaging Assay Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SoftwareandVersion", + "@type": "rdfs:Class", + "rdfs:comment": "Name of software used to generate expression values. String", + "rdfs:label": "SoftwareandVersion", + "rdfs:subClassOf": [ { - "@id": "bts:StageIIC" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Software and Version", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:CommitSHA", + "@type": "rdfs:Class", + "rdfs:comment": "Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]", + "rdfs:label": "CommitSHA", + "rdfs:subClassOf": [ { - "@id": "bts:StageIIC1" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Commit SHA", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pre-processingCompleted", + "@type": "rdfs:Class", + "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingCompleted", + "rdfs:subClassOf": [ { - "@id": "bts:StageIII" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StageIIIA" + "@id": "bts:Illuminationcorrection" }, { - "@id": "bts:StageIIIB" + "@id": "bts:TileStitching" }, { - "@id": "bts:StageIIIC" + "@id": "bts:Channel/CycleRegistration" }, { - "@id": "bts:StageIIIC1" + "@id": "bts:TMAde-arraying" }, { - "@id": "bts:StageIIIC2" + "@id": "bts:None" }, { - "@id": "bts:StageIS" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Completed", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Pre-processingRequired", + "@type": "rdfs:Class", + "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", + "rdfs:label": "Pre-processingRequired", + "rdfs:subClassOf": [ { - "@id": "bts:StageIV" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StageIVA" + "@id": "bts:Illuminationcorrection" }, { - "@id": "bts:StageIVB" + "@id": "bts:TileStitching" }, { - "@id": "bts:StageIVC" + "@id": "bts:Channel/CycleRegistration" }, { - "@id": "bts:StageTis" + "@id": "bts:TMAde-arraying" }, { - "@id": "bts:StageX" + "@id": "bts:None" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Pre-processing Required", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Comment", + "@type": "rdfs:Class", + "rdfs:comment": "Free text field (generally for QC comment)", + "rdfs:label": "Comment", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Imaging" } ], - "sms:displayName": "AJCC Clinical Stage", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Comment", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCClinicalT", + "@id": "bts:ImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.", - "rdfs:label": "AJCCClinicalT", + "rdfs:comment": "Raw and pre-processed image data", + "rdfs:label": "ImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:T0" + "@id": "bts:ImagingLevel1" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:T1" + "@id": "bts:Filename" }, { - "@id": "bts:T1a" + "@id": "bts:FileFormat" }, { - "@id": "bts:T1a1" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:T1a2" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:T1b" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:T1b1" + "@id": "bts:ChannelMetadataFilename" }, { - "@id": "bts:T1b2" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:T1c" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:T1mi" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:T2" + "@id": "bts:Microscope" }, { - "@id": "bts:T2a" + "@id": "bts:Objective" }, { - "@id": "bts:T2a1" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:T2a2" + "@id": "bts:LensNA" }, { - "@id": "bts:T2b" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:T2c" + "@id": "bts:WorkingDistanceUnit" }, { - "@id": "bts:T2d" + "@id": "bts:Immersion" }, { - "@id": "bts:T3" + "@id": "bts:Pyramid" }, { - "@id": "bts:T3a" + "@id": "bts:Zstack" }, { - "@id": "bts:T3b" + "@id": "bts:Tseries" }, { - "@id": "bts:T3c" + "@id": "bts:PassedQC" }, { - "@id": "bts:T3d" + "@id": "bts:Comment" }, { - "@id": "bts:T4" + "@id": "bts:FOVnumber" }, { - "@id": "bts:T4a" + "@id": "bts:FOVX" }, { - "@id": "bts:T4b" + "@id": "bts:FOVXUnit" }, { - "@id": "bts:T4c" + "@id": "bts:FOVY" }, { - "@id": "bts:T4d" + "@id": "bts:FOVYUnit" }, { - "@id": "bts:T4e" + "@id": "bts:FrameAveraging" }, { - "@id": "bts:TX" + "@id": "bts:ImageID" }, { - "@id": "bts:Ta" + "@id": "bts:DimensionOrder" }, { - "@id": "bts:Tis" + "@id": "bts:PhysicalSizeX" }, { - "@id": "bts:Tis(DCIS)" + "@id": "bts:PhysicalSizeXUnit" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:PhysicalSizeY" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:PhysicalSizeYUnit" }, { - "@id": "bts:Unknown" + "@id": "bts:PhysicalSizeZ" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "AJCC Clinical T", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:AJCCPathologicM", - "@type": "rdfs:Class", - "rdfs:comment": "Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicM", - "rdfs:subClassOf": [ + "@id": "bts:PhysicalSizeZUnit" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:PixelsBigEndian" + }, { - "@id": "bts:M0" + "@id": "bts:PlaneCount" }, { - "@id": "bts:M1" + "@id": "bts:SizeC" }, { - "@id": "bts:M1a" + "@id": "bts:SizeT" }, { - "@id": "bts:M1b" + "@id": "bts:SizeX" }, { - "@id": "bts:M1c" + "@id": "bts:SizeY" }, { - "@id": "bts:MX" + "@id": "bts:SizeZ" }, { - "@id": "bts:CM0(i+)" + "@id": "bts:PixelType" }, { - "@id": "bts:Unknown" + "@id": "bts:MERFISHPositionsFile" }, { - "@id": "bts:NotReported" + "@id": "bts:MERFISHCodebookFile" } ], - "sms:displayName": "AJCC Pathologic M", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicN", + "@id": "bts:ChannelMetadataFilename", "@type": "rdfs:Class", - "rdfs:comment": "The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.", - "rdfs:label": "AJCCPathologicN", + "rdfs:comment": "Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details", + "rdfs:label": "ChannelMetadataFilename", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ImagingLevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:N0" - }, - { - "@id": "bts:N0(i+)" - }, - { - "@id": "bts:N0(i-)" - }, + "sms:displayName": "Channel Metadata Filename", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Microscope", + "@type": "rdfs:Class", + "rdfs:comment": "Microscope type (manufacturer, model, etc) used for this experiment", + "rdfs:label": "Microscope", + "rdfs:subClassOf": [ { - "@id": "bts:N0(mol+)" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Microscope", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Objective", + "@type": "rdfs:Class", + "rdfs:comment": "Objective", + "rdfs:label": "Objective", + "rdfs:subClassOf": [ { - "@id": "bts:N0(mol-)" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Objective", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:NominalMagnification", + "@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:subClassOf": [ { - "@id": "bts:N1" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "NominalMagnification", + "sms:required": "sms:true", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:LensNA", + "@type": "rdfs:Class", + "rdfs:comment": "The numerical aperture of the lens. Floating point value > 0.", + "rdfs:label": "LensNA", + "rdfs:subClassOf": [ { - "@id": "bts:N1a" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "LensNA", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@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": [ { - "@id": "bts:N1b" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "WorkingDistance", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:N1bI" - }, + "@id": "bts:WorkingDistanceUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:WorkingDistanceUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "WorkingDistanceUnit", + "rdfs:subClassOf": [ { - "@id": "bts:N1bII" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:N1bIII" + "@id": "bts:Cm" }, { - "@id": "bts:N1bIV" + "@id": "bts:Mm" }, { - "@id": "bts:N1c" + "@id": "bts:Μm" }, { - "@id": "bts:N1mi" + "@id": "bts:Nm" }, { - "@id": "bts:N2" - }, + "@id": "bts:Å" + } + ], + "sms:displayName": "WorkingDistanceUnit", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Immersion", + "@type": "rdfs:Class", + "rdfs:comment": "Immersion medium", + "rdfs:label": "Immersion", + "rdfs:subClassOf": [ { - "@id": "bts:N2a" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:N2b" + "@id": "bts:Air" }, { - "@id": "bts:N2c" + "@id": "bts:Oil" }, { - "@id": "bts:N3" + "@id": "bts:Water" }, { - "@id": "bts:N3a" - }, + "@id": "bts:Other" + } + ], + "sms:displayName": "Immersion", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Pyramid", + "@type": "rdfs:Class", + "rdfs:comment": "Does data file contain pyramid of images", + "rdfs:label": "Pyramid", + "rdfs:subClassOf": [ { - "@id": "bts:N3b" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:N3c" + "@id": "bts:Yes" }, { - "@id": "bts:N4" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Pyramid", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Zstack", + "@type": "rdfs:Class", + "rdfs:comment": "Does data file contain a Z-stack of images", + "rdfs:label": "Zstack", + "rdfs:subClassOf": [ { - "@id": "bts:NX" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "AJCC Pathologic N", - "sms:required": "sms:false", + "sms:displayName": "Zstack", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicStage", + "@id": "bts:Tseries", "@type": "rdfs:Class", - "rdfs:comment": "The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.", - "rdfs:label": "AJCCPathologicStage", + "rdfs:comment": "Does data file contain a time-series of images", + "rdfs:label": "Tseries", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39640,293 +38260,150 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Stage0" + "@id": "bts:Yes" }, { - "@id": "bts:Stage0a" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Tseries", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PassedQC", + "@type": "rdfs:Class", + "rdfs:comment": "Did all channels pass QC (if not add free text Comment)", + "rdfs:label": "PassedQC", + "rdfs:subClassOf": [ { - "@id": "bts:Stage0is" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:StageI" + "@id": "bts:Yes" }, { - "@id": "bts:StageIA" - }, - { - "@id": "bts:StageIA1" - }, - { - "@id": "bts:StageIA2" - }, - { - "@id": "bts:StageIB" - }, - { - "@id": "bts:StageIB1" - }, - { - "@id": "bts:StageIB2" - }, - { - "@id": "bts:StageIC" - }, - { - "@id": "bts:StageII" - }, - { - "@id": "bts:StageIIA" - }, - { - "@id": "bts:StageIIA1" - }, - { - "@id": "bts:StageIIA2" - }, - { - "@id": "bts:StageIIB" - }, - { - "@id": "bts:StageIIC" - }, - { - "@id": "bts:StageIIC1" - }, - { - "@id": "bts:StageIII" - }, - { - "@id": "bts:StageIIIA" - }, - { - "@id": "bts:StageIIIB" - }, - { - "@id": "bts:StageIIIC" - }, - { - "@id": "bts:StageIIIC1" - }, - { - "@id": "bts:StageIIIC2" - }, - { - "@id": "bts:StageIS" - }, - { - "@id": "bts:StageIV" - }, - { - "@id": "bts:StageIVA" - }, - { - "@id": "bts:StageIVB" - }, - { - "@id": "bts:StageIVC" - }, - { - "@id": "bts:StageTis" - }, - { - "@id": "bts:StageX" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" + "@id": "bts:No-ChannelsQC" } ], - "sms:displayName": "AJCC Pathologic Stage", - "sms:required": "sms:false", + "sms:displayName": "Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AJCCPathologicT", + "@id": "bts:FOVnumber", "@type": "rdfs:Class", - "rdfs:comment": "Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).", - "rdfs:label": "AJCCPathologicT", + "rdfs:comment": "Index of FOV (as it pertains to its sequence order). Integer >= 1", + "rdfs:label": "FOVnumber", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:T0" - }, - { - "@id": "bts:T1" - }, - { - "@id": "bts:T1a" - }, - { - "@id": "bts:T1a1" - }, - { - "@id": "bts:T1a2" - }, - { - "@id": "bts:T1b" - }, - { - "@id": "bts:T1b1" - }, - { - "@id": "bts:T1b2" - }, - { - "@id": "bts:T1c" - }, - { - "@id": "bts:T1mi" - }, - { - "@id": "bts:T2" - }, - { - "@id": "bts:T2a" - }, - { - "@id": "bts:T2a1" - }, - { - "@id": "bts:T2a2" - }, - { - "@id": "bts:T2b" - }, - { - "@id": "bts:T2c" - }, - { - "@id": "bts:T2d" - }, - { - "@id": "bts:T3" - }, - { - "@id": "bts:T3a" - }, - { - "@id": "bts:T3b" - }, - { - "@id": "bts:T3c" - }, - { - "@id": "bts:T3d" - }, - { - "@id": "bts:T4" - }, - { - "@id": "bts:T4a" - }, - { - "@id": "bts:T4b" - }, - { - "@id": "bts:T4c" - }, - { - "@id": "bts:T4d" - }, - { - "@id": "bts:T4e" - }, + "sms:displayName": "FOV number", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:FOVX", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view X dimension. Floating point", + "rdfs:label": "FOVX", + "rdfs:subClassOf": [ { - "@id": "bts:TX" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "FOVX", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Ta" - }, + "@id": "bts:FOVXUnit" + } + ], + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:FOVXUnit", + "@type": "rdfs:Class", + "rdfs:comment": "Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVXUnit", + "rdfs:subClassOf": [ { - "@id": "bts:Tis" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:Tis(DCIS)" + "@id": "bts:Cm" }, { - "@id": "bts:Tis(LCIS)" + "@id": "bts:Mm" }, { - "@id": "bts:Tis(Paget's)" + "@id": "bts:Μm" }, { - "@id": "bts:Unknown" + "@id": "bts:Nm" }, { - "@id": "bts:NotReported" + "@id": "bts:Å" } ], - "sms:displayName": "AJCC Pathologic T", + "sms:displayName": "FOVXUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AJCCStagingSystemEdition", + "@id": "bts:FOVY", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.", - "rdfs:label": "AJCCStagingSystemEdition", + "rdfs:comment": "Field of view Y dimension. Floating point value", + "rdfs:label": "FOVY", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:1st" - }, - { - "@id": "bts:2nd" - }, - { - "@id": "bts:3rd" - }, - { - "@id": "bts:4th" - }, - { - "@id": "bts:5th" - }, - { - "@id": "bts:6th" - }, - { - "@id": "bts:7th" - }, - { - "@id": "bts:8th" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "FOVY", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:NotReported" + "@id": "bts:FOVYUnit" } ], - "sms:displayName": "AJCC Staging System Edition", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:AnaplasiaPresent", + "@id": "bts:FOVYUnit", "@type": "rdfs:Class", - "rdfs:comment": "Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.", - "rdfs:label": "AnaplasiaPresent", + "rdfs:comment": "Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "FOVYUnit", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39934,52 +38411,67 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-AnaplasiaPresent" + "@id": "bts:Cm" }, { - "@id": "bts:No" + "@id": "bts:Mm" }, { - "@id": "bts:Unknown" + "@id": "bts:Μm" }, { - "@id": "bts:NotReported" + "@id": "bts:Nm" + }, + { + "@id": "bts:Å" } ], - "sms:displayName": "Anaplasia Present", + "sms:displayName": "FOVYUnit", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yes-AnaplasiaPresent", + "@id": "bts:FrameAveraging", "@type": "rdfs:Class", - "rdfs:comment": "Indicates anaplasia is present", - "rdfs:label": "Yes-AnaplasiaPresent", + "rdfs:comment": "Number of frames averaged together (if no averaging, set to 1). Integer >= 1", + "rdfs:label": "FrameAveraging", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Anaplasia Present", + "sms:displayName": "Frame Averaging", "sms:required": "sms:false", - "sms:requiresDependency": [ + "sms:validationRules": [] + }, + { + "@id": "bts:ImageID", + "@type": "rdfs:Class", + "rdfs:comment": "Unique internal image identifier. eg \"Image:0\". (To be extracted from OME-XML)", + "rdfs:label": "ImageID", + "rdfs:subClassOf": [ { - "@id": "bts:AnaplasiaPresentType" + "@id": "bts:Imaging" } ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Image ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:AnaplasiaPresentType", + "@id": "bts:DimensionOrder", "@type": "rdfs:Class", - "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.", - "rdfs:label": "AnaplasiaPresentType", + "rdfs:comment": "The order in which the individual planes of data are interleaved.", + "rdfs:label": "DimensionOrder", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -39987,42 +38479,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" + "@id": "bts:XYZCT" }, { - "@id": "bts:Diffuse" + "@id": "bts:XYZTC" }, { - "@id": "bts:Equivocal" + "@id": "bts:XYCTZ" }, { - "@id": "bts:Focal" + "@id": "bts:XYCZT" }, { - "@id": "bts:Present" + "@id": "bts:XYTZC" }, { - "@id": "bts:Sclerosis" - }, + "@id": "bts:ZYX" + } + ], + "sms:displayName": "DimensionOrder", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@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:Unknown" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeX", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:NotReported" + "@id": "bts:PhysicalSizeXUnit" } ], - "sms:displayName": "Anaplasia Present Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BestOverallResponse", + "@id": "bts:PhysicalSizeXUnit", "@type": "rdfs:Class", - "rdfs:comment": "The best improvement achieved throughout the entire course of protocol treatment.", - "rdfs:label": "BestOverallResponse", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeXUnit", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -40030,113 +38538,111 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:AJ-AdjuvantTherapy" - }, - { - "@id": "bts:CPD-ClinicalProgression" - }, - { - "@id": "bts:CR-CompleteResponse" - }, - { - "@id": "bts:CRU-CompleteResponseUnconfirmed" - }, - { - "@id": "bts:DU-DiseaseUnchanged" - }, - { - "@id": "bts:IMR-Immunoresponse" - }, - { - "@id": "bts:IPD-Immunoprogression" - }, - { - "@id": "bts:MR-Minimal/MarginalResponse" - }, - { - "@id": "bts:MX-MixedResponse" - }, - { - "@id": "bts:Non-CR/Non-PD-Non-CR/Non-PD" - }, - { - "@id": "bts:NPB-NoPalliativeBenefit" - }, - { - "@id": "bts:NR-NoResponse" - }, - { - "@id": "bts:PA-PalliativeTherapy" - }, - { - "@id": "bts:PB-PalliativeBenefit" + "@id": "bts:Cm" }, { - "@id": "bts:PD-ProgressiveDisease" + "@id": "bts:Mm" }, { - "@id": "bts:PPD-Pseudoprogression" + "@id": "bts:Μm" }, { - "@id": "bts:PR-PartialResponse" + "@id": "bts:Nm" }, { - "@id": "bts:PSR-Pseudoresponse" - }, + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeXUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeY", + "@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:subClassOf": [ { - "@id": "bts:RD-ResponsiveDisease" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "PhysicalSizeY", + "sms:required": "sms:true", + "sms:requiresDependency": [ { - "@id": "bts:RP-Response" - }, + "@id": "bts:PhysicalSizeYUnit" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:PhysicalSizeYUnit", + "@type": "rdfs:Class", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeYUnit", + "rdfs:subClassOf": [ { - "@id": "bts:RPD-RadiographicProgressiveDisease" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:SCR-StringentCompleteResponse" + "@id": "bts:Cm" }, { - "@id": "bts:SD-StableDisease" + "@id": "bts:Mm" }, { - "@id": "bts:SPD-SurgicalProgression" + "@id": "bts:Μm" }, { - "@id": "bts:TE-TooEarly" + "@id": "bts:Nm" }, { - "@id": "bts:VGPR-VeryGoodPartialResponse" + "@id": "bts:Å" } ], - "sms:displayName": "Best Overall Response", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeYUnit", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreslowThickness", + "@id": "bts:PhysicalSizeZ", "@type": "rdfs:Class", - "rdfs:comment": "The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.", - "rdfs:label": "BreslowThickness", + "rdfs:comment": "Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.", + "rdfs:label": "PhysicalSizeZ", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breslow Thickness", - "sms:required": "sms:false", + "sms:displayName": "PhysicalSizeZ", + "sms:required": "sms:true", + "sms:requiresDependency": [ + { + "@id": "bts:PhysicalSizeZUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:ClassificationofTumor", + "@id": "bts:PhysicalSizeZUnit", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.", - "rdfs:label": "ClassificationofTumor", + "rdfs:comment": "The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)", + "rdfs:label": "PhysicalSizeZUnit", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -40144,118 +38650,170 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Primary" + "@id": "bts:Cm" }, { - "@id": "bts:Metastasis" + "@id": "bts:Mm" }, { - "@id": "bts:Recurrence" + "@id": "bts:Μm" }, { - "@id": "bts:Other" + "@id": "bts:Nm" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:Å" + } + ], + "sms:displayName": "PhysicalSizeZUnit", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:PixelsBigEndian", + "@type": "rdfs:Class", + "rdfs:comment": "Boolean (True/False)", + "rdfs:label": "PixelsBigEndian", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:True" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:False" } ], - "sms:displayName": "Classification of Tumor", - "sms:required": "sms:false", + "sms:displayName": "Pixels BigEndian", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:DaystoDiagnosis", + "@id": "bts:PlaneCount", "@type": "rdfs:Class", - "rdfs:comment": "Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'", - "rdfs:label": "DaystoDiagnosis", + "rdfs:comment": "Number of Z-planes (not to be confused with downsampled \"pyramid\"). Integer >=1", + "rdfs:label": "PlaneCount", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Days to Diagnosis", - "sms:required": "sms:false", + "sms:displayName": "PlaneCount", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:SizeC", + "@type": "rdfs:Class", + "rdfs:comment": "Number of channels. Integer >= 1", + "rdfs:label": "SizeC", + "rdfs:subClassOf": [ + { + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeC", + "sms:required": "sms:true", "sms:validationRules": [ - "regex match \\d+$|Not\\sApplicable$|unknown$" + "int" ] }, { - "@id": "bts:FirstSymptomPriortoDiagnosis", + "@id": "bts:SizeT", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.", - "rdfs:label": "FirstSymptomPriortoDiagnosis", + "rdfs:comment": "Number of time points. Integer >= 1", + "rdfs:label": "SizeT", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:AlteredMentalStatus" - }, - { - "@id": "bts:Headaches" - }, - { - "@id": "bts:MotororMovementChanges" - }, - { - "@id": "bts:Seizures" - }, - { - "@id": "bts:SensoryChanges" - }, - { - "@id": "bts:VisualChanges" - }, + "sms:displayName": "SizeT", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeX", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: X dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeX", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeX", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:SizeY", + "@type": "rdfs:Class", + "rdfs:comment": "Size of image: Y dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeY", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Imaging" } ], - "sms:displayName": "First Symptom Prior to Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "SizeY", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:GrossTumorWeight", + "@id": "bts:SizeZ", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the gross pathologic tumor weight, measured in grams.", - "rdfs:label": "GrossTumorWeight", + "rdfs:comment": "Size of image: Z dimension (in pixels). Integer >= 1", + "rdfs:label": "SizeZ", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gross Tumor Weight", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "SizeZ", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:Laterality", + "@id": "bts:PixelType", "@type": "rdfs:Class", - "rdfs:comment": "For tumors in paired organs, designates the side on which the cancer originates.", - "rdfs:label": "Laterality", + "rdfs:comment": "Data type for each pixel value. E.g. \"uint16\"", + "rdfs:label": "PixelType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -40263,104 +38821,136 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Bilateral" + "@id": "bts:Int8" }, { - "@id": "bts:Left" + "@id": "bts:Int16" }, { - "@id": "bts:Midline" + "@id": "bts:Int32" }, { - "@id": "bts:Right" + "@id": "bts:Uint8" }, { - "@id": "bts:Unilateral" + "@id": "bts:Uint16" }, { - "@id": "bts:Unknown" + "@id": "bts:Uint32" }, { - "@id": "bts:NotReported" + "@id": "bts:Float" + }, + { + "@id": "bts:Double" + }, + { + "@id": "bts:Bit" } ], - "sms:displayName": "Laterality", - "sms:required": "sms:false", + "sms:displayName": "PixelType", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesPositive", + "@id": "bts:MERFISHPositionsFile", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes involved with disease as determined by pathologic examination.", - "rdfs:label": "LymphNodesPositive", + "rdfs:comment": "The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.", + "rdfs:label": "MERFISHPositionsFile", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Positive", + "sms:displayName": "MERFISH Positions File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphNodesTested", + "@id": "bts:MERFISHCodebookFile", "@type": "rdfs:Class", - "rdfs:comment": "The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.", - "rdfs:label": "LymphNodesTested", + "rdfs:comment": "The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.", + "rdfs:label": "MERFISHCodebookFile", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Lymph Nodes Tested", + "sms:displayName": "MERFISH Codebook File", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LymphaticInvasionPresent", + "@id": "bts:ImagingLevel3Segmentation", "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement", - "rdfs:label": "LymphaticInvasionPresent", + "rdfs:comment": "Object segmentations", + "rdfs:label": "ImagingLevel3Segmentation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging Level 3 Segmentation", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Yes" + "@id": "bts:ImagingLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:No" + "@id": "bts:Filename" }, { - "@id": "bts:Unknown" + "@id": "bts:FileFormat" }, { - "@id": "bts:NotReported" + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:ImagingSegmentationDataType" + }, + { + "@id": "bts:Parameterfile" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:CommitSHA" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:NumberofObjects" } ], - "sms:displayName": "Lymphatic Invasion Present", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosis", + "@id": "bts:ImagingSegmentationDataType", "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the extent of metastatic disease present at diagnosis.", - "rdfs:label": "MetastasisatDiagnosis", + "rdfs:comment": "Specifies how the segmentation is stored", + "rdfs:label": "ImagingSegmentationDataType", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -40368,36 +38958,50 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DistantMetastasis" + "@id": "bts:Mask" }, { - "@id": "bts:MetastasisNOS" + "@id": "bts:Outline" }, { - "@id": "bts:NoMetastasis" + "@id": "bts:Polygon" }, { - "@id": "bts:RegionalMetastasis" + "@id": "bts:ProbabilityMap" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:Point" + } + ], + "sms:displayName": "Imaging Segmentation Data Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Parameterfile", + "@type": "rdfs:Class", + "rdfs:comment": "Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis", + "rdfs:label": "Parameterfile", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Imaging" } ], - "sms:displayName": "Metastasis at Diagnosis", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Parameter file", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MetastasisatDiagnosisSite", + "@id": "bts:ImagingObjectClass", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify an anatomic site in which metastatic disease involvement is found.", - "rdfs:label": "MetastasisatDiagnosisSite", + "rdfs:comment": "Defines the structure that the mask delineates", + "rdfs:label": "ImagingObjectClass", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -40405,384 +39009,363 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Abdomen" + "@id": "bts:Nucleus" }, { - "@id": "bts:AdrenalGland" + "@id": "bts:Cytoplasm" }, { - "@id": "bts:Ascites" + "@id": "bts:Plasmamembrane" }, { - "@id": "bts:Bone" + "@id": "bts:Wholecell" }, { - "@id": "bts:BoneMarrow" + "@id": "bts:Spot" }, { - "@id": "bts:Brain" - }, + "@id": "bts:ImagingObjectClassOther" + } + ], + "sms:displayName": "Imaging Object Class", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] + }, + { + "@id": "bts:NumberofObjects", + "@type": "rdfs:Class", + "rdfs:comment": "The number of objects (eg cells) described", + "rdfs:label": "NumberofObjects", + "rdfs:subClassOf": [ { - "@id": "bts:CerebrospinalFluid" - }, + "@id": "bts:Imaging" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Number of Objects", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:ImagingLevel3Image", + "@type": "rdfs:Class", + "rdfs:comment": "Quality controlled imaging data", + "rdfs:label": "ImagingLevel3Image", + "rdfs:subClassOf": [ { - "@id": "bts:CentralNervousSystem" - }, + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Imaging Level 3 Image", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Colon" + "@id": "bts:ImagingLevel3Channels" }, { - "@id": "bts:DistantNodes" + "@id": "bts:ImagingLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:DistantOrgan" + "@id": "bts:Filename" }, { - "@id": "bts:Groin" + "@id": "bts:FileFormat" }, { - "@id": "bts:Kidney" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Liver" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Lung" + "@id": "bts:HTANParentChannelMetadataID" }, { - "@id": "bts:LymphNode" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Axillary" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:LymphNode" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Inguinal" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:LymphNodeNOS" + "@id": "bts:Microscope" }, { - "@id": "bts:Mediastinum" + "@id": "bts:Objective" }, { - "@id": "bts:Omentum" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:Ovary" + "@id": "bts:LensNA" }, { - "@id": "bts:Pelvis" + "@id": "bts:WorkingDistance" }, { - "@id": "bts:PeritonealCavity" + "@id": "bts:Immersion" }, { - "@id": "bts:Peritoneum" + "@id": "bts:Pyramid" }, { - "@id": "bts:Pleura" + "@id": "bts:Zstack" }, { - "@id": "bts:Scalp" + "@id": "bts:Tseries" }, { - "@id": "bts:Skin" + "@id": "bts:PassedQC" }, { - "@id": "bts:SmallIntestine" + "@id": "bts:Comment" }, { - "@id": "bts:SoftTissue" + "@id": "bts:FOVnumber" }, { - "@id": "bts:SpinalCord" + "@id": "bts:FOVX" }, { - "@id": "bts:Unknown" + "@id": "bts:FOVY" }, { - "@id": "bts:NotReported" + "@id": "bts:FrameAveraging" } ], - "sms:displayName": "Metastasis at Diagnosis Site", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethodofDiagnosis", + "@id": "bts:HTANParentChannelMetadataID", "@type": "rdfs:Class", - "rdfs:comment": "Text term used to describe the method used to confirm the patients malignant diagnosis.", - "rdfs:label": "MethodofDiagnosis", + "rdfs:comment": "HTAN ID for a level 3 channels table.", + "rdfs:label": "HTANParentChannelMetadataID", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:ImagingLevel4" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "HTAN Parent Channel Metadata ID", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:ImagingLevel3Channels", + "@type": "rdfs:Class", + "rdfs:comment": "Channel-level Metadata Attributes", + "rdfs:label": "ImagingLevel3Channels", + "rdfs:subClassOf": [ { - "@id": "bts:Autopsy" + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Imaging Level 3 Channels", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:HTANChannelMetadataID" }, { - "@id": "bts:Biopsy" + "@id": "bts:ChannelID" }, { - "@id": "bts:BloodDraw" + "@id": "bts:ChannelName" }, { - "@id": "bts:BoneMarrowAspirate" + "@id": "bts:ChannelPassedQC" }, { - "@id": "bts:CoreBiopsy" + "@id": "bts:CycleNumber" }, { - "@id": "bts:Cytology" + "@id": "bts:SubCycleNumber" }, { - "@id": "bts:Cystoscopy" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:Debulking" + "@id": "bts:TargetName" }, { - "@id": "bts:DiagnosticImaging" + "@id": "bts:AntibodyName" }, { - "@id": "bts:DilationandCurettageProcedure" + "@id": "bts:RRIDidentifier" }, { - "@id": "bts:Enucleation" + "@id": "bts:Fluorophore" }, { - "@id": "bts:ExcisionalBiopsy" + "@id": "bts:Clone" }, { - "@id": "bts:FineNeedleAspiration" + "@id": "bts:Lot" }, { - "@id": "bts:IncisionalBiopsy" + "@id": "bts:Vendor" }, { - "@id": "bts:Laparoscopy" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:Laparotomy" + "@id": "bts:ExcitationWavelength" }, { - "@id": "bts:Other" + "@id": "bts:EmissionWavelength" }, { - "@id": "bts:PapSmear" + "@id": "bts:ExcitationBandwidth" }, { - "@id": "bts:PhysicalExam" + "@id": "bts:EmissionBandwidth" }, { - "@id": "bts:PathologicReview" + "@id": "bts:MetalIsotopeElement" }, { - "@id": "bts:SurgicalResection" + "@id": "bts:MetalIsotopeMass" }, { - "@id": "bts:Thoracentesis" + "@id": "bts:OligoBarcodeUpperStrand" }, { - "@id": "bts:UltrasoundGuidedBiopsy" + "@id": "bts:OligoBarcodeLowerStrand" }, { - "@id": "bts:Unknown" + "@id": "bts:Dilution" }, { - "@id": "bts:NotReported" + "@id": "bts:Concentration" } ], - "sms:displayName": "Method of Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MitoticCount", - "@type": "rdfs:Class", - "rdfs:comment": "The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.", - "rdfs:label": "MitoticCount", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Mitotic Count", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PercentTumorInvasion", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "@type": "rdfs:Class", - "rdfs:comment": "The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.", - "rdfs:label": "PercentTumorInvasion", + "rdfs:comment": "Files contain raw RNA-seq data associated with spot/slide data.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel1", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Percent Tumor Invasion", + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PeritonealFluidCytologicalStatus", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.", - "rdfs:label": "PeritonealFluidCytologicalStatus", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:Diagnosis" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Atypical" + "@id": "bts:Component" }, { - "@id": "bts:Malignant" + "@id": "bts:Filename" }, { - "@id": "bts:Non-Malignant" + "@id": "bts:RunID" }, { - "@id": "bts:Unsatisfactory" + "@id": "bts:FileFormat" }, { - "@id": "bts:Unknown" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Peritoneal Fluid Cytological Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:PerineuralInvasionPresent", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.", - "rdfs:label": "PerineuralInvasionPresent", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentBiospecimenID" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ReadIndicator" + }, { - "@id": "bts:Yes" + "@id": "bts:SpatialRead1" }, { - "@id": "bts:No" + "@id": "bts:SpatialRead2" }, { - "@id": "bts:Unknown" + "@id": "bts:SpatialLibraryConstructionMethod" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Perineural Invasion Present", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ResidualDisease", - "@type": "rdfs:Class", - "rdfs:comment": "Text terms to describe the status of a tissue margin following surgical resection.", - "rdfs:label": "ResidualDisease", - "rdfs:subClassOf": [ + "@id": "bts:LibraryPreparationDaysfromIndex" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SequencingLibraryConstructionDaysfromIndex" + }, { - "@id": "bts:R0" + "@id": "bts:EndBias" }, { - "@id": "bts:R1" + "@id": "bts:ReverseTranscriptionPrimer" }, { - "@id": "bts:R2" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:RX" + "@id": "bts:CaptureArea" }, { - "@id": "bts:Unknown" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Residual Disease", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:SynchronousMalignancy", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.", - "rdfs:label": "SynchronousMalignancy", - "rdfs:subClassOf": [ + "@id": "bts:SlideVersion" + }, { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SlideID" + }, { - "@id": "bts:Yes" + "@id": "bts:ImageRe-orientation" }, { - "@id": "bts:No" + "@id": "bts:PermeabilizationTime" }, { - "@id": "bts:Unknown" + "@id": "bts:RIN" }, { - "@id": "bts:NotReported" + "@id": "bts:DV200" } ], - "sms:displayName": "Synchronous Malignancy", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TumorConfinedtoOrganofOrigin", + "@id": "bts:CaptureArea", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.", - "rdfs:label": "TumorConfinedtoOrganofOrigin", + "rdfs:comment": "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.", + "rdfs:label": "CaptureArea", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -40790,78 +39373,42 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:A" }, { - "@id": "bts:No" + "@id": "bts:B" }, { - "@id": "bts:Unknown" + "@id": "bts:C" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Confined to Organ of Origin", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorFocality", - "@type": "rdfs:Class", - "rdfs:comment": "The text term used to describe whether the patient's disease originated in a single location or multiple locations.", - "rdfs:label": "TumorFocality", - "rdfs:subClassOf": [ - { - "@id": "bts:Diagnosis" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Multifocal" + "@id": "bts:D" }, { - "@id": "bts:Unifocal" + "@id": "bts:A1" }, { - "@id": "bts:Unknown" + "@id": "bts:B1" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Tumor Focality", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:TumorLargestDimensionDiameter", - "@type": "rdfs:Class", - "rdfs:comment": "Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.", - "rdfs:label": "TumorLargestDimensionDiameter", - "rdfs:subClassOf": [ + "@id": "bts:C1" + }, { - "@id": "bts:Diagnosis" + "@id": "bts:D1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Tumor Largest Dimension Diameter", + "sms:displayName": "Capture Area", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionPresent", + "@id": "bts:SlideVersion", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.", - "rdfs:label": "VascularInvasionPresent", + "rdfs:comment": "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label": "SlideVersion", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -40869,55 +39416,47 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes-VascularInvasionPresent" - }, - { - "@id": "bts:No" + "@id": "bts:V1" }, { - "@id": "bts:Unknown" + "@id": "bts:V2" }, { - "@id": "bts:NotReported" + "@id": "bts:V3" }, { - "@id": "bts:NotAllowedToCollect" + "@id": "bts:V4" } ], - "sms:displayName": "Vascular Invasion Present", + "sms:displayName": "Slide Version", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Yes-VascularInvasionPresent", + "@id": "bts:SlideID", "@type": "rdfs:Class", - "rdfs:comment": "Indicates venous invasion was detected by surgery or presence in a tumor specimen", - "rdfs:label": "Yes-VascularInvasionPresent", + "rdfs:comment": "The unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123.", + "rdfs:label": "SlideID", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Yes - Vascular Invasion Present", + "sms:displayName": "Slide ID", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:VascularInvasionType" - } - ], "sms:validationRules": [] }, { - "@id": "bts:VascularInvasionType", + "@id": "bts:ImageRe-orientation", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the type of vascular tumor invasion.", - "rdfs:label": "VascularInvasionType", + "rdfs:comment": "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.", + "rdfs:label": "ImageRe-orientation", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { @@ -40925,1262 +39464,2575 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Extramural" - }, - { - "@id": "bts:Intramural" - }, - { - "@id": "bts:Macro" - }, - { - "@id": "bts:Micro" - }, - { - "@id": "bts:NoVascularInvasion" - }, - { - "@id": "bts:Unknown" + "@id": "bts:TRUE" }, { - "@id": "bts:NotReported" + "@id": "bts:FALSE" } ], - "sms:displayName": "Vascular Invasion Type", + "sms:displayName": "Image Re-orientation", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearofDiagnosis", + "@id": "bts:PermeabilizationTime", "@type": "rdfs:Class", - "rdfs:comment": "Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.", - "rdfs:label": "YearofDiagnosis", + "rdfs:comment": "Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.", + "rdfs:label": "PermeabilizationTime", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year of Diagnosis", + "sms:displayName": "Permeabilization Time", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Morphology", + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "@type": "rdfs:Class", - "rdfs:comment": "The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.", - "rdfs:label": "Morphology", + "rdfs:comment": "Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel2", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:SpatialTranscriptomics" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Morphology", - "sms:required": "sms:true", - "sms:validationRules": [] - }, - { - "@id": "bts:TopographyCode", - "@type": "rdfs:Class", - "rdfs:comment": "Topography Code, indicating site within the body, based on ICD-O-3.", - "rdfs:label": "TopographyCode", - "rdfs:subClassOf": [ + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Diagnosis" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:C00.0" - }, - { - "@id": "bts:C00.1" - }, - { - "@id": "bts:C00.2" - }, - { - "@id": "bts:C00.3" - }, - { - "@id": "bts:C00.4" - }, + "sms:requiresDependency": [ { - "@id": "bts:C00.5" + "@id": "bts:Component" }, { - "@id": "bts:C00.6" + "@id": "bts:Filename" }, { - "@id": "bts:C00.8" + "@id": "bts:FileFormat" }, { - "@id": "bts:C01.9" + "@id": "bts:Checksum" }, { - "@id": "bts:C02.0" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:C02.1" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:C02.2" + "@id": "bts:UMITag" }, { - "@id": "bts:C02.3" + "@id": "bts:WhitelistSpatialBarcodeFileLink" }, { - "@id": "bts:C02.4" + "@id": "bts:SpatialBarcodeTag" }, { - "@id": "bts:C02.8" + "@id": "bts:AppliedHardTrimming" }, { - "@id": "bts:C02.9" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:C03.0" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:C03.1" + "@id": "bts:GenomicReference" }, { - "@id": "bts:C03.9" + "@id": "bts:GenomicReferenceURL" }, { - "@id": "bts:C04.0" + "@id": "bts:GenomeAnnotationURL" }, { - "@id": "bts:C04.1" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:C04.8" + "@id": "bts:RunID" }, { - "@id": "bts:C04.9" - }, + "@id": "bts:CaptureArea" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:WhitelistSpatialBarcodeFileLink", + "@type": "rdfs:Class", + "rdfs:comment": "Link