From 1425200a6b6d5617168ba0fa10a9aa100ac262b8 Mon Sep 17 00:00:00 2001 From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com> Date: Wed, 27 Mar 2024 13:05:41 -0600 Subject: [PATCH] Update Parameter.yaml (#412) * Update Parameter.yaml * Rebuild NF.jsonld, json --------- Co-authored-by: nf-osi[bot] --- NF.jsonld | 11937 +++++++++++++++++---------------- modules/Assay/Parameter.yaml | 2 + 2 files changed, 5977 insertions(+), 5962 deletions(-) diff --git a/NF.jsonld b/NF.jsonld index 6eb471f3..c6ba7311 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -867,3753 +867,4303 @@ "sms:displayName" : "GenePerturbationTechnologyEnum", "sms:required" : "sms:false" }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:ProteinAssayTemplate" - } ], - "@id" : "bts:MassSpecAssayTemplate", + "rdfs:subClassOf" : [ ], + "@id" : "bts:institution", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "MassSpecAssayTemplate", - "rdfs:comment" : "Template for raw mass spec-based proteomics data.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "schema:rangeIncludes" : [ { + "@id" : "bts:EutropicsPharmaceuticals" }, { - "@id" : "bts:Filename" + "@id" : "bts:CincinnatiChildren'sHospitalMedicalCenter" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:MemorialSloaneKetteringCancerCenter" }, { - "@id" : "bts:resourceType" + "@id" : "bts:Dana-FarberCancerInstitute" }, { - "@id" : "bts:dataType" + "@id" : "bts:MassachusettsGeneralHospital" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:UniversityofTennessee,HealthScienceCenter" }, { - "@id" : "bts:assay" + "@id" : "bts:DartmouthCollege" }, { - "@id" : "bts:individualID" + "@id" : "bts:TexasA&MUniversity" }, { - "@id" : "bts:species" + "@id" : "bts:ColdSpringHarborLaboratory" }, { - "@id" : "bts:sex" + "@id" : "bts:UniversityofAlaska,Fairbanks" }, { - "@id" : "bts:age" + "@id" : "bts:UniversityofTexas,Arlington" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:NorthwesternUniversity" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:IcahnSchoolofMedicineatMountSinai" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:UniversityofCentralFlorida" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:UniversityofMissouri,KansasCity" }, { - "@id" : "bts:tumorType" + "@id" : "bts:UtahStateUniversity" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:UniversityofNewOrleans" }, { - "@id" : "bts:organ" + "@id" : "bts:SyracuseUniversity" }, { - "@id" : "bts:comments" + "@id" : "bts:RiceUniversity" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:WashingtonStateUniversity" }, { - "@id" : "bts:specimenID" + "@id" : "bts:UniversityofConnecticut" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:NewJerseyInstituteofTechnology" }, { - "@id" : "bts:platform" + "@id" : "bts:StateUniversityofNewYorkPolytechnicInstitute" }, { - "@id" : "bts:proteinExtractSource" + "@id" : "bts:MarshallUniversity" }, { - "@id" : "bts:dataCollectionMode" - } ], - "sms:displayName" : "MassSpecAssayTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:BiologicalAssayDataTemplate" - } ], - "@id" : "bts:ClinicalAssayTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ClinicalAssayTemplate", - "rdfs:comment" : "General template for typically tabular **individual-level** data. This can include repeated measures and a drug treatment context.\n", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:IndianaUniversity" }, { - "@id" : "bts:Filename" + "@id" : "bts:IndianaUniversity,Bloomington" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:Institutd'InvestigacióenCiènciesdelaSalutGermansTriasiPujol" }, { - "@id" : "bts:resourceType" + "@id" : "bts:Institutd'InvestigacióBiomédicadeBellvitge" }, { - "@id" : "bts:dataType" + "@id" : "bts:UniversityofMassachusetts,Lowell" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:NorthernIllinoisUniversity" }, { - "@id" : "bts:assay" + "@id" : "bts:NortheasternUniversity" }, { - "@id" : "bts:individualID" + "@id" : "bts:UniversityofMississippi" }, { - "@id" : "bts:species" + "@id" : "bts:UniversityofNorthCarolina,ChapelHill" }, { - "@id" : "bts:sex" + "@id" : "bts:ArizonaStateUniversity" }, { - "@id" : "bts:age" + "@id" : "bts:UniversityofBaltimore" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:CityofHope" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:TuskegeeUniversity" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:UniversityofMinnesota,TwinCities" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:UniversityofSouthernCalifornia" }, { - "@id" : "bts:tumorType" + "@id" : "bts:GeorgeWashingtonUniversity" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:LongIslandUniversity" }, { - "@id" : "bts:organ" + "@id" : "bts:PurdueUniversity,WestLafayette" }, { - "@id" : "bts:comments" + "@id" : "bts:UniversityofPennsylvania" }, { - "@id" : "bts:experimentalFactor" + "@id" : "bts:UniversityofSouthernMississippi" }, { - "@id" : "bts:experimentalCondition" + "@id" : "bts:UniversityofNevada,Reno" }, { - "@id" : "bts:timepointUnit" + "@id" : "bts:CaliforniaStateUniversity,LongBeach" }, { - "@id" : "bts:compoundName" + "@id" : "bts:L’InsermdansParisetl’Île-de-FranceCentreNord" }, { - "@id" : "bts:compoundDose" + "@id" : "bts:IowaStateUniversity" }, { - "@id" : "bts:compoundDoseUnit" - } ], - "sms:displayName" : "ClinicalAssayTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:ScSequencingAssayTemplate" - } ], - "@id" : "bts:ScRNASeqTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ScRNASeqTemplate", - "rdfs:comment" : "Template for describing raw data from single-cell RNA-seq.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:VanAndelResearchInstitute" }, { - "@id" : "bts:Filename" + "@id" : "bts:UniversityofCalifornia,Irvine" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:UniversityofCambridge" }, { - "@id" : "bts:resourceType" + "@id" : "bts:UniversityofNorthCarolina,Greensboro" }, { - "@id" : "bts:dataType" + "@id" : "bts:UniversityofToledo" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:UniversityofLouisville" }, { - "@id" : "bts:assay" + "@id" : "bts:UniversityofPlymouth" }, { - "@id" : "bts:individualID" + "@id" : "bts:UniversityofTurku" }, { - "@id" : "bts:species" + "@id" : "bts:HarvardUniversity" }, { - "@id" : "bts:sex" + "@id" : "bts:MichiganStateUniversity" }, { - "@id" : "bts:age" + "@id" : "bts:UniversityofWisconsin-Madison" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:TexasStateUniversity" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:UniversityofMassachusetts,Dartmouth" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:AlliantInternationalUniversity" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:UniversityofAlabama,Birmingham" }, { - "@id" : "bts:tumorType" + "@id" : "bts:CUNY,QueensCollege" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:StateUniversityofNewYork,Albany" }, { - "@id" : "bts:organ" + "@id" : "bts:MichiganTechnologicalUniversity" }, { - "@id" : "bts:comments" + "@id" : "bts:WesternMichiganUniversity" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:StevensInstituteofTechnology" }, { - "@id" : "bts:specimenID" + "@id" : "bts:MissouriUniversityofScienceandTechnology" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:UniversityofLouisianaatLafayette" }, { - "@id" : "bts:platform" + "@id" : "bts:BowlingGreenStateUniversity" }, { - "@id" : "bts:nucleicAcidSource" + "@id" : "bts:ColumbiaU.intheCityofNewYork" }, { - "@id" : "bts:specimenPreparationMethod" + "@id" : "bts:OhioStateUniversity" }, { - "@id" : "bts:cellType" + "@id" : "bts:CarnegieMellonUniversity" }, { - "@id" : "bts:isCellLine" + "@id" : "bts:KentStateUniversity" }, { - "@id" : "bts:cellID" + "@id" : "bts:WashingtonUniversityinSt.Louis" }, { - "@id" : "bts:dissociationMethod" + "@id" : "bts:UniversityofWashington,Seattle" }, { - "@id" : "bts:runType" + "@id" : "bts:WayneStateUniversity" }, { - "@id" : "bts:libraryStrand" + "@id" : "bts:MemorialSloanKetteringCancerCenter" }, { - "@id" : "bts:libraryPrep" + "@id" : "bts:OklahomaStateUniversity,Stillwater" }, { - "@id" : "bts:libraryPreparationMethod" + "@id" : "bts:NorthCarolinaCentralUniversity" }, { - "@id" : "bts:readPair" + "@id" : "bts:JohnsHopkinsUniversity" }, { - "@id" : "bts:readLength" + "@id" : "bts:UniversityofArkansas,Fayetteville" }, { - "@id" : "bts:readDepth" + "@id" : "bts:AuburnUniversity,Auburn" }, { - "@id" : "bts:targetDepth" + "@id" : "bts:UniversityofNevada,LasVegas" }, { - "@id" : "bts:batchID" + "@id" : "bts:UniversityofMassachusetts,Boston" }, { - "@id" : "bts:auxiliaryAsset" - } ], - "sms:displayName" : "ScRNASeqTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:BiologicalAssayDataTemplate" - } ], - "@id" : "bts:ProteinAssayTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "ProteinAssayTemplate", - "rdfs:comment" : "Abstract template for data from some assay of protein structure and function. Data should be instantiated with more specific template.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:ScrippsResearchInstitute" }, { - "@id" : "bts:Filename" + "@id" : "bts:SanFranciscoStateUniversity" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:CaliforniaPolytechnicStateUniversity,SanLuisObispo" }, { - "@id" : "bts:resourceType" + "@id" : "bts:TempleUniversity" }, { - "@id" : "bts:dataType" + "@id" : "bts:UniversityHealthNetwork" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:UniversityofGlasgow" }, { - "@id" : "bts:assay" + "@id" : "bts:UniversityofNewHampshire" }, { - "@id" : "bts:individualID" + "@id" : "bts:UniversityofMiami" }, { - "@id" : "bts:species" + "@id" : "bts:UniversityofTexasRioGrandeValley" }, { - "@id" : "bts:sex" + "@id" : "bts:UniversityofTennessee,Knoxville" }, { - "@id" : "bts:age" + "@id" : "bts:UniversityofAlabama,Huntsville" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:CaliforniaStateUniversity,Northridge" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:StateUniversityofNewYork,Buffalo" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:SeattleChildren's" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:PrairieViewA&MUniversity" }, { - "@id" : "bts:tumorType" + "@id" : "bts:TennesseeStateUniversity" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:UniversityofNorthCarolina,Charlotte" }, { - "@id" : "bts:organ" + "@id" : "bts:MedicalUniversityofSouthCarolina" }, { - "@id" : "bts:comments" + "@id" : "bts:NewYorkMedicalCollege" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:RushUniversity" }, { - "@id" : "bts:specimenID" + "@id" : "bts:UniversityofTexas,SanAntonio" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:UniversityofOklahoma" }, { - "@id" : "bts:platform" + "@id" : "bts:VirginiaCommonwealthUniversity" }, { - "@id" : "bts:proteinExtractSource" - } ], - "sms:displayName" : "ProteinAssayTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:BiologicalAssayDataTemplate" - } ], - "@id" : "bts:GeneralMeasureDataTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "GeneralMeasureDataTemplate", - "rdfs:comment" : "General template for data in tabular form that aggregates tissue-level or cellular-level data.\n", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:UniversityofHouston" }, { - "@id" : "bts:Filename" + "@id" : "bts:GeorgiaInstituteofTechnology" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:FordhamUniversity" }, { - "@id" : "bts:resourceType" + "@id" : "bts:UniversityofMassachusetts,Amherst" }, { - "@id" : "bts:dataType" + "@id" : "bts:SaintLouisUniversity" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:RensselaerPolytechnicInstitute" }, { - "@id" : "bts:assay" + "@id" : "bts:JAX" }, { - "@id" : "bts:individualID" + "@id" : "bts:UniversityofNewMexico" }, { - "@id" : "bts:species" + "@id" : "bts:UniversityofMissouri,SaintLouis" }, { - "@id" : "bts:sex" + "@id" : "bts:VirginiaPolytechnicInstituteandStateUniversity" }, { - "@id" : "bts:age" + "@id" : "bts:UniversityofMinnesota,Duluth" }, { - "@id" : "bts:ageUnit" + "@id" : "bts:FloridaInstituteofTechnology" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:SUNY,DownstateHealthSciencesUniversity" }, { - "@id" : "bts:nf1Genotype" + "@id" : "bts:UniversityofKansas" }, { - "@id" : "bts:nf2Genotype" + "@id" : "bts:UniversityofRhodeIsland" }, { - "@id" : "bts:tumorType" + "@id" : "bts:CentralMichiganUniversity" }, { - "@id" : "bts:modelSystemName" + "@id" : "bts:UniversityofRochester" }, { - "@id" : "bts:organ" + "@id" : "bts:UniversityofCalifornia,Davis" }, { - "@id" : "bts:comments" + "@id" : "bts:UniversityofMontana,Missoula" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:KansasStateUniversity" }, { - "@id" : "bts:specimenID" + "@id" : "bts:UniversityofCalifornia,Riverside" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:LouisianaTechUniversity" }, { - "@id" : "bts:experimentalFactor" + "@id" : "bts:UniversityofFlorida" }, { - "@id" : "bts:experimentalCondition" + "@id" : "bts:BostonCollege" }, { - "@id" : "bts:experimentalTimepoint" + "@id" : "bts:ChapmanUniversity" }, { - "@id" : "bts:timepointUnit" + "@id" : "bts:LouisianaStateUniversity,HealthSciencesCenter,Shreveport" }, { - "@id" : "bts:compoundName" + "@id" : "bts:UniversityofNorthCarolina,Wilmington" }, { - "@id" : "bts:compoundDose" + "@id" : "bts:MiamiUniversity" }, { - "@id" : "bts:compoundDoseUnit" + "@id" : "bts:EmoryUniversity" }, { - "@id" : "bts:genePerturbed" + "@id" : "bts:PortlandStateUniversity" }, { - "@id" : "bts:genePerturbationType" + "@id" : "bts:CaliforniaInstituteofTechnology" }, { - "@id" : "bts:genePerturbationTechnology" - } ], - "sms:displayName" : "GeneralMeasureDataTemplate" - }, { - "rdfs:subClassOf" : [ { - "@id" : "bts:NonBiologicalAssayDataTemplate" - } ], - "@id" : "bts:MaterialScienceAssayTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "MaterialScienceAssayTemplate", - "rdfs:comment" : "General template for describing data for a materials science assay.