to file listing all possible spatial barcodes. URL", + "rdfs:label": "WhitelistSpatialBarcodeFileLink", + "rdfs:subClassOf": [ { - "@id": "bts:C05.0" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Whitelist Spatial Barcode File Link", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "@type": "rdfs:Class", + "rdfs:comment": "Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-AuxiliaryFiles", + "rdfs:subClassOf": [ { - "@id": "bts:C05.1" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - Auxiliary Files", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:C05.2" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel1" }, { - "@id": "bts:C05.8" - }, + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:C05.9" + "@id": "bts:Component" }, { - "@id": "bts:C06.0" + "@id": "bts:Filename" }, { - "@id": "bts:C06.1" + "@id": "bts:FileFormat" }, { - "@id": "bts:C06.2" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:C06.8" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:C06.9" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:C07.9" + "@id": "bts:RunID" }, { - "@id": "bts:C08.0" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:C08.1" + "@id": "bts:SlideID" }, { - "@id": "bts:C08.8" + "@id": "bts:CaptureArea" }, { - "@id": "bts:C08.9" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:C09.0" - }, + "@id": "bts:WorkflowLink" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:VisiumFileType", + "@type": "rdfs:Class", + "rdfs:comment": "The file type generated for the visium experiment.", + "rdfs:label": "VisiumFileType", + "rdfs:subClassOf": [ { - "@id": "bts:C09.1" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ { - "@id": "bts:C09.8" + "@id": "bts:Referencepng" }, { - "@id": "bts:C09.9" + "@id": "bts:Referencejpg" }, { - "@id": "bts:C10.0" + "@id": "bts:Jsonscalefactors" }, { - "@id": "bts:C10.1" + "@id": "bts:Probedatasetcsv" }, { - "@id": "bts:C10.2" + "@id": "bts:Qcresulthtml" }, { - "@id": "bts:C10.3" + "@id": "bts:Filteredmex" }, { - "@id": "bts:C10.4" + "@id": "bts:Unfilteredmex" }, { - "@id": "bts:C10.8" + "@id": "bts:TissuePositions" }, { - "@id": "bts:C10.9" + "@id": "bts:Barcodes" }, { - "@id": "bts:C11.0" + "@id": "bts:Features" }, { - "@id": "bts:C11.1" + "@id": "bts:Fiducialimagepng" }, { - "@id": "bts:C11.2" + "@id": "bts:Fiducialimagejpg" }, { - "@id": "bts:C11.3" + "@id": "bts:Detectedimagepng" }, { - "@id": "bts:C11.8" + "@id": "bts:Detectedjpg" }, { - "@id": "bts:C11.9" + "@id": "bts:Highresimage" }, { - "@id": "bts:C12.9" - }, + "@id": "bts:Lowresimage" + } + ], + "sms:displayName": "Visium File Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.", + "rdfs:label": "10xVisiumSpatialTranscriptomics-RNA-seqLevel3", + "rdfs:subClassOf": [ { - "@id": "bts:C13.0" - }, + "@id": "bts:SpatialTranscriptomics" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "10x Visium Spatial Transcriptomics - RNA-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:C13.1" + "@id": "bts:10xVisiumSpatialTranscriptomics-RNA-seqLevel2" }, { - "@id": "bts:C13.2" - }, + "@id": "bts:10xVisiumSpatialTranscriptomics-AuxiliaryFiles" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:C13.8" + "@id": "bts:Component" }, { - "@id": "bts:C13.9" + "@id": "bts:Filename" }, { - "@id": "bts:C14.0" + "@id": "bts:FileFormat" }, { - "@id": "bts:C14.2" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:C14.8" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:C15.0" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:C15.1" + "@id": "bts:RunID" }, { - "@id": "bts:C15.2" + "@id": "bts:VisiumFileType" }, { - "@id": "bts:C15.3" + "@id": "bts:WorkflowVersion" }, { - "@id": "bts:C15.4" + "@id": "bts:WorkflowLink" }, { - "@id": "bts:C15.5" + "@id": "bts:CaptureArea" }, { - "@id": "bts:C15.8" + "@id": "bts:Spotsundertissue" }, { - "@id": "bts:C15.9" + "@id": "bts:MeanReadsperSpatialSpot" }, { - "@id": "bts:C16.0" + "@id": "bts:MedianNumberGenesperSpatialSpot" }, { - "@id": "bts:C16.1" + "@id": "bts:SequencingSaturation" }, { - "@id": "bts:C16.2" + "@id": "bts:ProportionReadsMapped" }, { - "@id": "bts:C16.3" + "@id": "bts:ProportionReadsMappedtoTranscriptome" }, { - "@id": "bts:C16.4" - }, + "@id": "bts:MedianUMICountsperSpot" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:Spotsundertissue", + "@type": "rdfs:Class", + "rdfs:comment": "The number of barcodes associated with a spot under tissue.", + "rdfs:label": "Spotsundertissue", + "rdfs:subClassOf": [ { - 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"@id": "bts:C77.9" - }, + "@id": "bts:NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Tissue Stain", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Slidename", + "@type": "rdfs:Class", + "rdfs:comment": "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).", + "rdfs:label": "Slidename", + "rdfs:subClassOf": [ { - "@id": "bts:C80.9" - }, + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Slide name", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Rawreads", + "@type": "rdfs:Class", + "rdfs:comment": "Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.", + "rdfs:label": "Rawreads", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Raw reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Stitchedreads", + "@type": "rdfs:Class", + "rdfs:comment": "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads", + "rdfs:label": "Stitchedreads", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], - "sms:displayName": "Topography Code", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Stitched reads", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AdditionalTopography", + "@id": "bts:Alignedreads", "@type": "rdfs:Class", - "rdfs:comment": "Topography not included in the ICD-O-3 Topography codes.", - "rdfs:label": "AdditionalTopography", + "rdfs:comment": "Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.", + "rdfs:label": "Alignedreads", "rdfs:subClassOf": [ { - "@id": "bts:Diagnosis" + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Aligned reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Deduplicatedreads", + "@type": "rdfs:Class", + "rdfs:comment": "Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.", + "rdfs:label": "Deduplicatedreads", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofscalp" - }, + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Deduplicated reads", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:InSituNegativemedian", + "@type": "rdfs:Class", + "rdfs:comment": "Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.", + "rdfs:label": "InSituNegativemedian", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofeyelid" - }, + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "In Situ Negative median", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Biologicalprobemedian", + "@type": "rdfs:Class", + "rdfs:comment": "Is the median count from all probes except the negative control probes. A measure of signal to background for each segment", + "rdfs:label": "Biologicalprobemedian", + "rdfs:subClassOf": [ { - "@id": "bts:Skinofnose" - }, + "@id": "bts:NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Biological probe median", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HI-C-seqLevel1", + "@type": "rdfs:Class", + "rdfs:comment": "Unaligned sequence data", + "rdfs:label": "HI-C-seqLevel1", + "rdfs:subClassOf": [ { - "@id": "bts:Skinoflip" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HI-C-seq Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Skinofear" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Skinofneck" + "@id": "bts:Component" }, { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Skinofchest" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Skinofback" + "@id": "bts:Filename" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:FileFormat" }, { - "@id": "bts:Skinoftrunk" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Skinofbreast" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:NucleicAcidSource" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:TechnicalReplicateGroup" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:TranspositionReaction" }, { - "@id": "bts:Skinofsole" + "@id": "bts:CrosslinkingCondtion" }, { - "@id": "bts:Skinofpenis" + "@id": "bts:DNADigestionCondition" }, { - "@id": "bts:Skinofscrotum" + "@id": "bts:NucleiPermeabilizationMethod" }, { - "@id": "bts:Skinofvulva" + "@id": "bts:LigationCondition" }, { - "@id": "bts:SkinNOS" + "@id": "bts:BiotinEnrichment" }, { - "@id": "bts:HilarAirway" + "@id": "bts:DNAInputAmount" }, { - "@id": "bts:Peri-tumoralAirway" + "@id": "bts:TotalReads" }, { - "@id": "bts:NotReported" + "@id": "bts:ProtocolLink" } ], - "sms:displayName": "Additional Topography", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungCancerDetectionMethodType", + "@id": "bts:CrosslinkingCondtion", "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer", - "rdfs:label": "LungCancerDetectionMethodType", + "rdfs:comment": "Detailed condition for DNA crosslinking", + "rdfs:label": "CrosslinkingCondtion", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:LowDoseComputedTomography(LDCT)" - }, - { - "@id": "bts:ChestX-ray" - }, - { - "@id": "bts:ChestCT" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - }, + "sms:displayName": "Crosslinking Condtion", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DNADigestionCondition", + "@type": "rdfs:Class", + "rdfs:comment": "Enzymes and treatment length/temperature for genome digestion", + "rdfs:label": "DNADigestionCondition", + "rdfs:subClassOf": [ { - "@id": "bts:Other" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Lung Cancer Detection Method Type", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DNA Digestion Condition", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LungCancerParticipantProcedureHistory", + "@id": "bts:NucleiPermeabilizationMethod", "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.", - "rdfs:label": "LungCancerParticipantProcedureHistory", + "rdfs:comment": "Detergent and treatment condition for nuclei permeabilization and crosslinking softening", + "rdfs:label": "NucleiPermeabilizationMethod", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:LobectomyBilateral" - }, - { - "@id": "bts:LobectomyLeft" - }, - { - "@id": "bts:LobectomyRight" - }, - { - "@id": "bts:LungWedgeResectionBilateral" - }, - { - "@id": "bts:LungWedgeResectionLeft" - }, - { - "@id": "bts:LungWedgeResectionMultiple" - }, - { - "@id": "bts:LungWedgeResectionRight" - }, - { - "@id": "bts:PneumonectomyLeft" - }, - { - "@id": "bts:PneumonectomyRight" - }, - { - "@id": "bts:Endobronchialbiopsy" - }, - { - "@id": "bts:Mediastinoscopy" - }, - { - "@id": "bts:VATSSclerosis" - }, - { - "@id": "bts:Brainresection" - }, - { - "@id": "bts:Segmentectomy" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Other" - }, + "sms:displayName": "Nuclei Permeabilization Method", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LigationCondition", + "@type": "rdfs:Class", + "rdfs:comment": "Name of ligase and condition for proximity ligation", + "rdfs:label": "LigationCondition", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:Sequencing" } ], - "sms:displayName": "Lung Cancer Participant Procedure History", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ligation Condition", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LungAdjacentHistologyType", + "@id": "bts:BiotinEnrichment", "@type": "rdfs:Class", - "rdfs:comment": "The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth", - "rdfs:label": "LungAdjacentHistologyType", + "rdfs:comment": "Whether biotin is used for enriching ligation product", + "rdfs:label": "BiotinEnrichment", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { @@ -42188,100 +42040,114 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Lungadenocarcinoma" - }, - { - "@id": "bts:Adenosquamouscarcinoma" + "@id": "bts:Yes" }, { - "@id": "bts:Carcinoidtumorandlungatypicalcarcinoidtumor" - }, + "@id": "bts:No" + } + ], + "sms:displayName": "Biotin Enrichment", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:DNAInputAmount", + "@type": "rdfs:Class", + "rdfs:comment": "Amount of DNA for library construction, in nanograms.", + "rdfs:label": "DNAInputAmount", + "rdfs:subClassOf": [ { - "@id": "bts:Lungadenocarcinomainsitu" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "DNA Input Amount", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] + }, + { + "@id": "bts:HI-C-seqLevel2", + "@type": "rdfs:Class", + "rdfs:comment": "Aligned read pairs, contact matrix", + "rdfs:label": "HI-C-seqLevel2", + "rdfs:subClassOf": [ { - "@id": "bts:Largecelllungcarcinoma" - }, + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HI-C-seq Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Largecellneuroendocrinecarcinoma" - }, + "@id": "bts:HI-C-seqLevel1" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Lunglymphoepithelioma-likecarcinoma" + "@id": "bts:Component" }, { - "@id": "bts:Bronchioalveolarcarcinoma" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:ThoracicNUTcarcinoma" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Sarcomatoidcarcinoma" + "@id": "bts:Filename" }, { - "@id": "bts:Smallcelllungcarcinoma" + "@id": "bts:FileFormat" }, { - "@id": "bts:Squamouscelllungcarcinoma" + "@id": "bts:GenomicReference" }, { - "@id": "bts:Lungsquamouscellcarcinomainsitu" + "@id": "bts:AlignedReadLength" }, { - "@id": "bts:Other" + "@id": "bts:Tool" }, { - "@id": "bts:Unknown" + "@id": "bts:Resolution" }, { - "@id": "bts:NotReported" + "@id": "bts:NormalizationMethod" } ], - "sms:displayName": "Lung Adjacent Histology Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLocationAnatomicSite", + "@id": "bts:AlignedReadLength", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic location of the tumor inside the lung", - "rdfs:label": "LungTumorLocationAnatomicSite", + "rdfs:comment": "Read length used for alignment if hard trimming was applied", + "rdfs:label": "AlignedReadLength", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Maincarina" - }, - { - "@id": "bts:Left" - }, - { - "@id": "bts:Right" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Tumor Location Anatomic Site", - "sms:required": "sms:false", + "sms:displayName": "Aligned Read Length", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:LungTumorLobeBronchialLocation", + "@id": "bts:Tool", "@type": "rdfs:Class", - "rdfs:comment": "Anatomic lobe and bronchial location of the tumor inside the lung", - "rdfs:label": "LungTumorLobeBronchialLocation", + "rdfs:comment": "Were any software or computational tools generated for this content", + "rdfs:label": "Tool", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Publication" } ], "schema:isPartOf": { @@ -42289,904 +42155,928 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Upperlobe" - }, - { - "@id": "bts:Middlelobe" - }, - { - "@id": "bts:Lowerlobe" - }, - { - "@id": "bts:Stump" - }, - { - "@id": "bts:Bronchus" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No" } ], - "sms:displayName": "Lung Tumor Lobe Bronchial Location", - "sms:required": "sms:false", + "sms:displayName": "Tool", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CurrentLungCancerSymptoms", + "@id": "bts:Resolution", "@type": "rdfs:Class", - "rdfs:comment": "Reported lung cancer related symptoms person is currently experiencing", - "rdfs:label": "CurrentLungCancerSymptoms", + "rdfs:comment": "Binning size used for generating contact matrix, in basepair.", + "rdfs:label": "Resolution", "rdfs:subClassOf": [ { - "@id": "bts:LungCancerTier3" + "@id": "bts:Sequencing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Asbestosis" + "sms:displayName": "Resolution", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:NormalizationMethod", + "@type": "rdfs:Class", + "rdfs:comment": "Description of Normalization Process", + "rdfs:label": "NormalizationMethod", + "rdfs:subClassOf": [ + { + "@id": "bts:RPPALevel2" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Normalization Method", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HI-C-seqLevel3", + "@type": "rdfs:Class", + "rdfs:comment": "Summary data for the HI-C-seq assay.", + "rdfs:label": "HI-C-seqLevel3", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HI-C-seq Level 3", + "sms:required": "sms:false", + "sms:requiresComponent": [ + { + "@id": "bts:HI-C-seqLevel2" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - 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Can be an integer or int/int, indicating bin size and sliding window size if different.", + "rdfs:label": "StripeWindow", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:HiCCUPS" }, { - "@id": "bts:Dysphagia" + "@id": "bts:Cooltools" }, { - "@id": "bts:Pneumonia" + "@id": "bts:Other" + } + ], + "sms:displayName": "Stripe Window", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:LoopCalling", + "@type": "rdfs:Class", + "rdfs:comment": "Tool used for identifying loop interactions", + "rdfs:label": "LoopCalling", + "rdfs:subClassOf": [ + { + "@id": "bts:Sequencing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Loop Calling", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Yes", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Yes", + "rdfs:subClassOf": [ + { + "@id": "bts:BiotinEnrichment" }, { - 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"@id": "bts:V600KBRAFmutation" + "@id": "bts:ImmunosuppressiveTreatmentType" }, { - "@id": "bts:V600RBRAFmutation" + "@id": "bts:LungCancerDetectionMethodType" }, { - "@id": "bts:K601EBRAFmutation" + "@id": "bts:ColorectalCancerDetectionMethodType" }, { - "@id": "bts:D963spliceMETmutation" + "@id": "bts:BreastBiopsyProcedureFindingType" }, { - "@id": "bts:D1010NMETmutation" + "@id": "bts:BreastCancerAssessmentTests" }, { - "@id": "bts:D1010spliceMETmutation" + "@id": "bts:ProstateCancerCytologicMorphologicSubtypes" }, { - "@id": "bts:Intron13mutation" + "@id": "bts:SarcomaTumorExtensionType" }, { - "@id": "bts:Intron14mutation" + "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype" }, { - "@id": "bts:Exon14mutation" + "@id": "bts:Pre-processingCompleted" }, { - "@id": "bts:Exon14deletion" + "@id": "bts:Pre-processingRequired" }, { - "@id": "bts:Other" + "@id": "bts:MSSource" }, { - "@id": "bts:Unknown" + "@id": "bts:Race" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Lung Cancer Harboring Genomic Aberrations", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer", - "rdfs:label": "ColorectalCancerDetectionMethodType", - "rdfs:subClassOf": [ + "@id": "bts:DataCategory" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ExtentofTumorResection" + }, { - "@id": "bts:Fecaloccultbloodtest" + "@id": "bts:ColorectalPolypType" }, { - "@id": "bts:Sigmoidoscopy" + "@id": "bts:BreastCarcinomaERStainingIntensity" }, { - "@id": "bts:Colonoscopy" + "@id": "bts:BreastCarcinomaPRStainingIntensity" }, { - "@id": "bts:Virtualcolonoscopy" + "@id": "bts:SarcomaSubtype" }, { - "@id": "bts:DNAstooltest" + "@id": "bts:LibrarySelectionMethod" }, { - "@id": "bts:Other" + "@id": "bts:CutaneousMelanomaAdditionalFindings" }, { - "@id": "bts:Unknown" + "@id": "bts:DiabetesTreatmentType" }, { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Colorectal Cancer Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofPriorColonPolyps", - "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "HistoryofPriorColonPolyps", - "rdfs:subClassOf": [ + "@id": "bts:OvarianCancerHistologicSubtype" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory" + }, { - "@id": "bts:Yes" + "@id": "bts:ProstateCarcinomaHistologicType" }, { - "@id": "bts:No" + "@id": "bts:ScRNAseqWorkflowType" }, { - "@id": "bts:NotApplicable" + "@id": "bts:MolecularAnalysisMethod" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "History of Prior Colon Polyps", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyColonCancerHistoryIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "The indicator to designate if any first degree relative has a history of colorectal cancer.", - "rdfs:label": "FamilyColonCancerHistoryIndicator", - "rdfs:subClassOf": [ + "@id": "bts:LungAdjacentHistologyType" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:VariantType" + }, { - "@id": "bts:Yes" + "@id": "bts:LungCancerParticipantProcedureHistory" }, { - "@id": "bts:No" + "@id": "bts:MethodofDiagnosis" }, { - "@id": "bts:NotApplicable" + "@id": "bts:FixativeType" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Colon Cancer History Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyMedicalHistoryColorectalPolypDiagnosis", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyMedicalHistoryColorectalPolypDiagnosis", - "rdfs:subClassOf": [ + "@id": "bts:HPVPositiveType" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:ConcomitantMedicationReceivedType" + }, { - "@id": "bts:Yes" + "@id": "bts:TreatmentType" }, { - "@id": "bts:No" + "@id": "bts:CurrentLungCancerSymptoms" }, { - "@id": "bts:NotApplicable" + "@id": "bts:SequencingPlatform" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Family Medical History Colorectal Polyp Diagnosis", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryEndometrialCancer", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryEndometrialCancer", - "rdfs:subClassOf": [ + "@id": "bts:MutationalSignatures" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LungCancerHarboringGenomicAberrations" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:RelationshipType" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:LungTopography" }, { - "@id": "bts:Unknown" + "@id": "bts:Comorbidity" }, { - "@id": "bts:NotApplicable" + "@id": "bts:PriorSitesofRadiation" + }, + { + "@id": "bts:License" } ], - "sms:displayName": "Immediate Family History Endometrial Cancer", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "other", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ImmediateFamilyHistoryOvarianCancer", + "@id": "bts:HiCCUPS", "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryOvarianCancer", + "rdfs:comment": "TBD", + "rdfs:label": "HiCCUPS", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:StripeWindow" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Beforeage50" - }, - { - "@id": "bts:Notbeforeage50" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Immediate Family History Ovarian Cancer", + "sms:displayName": "HiCCUPS", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "@id": "bts:Cooltools", "@type": "rdfs:Class", - "rdfs:comment": "The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).", - "rdfs:label": "PatientInflammatoryBowelDiseasePersonalMedicaHistory", + "rdfs:comment": "TBD", + "rdfs:label": "Cooltools", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:StripeWindow" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes-Crohn'sdisease" - }, - { - "@id": "bts:Yes-Ulcerativecolitis" - }, - { - "@id": "bts:No" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Patient Inflammatory Bowel Disease Personal Medica History", + "sms:displayName": "Cooltools", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PatientColonoscopyPerformedIndicator", + "@id": "bts:ImagingLevel4", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no indicator that records if the subject has undergone a previous colonoscopy.", - "rdfs:label": "PatientColonoscopyPerformedIndicator", + "rdfs:comment": "Derived imaging data: Object-by-feature array", + "rdfs:label": "ImagingLevel4", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging Level 4", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Yes" + "@id": "bts:ImagingLevel3Channels" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:No" + "@id": "bts:Filename" }, { - "@id": "bts:NotApplicable" + "@id": "bts:FileFormat" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Patient Colonoscopy Performed Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalCancerTumorBorderConfiguration", - "@type": "rdfs:Class", - "rdfs:comment": "The description of the border configuration of a colorectal tumor at pathologic assessment.", - "rdfs:label": "ColorectalCancerTumorBorderConfiguration", - "rdfs:subClassOf": [ + "@id": "bts:HTANParentDataFileID" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HTANParentChannelMetadataID" + }, { - "@id": "bts:Indeterminate" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Infiltrating" + "@id": "bts:Parameterfile" }, { - "@id": "bts:Other" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:Pushing" + "@id": "bts:CommitSHA" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NumberofObjects" + }, + { + "@id": "bts:NumberofFeatures" + }, + { + "@id": "bts:ImagingObjectClass" + }, + { + "@id": "bts:ImagingSummaryStatistic" } ], - "sms:displayName": "Colorectal Cancer Tumor Border Configuration", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MLH1PromoterMethylationStatus", + "@id": "bts:NumberofFeatures", "@type": "rdfs:Class", - "rdfs:comment": "Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.", - "rdfs:label": "MLH1PromoterMethylationStatus", + "rdfs:comment": "The number of features (eg channels) described", + "rdfs:label": "NumberofFeatures", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Imaging" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:NotAssessed" - }, - { - "@id": "bts:Present" - } - ], - "sms:displayName": "MLH1 Promoter Methylation Status", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Number of Features", + "sms:required": "sms:true", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:ColorectalCancerKRASIndicator", + "@id": "bts:ImagingSummaryStatistic", "@type": "rdfs:Class", - "rdfs:comment": "The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.", - "rdfs:label": "ColorectalCancerKRASIndicator", + "rdfs:comment": "Function used to summarize object/feature intensity", + "rdfs:label": "ImagingSummaryStatistic", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Imaging" } ], "schema:isPartOf": { @@ -43194,523 +43084,347 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:Mean" }, { - "@id": "bts:Unknown" + "@id": "bts:Median" }, { - "@id": "bts:NotApplicable" + "@id": "bts:NotSpecified" } ], - "sms:displayName": "Colorectal Cancer KRAS Indicator", + "sms:displayName": "Imaging Summary Statistic", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColonPolypOccurenceIndicator", + "@id": "bts:SRRSImagingLevel2", "@type": "rdfs:Class", - "rdfs:comment": "Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).", - "rdfs:label": "ColonPolypOccurenceIndicator", + "rdfs:comment": "SRRS-specific HTAN raw and pre-processed image data", + "rdfs:label": "SRRSImagingLevel2", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "SRRS Imaging Level 2", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Yes" + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ + { + "@id": "bts:Component" }, { - "@id": "bts:No" + "@id": "bts:Filename" }, { - "@id": "bts:Unknown" + "@id": "bts:FileFormat" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colon Polyp Occurence Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:FamilyHistoryColorectalPolyp", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.", - "rdfs:label": "FamilyHistoryColorectalPolyp", - "rdfs:subClassOf": [ + "@id": "bts:HTANParticipantID" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:HTANParentBiospecimenID" + }, { - "@id": "bts:Yes" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:No" + "@id": "bts:ChannelMetadataFilename" }, { - "@id": "bts:Unknown" + "@id": "bts:ImagingAssayType" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Family History Colorectal Polyp", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypNewIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.", - "rdfs:label": "ColorectalPolypNewIndicator", - "rdfs:subClassOf": [ + "@id": "bts:ProtocolLink" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:SoftwareandVersion" + }, { - "@id": "bts:Yes" + "@id": "bts:Microscope" }, { - "@id": "bts:No" + "@id": "bts:Objective" }, { - "@id": "bts:Unknown" + "@id": "bts:NominalMagnification" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp New Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypShape", - "@type": "rdfs:Class", - "rdfs:comment": "Shape of polyp identified in the participant", - "rdfs:label": "ColorectalPolypShape", - "rdfs:subClassOf": [ + "@id": "bts:Pyramid" + }, { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Zstack" + }, { - "@id": "bts:Pedunculated" + "@id": "bts:Tseries" }, { - "@id": "bts:Sessile" + "@id": "bts:PassedQC" }, { - "@id": "bts:Flat" + "@id": "bts:FrameAveraging" }, { - "@id": "bts:Notstated" + "@id": "bts:ImageID" }, { - "@id": "bts:NotApplicable" + "@id": "bts:DimensionOrder" + }, + { + "@id": "bts:PhysicalSizeX" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeY" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PixelsBigEndian" + }, + { + "@id": "bts:PlaneCount" + }, + { + "@id": "bts:SizeC" + }, + { + "@id": "bts:SizeT" + }, + { + "@id": "bts:SizeX" + }, + { + "@id": "bts:SizeY" + }, + { + "@id": "bts:SizeZ" + }, + { + "@id": "bts:PixelType" } ], - "sms:displayName": "Colorectal Polyp Shape", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SizeofPolypRemoved", + "@id": "bts:RPPALevel2", "@type": "rdfs:Class", - "rdfs:comment": "Size of the polyp removed in cm", - "rdfs:label": "SizeofPolypRemoved", + "rdfs:comment": "Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.", + "rdfs:label": "RPPALevel2", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Size of Polyp Removed", + "sms:displayName": "RPPA Level 2", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypCount", - "@type": "rdfs:Class", - "rdfs:comment": "The total number of polyps detected", - "rdfs:label": "ColorectalPolypCount", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Colorectal Polyp Count", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ColorectalPolypType", - "@type": "rdfs:Class", - "rdfs:comment": "Type of polyp found in the participant", - "rdfs:label": "ColorectalPolypType", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:ColorectalCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Component" + }, { - "@id": "bts:Adenoma" + "@id": "bts:Filename" }, { - "@id": "bts:Hyperplastic" + "@id": "bts:FileFormat" }, { - "@id": "bts:Mixed" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Papillomatous" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Normal" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Cancer" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Other" + "@id": "bts:HTANRPPAAntibodyTable" }, { - "@id": "bts:Unknown" + "@id": "bts:AssayType" + }, + { + "@id": "bts:ProtocolLink" + }, + { + "@id": "bts:SoftwareandVersion" } ], - "sms:displayName": "Colorectal Polyp Type", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ColorectalPolypAdenomaType", + "@id": "bts:HTANRPPAAntibodyTable", "@type": "rdfs:Class", - "rdfs:comment": "Type of adenoma associated with the polyp", - "rdfs:label": "ColorectalPolypAdenomaType", + "rdfs:comment": "A table containing antibody level metadata for RPPA", + "rdfs:label": "HTANRPPAAntibodyTable", "rdfs:subClassOf": [ { - "@id": "bts:ColorectalCancerTier3" + "@id": "bts:RPPALevel2" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Tubular" - }, + "sms:displayName": "HTAN RPPA Antibody Table", + "sms:required": "sms:true", + "sms:requiresComponent": [ { - "@id": "bts:Villous" - }, + "@id": "bts:RPPALevel2" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Tubulovillous" + "@id": "bts:HTANRPPAAntibodyTableID" }, { - "@id": "bts:Sessileserrated" + "@id": "bts:Filename" }, { - "@id": "bts:Traditionalserrated" + "@id": "bts:FileFormat" }, { - "@id": "bts:Serratednotspecified" + "@id": "bts:AbNameReportedonDataset" }, { - "@id": "bts:Notstated" + "@id": "bts:GENCODEGeneSymbolTarget" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Colorectal Polyp Adenoma Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaDetectionMethodType", - "@type": "rdfs:Class", - "rdfs:comment": "The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.", - "rdfs:label": "BreastCarcinomaDetectionMethodType", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:ClinicalExam" + "@id": "bts:UNIPROTProteinIDTarget" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:PhosphoproteinFlag" }, { - "@id": "bts:NippleDischarge" + "@id": "bts:Vendor" }, { - "@id": "bts:Other" + "@id": "bts:CatalogNumber" }, { - "@id": "bts:ScreeningMammography" + "@id": "bts:InternalAbID" }, { - "@id": "bts:ScreeningMRI" + "@id": "bts:Species" }, { - "@id": "bts:Selfexam" + "@id": "bts:RPPADilution" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma Detection Method Type", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHistologyCategory", - "@type": "rdfs:Class", - "rdfs:comment": "Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.", - "rdfs:label": "BreastCarcinomaHistologyCategory", - "rdfs:subClassOf": [ - { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Infiltratingductalcarcinoma" + "@id": "bts:PhosphoSite" }, { - "@id": "bts:Infiltratinglobularcarcinoma" + "@id": "bts:RPPAValidationStatus" }, { - "@id": "bts:InvasivemammarycarcinomaNOS" + "@id": "bts:Clone" }, { - "@id": "bts:Invasivemixedductalandlobularcarcinoma" + "@id": "bts:Clonality" }, { - "@id": "bts:Other" + "@id": "bts:AntibodyNotes" } ], - "sms:displayName": "Breast Carcinoma Histology Category", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InvasiveLobularBreastCarcinomaHistologicCategory", + "@id": "bts:HTANRPPAAntibodyTableID", "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for an infiltrating lobular carcinoma of the breast.", - "rdfs:label": "InvasiveLobularBreastCarcinomaHistologicCategory", + "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", + "rdfs:label": "HTANRPPAAntibodyTableID", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Alveolartype" - }, - { - "@id": "bts:Classicaltype" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Pleomorphictype" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Invasive Lobular Breast Carcinoma Histologic Category", - "sms:required": "sms:false", + "sms:displayName": "HTAN RPPA Antibody Table ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InvasiveDuctalBreastCarcinomaHistologicCategory", + "@id": "bts:AbNameReportedonDataset", "@type": "rdfs:Class", - "rdfs:comment": "The histologic subtype for the most common type of invasive breast carcinoma.", - "rdfs:label": "InvasiveDuctalBreastCarcinomaHistologicCategory", + "rdfs:comment": "The antibody name.", + "rdfs:label": "AbNameReportedonDataset", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Classicaltype" - }, - { - "@id": "bts:Invasivecarcinoma-typecannotbedetermined" - }, - { - "@id": "bts:Invasivecribriformcarcinoma" - }, - { - "@id": "bts:Invasivemicropapillarycarcinoma" - }, - { - "@id": "bts:Invasivepapillarycarcinoma" - }, - { - "@id": "bts:Invasivetubularcarcinoma" - }, - { - "@id": "bts:Medullarycarcinoma" - }, - { - "@id": "bts:Mucinouscarcinoma" - }, - { - "@id": "bts:Tubulolobularcarcinoma" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Invasive Ductal Breast Carcinoma Histologic Category", - "sms:required": "sms:false", + "sms:displayName": "Ab Name Reported on Dataset", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastBiopsyProcedureFindingType", + "@id": "bts:GENCODEGeneSymbolTarget", "@type": "rdfs:Class", - "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": "BreastBiopsyProcedureFindingType", + "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", + "rdfs:label": "GENCODEGeneSymbolTarget", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Atypicalhyperplasia" - }, - { - "@id": "bts:DCIS" - }, - { - "@id": "bts:LCIS" - }, - { - "@id": "bts:Cancer" - }, - { - "@id": "bts:Nocancer" - }, - { - "@id": "bts:Other" - } - ], - "sms:displayName": "Breast Biopsy Procedure Finding Type", - "sms:required": "sms:false", + "sms:displayName": "GENCODE Gene Symbol Target", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastQuadrantSite", + "@id": "bts:UNIPROTProteinIDTarget", "@type": "rdfs:Class", - "rdfs:comment": "The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.", - "rdfs:label": "BreastQuadrantSite", + "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", + "rdfs:label": "UNIPROTProteinIDTarget", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Upperouterquadrant" - }, - { - "@id": "bts:Lowerouterquadrant" - }, - { - "@id": "bts:Upperinnerquadrant" - }, - { - "@id": "bts:Lowerinnerquadrant" - }, - { - "@id": "bts:Central" - }, - { - "@id": "bts:Nipple" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Datanotavailable" - } - ], - "sms:displayName": "Breast Quadrant Site", - "sms:required": "sms:false", + "sms:displayName": "UNIPROT Protein ID Target", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastCancerAssessmentTests", + "@id": "bts:PhosphoproteinFlag", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify assessment tests done in participants during diagnosis", - "rdfs:label": "BreastCancerAssessmentTests", + "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", + "rdfs:label": "PhosphoproteinFlag", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -43718,147 +43432,75 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:EstrogenreceptorIHC" - }, - { - "@id": "bts:ProgesteronereceptorIHC" - }, - { - "@id": "bts:HER2IHC" - }, - { - "@id": "bts:HER2FISH-CISH" - }, - { - "@id": "bts:HER2FISH" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" + "@id": "bts:True" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:False" } ], - "sms:displayName": "Breast Cancer Assessment Tests", - "sms:required": "sms:false", + "sms:displayName": "Phosphoprotein Flag", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastCancerGenomicTestPerformed", + "@id": "bts:Vendor", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the name of the genomic test performed for breast cancer.", - "rdfs:label": "BreastCancerGenomicTestPerformed", + "rdfs:comment": "Vendor", + "rdfs:label": "Vendor", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Oncotype" - }, - { - "@id": "bts:MammaPrint" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:Notperformed" - } - ], - "sms:displayName": "Breast Cancer Genomic Test Performed", + "sms:displayName": "Vendor", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MammaprintRiskGroup", + "@id": "bts:CatalogNumber", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.", - "rdfs:label": "MammaprintRiskGroup", + "rdfs:comment": "Catalog Number", + "rdfs:label": "CatalogNumber", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Highrisk" - }, - { - "@id": "bts:Intermediaterisk" - }, - { - "@id": "bts:Lowrisk" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Mammaprint Risk Group", + "sms:displayName": "Catalog Number", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OncotypeRiskGroup", + "@id": "bts:InternalAbID", "@type": "rdfs:Class", - "rdfs:comment": "Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.", - "rdfs:label": "OncotypeRiskGroup", + "rdfs:comment": "Internal lab ID for an antibody.", + "rdfs:label": "InternalAbID", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Highrisk" - }, - { - "@id": "bts:Intermediaterisk" - }, - { - "@id": "bts:Lowrisk" - }, - { - "@id": "bts:Datanotavailable" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Oncotype Risk Group", - "sms:required": "sms:false", + "sms:displayName": "Internal Ab ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaEstrogenReceptorStatus", + "@id": "bts:Species", "@type": "rdfs:Class", - "rdfs:comment": "Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaEstrogenReceptorStatus", + "rdfs:comment": "Host animal.", + "rdfs:label": "Species", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -43866,137 +43508,66 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Borderline" - }, - { - "@id": "bts:Equivocal" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Negative" - }, - { - "@id": "bts:NotPerformed" - }, - { - "@id": "bts:PerformedbutNotAvailable" + "@id": "bts:Mouse" }, { - "@id": "bts:Positive" + "@id": "bts:Rabbit" }, { - "@id": "bts:Unknown" + "@id": "bts:Goat" } ], - "sms:displayName": "Breast Carcinoma Estrogen Receptor Status", - "sms:required": "sms:false", + "sms:displayName": "Species", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaProgesteronerReceptorStatus", + "@id": "bts:RPPADilution", "@type": "rdfs:Class", - "rdfs:comment": "Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaProgesteronerReceptorStatus", + "rdfs:comment": "The dilution ratio.", + "rdfs:label": "RPPADilution", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Borderline" - }, - { - "@id": "bts:Equivocal" - }, - { - "@id": "bts:Indeterminate" - }, - { - "@id": "bts:Negative" - }, - { - "@id": "bts:NotPerformed" - }, - { - "@id": "bts:PerformedbutNotAvailable" - }, - { - "@id": "bts:Positive" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma Progesteroner Receptor Status", + "sms:displayName": "RPPA Dilution", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCancerAllredEstrogenReceptorScore", + "@id": "bts:PhosphoSite", "@type": "rdfs:Class", - "rdfs:comment": "The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.", - "rdfs:label": "BreastCancerAllredEstrogenReceptorScore", + "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", + "rdfs:label": "PhosphoSite", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:0" - }, - { - "@id": "bts:1" - }, - { - "@id": "bts:2" - }, - { - "@id": "bts:3" - }, - { - "@id": "bts:4" - }, - { - "@id": "bts:5" - }, - { - "@id": "bts:6" - }, - { - "@id": "bts:7" - }, - { - "@id": "bts:8" - }, - { - "@id": "bts:10" - }, + "sms:displayName": "Phospho Site", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Unknown" + "@id": "bts:PhosphoproteinFlag" } ], - "sms:displayName": "Breast Cancer Allred Estrogen Receptor Score", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PriorInvasiveBreastDisease", + "@id": "bts:RPPAValidationStatus", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate prior invasive breast condition in the participant", - "rdfs:label": "PriorInvasiveBreastDisease", + "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", + "rdfs:label": "RPPAValidationStatus", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { @@ -44004,378 +43575,317 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:DCIS" - }, - { - "@id": "bts:LCIS" - }, - { - "@id": "bts:Invasivebreastcancer(unrelatedtothecurrentcancer)" + "@id": "bts:Valid" }, { - "@id": "bts:Other" + "@id": "bts:UsewithCaution" }, { - "@id": "bts:Unknown" + "@id": "bts:UnderEvaluation" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:UsedforQC" } ], - "sms:displayName": "Prior Invasive Breast