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:Component" + "@id" : "bts:UniversityofGeorgia" }, { - "@id" : "bts:Filename" + "@id" : "bts:DelawareStateUniversity" }, { - "@id" : "bts:fileFormat" + "@id" : "bts:UniversityofTexasHealthScienceCenter,SanAntonio" }, { - "@id" : "bts:resourceType" + "@id" : "bts:GeorgeMasonUniversity" }, { - "@id" : "bts:dataType" + "@id" : "bts:BoiseStateUniversity" }, { - "@id" : "bts:dataSubtype" + "@id" : "bts:UniversityofSouthFlorida,SaintPetersburg" }, { - "@id" : "bts:assay" + "@id" : "bts:UniversityofNorthTexas,Denton" }, { - "@id" : "bts:platform" + "@id" : "bts:DuquesneUniversity" }, { - "@id" : "bts:specimenID" + "@id" : "bts:OregonHealthandScienceUniversity" }, { - "@id" : "bts:materialType" + "@id" : "bts:OhioUniversity" }, { - "@id" : "bts:concentrationMaterial" + "@id" : "bts:VanderbiltUniversity" }, { - "@id" : "bts:concentrationMaterialUnit" + "@id" : "bts:SouthernIllinoisUniversity,Carbondale" }, { - "@id" : "bts:concentrationNaCl" + "@id" : "bts:UniversityofPittsburgh,Pittsburgh" }, { - 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}, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:Template", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "Template", - "rdfs:comment" : "A collection of fields representing some entity.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ ], - "sms:displayName" : "Template" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:BiospecimenTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "BiospecimenTemplate", - "rdfs:comment" : "Specimen-level data, whether from human or animal.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:individualID" + "@id" : "bts:SouthernMethodistUniversity" }, { - "@id" : "bts:parentSpecimenID" + "@id" : "bts:ColoradoStateUniversity,FortCollins" }, { - "@id" : "bts:specimenID" + "@id" : "bts:UniversityofChicago" }, { - "@id" : "bts:aliquotID" + "@id" : "bts:TulaneUniversity" }, { - "@id" : "bts:tumorType" + "@id" : "bts:IdahoStateUniversity" }, { - "@id" : "bts:bodySite" + "@id" : "bts:UniversityofAlabama,Tuscaloosa" }, { - "@id" : "bts:experimentalCondition" - } ], - "sms:displayName" : "BiospecimenTemplate" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:PartialTemplate", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "PartialTemplate", - "rdfs:comment" : "A template for collecting a subset of contextual data; not intended to be a standalone template but rather a subdocument.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ ], - "sms:displayName" : "PartialTemplate" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:PortalStudy", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "sms:requiresComponent" : null, - "rdfs:label" : "PortalStudy", - 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"@id" : "bts:averageReadLength" + "@id" : "bts:absentbyimaging" }, { - "@id" : "bts:averageBaseQuality" + "@id" : "bts:single" }, { - "@id" : "bts:pairsOnDifferentChr" + "@id" : "bts:multiple" }, { - "@id" : "bts:readsDuplicatedPercent" + "@id" : "bts:unknown" + } ], + "rdfs:label" : "spinalSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Spinal schwannoma.", + "@type" : "rdfs:Class", + "sms:displayName" : "spinalSchwannoma" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:accessType", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:PublicAccess" }, { - "@id" : "bts:readsMappedPercent" + "@id" : "bts:OpenAccess" }, { - "@id" : "bts:meanCoverage" + "@id" : "bts:ControlledAccess" + } ], + "rdfs:label" : "accessType", + "rdfs:comment" : "Indicates access type / possible procedures needed for access to the resource.", + "@type" : "rdfs:Class", + "sms:displayName" : "accessType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:spinalNeurofibromas", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:notimaged" }, { - "@id" : "bts:proportionCoverage10x" + "@id" : "bts:absent" }, { - "@id" : "bts:proportionCoverage30x" + "@id" : "bts:levels1-3" }, { - "@id" : "bts:readDepth" + "@id" : "bts:alllevels" + } ], + "rdfs:label" : "spinalNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Spinal neurofibromas.", + "@type" : "rdfs:Class", + "sms:displayName" : "spinalNeurofibromas" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:opticGlioma", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" }, { - "@id" : "bts:totalReads" + "@id" : "bts:present-asymptomatic" }, { - "@id" : "bts:workflow" + "@id" : "bts:present-symptomatic-nottreated" }, { - "@id" : "bts:workflowLink" + "@id" : "bts:present-symptomatic-treated" }, { - "@id" : "bts:auxiliaryAsset" + "@id" : "bts:unknown" } ], - "sms:displayName" : "ProcessedAlignedReadsTemplate" + "rdfs:label" : "opticGlioma", + "rdfs:comment" : "Characterization of the manifestation of Optic glioma.", + "@type" : "rdfs:Class", + "sms:displayName" : "opticGlioma" + }, { + "@id" : "bts:createdOn", + "@type" : "rdfs:Class", + "rdfs:comment" : "Refers to when the resource was created.", + "rdfs:label" : "createdOn", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "createdOn", + "sms:required" : "sms:false" }, { + "@id" : "bts:protocolPurpose", + "@type" : "rdfs:Class", + "rdfs:comment" : "Brief description of the protocol purpose.", + "rdfs:label" : "protocolPurpose", "rdfs:subClassOf" : [ ], - "@id" : "bts:HumanCohortTemplate", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "protocolPurpose", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:grantDOI", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:requiresComponent" : "", - "rdfs:label" : "HumanCohortTemplate", - "rdfs:comment" : "Data of biosamples from human patients. Adapted from Table 2 of http://nrs.harvard.edu/urn-3:HUL.InstRepos:32725809. This template should be used when biosamples are from NF patients to provides a more valuable characterization and make additional gene-phenotype insights possible.\n", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "grantDOI", + "rdfs:comment" : "Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity.", "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:individualID" - }, { - "@id" : "bts:sex" - }, { - "@id" : "bts:age" - }, { - "@id" : "bts:ageUnit" + "sms:displayName" : "grantDOI" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:breastCancer", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" }, { - "@id" : "bts:diagnosis" + "@id" : "bts:present" }, { - "@id" : "bts:diagnosisAgeGroup" + "@id" : "bts:unknown" + } ], + "rdfs:label" : "breastCancer", + "rdfs:comment" : "Characterization of the manifestation of Breast