Disease", + "sms:displayName": "RPPA Validation Status", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaERStatusPercentageValue", + "@id": "bts:Clone", "@type": "rdfs:Class", - "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:comment": "Clone", + "rdfs:label": "Clone", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breast Carcinoma ER Status Percentage Value", + "sms:displayName": "Clone", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaPRStatusPercentageValue", + "@id": "bts:AntibodyNotes", "@type": "rdfs:Class", - "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:comment": "Notes on antibodies replacements and antibody recognition observations.", + "rdfs:label": "AntibodyNotes", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:HTANRPPAAntibodyTable" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breast Carcinoma PR Status Percentage Value", + "sms:displayName": "Antibody Notes", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HER2BreastCarcinomaCopyNumberTotal", + "@id": "bts:RPPALevel3", "@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": "Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.", + "rdfs:label": "RPPALevel3", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HER2 Breast Carcinoma Copy Number Total", + "sms:displayName": "RPPA Level 3", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@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": [ + "sms:requiresComponent": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Biospecimen" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Carcinoma Centromere 17 Copy Number", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaHER2Centromere17CopynumberTotal", - "@type": "rdfs:Class", - "rdfs:comment": "Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaHER2Centromere17CopynumberTotal", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Component" + }, + { + "@id": "bts:Filename" + }, + { + "@id": "bts:FileFormat" + }, + { + "@id": "bts:HTANParticipantID" + }, + { + "@id": "bts:HTANParentBiospecimenID" + }, + { + "@id": "bts:HTANParentDataFileID" + }, + { + "@id": "bts:HTANDataFileID" + }, + { + "@id": "bts:AssayType" + }, + { + "@id": "bts:SoftwareandVersion" + }, + { + "@id": "bts:NormalizationMethod" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Breast Carcinoma HER2 Centromere17 Copynumber Total", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaHER2Chromosome17Ratio", + "@id": "bts:RPPALevel4", "@type": "rdfs:Class", - "rdfs:comment": "HER2 chromosome 17 ratio in participants with breast cancer", - "rdfs:label": "BreastCarcinomaHER2Chromosome17Ratio", + "rdfs:comment": "Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.", + "rdfs:label": "RPPALevel4", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breast Carcinoma HER2 Chromosome17 Ratio", + "sms:displayName": "RPPA Level 4", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaSurgicalProcedureName", - "@type": "rdfs:Class", - "rdfs:comment": "Text name of a surgical procedure performed for a person with a diagnosis of breast cancer", - "rdfs:label": "BreastCarcinomaSurgicalProcedureName", - "rdfs:subClassOf": [ + "sms:requiresComponent": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:RPPALevel2" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "sms:requiresDependency": [ { - "@id": "bts:Lumpectomy" + "@id": "bts:Component" }, { - "@id": "bts:Radicalmastectomy" + "@id": "bts:Filename" }, { - "@id": "bts:Modifiedradicalmastectomy" + "@id": "bts:FileFormat" }, { - "@id": "bts:Other" + "@id": "bts:HTANParticipantID" }, { - "@id": "bts:Partialmastectomy" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Re-excision" + "@id": "bts:HTANParentDataFileID" }, { - "@id": "bts:Simplemastectomy" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:Surgerynotperformed" + "@id": "bts:AssayType" }, { - "@id": "bts:Unknown" + "@id": "bts:BatchCorrectionMethod" } ], - "sms:displayName": "Breast Carcinoma Surgical Procedure Name", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaHER2RatioDiagnosis", + "@id": "bts:BatchCorrectionMethod", "@type": "rdfs:Class", - "rdfs:comment": "HER2 ratio of the participant at diagnosis", - "rdfs:label": "BreastCarcinomaHER2RatioDiagnosis", + "rdfs:comment": "Method that was used to batch correct Level 3 data", + "rdfs:label": "BatchCorrectionMethod", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:RPPALevel3" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Breast Carcinoma HER2 Ratio Diagnosis", + "sms:displayName": "Batch Correction Method", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BreastCarcinomaHER2Status", + "@id": "bts:MassSpectrometryLevel1", "@type": "rdfs:Class", - "rdfs:comment": "Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaHER2Status", + "rdfs:comment": "Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1", + "rdfs:label": "MassSpectrometryLevel1", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Assay" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Mass Spectrometry Level 1", + "sms:required": "sms:false", + "sms:requiresComponent": [ { - "@id": "bts:Positive" - }, + "@id": "bts:Biospecimen" + } + ], + "sms:requiresDependency": [ { - "@id": "bts:Negative" + "@id": "bts:Component" }, { - "@id": "bts:Amplified" + "@id": "bts:Filename" }, { - "@id": "bts:Non-amplified" + "@id": "bts:FileFormat" }, { - "@id": "bts:Equivocal" + "@id": "bts:HTANParentBiospecimenID" }, { - "@id": "bts:Indeterminate" + "@id": "bts:HTANDataFileID" }, { - "@id": "bts:NotPerformed" + "@id": "bts:MSBatchID" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma HER2 Status", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HormoneTherapyBreastCancerPreventionIndicator", - "@type": "rdfs:Class", - "rdfs:comment": "Did the patient receive hormonal therapy for prevention of breast cancer?", - "rdfs:label": "HormoneTherapyBreastCancerPreventionIndicator", - "rdfs:subClassOf": [ + "@id": "bts:MS-basedAssayType" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:AnalyteType" + }, { - "@id": "bts:Yes" + "@id": "bts:MS-basedTargeted" }, { - "@id": "bts:No" + "@id": "bts:MSInstrumentVendorandModel" }, { - "@id": "bts:Unknown" + "@id": "bts:MSSource" }, { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Hormone Therapy Breast Cancer Prevention Indicator", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaERStainingIntensity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaERStainingIntensity", - "rdfs:subClassOf": [ + "@id": "bts:Polarity" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:MassRangeLowValue" + }, { - "@id": "bts:Strong" + "@id": "bts:MassRangeHighValue" }, { - "@id": "bts:Moderate" + "@id": "bts:DataCollectionMode" }, { - "@id": "bts:Weak" + "@id": "bts:MSScanMode" }, { - "@id": "bts:Weak-Moderate" + "@id": "bts:MSLabeling" }, { - "@id": "bts:Moderate-Strong" + "@id": "bts:ProtocolLink" }, { - "@id": "bts:Weak-Strong" + "@id": "bts:LCInstrumentVendorandModel" }, { - "@id": "bts:Other" + "@id": "bts:LCColumnVendorandModel" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Breast Carcinoma ER Staining Intensity", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BreastCarcinomaPRStainingIntensity", - "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer", - "rdfs:label": "BreastCarcinomaPRStainingIntensity", - "rdfs:subClassOf": [ + "@id": "bts:LCResin" + }, { - "@id": "bts:BreastCancerTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:LCLengthValue" + }, { - "@id": "bts:Strong" + "@id": "bts:LCTempValue" }, { - "@id": "bts:Moderate" + "@id": "bts:LCIDValue" }, { - "@id": "bts:Weak" + "@id": "bts:LCFlowRate" }, { - "@id": "bts:Weak-Moderate" + "@id": "bts:LCGradient" }, { - "@id": "bts:Moderate-Strong" + "@id": "bts:LCMobilePhaseA" }, { - "@id": "bts:Weak-Strong" + "@id": "bts:LCMobilePhaseB" }, { - "@id": "bts:Other" + "@id": "bts:SoftwareandVersion" }, { - "@id": "bts:Unknown" + "@id": "bts:MSInstrumentMetadataFile" } ], - "sms:displayName": "Breast Carcinoma PR Staining Intensity", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OncotypeScore", + "@id": "bts:MSBatchID", "@type": "rdfs:Class", - "rdfs:comment": "OncotypeDX recurrence score", - "rdfs:label": "OncotypeScore", + "rdfs:comment": "Batch ID indicating a set of samples that were run together.", + "rdfs:label": "MSBatchID", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Oncotype Score", - "sms:required": "sms:false", + "sms:displayName": "MS Batch ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BreastImagingPerformedType", + "@id": "bts:MS-basedAssayType", "@type": "rdfs:Class", - "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).", - "rdfs:label": "BreastImagingPerformedType", + "rdfs:comment": "Analytes are the target molecules being measured with the assay.", + "rdfs:label": "MS-basedAssayType", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44383,42 +43893,30 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Mammogram" - }, - { - "@id": "bts:Ultrasound" - }, - { - "@id": "bts:MRI" - }, - { - "@id": "bts:PET/CT" - }, - { - "@id": "bts:CT" + "@id": "bts:LC-MS" }, { - "@id": "bts:Multipleimagingmodalities" + "@id": "bts:MS" }, { - "@id": "bts:Unknown" + "@id": "bts:TMT" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:LC-MS/MS" } ], - "sms:displayName": "Breast Imaging Performed Type", - "sms:required": "sms:false", + "sms:displayName": "MS-based Assay Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MultifocalBreastCarcinomaPresentIndicator", + "@id": "bts:AnalyteType", "@type": "rdfs:Class", - "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": "MultifocalBreastCarcinomaPresentIndicator", + "rdfs:comment": "The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteType", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { @@ -44426,30 +43924,60 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" + "@id": "bts:CfDNAAnalyte" }, { - "@id": "bts:No" + "@id": "bts:DNAAnalyte" }, { - "@id": "bts:Unknown" + "@id": "bts:RNAAnalyte" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:TotalRNAAnalyte" + }, + { + "@id": "bts:TissueBlockAnalyte" + }, + { + "@id": "bts:TissueSectionAnalyte" + }, + { + "@id": "bts:PBMCsorPlasmaorSerumAnalyte" + }, + { + "@id": "bts:CDNALibrariesAnalyte" + }, + { + "@id": "bts:PBMCs" + }, + { + "@id": "bts:Plasma" + }, + { + "@id": "bts:SerumAnalyte" + }, + { + "@id": "bts:Lipid" + }, + { + "@id": "bts:Protein" + }, + { + "@id": "bts:Metabolite" } ], - "sms:displayName": "Multifocal Breast Carcinoma Present Indicator", - "sms:required": "sms:false", + "sms:displayName": "Analyte Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MulticentricBreastCarcinomaPresentIndicator", + "@id": "bts:MS-basedTargeted", "@type": "rdfs:Class", - "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.", - "rdfs:label": "MulticentricBreastCarcinomaPresentIndicator", + "rdfs:comment": "Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.", + "rdfs:label": "MS-basedTargeted", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44457,30 +43985,41 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Yes" - }, - { - "@id": "bts:No" + "@id": "bts:Targeted" }, { - "@id": "bts:Unknown" - }, + "@id": "bts:Untargeted" + } + ], + "sms:displayName": "MS-based Targeted", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:MSInstrumentVendorandModel", + "@type": "rdfs:Class", + "rdfs:comment": "An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.", + "rdfs:label": "MSInstrumentVendorandModel", + "rdfs:subClassOf": [ { - "@id": "bts:Datanotavailable" + "@id": "bts:MassSpectrometryLevel1" } ], - "sms:displayName": "Multicentric Breast Carcinoma Present Indicator", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "MS Instrument Vendor and Model", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:BIRADSMammographyBreastDensityCategory", + "@id": "bts:MSSource", "@type": "rdfs:Class", - "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.", - "rdfs:label": "BIRADSMammographyBreastDensityCategory", + "rdfs:comment": "The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)", + "rdfs:label": "MSSource", "rdfs:subClassOf": [ { - "@id": "bts:BreastCancerTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44488,36 +44027,36 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Predominantlyfatty" + "@id": "bts:MALDI" }, { - "@id": "bts:Scatteredfibroglandulardensities" + "@id": "bts:MALDI-2" }, { - "@id": "bts:Heterogeneouslydense" + "@id": "bts:DESI" }, { - "@id": "bts:Extremelydense" + "@id": "bts:SIMS" }, { - "@id": "bts:Unknown" + "@id": "bts:NESI" }, { - "@id": "bts:Datanotavailable" + "@id": "bts:Other" } ], - "sms:displayName": "BIRADS Mammography Breast Density Category", - "sms:required": "sms:false", + "sms:displayName": "MS Source", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CNSTumorPrimaryAnatomicSite", + "@id": "bts:Polarity", "@type": "rdfs:Class", - "rdfs:comment": "Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2", - "rdfs:label": "CNSTumorPrimaryAnatomicSite", + "rdfs:comment": "The polarity of the mass analysis (positive or negative ion modes)", + "rdfs:label": "Polarity", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44525,143 +44064,58 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Thalamus" - }, - { - "@id": "bts:Ventricles" + "@id": "bts:Positive" }, { - "@id": "bts:Intracranial/Leptomeningeal" - }, - { - "@id": "bts:Suprasellar/Hypothalamic/Pituitary" - }, - { - "@id": "bts:Cerebellar/Posteriorfossa" - }, - { - "@id": "bts:Brainstem-Medulla" - }, - { - "@id": "bts:Brainstem-Midbrain/Tectum" - }, - { - "@id": "bts:Brainstem-Pons" - }, - { - "@id": "bts:Spinalcord-Cervical" - }, - { - "@id": "bts:Spinalcord-Thoracic" - }, - { - "@id": "bts:Spinalcord-Lumbar" - }, - { - "@id": "bts:Opticpathway" - }, - { - "@id": "bts:OtherlocationsNOS" - }, - { - "@id": "bts:Paraspinalganglion" - }, - { - "@id": "bts:Basalganglia" - }, - { - "@id": "bts:Hippocampus" - }, - { - "@id": "bts:Meninges/Dura" - }, - { - "@id": "bts:Otherlymphnodes" + "@id": "bts:Negative" } ], - "sms:displayName": "CNS Tumor Primary Anatomic Site", - "sms:required": "sms:false", + "sms:displayName": "Polarity", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificMetastasisSites", + "@id": "bts:MassRangeLowValue", "@type": "rdfs:Class", - "rdfs:comment": "Evidence of active brain metastasis including leptomeningeal involvement", - "rdfs:label": "GliomaSpecificMetastasisSites", + "rdfs:comment": "The low value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeLowValue", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:CSF" - }, - { - "@id": "bts:Spine" - }, - { - "@id": "bts:Bonemarrow" - }, - { - "@id": "bts:Brain" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Leptomeningeal" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Glioma Specific Metastasis Sites", - "sms:required": "sms:false", + "sms:displayName": "Mass Range Low Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:GliomaSpecificRadiationField", + "@id": "bts:MassRangeHighValue", "@type": "rdfs:Class", - "rdfs:comment": "A description of the location on or within the CNS where radiation was administered in a partcipant with glioma", - "rdfs:label": "GliomaSpecificRadiationField", + "rdfs:comment": "The high value of the scanned mass range for MS1 in m/z.", + "rdfs:label": "MassRangeHighValue", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Craniospinal" - }, - { - "@id": "bts:Focal-tumorbed" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotApplicable" - } - ], - "sms:displayName": "Glioma Specific Radiation Field", - "sms:required": "sms:false", + "sms:displayName": "Mass Range High Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SupraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:DataCollectionMode", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a supra tentorial ependymoma", - "rdfs:label": "SupraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", + "rdfs:label": "DataCollectionMode", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44669,30 +44123,27 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ST-EPN-RELA" - }, - { - "@id": "bts:ST-EPN-YAP1" + "@id": "bts:DDA" }, { - "@id": "bts:Unknown" + "@id": "bts:DIA" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Other" } ], - "sms:displayName": "Supra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", + "sms:displayName": "Data Collection Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:InfraTentorialEpendymomaMolecularSubgroup", + "@id": "bts:MSScanMode", "@type": "rdfs:Class", - "rdfs:comment": "Text term to identify the molecular subgroup in a infra tentorial ependymoma", - "rdfs:label": "InfraTentorialEpendymomaMolecularSubgroup", + "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", + "rdfs:label": "MSScanMode", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { @@ -44700,875 +44151,489 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:PF-EPN-A" - }, - { - "@id": "bts:PF-EPN-B" + "@id": "bts:MS" }, { - "@id": "bts:Myxopapillaryependymoma" + "@id": "bts:MS/MS" }, { - "@id": "bts:Unknown" + "@id": "bts:MS3" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Other" } ], - "sms:displayName": "Infra Tentorial Ependymoma Molecular Subgroup", - "sms:required": "sms:false", + "sms:displayName": "MS Scan Mode", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:NeuroblastomaMYCNGeneAmplificationStatus", + "@id": "bts:MSLabeling", "@type": "rdfs:Class", - "rdfs:comment": "Neuroblastoma MYCN amplification or over-expression status", - "rdfs:label": "NeuroblastomaMYCNGeneAmplificationStatus", + "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", + "rdfs:label": "MSLabeling", "rdfs:subClassOf": [ { - "@id": "bts:NeuroblastomaandGliomaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Amplified" - }, - { - "@id": "bts:Notamplified" - }, - { - "@id": "bts:Notdone" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Neuroblastoma MYCN Gene Amplification Status", - "sms:required": "sms:false", + "sms:displayName": "MS Labeling", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SpecimenBlastCountPercentageValue", + "@id": "bts:LCInstrumentVendorandModel", "@type": "rdfs:Class", - "rdfs:comment": "The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis", - "rdfs:label": "SpecimenBlastCountPercentageValue", + "rdfs:comment": "The manufacturer of the instrument used for LC.", + "rdfs:label": "LCInstrumentVendorandModel", "rdfs:subClassOf": [ { - "@id": "bts:AcuteLymphoblasticLeukemiaTier3" + "@id": "bts:MassSpectrometryLevel1" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - 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{ - "@id": "bts:BoneSarcoma" - }, - { - "@id": "bts:MusculoskeletalSarcoma" - }, - { - "@id": "bts:SoftTissueSarcoma" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sarcoma Diagnosis Classification Category", - "sms:required": "sms:false", + "sms:displayName": "HTAN Channel Metadata ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SarcomaTumorExtensionType", + "@id": "bts:ChannelID", "@type": "rdfs:Class", - "rdfs:comment": "The field to indicate the organs and structures to which the tumor has become adherent or has invaded.", - "rdfs:label": "SarcomaTumorExtensionType", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')", + "rdfs:label": "ChannelID", "rdfs:subClassOf": [ { - "@id": "bts:SarcomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Extraosseous" - }, - { - "@id": "bts:Intracranial" - }, - { - "@id": "bts:Lymphnodes" - }, - { - "@id": "bts:Parameningeal" - }, - { - "@id": "bts:Thoraciccavity" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Sarcoma Tumor Extension Type", - "sms:required": "sms:false", + "sms:displayName": "Channel ID", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PancreasPrecancerHistopathologicGrade", + "@id": "bts:ChannelName", "@type": "rdfs:Class", - "rdfs:comment": "The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.", - "rdfs:label": "PancreasPrecancerHistopathologicGrade", + "rdfs:comment": "This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')", + "rdfs:label": "ChannelName", "rdfs:subClassOf": [ { - "@id": "bts:PancreaticCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:IPMN-Adenoma" - }, - { - "@id": "bts:IPMN-Borderline" - }, - { - "@id": "bts:IPMN-Carcinomainsitu" - }, - { - "@id": "bts:IPMN-Invasivecarcinoma" - }, - { - "@id": "bts:PanIN1" - }, - { - "@id": "bts:PanIN1A" - }, - { - "@id": "bts:PanIN1B" - }, - { - "@id": "bts:PanIN2" - }, - { - "@id": "bts:PanIN3" - }, - { - "@id": "bts:Unknown" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreas Precancer Histopathologic Grade", - "sms:required": "sms:false", + "sms:displayName": "Channel Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PancreaticIPMNPathologyEpithelialSubtype", + "@id": "bts:ChannelPassedQC", "@type": "rdfs:Class", - "rdfs:comment": "The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen", - "rdfs:label": "PancreaticIPMNPathologyEpithelialSubtype", + "rdfs:comment": "Identify stains that did not pass QC but are included in the dataset.", + "rdfs:label": "ChannelPassedQC", "rdfs:subClassOf": [ { - "@id": "bts:PancreaticCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -45576,110 +44641,62 