cancer.", + "@type" : "rdfs:Class", + "sms:displayName" : "breastCancer" + }, { + "@id" : "bts:reporterSubstance", + "@type" : "rdfs:Class", + "rdfs:comment" : "A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.", + "rdfs:label" : "reporterSubstance", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "reporterSubstance", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:slideVersion", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:V1" }, { - "@id" : "bts:inheritance" + "@id" : "bts:V2" }, { - "@id" : "bts:mosaicism" + "@id" : "bts:V3" }, { - "@id" : "bts:nf1Genotype" - }, { - "@id" : "bts:nf2Genotype" - }, { - "@id" : "bts:germlineMutationIndicator" - }, { - "@id" : "bts:species" - }, { - "@id" : "bts:vitalStatus" - }, { - "@id" : "bts:WHOPerformanceStatus" - }, { - "@id" : "bts:painStatus" - }, { - "@id" : "bts:tumorTreatmentStatus" - }, { - "@id" : "bts:cafeaulaitMacules" - }, { - "@id" : "bts:skinFoldFreckling" - }, { - "@id" : "bts:IrisLischNodules" - }, { - "@id" : "bts:dermalNeurofibromas" - }, { - "@id" : "bts:subcutaneousNodularNeurofibromas" - }, { - "@id" : "bts:diffuseDermalNeurofibromas" + "@id" : "bts:V4" + } ], + "rdfs:label" : "slideVersion", + "rdfs:comment" : "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "@type" : "rdfs:Class", + "sms:displayName" : "slideVersion" + }, { + "@id" : "bts:reporterGene", + "@type" : "rdfs:Class", + "rdfs:comment" : "A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.", + "rdfs:label" : "reporterGene", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "reporterGene", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:nf1Genotype", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:-/-" }, { - "@id" : "bts:spinalNeurofibromas" + "@id" : "bts:+/-" }, { - "@id" : "bts:plexiformNeurofibromas" + "@id" : "bts:+/+" }, { - "@id" : "bts:opticGlioma" + "@id" : "bts:Unknown" }, { - "@id" : "bts:heartDefect" + "@id" : "bts:Unknown" + } ], + "rdfs:label" : "nf1Genotype", + "rdfs:comment" : "Genotype of NF1 gene in the biospecimen from which the data were derived, if known.", + "@type" : "rdfs:Class", + "sms:displayName" : "nf1Genotype" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:diagnosis", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Neurofibromatosistype1" }, { - "@id" : "bts:vascularDisease" + "@id" : "bts:Schwannomatosis" }, { - "@id" : "bts:pubertyOnset" + "@id" : "bts:NF2-relatedschwannomatosis" }, { - "@id" : "bts:stature" + "@id" : "bts:SMARCB1-relatedschwannomatosis" }, { - "@id" : "bts:peripheralNeuropathy" + "@id" : "bts:LZTR1-relatedschwannomatosis" }, { - "@id" : "bts:aqueductalStenosis" + "@id" : "bts:22q-relatedschwannomatosis" }, { - "@id" : "bts:longBoneDysplasia" + "@id" : "bts:Schwannomatosis-NOS" }, { - "@id" : "bts:sphenoidDysplasia" + "@id" : "bts:Schwannomatosis-NEC" }, { - "@id" : "bts:scoliosis" + "@id" : "bts:SporadicSchwannoma" + } ], + "rdfs:label" : "diagnosis", + "rdfs:comment" : "Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.", + "@type" : "rdfs:Class", + "sms:displayName" : "diagnosis" + }, { + "@id" : "bts:targetDepth", + "@type" : "rdfs:Class", + "rdfs:comment" : "The targeted read depth prior to sequencing.", + "rdfs:label" : "targetDepth", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "targetDepth", + "sms:required" : "sms:false" + }, { + "@id" : "bts:accessRequirements", + "@type" : "rdfs:Class", + "rdfs:comment" : "Statement describing access requirements for an entity.", + "rdfs:label" : "accessRequirements", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "accessRequirements", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:creator", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "creator", + "rdfs:comment" : "An entity responsible for making the resource.", + "@type" : "rdfs:Class", + "sms:displayName" : "creator" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:age", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "age", + "rdfs:comment" : "A numeric value representing age of the individual. Use with `ageUnit`.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:ageUnit" + } ], + "sms:displayName" : "age" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:isCellLine", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:Yes" }, { - "@id" : "bts:intellectualDisability" + "@id" : "bts:No" + } ], + "rdfs:label" : "isCellLine", + "rdfs:comment" : "Whether or not sample source is a cell line (Yes; No)", + "@type" : "rdfs:Class", + "sms:displayName" : "isCellLine" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:libraryPreparationMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:10x" }, { - "@id" : "bts:learningDisability" + "@id" : "bts:CEL-seq" }, { - "@id" : "bts:attentionDeficitDisorder" + "@id" : "bts:Drop-Seq" }, { - "@id" : "bts:pheochromocytoma" + "@id" : "bts:GTAC@WUSTLin-houseprep" }, { - 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"@id" : "bts:UniversityofIllinois,Chicago" + "@id" : "bts:SC4[Mouseschwannoma]" }, { - "@id" : "bts:IndianaUniversity-PurdueUniversityatIndianapolis" + "@id" : "bts:cNF18.1a" }, { - "@id" : "bts:UniversityofMemphis" + "@id" : "bts:Nf1Arg681*/Arg681*ES" }, { - "@id" : "bts:PacificNorthwestNationalLaboratory" + "@id" : "bts:GM11601" }, { - "@id" : "bts:NorthDakotaStateUniversity" + "@id" : "bts:HEK293NF1-/-withR2550XmNf1cDNA" }, { - "@id" : "bts:NCICenterforCancerResearch" + "@id" : "bts:JH-2-103-CL" }, { - "@id" : "bts:UniversityofTexasHealthScienceCenter,Houston" + "@id" : "bts:HS-Sch-2" }, { - "@id" : "bts:NovaSoutheasternUniversity" + "@id" : "bts:hTERTNF1ipn02.32λ" }, { - "@id" : "bts:EastTennesseeStateUniversity" + "@id" : "bts:ELK-TADLuciferaseReporterHEK293Stable" }, { - "@id" : "bts:CUNY,CityCollege" + "@id" : "bts:6PNF_SiPSrv_PM_2" }, { - "@id" : "bts:PennsylvaniaStateUniversity,UniversityParkandHersheyMedicalCenter" + "@id" : "bts:hTERTNF1ipNF03.3" }, { - "@id" : "bts:StonyBrookUniversity" + "@id" : "bts:JH-2-079-CL" }, { - "@id" : "bts:ClarksonUniversity" + "@id" : "bts:hTERTNF1ipNF04.4" }, { - "@id" : "bts:IllinoisInstituteofTechnology" + "@id" : "bts:Nf1Arg681*/Arg681*MEFs" }, { - "@id" : "bts:UniversityofPuertoRico,RioPiedras" + "@id" : "bts:Nf1Arg681*/+ES" }, { - "@id" : "bts:MississippiStateUniversity" + "@id" : "bts:cNF97.2a" }, { - "@id" : "bts:CornellUniversity" + "@id" : "bts:Schwanncelli28cNFNF1-/-(#14)" }, { - "@id" : "bts:UniversityofPuertoRico,Mayaguez" + "@id" : "bts:hTERTNF1ipNF00.6" }, { - "@id" : "bts:UniversityofMissouri,Columbia" + "@id" : "bts:NCC-MPNST3-X2-C1" }, { - "@id" : "bts:William&Mary" + "@id" : "bts:JHU2-002-PDX" }, { - "@id" : "bts:UniversityofIdaho" + "@id" : "bts:hTERTNF1ipNF95.11bC" }, { - "@id" : "bts:Children'sHospitalofPhiladelphia" + "@id" : "bts:5PNF_TDiPSsv_MM_4" }, { - "@id" : "bts:UniversityofCincinnati" + "@id" : "bts:hTERTNF1ipn06.2A" }, { - "@id" : "bts:UniversityofIowa" + "@id" : "bts:hTERTSCipn02.8" }, { - "@id" : "bts:UniversityCollegeofLondon" + "@id" : "bts:SZ-NF2" }, { - "@id" : "bts:LangstonUniversity" + "@id" : "bts:sMPNST" }, { - "@id" : "bts:UniversityofWestFlorida" + "@id" : "bts:B6;129S2-Trp53tm1TyjNf1tm1Tyj/J" }, { - "@id" : "bts:HowardUniversity" + "@id" : "bts:Prss56Cre;R26mT" }, { - "@id" : "bts:AugustaUniversity" + "@id" : "bts:B6.129S1-Nf1tm1Cbr/J" }, { - "@id" : "bts:UniversityofCalifornia,SanDiego" + "@id" : "bts:Nf1-OPG" }, { - "@id" : "bts:UniversityofCalifornia,Merced" + "@id" : "bts:C57BL/6J" }, { - "@id" : "bts:UniversityofNebraska,MedicalCenter" + "@id" : "bts:NRG" }, { - "@id" : "bts:WichitaStateUniversity" + "@id" : "bts:Nf1-OPG-Arg816" }, { - "@id" : "bts:UniversityofCalifornia,SanFrancisco" + "@id" : "bts:NODscidgamma" }, { - "@id" : "bts:SouthDakotaStateUniversity" + "@id" : "bts:B6.129S2-Nf1tm1Tyj/J" }, { - "@id" : "bts:UniversityofWyoming" + "@id" : "bts:B6;129-Trp53tm1TyjNf1tm1TyjSuz12Gt(Betageo)1Khe/KcichJ" }, { - "@id" : "bts:UniformedServicesUniversityoftheHealthSciences" + "@id" : "bts:B6.129(Cg)-Nf1tm1Par/J" }, { - "@id" : "bts:SouthernIllinoisUniversity,Edwardsville" + "@id" : "bts:GFAP-Cre;Nf1-G848R/Flox" }, { - "@id" : "bts:UniversityofArizona" + "@id" : "bts:GFAP-Cre;Nf1-R681X/Flox" }, { - "@id" : "bts:AmericanUniversity" + "@id" : "bts:GFAP-Cre;Nf1-C383X/Flox" }, { - "@id" : "bts:UniversityofIllinois,Urbana-Champaign" + "@id" : "bts:Nf1-C848R/Flox" }, { - "@id" : "bts:UniversityofNebraska,Omaha" + "@id" : "bts:Nf1-R681X/Flox" }, { - "@id" : "bts:MorehouseSchoolofMedicine" + "@id" : "bts:Nf1-C383X/Flox" }, { - "@id" : "bts:VillanovaUniversity" + "@id" : "bts:Nf1flox/flox" } ], - "rdfs:label" : "institution", - "rdfs:comment" : "Link to affiliated institution.", + "rdfs:label" : "modelSystemName", + "rdfs:comment" : "A group of presumed common ancestry with clear-cut physiological but usually not morphological distinctions such as an animal model or cell line. EXAMPLE(S): HEK293 (cell line), Minnesota5 (swine strain), DXL (poultry strain), RB51 (vaccine strain of Brucella abortus)", "@type" : "rdfs:Class", - "sms:displayName" : "institution" + "sms:displayName" : "modelSystemName" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:proportionCoverage30x", + "@id" : "bts:dermalNeurofibromas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "proportionCoverage30x", - "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", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:scattered" + }, { + "@id" : "bts:dense" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "dermalNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Dermal neurofibromas.", "@type" : "rdfs:Class", - "sms:displayName" : "proportionCoverage30x" + "sms:displayName" : "dermalNeurofibromas" }, { + "@id" : "bts:plateWell", + "@type" : "rdfs:Class", + "rdfs:comment" : "User-specified identifier for the specific well of the plate used to prepare the sample for analysis.", + "rdfs:label" : "plateWell", "rdfs:subClassOf" : [ ], - "@id" : "bts:description", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "description", - "rdfs:comment" : "Text describing a resource.", - "@type" : "rdfs:Class", - "sms:displayName" : "description" + "sms:displayName" : "plateWell", + "sms:required" : "sms:false" }, { - "@id" : "bts:compoundDoseUnit", + "@id" : "bts:chipID", "@type" : "rdfs:Class", - "rdfs:comment" : "A unit associated with the value(s) in compoundDose.", - "rdfs:label" : "compoundDoseUnit", + "rdfs:comment" : "User-specified identifier for the chip used to perform the methylation microarray.", + "rdfs:label" : "chipID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "compoundDoseUnit", + "sms:displayName" : "chipID", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:isStranded", + "@id" : "bts:proteinExtractSource", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Yes" + "@id" : "bts:celllysate" }, { - "@id" : "bts:No" + "@id" : "bts:cytoplasm" + }, { + "@id" : "bts:mitochondria" + }, { + "@id" : "bts:nuclearextract" } ], - "rdfs:label" : "isStranded", - "rdfs:comment" : "Whether or not the library is stranded (Yes; No)", + "rdfs:label" : "proteinExtractSource", + "rdfs:comment" : "Source of the extracted protein used in the experiment", "@type" : "rdfs:Class", - "sms:displayName" : "isStranded" + "sms:displayName" : "proteinExtractSource" }, { - "@id" : "bts:genomicReferenceLink", - "@type" : "rdfs:Class", - "rdfs:comment" : "Link to genome reference data file used for alignment in processing workflow", - "rdfs:label" : "genomicReferenceLink", "rdfs:subClassOf" : [ ], + "@id" : "bts:dataCollectionMode", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "genomicReferenceLink", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:DDA" + }, { + "@id" : "bts:DIA" + }, { + "@id" : "bts:Other" + } ], + "rdfs:label" : "dataCollectionMode", + "rdfs:comment" : "Mode of data collection in tandem MS assays. Either DDA (data-dependent acquisition) or DIA (data-independent) acquisition.", + "@type" : "rdfs:Class", + "sms:displayName" : "dataCollectionMode" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:programmingLanguage", + "@id" : "bts:bodySite", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Python" + "@id" : "bts:axilla" }, { - "@id" : "bts:R" + "@id" : "bts:groin" }, { - "@id" : "bts:MATLAB" + "@id" : "bts:leg" }, { - "@id" : "bts:Java" + "@id" : "bts:thoracicspine" }, { - "@id" : "bts:C" + "@id" : "bts:forearm" }, { - "@id" : "bts:C++" + "@id" : "bts:acetabulum" }, { - "@id" : "bts:C#" + "@id" : "bts:muscle" }, { - "@id" : "bts:Javascript" + "@id" : "bts:finger" }, { - "@id" : "bts:bash" - } ], - "rdfs:label" : "programmingLanguage", - "rdfs:comment" : "A computer programming language", - "@type" : "rdfs:Class", - "sms:displayName" : "programmingLanguage" - }, { - "@id" : "bts:slideID", - "@type" : "rdfs:Class", - "rdfs:comment" : "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.\n", - "rdfs:label" : "slideID", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "slideID", - "sms:required" : "sms:false" - }, { - "@id" : "bts:sourceName", + "@id" : "bts:iliacspine" + }, { + "@id" : "bts:head" + }, { + "@id" : "bts:neck" + }, { + "@id" : "bts:shoulder" + }, { + "@id" : "bts:back" + }, { + "@id" : "bts:spine" + }, { + "@id" : "bts:scalp" + }, { + "@id" : "bts:scapula" + }, { + "@id" : "bts:pelvis" + }, { + "@id" : "bts:dorsolateralprefrontalcortex" + }, { + "@id" : "bts:occcipitallobe" + } ], + "rdfs:label" : "bodySite", + "rdfs:comment" : "Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts.", "@type" : "rdfs:Class", - "rdfs:comment" : "Intended for non-biological samples, tf the sample is a nanoparticle sample or some chemical substance not derived from a biological material, the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.