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:GastricFoveolar" - }, - { - "@id": "bts:Intestinal" - }, - { - "@id": "bts:IntraductalTubopapillary" - }, - { - "@id": "bts:Pancreatobiliary" - }, - { - "@id": "bts:Oncocytic" - }, - { - "@id": "bts:Other" - }, - { - "@id": "bts:Unknown" + "@id": "bts:Yes" }, { - "@id": "bts:NotReported" + "@id": "bts:No-ChannelFailedQC" } ], - "sms:displayName": "Pancreatic IPMN Pathology Epithelial Subtype", - "sms:required": "sms:false", + "sms:displayName": "Channel Passed QC", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:PancreaticDuctFinalPathologyType", + "@id": "bts:CycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "The final pathology result of the pancreatic duct communication type.", - "rdfs:label": "PancreaticDuctFinalPathologyType", + "rdfs:comment": "The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)", + "rdfs:label": "CycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:PancreaticCancerTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Side-Branch" - }, - { - "@id": "bts:MainDuct" - }, - { - "@id": "bts:Mixed" - }, - { - "@id": "bts:NotSpecified" - }, - { - "@id": "bts:None" - }, - { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Pancreatic Duct Final Pathology Type", + "sms:displayName": "Cycle Number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:CutaneousMelanomaTumorInfiltratingLymphocytes", + "@id": "bts:SubCycleNumber", "@type": "rdfs:Class", - "rdfs:comment": "Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaTumorInfiltratingLymphocytes", + "rdfs:comment": "Sub cycle number", + "rdfs:label": "SubCycleNumber", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Absent" - }, - { - "@id": "bts:Brisk" - }, - { - "@id": "bts:Nonbrisk" - }, - { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Cutaneous Melanoma Tumor Infiltrating Lymphocytes", + "sms:displayName": "Sub Cycle Number", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:CutaneousMelanomaTumorRegressionRange", + "@id": "bts:AntibodyRole", "@type": "rdfs:Class", - "rdfs:comment": "Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.", - "rdfs:label": "CutaneousMelanomaTumorRegressionRange", + "rdfs:comment": "\"Is this antibody acting as a primary or secondary antibody\"", + "rdfs:label": "AntibodyRole", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -45687,152 +44704,187 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Absent" - }, - { - "@id": "bts:Presentinvolving75%ormore" - }, - { - "@id": "bts:Presentinvolvinglessthan75%" + "@id": "bts:Primary" }, { - "@id": "bts:Unknown" + "@id": "bts:Secondary" } ], - "sms:displayName": "Cutaneous Melanoma Tumor Regression Range", - "sms:required": "sms:false", + "sms:displayName": "Antibody Role", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:MelanomaSpecimenClarkLevelValue", + "@id": "bts:TargetName", "@type": "rdfs:Class", - "rdfs:comment": "Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.", - "rdfs:label": "MelanomaSpecimenClarkLevelValue", + "rdfs:comment": "Short descriptive name (abbreviation) for this target (antigen)", + "rdfs:label": "TargetName", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:I" - }, - { - "@id": "bts:II" - }, - { - "@id": "bts:III" - }, - { - "@id": "bts:IV" - }, - { - "@id": "bts:V" - }, - { - "@id": "bts:NoSourceDocumentation" - }, + "sms:displayName": "Target Name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AntibodyName", + "@type": "rdfs:Class", + "rdfs:comment": "Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))", + "rdfs:label": "AntibodyName", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:displayName": "Melanoma Specimen Clark Level Value", - "sms:required": "sms:false", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Antibody Name", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:CutaneousMelanomaSurgicalMargins", + "@id": "bts:RRIDidentifier", "@type": "rdfs:Class", - "rdfs:comment": "Text term to indicate presence of tumor at resection margins", - "rdfs:label": "CutaneousMelanomaSurgicalMargins", + "rdfs:comment": "Research Resource Identifier (eg “RRID: AB_394606”)", + "rdfs:label": "RRIDidentifier", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Positive" - }, - { - "@id": "bts:Negative" - }, - { - "@id": "bts:Unknown" - }, + "sms:displayName": "RRID identifier", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match AB_\\d+" + ] + }, + { + "@id": "bts:Fluorophore", + "@type": "rdfs:Class", + "rdfs:comment": "Fluorescent dye label (eg Alexa Fluor 488)", + "rdfs:label": "Fluorophore", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:displayName": "Cutaneous Melanoma Surgical Margins", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fluorophore", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MelanomaLesionSize", + "@id": "bts:Lot", "@type": "rdfs:Class", - "rdfs:comment": "Diameter of lesion determined on skin examination (pre-bx), in mm", - "rdfs:label": "MelanomaLesionSize", + "rdfs:comment": "Lot number from vendor", + "rdfs:label": "Lot", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Melanoma Lesion Size", + "sms:displayName": "Lot", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HistoryofAtypicalNevi", + "@id": "bts:ExcitationWavelength", "@type": "rdfs:Class", - "rdfs:comment": "Patient has a history of atypical nevi", - "rdfs:label": "HistoryofAtypicalNevi", + "rdfs:comment": "Center/peak of the excitation spectrum (nm)", + "rdfs:label": "ExcitationWavelength", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Yes(morethan50)" - }, - { - "@id": "bts:Yes(lessthan50)" - }, + "sms:displayName": "Excitation Wavelength", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:EmissionWavelength", + "@type": "rdfs:Class", + "rdfs:comment": "Center/peak of the emission spectrum (nm)", + "rdfs:label": "EmissionWavelength", + "rdfs:subClassOf": [ { - "@id": "bts:No" - }, + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Emission Wavelength", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:ExcitationBandwidth", + "@type": "rdfs:Class", + "rdfs:comment": "Nominal width of excitation spectrum (nm)", + "rdfs:label": "ExcitationBandwidth", + "rdfs:subClassOf": [ { - "@id": "bts:Unknown" - }, + "@id": "bts:ImagingLevel3Channels" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Excitation Bandwidth", + "sms:required": "sms:false", + "sms:validationRules": [ + "num" + ] + }, + { + "@id": "bts:EmissionBandwidth", + "@type": "rdfs:Class", + "rdfs:comment": "Nominal width of emission spectrum (nm)", + "rdfs:label": "EmissionBandwidth", + "rdfs:subClassOf": [ { - "@id": "bts:NotReported" + "@id": "bts:ImagingLevel3Channels" } ], - "sms:displayName": "History of Atypical Nevi", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Emission Bandwidth", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "num" + ] }, { - "@id": "bts:FitzpatrickSkinTone", + "@id": "bts:MetalIsotopeElement", "@type": "rdfs:Class", - "rdfs:comment": "The Fitzpatrick classification of skin phototype", - "rdfs:label": "FitzpatrickSkinTone", + "rdfs:comment": "Element abbreviation. eg “La” or “Nd”", + "rdfs:label": "MetalIsotopeElement", "rdfs:subClassOf": [ { - "@id": "bts:MelanomaTier3" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -45840,447 +44892,483 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:I" + "@id": "bts:H" }, { - "@id": "bts:II" + "@id": "bts:He" }, { - "@id": "bts:III" + "@id": "bts:Li" }, { - "@id": "bts:IV" + "@id": "bts:Be" + }, + { + "@id": "bts:B" + }, + { + "@id": "bts:C" + }, + { + "@id": "bts:N" + }, + { + "@id": "bts:O" + }, + { + "@id": "bts:F" + }, + { + "@id": "bts:Ne" + }, + { + "@id": "bts:Na" + }, + { + "@id": "bts:Mg" + }, + { + "@id": "bts:Al" + }, + { + "@id": "bts:Si" + }, + { + "@id": "bts:P" + }, + { + "@id": "bts:S" + }, + { + "@id": "bts:Cl" + }, + { + "@id": "bts:Ar" + }, + { + "@id": "bts:K" + }, + { + "@id": "bts:Ca" + }, + { + "@id": "bts:Sc" + }, + { + "@id": "bts:Ti" }, { "@id": "bts:V" }, { - "@id": "bts:VI" + "@id": "bts:Cr" }, { - "@id": "bts:Unknown" + "@id": "bts:Mn" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Fitzpatrick Skin Tone", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofChronicUVExposure", - "@type": "rdfs:Class", - "rdfs:comment": "History of chronic UV exposure", - "rdfs:label": "HistoryofChronicUVExposure", - "rdfs:subClassOf": [ + "@id": "bts:Fe" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Co" + }, { - "@id": "bts:Outdooroccupational" + "@id": "bts:Ni" }, { - "@id": "bts:Outdoorrecreational" + "@id": "bts:Cu" }, { - "@id": "bts:Therapeutic" + "@id": "bts:Zn" }, { - "@id": "bts:None" + "@id": "bts:Ga" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Chronic UV Exposure", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofBlisteringSunburn", - "@type": "rdfs:Class", - "rdfs:comment": "Patient has history of blistering sunburn", - "rdfs:label": "HistoryofBlisteringSunburn", - "rdfs:subClassOf": [ + "@id": "bts:Ge" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:As" + }, { - "@id": "bts:Yes" + "@id": "bts:Se" }, { - "@id": "bts:No" + "@id": "bts:Br" }, { - "@id": "bts:Unknown" + "@id": "bts:Kr" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Blistering Sunburn", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:HistoryofTanningBedUse", - "@type": "rdfs:Class", - "rdfs:comment": "History of tanning bed use of the patient", - "rdfs:label": "HistoryofTanningBedUse", - "rdfs:subClassOf": [ + "@id": "bts:Rb" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Sr" + }, { - "@id": "bts:Never" + "@id": "bts:Y" }, { - "@id": "bts:Lessthan10times" + "@id": "bts:Zr" }, { - "@id": "bts:10-50times" + "@id": "bts:Nb" }, { - "@id": "bts:50-100times" + "@id": "bts:Mo" }, { - "@id": "bts:Morethan100times" + "@id": "bts:Tc" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "History of Tanning Bed Use", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:ImmediateFamilyHistoryMelanoma", - "@type": "rdfs:Class", - "rdfs:comment": "Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.", - "rdfs:label": "ImmediateFamilyHistoryMelanoma", - "rdfs:subClassOf": [ + "@id": "bts:Ru" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Rh" + }, { - "@id": "bts:Beforeage50" + "@id": "bts:Pd" }, { - "@id": "bts:Notbeforeage50" + "@id": "bts:Ag" }, { - "@id": "bts:Unknown" - } - ], - "sms:displayName": "Immediate Family History Melanoma", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:MelanomaBiopsyResectionSites", - "@type": "rdfs:Class", - "rdfs:comment": "Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)", - "rdfs:label": "MelanomaBiopsyResectionSites", - "rdfs:subClassOf": [ + "@id": "bts:Cd" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:In" + }, { - "@id": "bts:Skinofscalp" + "@id": "bts:Sn" }, { - "@id": "bts:Skinofeyelid" + "@id": "bts:Sb" }, { - "@id": "bts:Skinofnose" + "@id": "bts:Te" }, { - "@id": "bts:Skinoflip" + "@id": "bts:I" }, { - "@id": "bts:Skinofear" + "@id": "bts:Xe" }, { - "@id": "bts:Skinofneck" + "@id": "bts:Cs" }, { - "@id": "bts:Skinofotherpartsofface" + "@id": "bts:Ba" }, { - "@id": "bts:Skinofchest" + "@id": "bts:La" }, { - "@id": "bts:Skinofback" + "@id": "bts:Ce" }, { - "@id": "bts:Skinofabdomen" + "@id": "bts:Pr" }, { - "@id": "bts:Skinoftrunk-other" + "@id": "bts:Nd" }, { - "@id": "bts:Skinofbreast" + "@id": "bts:Pm" }, { - "@id": "bts:Skinofupperlimbandshoulder" + "@id": "bts:Sm" }, { - "@id": "bts:Skinofpalm" + "@id": "bts:Eu" }, { - "@id": "bts:Skinoflowerlimbandhip" + "@id": "bts:Gd" }, { - "@id": "bts:Skinofsole" + "@id": "bts:Tb" }, { - "@id": "bts:Skinofpenis" + "@id": "bts:Dy" }, { - "@id": "bts:Skinofscrotum" + "@id": "bts:Ho" }, { - "@id": "bts:Skinofvulva" + "@id": "bts:Er" }, { - "@id": "bts:Skinother" + "@id": "bts:Tm" }, { - "@id": "bts:SkinNOS" + "@id": "bts:Yb" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Melanoma Biopsy Resection Sites", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaUlceration", - "@type": "rdfs:Class", - "rdfs:comment": "Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaUlceration", - "rdfs:subClassOf": [ + "@id": "bts:Lu" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Hf" + }, { - "@id": "bts:Absent" + "@id": "bts:Ta" }, { - "@id": "bts:Present" + "@id": "bts:W" }, { - "@id": "bts:Unknown" + "@id": "bts:Re" }, { - "@id": "bts:NotReported" - } - ], - "sms:displayName": "Cutaneous Melanoma Ulceration", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:CutaneousMelanomaAdditionalFindings", - "@type": "rdfs:Class", - "rdfs:comment": "Significant pathologic finding present in addition to the cutaneous melanoma.", - "rdfs:label": "CutaneousMelanomaAdditionalFindings", - "rdfs:subClassOf": [ + "@id": "bts:Os" + }, { - "@id": "bts:MelanomaTier3" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:Ir" + }, { - "@id": "bts:ActinicKeratosis" + "@id": "bts:Pt" }, { - "@id": "bts:NevusRemnant" + "@id": "bts:Au" }, { - "@id": "bts:SolarElastosis" + "@id": "bts:Hg" }, { - "@id": "bts:FibrosingRegression" + "@id": "bts:Tl" }, { - "@id": "bts:NestingMelanoma" + "@id": "bts:Pb" }, { - "@id": "bts:PagetoidSpread" + "@id": "bts:Bi" }, { - "@id": "bts:VascularProliferation" + "@id": "bts:Po" }, { - "@id": "bts:Other" + "@id": "bts:At" }, { - "@id": "bts:Unknown" + "@id": "bts:Rn" }, { - "@id": "bts:NotApplicable" + "@id": "bts:Fr" + }, + { + "@id": "bts:Ra" + }, + { + "@id": "bts:Ac" + }, + { + "@id": "bts:Th" + }, + { + "@id": "bts:Pa" + }, + { + "@id": "bts:U" + }, + { + "@id": "bts:Np" + }, + { + "@id": "bts:Pu" + }, + { + "@id": "bts:Am" + }, + { + "@id": "bts:Bk" + }, + { + "@id": "bts:Cf" + }, + { + "@id": "bts:Es" + }, + { + "@id": "bts:Fm" + }, + { + "@id": "bts:Md" + }, + { + "@id": "bts:No" + }, + { + "@id": "bts:Lr" + }, + { + "@id": "bts:Rf" + }, + { + "@id": "bts:Db" + }, + { + "@id": "bts:Sg" + }, + { + "@id": "bts:Bh" + }, + { + "@id": "bts:Hs" + }, + { + "@id": "bts:Mt" + }, + { + "@id": "bts:Ds" + }, + { + "@id": "bts:Rg" + }, + { + "@id": "bts:Cn" + }, + { + "@id": "bts:Nh" + }, + { + "@id": "bts:Fl" + }, + { + "@id": "bts:Mc" + }, + { + "@id": "bts:Lv" + }, + { + "@id": "bts:Ts" + }, + { + "@id": "bts:Og" } ], - "sms:displayName": "Cutaneous Melanoma Additional Findings", + "sms:displayName": "Metal Isotope Element", "sms:required": "sms:false", - "sms:validationRules": [] + "sms:validationRules": [ + "str" + ] }, { - "@id": "bts:HTANRPPAAntibodyTableID", + "@id": "bts:MetalIsotopeMass", "@type": "rdfs:Class", - "rdfs:comment": "HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.", - "rdfs:label": "HTANRPPAAntibodyTableID", + "rdfs:comment": "Element mass number", + "rdfs:label": "MetalIsotopeMass", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN RPPA Antibody Table ID", - "sms:required": "sms:true", - "sms:validationRules": [] + "sms:displayName": "Metal Isotope Mass", + "sms:required": "sms:false", + "sms:validationRules": [ + "int" + ] }, { - "@id": "bts:AbNameReportedonDataset", + "@id": "bts:OligoBarcodeUpperStrand", "@type": "rdfs:Class", - "rdfs:comment": "The antibody name.", - "rdfs:label": "AbNameReportedonDataset", + "rdfs:comment": "Oligo Barcode - Upper Strand", + "rdfs:label": "OligoBarcodeUpperStrand", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ab Name Reported on Dataset", - "sms:required": "sms:true", + "sms:displayName": "Oligo Barcode Upper Strand", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:GENCODEGeneSymbolTarget", + "@id": "bts:OligoBarcodeLowerStrand", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of gene symbols targeted by the antibody.", - "rdfs:label": "GENCODEGeneSymbolTarget", + "rdfs:comment": "Oligo Barcode - Lower Strand", + "rdfs:label": "OligoBarcodeLowerStrand", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "GENCODE Gene Symbol Target", - "sms:required": "sms:true", + "sms:displayName": "Oligo Barcode Lower Strand", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:UNIPROTProteinIDTarget", + "@id": "bts:Dilution", "@type": "rdfs:Class", - "rdfs:comment": "The comma separated list of UNIPROT IDs targeted by the antibody.", - "rdfs:label": "UNIPROTProteinIDTarget", + "rdfs:comment": "Dilution (eg 1:1000)", + "rdfs:label": "Dilution", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UNIPROT Protein ID Target", - "sms:required": "sms:true", + "sms:displayName": "Dilution", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoproteinFlag", + "@id": "bts:Concentration", "@type": "rdfs:Class", - "rdfs:comment": "A flag the denotes if an antibody targets a phosphoprotein.", - "rdfs:label": "PhosphoproteinFlag", + "rdfs:comment": "Concentration (eg 10ug/mL)", + "rdfs:label": "Concentration", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:True" - }, - { - "@id": "bts:False" - } - ], - "sms:displayName": "Phosphoprotein Flag", - "sms:required": "sms:true", + "sms:displayName": "Concentration", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:InternalAbID", + "@id": "bts:No-ChannelFailedQC", "@type": "rdfs:Class", - "rdfs:comment": "Internal lab ID for an antibody.", - "rdfs:label": "InternalAbID", + "rdfs:comment": "Channel failed QC", + "rdfs:label": "No-ChannelFailedQC", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelPassedQC" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Internal Ab ID", - "sms:required": "sms:true", + "sms:displayName": "No - Channel Failed QC", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ChannelQCFailureType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Species", + "@id": "bts:ChannelQCFailureType", "@type": "rdfs:Class", - "rdfs:comment": "Host animal.", - "rdfs:label": "Species", + "rdfs:comment": "Reason the channel failed QC", + "rdfs:label": "ChannelQCFailureType", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { @@ -46288,24947 +45376,27160 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:Mouse" + "@id": "bts:Off-targetstaining" }, { - "@id": "bts:Rabbit" + "@id": "bts:Auto-fluoresence" }, { - "@id": "bts:Goat" + "@id": "bts:Stainingartefacet" + }, + { + "@id": "bts:Imagingartefact" + }, + { + "@id": "bts:Other/multiplechannelQCfaliuretypes" } ], - "sms:displayName": "Species", - "sms:required": "sms:true", + "sms:displayName": "Channel QC Failure Type", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RPPADilution", + "@id": "bts:Off-targetstaining", "@type": "rdfs:Class", - "rdfs:comment": "The dilution ratio.", - "rdfs:label": "RPPADilution", + "rdfs:comment": "TBD", + "rdfs:label": "Off-targetstaining", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "RPPA Dilution", + "sms:displayName": "Off-target staining", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PhosphoSite", + "@id": "bts:Auto-fluoresence", "@type": "rdfs:Class", - "rdfs:comment": "The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)", - "rdfs:label": "PhosphoSite", + "rdfs:comment": "TBD", + "rdfs:label": "Auto-fluoresence", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Phospho Site", + "sms:displayName": "Auto-fluoresence", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:PhosphoproteinFlag" - } - ], "sms:validationRules": [] }, { - "@id": "bts:RPPAValidationStatus", + "@id": "bts:Stainingartefacet", "@type": "rdfs:Class", - "rdfs:comment": "Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)", - "rdfs:label": "RPPAValidationStatus", + "rdfs:comment": "TBD", + "rdfs:label": "Stainingartefacet", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Valid" - }, - { - "@id": "bts:UsewithCaution" - }, - { - "@id": "bts:UnderEvaluation" - }, - { - "@id": "bts:UsedforQC" - } - ], - "sms:displayName": "RPPA Validation Status", + "sms:displayName": "Staining artefacet", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:AntibodyNotes", + "@id": "bts:Imagingartefact", "@type": "rdfs:Class", - "rdfs:comment": "Notes on antibodies replacements and antibody recognition observations.", - "rdfs:label": "AntibodyNotes", + "rdfs:comment": "TBD", + "rdfs:label": "Imagingartefact", "rdfs:subClassOf": [ { - "@id": "bts:HTANRPPAAntibodyTable" + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Antibody Notes", + "sms:displayName": "Imaging artefact", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingCompleted", + "@id": "bts:Other/multiplechannelQCfaliuretypes", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps completed to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingCompleted", + "rdfs:comment": "QC failure type not speficied", + "rdfs:label": "Other/multiplechannelQCfaliuretypes", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ImagingLevel3Channels" + }, + { + "@id": "bts:ChannelQCFailureType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, - { - "@id": "bts:TMAde-arraying" - }, - { - "@id": "bts:None" - }, + "sms:displayName": "Other/multiple channel QC faliure types", + "sms:required": "sms:false", + "sms:requiresDependency": [ { - "@id": "bts:Other" + "@id": "bts:ChannelQCFailureComment" } ], - "sms:displayName": "Pre-processing Completed", - "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Pre-processingRequired", + "@id": "bts:ChannelQCFailureComment", "@type": "rdfs:Class", - "rdfs:comment": "Pre-processing steps required to convert level 1 raw data to a single level 2 image", - "rdfs:label": "Pre-processingRequired", + "rdfs:comment": "Custom comment on channel QC faliure", + "rdfs:label": "ChannelQCFailureComment", "rdfs:subClassOf": [ { - "@id": "bts:Imaging" + "@id": "bts:ImagingLevel3Channels" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Illuminationcorrection" - }, - { - "@id": "bts:TileStitching" - }, - { - "@id": "bts:Channel/CycleRegistration" - }, + "sms:displayName": "Channel