\n", - "rdfs:label" : "sourceName", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "sourceName", - "sms:required" : "sms:false" + "sms:displayName" : "bodySite" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:mosaicism", + "@id" : "bts:longBoneDysplasia", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:mosaic" + "@id" : "bts:absent" }, { - "@id" : "bts:notmosaic" + "@id" : "bts:present" }, { "@id" : "bts:unknown" } ], - "rdfs:label" : "mosaicism", - "rdfs:comment" : "Whether individual is mosaic.", + "rdfs:label" : "longBoneDysplasia", + "rdfs:comment" : "Characterization of the manifestation of Long bone dysplasia.", "@type" : "rdfs:Class", - "sms:displayName" : "mosaicism" + "sms:displayName" : "longBoneDysplasia" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:readPairOrientation", + "@id" : "bts:libraryPrep", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:fr-firststrand" + "@id" : "bts:lncRNAenrichment" }, { - "@id" : "bts:inward" + "@id" : "bts:miRNAenrichment" }, { - "@id" : "bts:matching" + "@id" : "bts:polyAselection" }, { - "@id" : "bts:outward" + "@id" : "bts:rRNAdepletion" } ], - "rdfs:label" : "readPairOrientation", - "rdfs:comment" : "The relative orientation of the reads in a paired-end protocol", - "@type" : "rdfs:Class", - "sms:displayName" : "readPairOrientation" - }, { - "@id" : "bts:fileSize", + "rdfs:label" : "libraryPrep", + "rdfs:comment" : "The general strategy by which the library was prepared", "@type" : "rdfs:Class", - "rdfs:comment" : "Size of file in bytes.", - "rdfs:label" : "fileSize", - "rdfs:subClassOf" : [ ], - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:displayName" : "fileSize", - "sms:required" : "sms:false" + "sms:displayName" : "libraryPrep" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:dermalSchwannoma", + "@id" : "bts:tumorType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", + "sms:required" : "sms:true", "schema:rangeIncludes" : [ { - "@id" : "bts:absent" + "@id" : "bts:DiffuseAstrocytoma" }, { - "@id" : "bts:present" + "@id" : "bts:SubcutaneousNeurofibroma" }, { - "@id" : "bts:unknown" + "@id" : "bts:PilomyxoidAstrocytoma" + }, { + "@id" : "bts:JuvenileMyelomonocyticLeukemia" + }, { + "@id" : "bts:AnaplasticAstrocytoma" + }, { + "@id" : "bts:MalignantPeripheralNerveSheathTumor" + }, { + "@id" : "bts:LocalizedNeurofibroma" + }, { + "@id" : "bts:CutaneousNeurofibroma" + }, { + "@id" : "bts:ColorectalAdenocarcinoma" + }, { + "@id" : "bts:AnaplasticPilocyticAstrocytoma" + }, { + "@id" : "bts:Schwannoma" + }, { + "@id" : "bts:HemorrhagicNeoplasm" + }, { + "@id" : "bts:NotApplicable" + }, { + "@id" : "bts:PilocyticAstrocytoma" + }, { + "@id" : "bts:Ganglioglioma" + }, { + "@id" : "bts:PlexiformNeurofibroma" + }, { + "@id" : "bts:NF2-AssociatedTumor" + }, { + "@id" : "bts:Fibrosarcoma" + }, { + "@id" : "bts:Low-GradeGliomaNOS" + }, { + "@id" : "bts:Glioblastoma" + }, { + "@id" : "bts:AnaplasticPleomorphicXanthoastrocytoma" + }, { + "@id" : "bts:GlioblastomaMultiforme" + }, { + "@id" : "bts:Unknown" + }, { + "@id" : "bts:AtypicalPilocyticAstrocytoma" + }, { + "@id" : "bts:OpticPathwayGlioma" + }, { + "@id" : "bts:DiffuseInfiltratingNeurofibroma" + }, { + "@id" : "bts:Fibromatosis" + }, { + "@id" : "bts:NeurofibromawithDegenerativeAtypia" + }, { + "@id" : "bts:NecroticNeoplasm" + }, { + "@id" : "bts:PleomorphicXanthoastrocytoma" + }, { + "@id" : "bts:Teratoma" + }, { + "@id" : "bts:Sarcoma" + }, { + "@id" : "bts:MassiveSoftTissueNeurofibroma" + }, { + "@id" : "bts:Glioma" + }, { + "@id" : "bts:Oligoastrocytoma" + }, { + "@id" : "bts:ColorectalCarcinoma" + }, { + "@id" : "bts:Meningioma" + }, { + "@id" : "bts:ANNUBP" + }, { + "@id" : "bts:High-GradeGliomaNOS" + }, { + "@id" : "bts:NF1-AssociatedTumor" + }, { + "@id" : "bts:AtypicalNeurofibroma" + }, { + "@id" : "bts:Neurofibroma" + }, { + "@id" : "bts:RecurrentMPNST" + }, { + "@id" : "bts:AnaplasticGanglioglioma" + }, { + "@id" : "bts:tumor" + }, { + "@id" : "bts:metastatictumor" + }, { + "@id" : "bts:metastatic/recurrenttumor" + }, { + "@id" : "bts:recurrenttumor" + }, { + "@id" : "bts:Melanoma" + }, { + "@id" : "bts:NodularNeurofibroma" } ], - "rdfs:label" : "dermalSchwannoma", - "rdfs:comment" : "Characterization of the manifestation of Dermal schwannoma.", + "rdfs:label" : "tumorType", + "rdfs:comment" : "The type of tumor that the biospecimen used to generate the data were collected from.", "@type" : "rdfs:Class", - "sms:displayName" : "dermalSchwannoma" + "sms:displayName" : "tumorType" }, { - "@id" : "bts:benefactorId", - "@type" : "rdfs:Class", - "rdfs:comment" : "The id of the resource from which access control is inherited.", - "rdfs:label" : "benefactorId", "rdfs:subClassOf" : [ ], + "@id" : "bts:workingDistance", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "benefactorId", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "workingDistance", + "rdfs:comment" : "Working distance of the lens expressed as a floating point number > 0.", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:workingDistanceUnit" + } ], + "sms:displayName" : "workingDistance" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:spinalSchwannoma", + "@id" : "bts:nonvestibularCranialSchwannoma", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -4623,274 +5173,282 @@ }, { "@id" : "bts:absentbyimaging" }, { - "@id" : "bts:single" - }, { - "@id" : "bts:multiple" + "@id" : "bts:present" }, { "@id" : "bts:unknown" } ], - "rdfs:label" : "spinalSchwannoma", - "rdfs:comment" : "Characterization of the manifestation of Spinal schwannoma.", + "rdfs:label" : "nonvestibularCranialSchwannoma", + "rdfs:comment" : "Characterization of the manifestation of Nonvestibular cranial schwannoma.", "@type" : "rdfs:Class", - "sms:displayName" : "spinalSchwannoma" + "sms:displayName" : "nonvestibularCranialSchwannoma" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:accessType", + "@id" : "bts:expressionUnit", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:PublicAccess" + "@id" : "bts:TPM" }, { - "@id" : "bts:OpenAccess" + "@id" : "bts:RPKM" }, { - "@id" : "bts:ControlledAccess" + "@id" : "bts:FPKM" + }, { + "@id" : "bts:Counts" + }, { + "@id" : "bts:RawCounts" + }, { + "@id" : "bts:NormalizedCounts" + }, { + "@id" : "bts:Other" } ], - "rdfs:label" : "accessType", - "rdfs:comment" : "Indicates access type / possible procedures needed for access to the resource.", + "rdfs:label" : "expressionUnit", + "rdfs:comment" : "Measure used for transcript expression quantification", "@type" : "rdfs:Class", - "sms:displayName" : "accessType" + "sms:displayName" : "expressionUnit" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:spinalNeurofibromas", + "@id" : "bts:pubertyOnset", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:notimaged" + "@id" : "bts:prebubertal" }, { - "@id" : "bts:absent" + "@id" : "bts:precocious" }, { - "@id" : "bts:levels1-3" + "@id" : "bts:normal" }, { - "@id" : "bts:alllevels" + "@id" : "bts:late" } ], - "rdfs:label" : "spinalNeurofibromas", - "rdfs:comment" : "Characterization of the manifestation of Spinal neurofibromas.", + "rdfs:label" : "pubertyOnset", + "rdfs:comment" : "Puberty onset.", "@type" : "rdfs:Class", - "sms:displayName" : "spinalNeurofibromas" + "sms:displayName" : "pubertyOnset" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:opticGlioma", + "@id" : "bts:readsMappedPercent", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" - }, { - "@id" : "bts:present-asymptomatic" - }, { - "@id" : "bts:present-symptomatic-nottreated" - }, { - "@id" : "bts:present-symptomatic-treated" - }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "opticGlioma", - "rdfs:comment" : "Characterization of the manifestation of Optic glioma.", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "readsMappedPercent", + "rdfs:comment" : "Percent of mapped reads collected from samtools", "@type" : "rdfs:Class", - "sms:displayName" : "opticGlioma" + "sms:displayName" : "readsMappedPercent" }, { - "@id" : "bts:createdOn", - "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to when the resource was created.", - "rdfs:label" : "createdOn", "rdfs:subClassOf" : [ ], + "@id" : "bts:glomusTumor", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdOn", - "sms:required" : "sms:false" - }, { - "@id" : "bts:protocolPurpose", + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "glomusTumor", + "rdfs:comment" : "Characterization of the manifestation of Glomus tumor.", "@type" : "rdfs:Class", - "rdfs:comment" : "Brief description of the protocol purpose.", - "rdfs:label" : "protocolPurpose", + "sms:displayName" : "glomusTumor" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:studyStatus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "protocolPurpose", - "sms:required" : "sms:false" + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:Active" + }, { + "@id" : "bts:Completed" + }, { + "@id" : "bts:Withdrawn" + } ], + "rdfs:label" : "studyStatus", + "rdfs:comment" : "Status of a study.", + "@type" : "rdfs:Class", + "sms:displayName" : "studyStatus" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:grantDOI", + "@id" : "bts:sphenoidDysplasia", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "grantDOI", - "rdfs:comment" : "Doi of a grant (e.g. in ProposalCentral) that can be associated with the entity.", + "schema:rangeIncludes" : [ { + "@id" : "bts:absent" + }, { + "@id" : "bts:present" + }, { + "@id" : "bts:unknown" + } ], + "rdfs:label" : "sphenoidDysplasia", + "rdfs:comment" : "Characterization of the manifestation of Sphenoid dysplasia.", "@type" : "rdfs:Class", - "sms:displayName" : "grantDOI" + "sms:displayName" : "sphenoidDysplasia" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:breastCancer", + "@id" : "bts:nonvestibularSchwannomas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:absent" + "@id" : "bts:onlybyimagingevidence" }, { - "@id" : "bts:present" + "@id" : "bts:1pathogicallyconfirmed" + }, { + "@id" : "bts:2ormore,atleast1pathogicallyconfirmed" }, { "@id" : "bts:unknown" } ], - "rdfs:label" : "breastCancer", - "rdfs:comment" : "Characterization of the manifestation of Breast cancer.", + "rdfs:label" : "nonvestibularSchwannomas", + "rdfs:comment" : "Characterization of the manifestation of Nonvestibular schwannomas.", "@type" : "rdfs:Class", - "sms:displayName" : "breastCancer" + "sms:displayName" : "nonvestibularSchwannomas" }, { - "@id" : "bts:reporterSubstance", + "@id" : "bts:germlineMutation", "@type" : "rdfs:Class", - "rdfs:comment" : "A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.", - "rdfs:label" : "reporterSubstance", + "rdfs:comment" : "The individual's actual germline mutation.", + "rdfs:label" : "germlineMutation", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterSubstance", + "sms:displayName" : "germlineMutation", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:slideVersion", + "@id" : "bts:skinFoldFreckling", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:V1" - }, { - "@id" : "bts:V2" + "@id" : "bts:absent" }, { - "@id" : "bts:V3" + "@id" : "bts:present" }, { - "@id" : "bts:V4" + "@id" : "bts:unknown" } ], - "rdfs:label" : "slideVersion", - "rdfs:comment" : "Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.", + "rdfs:label" : "skinFoldFreckling", + "rdfs:comment" : "Characterization of skin fold freckling.", "@type" : "rdfs:Class", - "sms:displayName" : "slideVersion" + "sms:displayName" : "skinFoldFreckling" }, { - "@id" : "bts:reporterGene", + "@id" : "bts:contentType", "@type" : "rdfs:Class", - "rdfs:comment" : "A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.", - "rdfs:label" : "reporterGene", + "rdfs:comment" : "Refers to the type of content.", + "rdfs:label" : "contentType", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "reporterGene", + "sms:displayName" : "contentType", "sms:required" : "sms:false" }, { + "@id" : "bts:objective", + "@type" : "rdfs:Class", + "rdfs:comment" : "Microscope objective.", + "rdfs:label" : "objective", "rdfs:subClassOf" : [ ], - "@id" : "bts:nf1Genotype", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "objective", + "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:leukemia", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:-/-" - }, { - "@id" : "bts:+/-" - }, { - "@id" : "bts:+/+" + "@id" : "bts:absent" }, { - "@id" : "bts:Unknown" + "@id" : "bts:present" }, { - "@id" : "bts:Unknown" + "@id" : "bts:unknown" } ], - "rdfs:label" : "nf1Genotype", - "rdfs:comment" : "Genotype of NF1 gene in the biospecimen from which the data were derived, if known.", + "rdfs:label" : "leukemia", + "rdfs:comment" : "Characterization of the manifestation of Leukemia.", "@type" : "rdfs:Class", - "sms:displayName" : "nf1Genotype" + "sms:displayName" : "leukemia" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:diagnosis", + "@id" : "bts:subcutaneousNodularNeurofibromas", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Neurofibromatosistype1" - }, { - "@id" : "bts:Schwannomatosis" - }, { - "@id" : "bts:NF2-relatedschwannomatosis" - }, { - "@id" : "bts:SMARCB1-relatedschwannomatosis" - }, { - "@id" : "bts:LZTR1-relatedschwannomatosis" - }, { - "@id" : "bts:22q-relatedschwannomatosis" + "@id" : "bts:absent" }, { - "@id" : "bts:Schwannomatosis-NOS" + "@id" : "bts:scattered" }, { - "@id" : "bts:Schwannomatosis-NEC" + "@id" : "bts:dense" }, { - "@id" : "bts:SporadicSchwannoma" + "@id" : "bts:unknown" } ], - "rdfs:label" : "diagnosis", - "rdfs:comment" : "Diagnosis for the individual given signs and symptoms. Use the most specific diagnosis term that applies.", + "rdfs:label" : "subcutaneousNodularNeurofibromas", + "rdfs:comment" : "Characterization of the manifestation of Subcutaneous nodular neurofibromas.", "@type" : "rdfs:Class", - "sms:displayName" : "diagnosis" + "sms:displayName" : "subcutaneousNodularNeurofibromas" }, { - "@id" : "bts:targetDepth", + "@id" : "bts:averageInsertSize", "@type" : "rdfs:Class", - "rdfs:comment" : "The targeted read depth prior to sequencing.", - "rdfs:label" : "targetDepth", + "rdfs:comment" : "Average insert size as reported by samtools", + "rdfs:label" : "averageInsertSize", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "targetDepth", + "sms:displayName" : "averageInsertSize", "sms:required" : "sms:false" }, { - "@id" : "bts:accessRequirements", + "@id" : "bts:cellID", "@type" : "rdfs:Class", - "rdfs:comment" : "Statement describing access requirements for an