QC Failure Comment", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Primary", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Primary", + "rdfs:subClassOf": [ { - "@id": "bts:TMAde-arraying" + "@id": "bts:AntibodyRole" }, { - "@id": "bts:None" + "@id": "bts:ClassificationofTumor" }, { - "@id": "bts:Other" + "@id": "bts:TumorTissueType" } ], - "sms:displayName": "Pre-processing Required", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Primary", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Publication", + "@id": "bts:Secondary", "@type": "rdfs:Class", - "rdfs:comment": "An empty parent attribute for publications", - "rdfs:label": "Publication", + "rdfs:comment": "TBD", + "rdfs:label": "Secondary", "rdfs:subClassOf": [ { - "@id": "schema:Thing" + "@id": "bts:AntibodyRole" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Publication", + "sms:displayName": "Secondary", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PublicationManifest", + "@id": "bts:H", "@type": "rdfs:Class", - "rdfs:comment": "Publication specific attributes.", - "rdfs:label": "PublicationManifest", + "rdfs:comment": "TBD", + "rdfs:label": "H", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Publication Manifest", + "sms:displayName": "H", "sms:required": "sms:false", - "sms:requiresDependency": [ - { - "@id": "bts:Component" - }, - { - "@id": "bts:Publication-associatedHTANParentDataFileID" - }, - { - "@id": "bts:HTANGrantID" - }, - { - "@id": "bts:HTANCenterID" - }, - { - "@id": "bts:PublicationContentType" - }, - { - "@id": "bts:DOI" - }, - { - "@id": "bts:Title" - }, - { - "@id": "bts:Authors" - }, - { - "@id": "bts:CorrespondingAuthor" - }, - { - "@id": "bts:CorrespondingAuthorORCID" - }, - { - "@id": "bts:YearofPublication" - }, - { - "@id": "bts:LocationofPublication" - }, - { - "@id": "bts:PublicationAbstract" - }, - { - "@id": "bts:License" - }, - { - "@id": "bts:PMID" - }, - { - "@id": "bts:PublicationcontainsHTANID" - }, - { - "@id": "bts:DataType" - }, - { - "@id": "bts:Tool" - }, - { - "@id": "bts:SupportingLink" - }, - { - "@id": "bts:SupportingLinkDescription" - } - ], "sms:validationRules": [] }, { - "@id": "bts:Publication-associatedHTANParentDataFileID", + "@id": "bts:He", "@type": "rdfs:Class", - "rdfs:comment": "HTAN Data File Identifier(s) of the files associated with the content presented/published. Should be comma-separated lists.", - "rdfs:label": "Publication-associatedHTANParentDataFileID", + "rdfs:comment": "TBD", + "rdfs:label": "He", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Publication-associated HTAN Parent Data File ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] + "sms:displayName": "He", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANGrantID", + "@id": "bts:Li", "@type": "rdfs:Class", - "rdfs:comment": "HTAN grant number(s) (i.e. CA------ format) associated with the content presented/published.", - "rdfs:label": "HTANGrantID", + "rdfs:comment": "TBD", + "rdfs:label": "Li", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HTAN Grant ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] + "sms:displayName": "Li", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:HTANCenterID", + "@id": "bts:Be", "@type": "rdfs:Class", - "rdfs:comment": "List of HTAN Center ID(s) associated with the content presented/published.", - "rdfs:label": "HTANCenterID", + "rdfs:comment": "TBD", + "rdfs:label": "Be", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:HTA1" - }, - { - "@id": "bts:HTA2" - }, - { - "@id": "bts:HTA3" - }, - { - "@id": "bts:HTA4" - }, - { - "@id": "bts:HTA5" - }, - { - "@id": "bts:HTA6" - }, - { - "@id": "bts:HTA7" - }, - { - "@id": "bts:HTA8" - }, - { - "@id": "bts:HTA9" - }, - { - "@id": "bts:HTA10" - }, - { - "@id": "bts:HTA11" - }, - { - "@id": "bts:HTA12" - }, - { - "@id": "bts:HTA13" - }, - { - "@id": "bts:HTA14" - } - ], - "sms:displayName": "HTAN Center ID", - "sms:required": "sms:true", - "sms:validationRules": [ - "list like" - ] + "sms:displayName": "Be", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:PublicationContentType", + "@id": "bts:N", "@type": "rdfs:Class", - "rdfs:comment": "The type of content presented or published.", - "rdfs:label": "PublicationContentType", + "rdfs:comment": "TBD", + "rdfs:label": "N", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Preprint" - }, - { - "@id": "bts:Publishedmanuscript" - }, + "sms:displayName": "N", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:O", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "O", + "rdfs:subClassOf": [ { - "@id": "bts:Conferenceproceedings" + "@id": "bts:MetalIsotopeElement" } ], - "sms:displayName": "Publication Content Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "O", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:DOI", + "@id": "bts:F", "@type": "rdfs:Class", - "rdfs:comment": "The digital object identifier (DOI) of the content in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.", - "rdfs:label": "DOI", + "rdfs:comment": "TBD", + "rdfs:label": "F", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "DOI", - "sms:required": "sms:true", - "sms:validationRules": [ - "url" - ] + "sms:displayName": "F", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:CorrespondingAuthor", + "@id": "bts:Ne", "@type": "rdfs:Class", - "rdfs:comment": "The name(s) of the corresponding author(s) of the content presented/published. If more than one corresponding author, please list in the order they appear in the author list.", - "rdfs:label": "CorrespondingAuthor", + "rdfs:comment": "TBD", + "rdfs:label": "Ne", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Corresponding Author", - "sms:required": "sms:true", + "sms:displayName": "Ne", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CorrespondingAuthorORCID", + "@id": "bts:Na", "@type": "rdfs:Class", - "rdfs:comment": "The ORCiD(s) of the corresponding author(s) of the content presented/published. Should be a valid ORCiD url starting with https://orcid.org/ followed by a 16 digit identifier in dash separated groups of 4 (for example https://orcid.org/0000-0002-1825-0097). If more than one corresponding author, please list ORCiDs in the order the authors appear in the author list.", - "rdfs:label": "CorrespondingAuthorORCID", + "rdfs:comment": "TBD", + "rdfs:label": "Na", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Corresponding Author ORCID", - "sms:required": "sms:true", + "sms:displayName": "Na", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Title", + "@id": "bts:Mg", "@type": "rdfs:Class", - "rdfs:comment": "The title of the content presented or published.", - "rdfs:label": "Title", + "rdfs:comment": "TBD", + "rdfs:label": "Mg", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Title", - "sms:required": "sms:true", + "sms:displayName": "Mg", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Authors", + "@id": "bts:Al", "@type": "rdfs:Class", - "rdfs:comment": "The names of the author(s) of the content presented/published, in the order they appear.", - "rdfs:label": "Authors", + "rdfs:comment": "TBD", + "rdfs:label": "Al", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Authors", - "sms:required": "sms:true", + "sms:displayName": "Al", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:YearofPublication", + "@id": "bts:Si", "@type": "rdfs:Class", - "rdfs:comment": "The year the content was presented or published (format YYYY).", - "rdfs:label": "YearofPublication", + "rdfs:comment": "TBD", + "rdfs:label": "Si", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Year of Publication", - "sms:required": "sms:true", - "sms:validationRules": [ - "regex search ^(19|20)\\d{2}$" - ] + "sms:displayName": "Si", + "sms:required": "sms:false", + "sms:validationRules": [] }, { - "@id": "bts:LocationofPublication", + "@id": "bts:P", "@type": "rdfs:Class", - "rdfs:comment": "The name of the preprint server, journal, or conference where the content was presented/published.", - "rdfs:label": "LocationofPublication", + "rdfs:comment": "TBD", + "rdfs:label": "P", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Location of Publication", - "sms:required": "sms:true", + "sms:displayName": "P", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PublicationAbstract", + "@id": "bts:S", "@type": "rdfs:Class", - "rdfs:comment": "The abstract or short description of the content presented/published.", - "rdfs:label": "PublicationAbstract", + "rdfs:comment": "TBD", + "rdfs:label": "S", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Publication Abstract", - "sms:required": "sms:true", + "sms:displayName": "S", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:License", + "@id": "bts:Cl", "@type": "rdfs:Class", - "rdfs:comment": "The type of license applicable to the content.", - "rdfs:label": "License", + "rdfs:comment": "TBD", + "rdfs:label": "Cl", "rdfs:subClassOf": [ { - "@id": "bts:Publication" + "@id": "bts:MetalIsotopeElement" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Cl", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ar", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ar", + "rdfs:subClassOf": [ { - "@id": "bts:0BSD" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ar", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:K", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "K", + "rdfs:subClassOf": [ { - "@id": "bts:AAL" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "K", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ca", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ca", + "rdfs:subClassOf": [ { - "@id": "bts:ADSL" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ca", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Sc", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Sc", + "rdfs:subClassOf": [ { - "@id": "bts:AFL-1.1" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sc", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ti", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ti", + "rdfs:subClassOf": [ { - "@id": "bts:AFL-1.2" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ti", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:V", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "V", + "rdfs:subClassOf": [ { - "@id": "bts:AFL-2.0" + "@id": "bts:MelanomaSpecimenClarkLevelValue" }, { - "@id": "bts:AFL-2.1" + "@id": "bts:FitzpatrickSkinTone" }, { - "@id": "bts:AFL-3.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "V", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cr", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cr", + "rdfs:subClassOf": [ { - "@id": "bts:AGPL-1.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cr", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Mn", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Mn", + "rdfs:subClassOf": [ { - "@id": "bts:AGPL-3.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mn", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Fe", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Fe", + "rdfs:subClassOf": [ { - "@id": "bts:AMDPLPA" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Fe", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Co", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Co", + "rdfs:subClassOf": [ { - "@id": "bts:AML" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Co", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ni", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ni", + "rdfs:subClassOf": [ { - "@id": "bts:AMPAS" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ni", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cu", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cu", + "rdfs:subClassOf": [ { - "@id": "bts:ANTLR-PD" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Cu", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Zn", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Zn", + "rdfs:subClassOf": [ { - "@id": "bts:APAFML" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Zn", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ga", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ga", + "rdfs:subClassOf": [ { - "@id": "bts:APL-1.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ga", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Ge", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Ge", + "rdfs:subClassOf": [ { - "@id": "bts:APSL-1.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Ge", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:As", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "As", + "rdfs:subClassOf": [ { - "@id": "bts:APSL-1.1" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "As", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Se", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Se", + "rdfs:subClassOf": [ { - "@id": "bts:APSL-1.2" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Se", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Br", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Br", + "rdfs:subClassOf": [ { - "@id": "bts:APSL-2.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Br", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Kr", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Kr", + "rdfs:subClassOf": [ { - "@id": "bts:Abstyles" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Kr", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Rb", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Rb", + "rdfs:subClassOf": [ { - "@id": "bts:Adobe-2006" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Rb", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Sr", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Sr", + "rdfs:subClassOf": [ { - "@id": "bts:Adobe-Glyph" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Sr", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Y", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Y", + "rdfs:subClassOf": [ { - "@id": "bts:Afmparse" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Y", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Zr", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Zr", + "rdfs:subClassOf": [ { - "@id": "bts:Aladdin" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Zr", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Nb", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Nb", + "rdfs:subClassOf": [ { - "@id": "bts:Apache-1.0" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Nb", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Mo", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Mo", + "rdfs:subClassOf": [ { - "@id": "bts:Apache-1.1" - }, + "@id": "bts:MetalIsotopeElement" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Mo", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Tc", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Tc", + "rdfs:subClassOf": [ { - 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Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. 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Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.", - "rdfs:label": "DataCollectionMode", + "rdfs:comment": "TBD", + "rdfs:label": "Imaging", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Thing" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ + "sms:displayName": "Imaging", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cm", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Cm", + "rdfs:subClassOf": [ { - "@id": "bts:DDA" + "@id": "bts:WorkingDistanceUnit" }, { - "@id": "bts:DIA" + "@id": "bts:FOVXUnit" }, { - "@id": "bts:Other" + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZUnit" + }, + { + "@id": "bts:DimensionsUnit" } ], - "sms:displayName": "Data Collection Mode", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cm", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSScanMode", + "@id": "bts:Mm", "@type": "rdfs:Class", - "rdfs:comment": "Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)", - "rdfs:label": "MSScanMode", + "rdfs:comment": "TBD", + "rdfs:label": "Mm", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ + "@id": "bts:DimensionsUnit" + }, { - "@id": "bts:MS" + "@id": "bts:WorkingDistanceUnit" }, { - "@id": "bts:MS/MS" + "@id": "bts:FOVXUnit" }, { - "@id": "bts:MS3" + "@id": "bts:FOVYUnit" }, { - "@id": "bts:Other" + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZUnit" } ], - "sms:displayName": "MS Scan Mode", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "mm", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSLabeling", + "@id": "bts:Μm", "@type": "rdfs:Class", - "rdfs:comment": "Indicates whether samples were labeled prior to MS analysis (e.g., TMT)", - "rdfs:label": "MSLabeling", + "rdfs:comment": "TBD", + "rdfs:label": "Μm", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZUnit" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MS Labeling", - "sms:required": "sms:true", + "sms:displayName": "µm", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCInstrumentVendorandModel", + "@id": "bts:Nm", "@type": "rdfs:Class", - "rdfs:comment": "The manufacturer of the instrument used for LC.", - "rdfs:label": "LCInstrumentVendorandModel", + "rdfs:comment": "TBD", + "rdfs:label": "Nm", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZUnit" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Instrument Vendor and Model", - "sms:required": "sms:true", + "sms:displayName": "nm", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCColumnVendorandModel", + "@id": "bts:Å", "@type": "rdfs:Class", - "rdfs:comment": "The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'", - "rdfs:label": "LCColumnVendorandModel", + "rdfs:comment": "TBD", + "rdfs:label": "Å", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:WorkingDistanceUnit" + }, + { + "@id": "bts:FOVXUnit" + }, + { + "@id": "bts:FOVYUnit" + }, + { + "@id": "bts:PhysicalSizeXUnit" + }, + { + "@id": "bts:PhysicalSizeYUnit" + }, + { + "@id": "bts:PhysicalSizeZUnit" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Column Vendor and Model", - "sms:required": "sms:true", + "sms:displayName": "Å", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCResin", + "@id": "bts:Air", "@type": "rdfs:Class", - "rdfs:comment": "Details of the resin used for lc, including vendor, particle size, pore size", - "rdfs:label": "LCResin", + "rdfs:comment": "TBD", + "rdfs:label": "Air", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Immersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Resin", - "sms:required": "sms:true", + "sms:displayName": "Air", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCLengthValue", + "@id": "bts:Oil", "@type": "rdfs:Class", - "rdfs:comment": "LC column length in cm.", - "rdfs:label": "LCLengthValue", + "rdfs:comment": "TBD", + "rdfs:label": "Oil", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Immersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Length Value", - "sms:required": "sms:true", + "sms:displayName": "Oil", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCTempValue", + "@id": "bts:Water", "@type": "rdfs:Class", - "rdfs:comment": "LC temperature in C.", - "rdfs:label": "LCTempValue", + "rdfs:comment": "TBD", + "rdfs:label": "Water", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Immersion" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Temp Value", - "sms:required": "sms:true", + "sms:displayName": "Water", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCIDValue", + "@id": "bts:No-ChannelsQC", "@type": "rdfs:Class", - "rdfs:comment": "LC column inner diameter in microns.", - "rdfs:label": "LCIDValue", + "rdfs:comment": "Not all channels passed QC", + "rdfs:label": "No-ChannelsQC", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:Imaging" + }, + { + "@id": "bts:PassedQC" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC ID Value", - "sms:required": "sms:true", + "sms:displayName": "No - Channels QC", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Comment" + } + ], "sms:validationRules": [] }, { - "@id": "bts:LCFlowRate", + "@id": "bts:XYZCT", "@type": "rdfs:Class", - "rdfs:comment": "LC flow rate in nL/min.", - "rdfs:label": "LCFlowRate", + "rdfs:comment": "TBD", + "rdfs:label": "XYZCT", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Flow Rate", - "sms:required": "sms:true", + "sms:displayName": "XYZCT", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCGradient", + "@id": "bts:XYZTC", "@type": "rdfs:Class", - "rdfs:comment": "The program dictates the mobile phase solvent composition over the course of the chromatographic run.", - "rdfs:label": "LCGradient", + "rdfs:comment": "TBD", + "rdfs:label": "XYZTC", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Gradient", - "sms:required": "sms:true", + "sms:displayName": "XYZTC", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCMobilePhaseA", + "@id": "bts:XYCTZ", "@type": "rdfs:Class", - "rdfs:comment": "Composition of mobile phase A", - "rdfs:label": "LCMobilePhaseA", + "rdfs:comment": "TBD", + "rdfs:label": "XYCTZ", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Mobile Phase A", - "sms:required": "sms:true", + "sms:displayName": "XYCTZ", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LCMobilePhaseB", + "@id": "bts:XYCZT", "@type": "rdfs:Class", - "rdfs:comment": "Composition of mobile phase B", - "rdfs:label": "LCMobilePhaseB", + "rdfs:comment": "TBD", + "rdfs:label": "XYCZT", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC Mobile Phase B", - "sms:required": "sms:true", + "sms:displayName": "XYCZT", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MSInstrumentMetadataFile", + "@id": "bts:XYTZC", "@type": "rdfs:Class", - "rdfs:comment": "Additional file containing instrument metadata details. Use either synapse_path or entity_Id", - "rdfs:label": "MSInstrumentMetadataFile", + "rdfs:comment": "TBD", + "rdfs:label": "XYTZC", "rdfs:subClassOf": [ { - "@id": "bts:MassSpectrometryLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "MS Instrument Metadata File", + "sms:displayName": "XYTZC", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BisulfiteConversion", + "@id": "bts:ZYX", "@type": "rdfs:Class", - "rdfs:comment": "Name of the kit used in bisulfite conversion.", - "rdfs:label": "BisulfiteConversion", + "rdfs:comment": "TBD", + "rdfs:label": "ZYX", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:DimensionOrder" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:ZimoEZDNAMethylationKit" - }, - { - "@id": "bts:ZimoEZ-96DNAMethylationShallowKit" - }, + "sms:displayName": "ZYX", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:True", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "True", + "rdfs:subClassOf": [ { - "@id": "bts:ZimoEZ-96DNAMethylationDeepKit" + "@id": "bts:PixelsBigEndian" }, { - "@id": "bts:NEBNextEnzymaticMethyl-seqKit" + "@id": "bts:PhosphoproteinFlag" }, { - "@id": "bts:AgilentSureSelectXTMethyl-Seq" + "@id": "bts:AgeIsObfuscated" } ], - "sms:displayName": "Bisulfite Conversion", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "true", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ReplicateType", + "@id": "bts:False", "@type": "rdfs:Class", - "rdfs:comment": "A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.", - "rdfs:label": "ReplicateType", + "rdfs:comment": "TBD", + "rdfs:label": "False", "rdfs:subClassOf": [ { - "@id": "bts:Sequencing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "schema:rangeIncludes": [ - { - "@id": "bts:Technicalreplicate" + "@id": "bts:PixelsBigEndian" }, { - "@id": "bts:Biologicalreplicate" + "@id": "bts:PhosphoproteinFlag" }, { - "@id": "bts:NotApplicable" + "@id": "bts:AgeIsObfuscated" } ], - "sms:displayName": "Replicate Type", - "sms:required": "sms:true", + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "false", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkMethylationAssayType", + "@id": "bts:Int8", "@type": "rdfs:Class", - "rdfs:comment": "Assay types normally determine genomic coverage", - "rdfs:label": "BulkMethylationAssayType", + "rdfs:comment": "TBD", + "rdfs:label": "Int8", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylation-seqLevel1" + "@id": "bts:PixelType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:Wholegenome" - }, - { - "@id": "bts:TargetedGenome" - }, - { - "@id": "bts:BeadchipArray" - } - ], - "sms:displayName": "Bulk Methylation Assay Type", - "sms:required": "sms:true", - "sms:requiresDependency": [ - { - "@id": "bts:TargetedGenome" - }, - { - "@id": "bts:BeadchipArray" - } - ], + "sms:displayName": "int8", + "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TargetedGenome", + "@id": "bts:Int16", "@type": "rdfs:Class", - "rdfs:comment": "Assay for analyzing specific mutations in a given sample", - "rdfs:label": "TargetedGenome", + "rdfs:comment": "TBD", + "rdfs:label": "Int16", "rdfs:subClassOf": [ { - "@id": "bts:BulkMethylationAssayType" + "@id": "bts:PixelType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "schema:rangeIncludes": [ - { - "@id": "bts:MeDIP" - 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"sms:displayName": "BWA with Mark Duplicates and BQSR", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Np", + "@id": "bts:STAR2-Pass", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Np", + "rdfs:label": "STAR2-Pass", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Np", + "sms:displayName": "STAR 2-Pass", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Pu", + "@id": "bts:STAR2-PassChimeric", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Pu", + "rdfs:label": "STAR2-PassChimeric", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pu", + "sms:displayName": "STAR 2-Pass Chimeric", "sms:required": "sms:false", "sms:validationRules": [] }, { - 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"@id": "http://schema.biothings.io" }, - "sms:displayName": "Lr", + "sms:displayName": "GSNAP", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Rf", + "@id": "bts:BSMAP", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Rf", + "rdfs:label": "BSMAP", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Rf", + "sms:displayName": "BSMAP", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Db", + "@id": "bts:BSmooth", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Db", + "rdfs:label": "BSmooth", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:DMCCallingTool" + }, + { + "@id": "bts:DMRCallingTool" + }, + { + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Db", + "sms:displayName": "BSmooth", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Sg", + "@id": "bts:BS-Seeker2", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Sg", + "rdfs:label": "BS-Seeker2", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Sg", + "sms:displayName": "BS-Seeker2", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bh", + "@id": "bts:BS-Seeker", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bh", + "rdfs:label": "BS-Seeker", "rdfs:subClassOf": [ { - "@id": "bts:MetalIsotopeElement" + "@id": "bts:AlignmentWorkflowType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Bh", + "sms:displayName": "BS-Seeker", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Hs", + "@id": "bts:RMAP", "@type": "rdfs:Class", "rdfs:comment": 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"@id": "bts:BiospecimenDimension1" + }, + { + "@id": "bts:BiospecimenDimension2" + }, + { + "@id": "bts:BiospecimenDimension3" + }, + { + "@id": "bts:SectionNumberinSequence" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Int32", + "@id": "bts:BloodBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Int32", + "rdfs:comment": "Blood biospecimen", + "rdfs:label": "BloodBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:Biospecimen" + }, + { + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "int32", + "sms:displayName": "Blood Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:ShippingConditionType" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Uint8", + "@id": "bts:AnalyteBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Uint8", + "rdfs:comment": "A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen", + "rdfs:label": "AnalyteBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:Biospecimen" + }, + { + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "uint8", + "sms:displayName": "Analyte Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@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:validationRules": [] }, { - "@id": "bts:Uint16", + "@id": "bts:MouthRinseBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Uint16", + "rdfs:label": "MouthRinseBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "uint16", + "sms:displayName": "Mouth Rinse Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Uint32", + "@id": "bts:StoolBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Uint32", + "rdfs:label": "StoolBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "uint32", + "sms:displayName": "Stool Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Float", + "@id": "bts:UrineBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Float", + "rdfs:comment": "Urine biospecimen", + "rdfs:label": "UrineBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:Biospecimen" + }, + { + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "float", + "sms:displayName": "Urine Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:IschemicTime" + }, + { + "@id": "bts:IschemicTemperature" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:SpecimenLaterality" + }, + { + "@id": "bts:PortionWeight" + }, + { + "@id": "bts:TotalVolume" + }, + { + "@id": "bts:TumorTissueType" + }, + { + "@id": "bts:HistologicMorphologyCode" + }, + { + "@id": "bts:PreservationMethod" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Double", + "@id": "bts:AscitesBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Double", + "rdfs:label": "AscitesBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "double", + "sms:displayName": "Ascites Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Bit", + "@id": "bts:SputumBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Bit", + "rdfs:label": "SputumBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:PixelType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "bit", + "sms:displayName": "Sputum Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mask", + "@id": "bts:FluidsBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Mask", + "rdfs:label": "FluidsBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mask", + "sms:displayName": "Fluids Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Outline", + "@id": "bts:BoneMarrowBiospecimenType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Outline", + "rdfs:comment": "Bone Marrow biospecimen", + "rdfs:label": "BoneMarrowBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:Biospecimen" + }, + { + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Outline", + "sms:displayName": "Bone Marrow Biospecimen Type", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:IschemicTime" + }, + { + "@id": "bts:IschemicTemperature" + }, + { + "@id": "bts:SiteofResectionorBiopsy" + }, + { + "@id": "bts:SpecimenLaterality" + }, + { + "@id": "bts:PortionWeight" + }, + { + "@id": "bts:TotalVolume" + }, + { + "@id": "bts:TumorTissueType" + }, + { + "@id": "bts:HistologicMorphologyCode" + }, + { + "@id": "bts:PreservationMethod" + }, + { + "@id": "bts:BiospecimenDimension1" + }, + { + "@id": "bts:BiospecimenDimension2" + }, + { + "@id": "bts:BiospecimenDimension3" + }, + { + "@id": "bts:SectionNumberinSequence" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Polygon", + "@id": "bts:CellsBiospecimenType", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Polygon", + "rdfs:label": "CellsBiospecimenType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:BiospecimenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Polygon", + "sms:displayName": "Cells Biospecimen Type", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ProbabilityMap", + "@id": "bts:FixationDuration", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ProbabilityMap", + "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": [ { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Probability Map", - "sms:required": "sms:false", + "sms:displayName": "Fixation Duration", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Point", + "@id": "bts:SlideChargeType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Point", + "rdfs:comment": "A description of the charge on the glass slide.", + "rdfs:label": "SlideChargeType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSegmentationDataType" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Point", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Uncharged" + }, + { + "@id": "bts:Charged" + }, + { + "@id": "bts:Coverslip" + }, + { + "@id": "bts:Notapplicable" + }, + { + "@id": "bts:Other" + } + ], + "sms:displayName": "Slide Charge Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Nucleus", + "@id": "bts:SectionThicknessValue", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Nucleus", + "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": [ { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nucleus", - "sms:required": "sms:false", + "sms:displayName": "Section Thickness Value", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Cytoplasm", + "@id": "bts:SectioningDaysfromIndex", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Cytoplasm", + "rdfs:comment": "Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable'", + "rdfs:label": "SectioningDaysfromIndex", "rdfs:subClassOf": [ { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cytoplasm", - "sms:required": "sms:false", - "sms:validationRules": [] + "sms:displayName": "Sectioning Days from Index", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match \\d+$|Not\\sApplicable$|unknown$" + ] }, { - "@id": "bts:Plasmamembrane", + "@id": "bts:ShippingConditionType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Plasmamembrane", + "rdfs:comment": "Text descriptor of the shipping environment of a biospecimen.", + "rdfs:label": "ShippingConditionType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "plasma membrane", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:AmbientPack" + }, + { + "@id": "bts:ColdPack" + }, + { + "@id": "bts:DryIce" + }, + { + "@id": "bts:IcePack" + }, + { + "@id": "bts:LiquidNitrogen" + }, + { + "@id": "bts:SpecimenatRoomTemperature" + }, + { + "@id": "bts:OtherShippingEnvironment" + }, + { + "@id": "bts:NotShipped" + } + ], + "sms:displayName": "Shipping Condition Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Wholecell", + "@id": "bts:SpecimenLaterality", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Wholecell", + "rdfs:comment": "For tumors in paired organs, designates the side on which the specimen was obtained.", + "rdfs:label": "SpecimenLaterality", "rdfs:subClassOf": [ { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "whole cell", - "sms:required": "sms:false", + "schema:rangeIncludes": [ + { + "@id": "bts:Bilateral" + }, + { + "@id": "bts:Left" + }, + { + "@id": "bts:Right" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:NotReported" + }, + { + "@id": "bts:NotApplicable" + } + ], + "sms:displayName": "Specimen Laterality", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:Spot", + "@id": "bts:PortionWeight", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Spot", + "rdfs:comment": "Numeric value that represents the sample portion weight, measured in milligrams.", + "rdfs:label": "PortionWeight", "rdfs:subClassOf": [ { - "@id": "bts:ImagingObjectClass" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "spot", + "sms:displayName": "Portion Weight", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Mean", + "@id": "bts:TotalVolume", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Mean", + "rdfs:comment": "Numeric value for the total amount of sample or specimen", + "rdfs:label": "TotalVolume", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSummaryStatistic" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Mean", + "sms:displayName": "Total Volume", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:TotalVolumeUnit" + } + ], "sms:validationRules": [] }, { - "@id": "bts:Median", + "@id": "bts:TumorTissueType", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Median", + "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": "TumorTissueType", "rdfs:subClassOf": [ { - "@id": "bts:ImagingSummaryStatistic" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Median", - "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:NotSpecified", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "NotSpecified", - "rdfs:subClassOf": [ + "schema:rangeIncludes": [ + { + "@id": "bts:AdditionalPrimary" + }, + { + "@id": "bts:Localrecurrence" + }, + { + "@id": "bts:Metastatic" + }, + { + "@id": "bts:Premalignant" + }, + { + "@id": "bts:Primary" + }, + { + "@id": "bts:Recurrent" + }, + { + "@id": "bts:Normal" + }, + { + "@id": "bts:Normaladjacent" + }, + { + "@id": "bts:Normaldistant" + }, + { + "@id": "bts:Posttherapy" + }, + { + "@id": "bts:Posttherapyneoadjuvant" + }, + { + "@id": "bts:Posttherapyadjuvant" + }, + { + "@id": "bts:NotOtherwiseSpecified" + }, + { + "@id": "bts:Premalignant-insitu" + }, + { + "@id": "bts:Atypia-hyperplasia" + }, { - "@id": "bts:ImagingSummaryStatistic" + "@id": "bts:Notanalyzed" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Not Specified", - "sms:required": "sms:false", + "sms:displayName": "Tumor Tissue Type", + "sms:required": "sms:true", "sms:validationRules": [] }, { - "@id": "bts:SingleCell", + "@id": "bts:BiospecimenDimension1", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SingleCell", + "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": [ { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell", + "sms:displayName": "Biospecimen Dimension 1", "sms:required": "sms:false", - "sms:validationRules": [] - }, - { - "@id": "bts:BulkWholeCell", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkWholeCell", - "rdfs:subClassOf": [ + "sms:requiresDependency": [ { - "@id": "bts:NucleicAcidSource" + "@id": "bts:DimensionsUnit" } ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Bulk Whole Cell", - "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SingleNucleus", + "@id": "bts:BiospecimenDimension2", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "SingleNucleus", + "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:subClassOf": [ { - "@id": "bts:NucleicAcidSource" + "@id": "bts:Biospecimen" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Nucleus", + "sms:displayName": "Biospecimen Dimension 2", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BulkNuclei", + "@id": "bts:BiospecimenDimension3", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "BulkNuclei", + "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": [ { - 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Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first \"Service Area\" column, adding the state in the 5th column may help direct you to the data. 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"@id": "bts:Egypt", + "@id": "bts:RelationshipGender", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Egypt", + "rdfs:comment": "The text term used to describe the gender of the patient's relative with a history of cancer.", + "rdfs:label": "RelationshipGender", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:FamilyHistory" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Egypt", + "schema:rangeIncludes": [ + { + "@id": "bts:Female" + }, + { + "@id": "bts:Male" + }, + { + "@id": "bts:Unknown" + }, + { + "@id": "bts:Unspecified" + }, + { + "@id": "bts:NotReported" + } + ], + "sms:displayName": "Relationship Gender", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ElSalvador", + "@id": "bts:RelationshipAgeatDiagnosis", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "ElSalvador", + "rdfs:comment": "The age (in years) when the patient's relative was first diagnosed.", + 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"sms:validationRules": [] }, { - "@id": "bts:Timor-Leste", + "@id": "bts:Sister-in-law", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Timor-Leste", + "rdfs:label": "Sister-in-law", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:RelationshipType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Timor-Leste", + "sms:displayName": "Sister-in-law", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Togo", + "@id": "bts:Son", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Togo", + "rdfs:label": "Son", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:RelationshipType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Togo", + "sms:displayName": "Son", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Tokelau", + "@id": "bts:Son-in-law", "@type": "rdfs:Class", "rdfs:comment": "TBD", - 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"sms:validationRules": [] }, { - "@id": "bts:VirginIslandsBritish", + "@id": "bts:Yes-SmokingExposure", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "VirginIslandsBritish", + "rdfs:comment": "Individual has been exposed to smoke; requires additional metadata", + "rdfs:label": "Yes-SmokingExposure", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:Exposure" + }, + { + "@id": "bts:SmokingExposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Virgin Islands British", + "sms:displayName": "Yes - Smoking Exposure", "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:YearsSmoked" + }, + { + "@id": "bts:PackYearsSmoked" + }, + { + "@id": "bts:CigarettesperDay" + }, + { + "@id": "bts:SmokingFrequency" + }, + { + "@id": "bts:TypeofSmokeExposure" + }, + { + "@id": "bts:TimebetweenWakingandFirstSmoke" + }, + { + "@id": "bts:TobaccoSmokingOnsetYear" + }, + { + "@id": 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"The average number of cigarettes smoked per day.", + "rdfs:label": "CigarettesperDay", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Wallis and Futuna", + "sms:displayName": "Cigarettes per Day", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WesternSahara", + "@id": "bts:SmokingFrequency", "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "WesternSahara", + "rdfs:comment": "The text term used to generally decribe how often the patient smokes.", + "rdfs:label": "SmokingFrequency", "rdfs:subClassOf": [ { - "@id": "bts:CountryofResidence" + "@id": "bts:Exposure" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Western Sahara", + "schema:rangeIncludes": [ + { + "@id": "bts:Everyday" + }, + { + "@id": "bts:Somedays" + }, + { + "@id": "bts:Unknown" + } + ], + "sms:displayName": "Smoking 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