entity.", - "rdfs:label" : "accessRequirements", + "rdfs:comment" : "Also known as cell barcode, this value can be added for single-cell experiments to identify data at the cell level.", + "rdfs:label" : "cellID", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "accessRequirements", + "sms:displayName" : "cellID", "sms:required" : "sms:false" }, { + "@id" : "bts:batchID", + "@type" : "rdfs:Class", + "rdfs:comment" : "Batch identifier, can be used in any context where added batch information is helpful, such as different sequencing runs or collection times.", + "rdfs:label" : "batchID", "rdfs:subClassOf" : [ ], - "@id" : "bts:creator", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "creator", - "rdfs:comment" : "An entity responsible for making the resource.", - "@type" : "rdfs:Class", - "sms:displayName" : "creator" + "sms:displayName" : "batchID", + "sms:required" : "sms:false" }, { + "@id" : "bts:individualID", + "@type" : "rdfs:Class", + "rdfs:comment" : "A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.", + "rdfs:label" : "individualID", "rdfs:subClassOf" : [ ], - "@id" : "bts:age", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "num" ], - "rdfs:label" : "age", - "rdfs:comment" : "A numeric value representing age of the individual. Use with `ageUnit`.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:ageUnit" - } ], - "sms:displayName" : "age" + "sms:displayName" : "individualID", + "sms:required" : "sms:true" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:isCellLine", + "@id" : "bts:failedQC", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -4900,117 +5458,104 @@ }, { "@id" : "bts:No" } ], - "rdfs:label" : "isCellLine", - "rdfs:comment" : "Whether or not sample source is a cell line (Yes; No)", + "rdfs:label" : "failedQC", + "rdfs:comment" : "Whether the sample or data failed QC checks (Yes, No)", "@type" : "rdfs:Class", - "sms:displayName" : "isCellLine" + "sms:displayName" : "failedQC" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:libraryPreparationMethod", + "@id" : "bts:vascularDisease", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:true", + "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:10x" - }, { - "@id" : "bts:CEL-seq" - }, { - "@id" : "bts:Drop-Seq" - }, { - "@id" : "bts:GTAC@WUSTLin-houseprep" - }, { - "@id" : "bts:IDTxGenExomeResearchPanel" - }, { - "@id" : "bts:IlluminaTruSeqDNANano" - }, { - "@id" : "bts:IlluminaTn5Transposase" - }, { - "@id" : "bts:KAPAHyperPrepKitPCR-free" - }, { - "@id" : "bts:KAPARNAHyperPrepKitwithRiboErase(HMR)" - }, { - "@id" : "bts:KAPAmRNAHyperPrepKit" - }, { - "@id" : "bts:NEBNextmRNALibraryPrepReagentSetforIllumina" - }, { - "@id" : "bts:Omni-ATAC" - }, { - "@id" : "bts:QuantSeqFWDV2withUDI" + "@id" : "bts:absent" }, { - "@id" : "bts:Smart-seq2" - }, { - "@id" : "bts:Smart-seq4" - }, { - "@id" : "bts:TruSeq" - }, { - "@id" : "bts:TruSeqstandardtotalRNAlibrarykit" - }, { - "@id" : "bts:OxfordNanoporeDirectRNASequencingKit" + "@id" : "bts:present" }, { "@id" : "bts:unknown" } ], - "rdfs:label" : "libraryPreparationMethod", - "rdfs:comment" : "Method by which library was prepared", + "rdfs:label" : "vascularDisease", + "rdfs:comment" : "Characterization of the manifestation of Vascular disease.", "@type" : "rdfs:Class", - "sms:displayName" : "libraryPreparationMethod" + "sms:displayName" : "vascularDisease" }, { + "@id" : "bts:compoundName", + "@type" : "rdfs:Class", + "rdfs:comment" : "Common name for a compound, e.g. “Selumetinib” (https://pubchem.ncbi.nlm.nih.gov/compound/10127622)", + "rdfs:label" : "compoundName", "rdfs:subClassOf" : [ ], - "@id" : "bts:publisher", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "publisher", - "rdfs:comment" : "An entity responsible for making the resource available.", + "sms:displayName" : "compoundName", + "sms:required" : "sms:false" + }, { + "@id" : "bts:nf1GermlineMutation", "@type" : "rdfs:Class", - "sms:displayName" : "publisher" + "rdfs:comment" : "NF1 germline mutation.", + "rdfs:label" : "nf1GermlineMutation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "nf1GermlineMutation", + "sms:required" : "sms:false" }, { - "@id" : "bts:averageBaseQuality", + "@id" : "bts:isFilteredReads", "@type" : "rdfs:Class", - "rdfs:comment" : "Average base quality collected from samtools", - "rdfs:label" : "averageBaseQuality", + "rdfs:comment" : "Whether the reads in the processed result has been filtered by adding a 'PASS' filter or other filters as determined by the data generator", + "rdfs:label" : "isFilteredReads", "rdfs:subClassOf" : [ ], "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "averageBaseQuality", + "sms:displayName" : "isFilteredReads", "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:sex", + "@id" : "bts:runType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", "schema:rangeIncludes" : [ { - "@id" : "bts:Male" - }, { - "@id" : "bts:Female" - }, { - "@id" : "bts:Unknown" + "@id" : "bts:pairedEnd" }, { - "@id" : "bts:NotApplicable" + "@id" : "bts:singleEnd" } ], - "rdfs:label" : "sex", - "rdfs:comment" : "Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.", + "rdfs:label" : "runType", + "rdfs:comment" : "Sequencing run type.", "@type" : "rdfs:Class", - "sms:displayName" : "sex" + "sms:displayName" : "runType" }, { - "@id" : "bts:createdBy", + "rdfs:subClassOf" : [ ], + "@id" : "bts:lensAperture", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "lensAperture", + "rdfs:comment" : "Numerical aperture of the lens. Floating point value > 0.", "@type" : "rdfs:Class", - "rdfs:comment" : "Refers to the user who created the resource.", - "rdfs:label" : "createdBy", + "sms:displayName" : "lensAperture" + }, { "rdfs:subClassOf" : [ ], + "@id" : "bts:referenceSet", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "createdBy", - "sms:required" : "sms:false" + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "referenceSet", + "rdfs:comment" : "A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data.", + "@type" : "rdfs:Class", + "sms:displayName" : "referenceSet" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:otherTumors", + "@id" : "bts:attentionDeficitDisorder", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, @@ -5022,4631 +5567,4088 @@ }, { "@id" : "bts:unknown" } ], - "rdfs:label" : "otherTumors", - "rdfs:comment" : "Characterization of the manifestation of other tumors.", + "rdfs:label" : "attentionDeficitDisorder", + "rdfs:comment" : "Characterization of the manifestation of Attention Deficit Disorder.", "@type" : "rdfs:Class", - "sms:displayName" : "otherTumors" + "sms:displayName" : "attentionDeficitDisorder" }, { + "@id" : "bts:parentId", + "@type" : "rdfs:Class", + "rdfs:comment" : "The id of the parent resource, i.e. the parent folder on the platform. ", + "rdfs:label" : "parentId", "rdfs:subClassOf" : [ ], - "@id" : "bts:genePerturbationType", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "genePerturbationType", - "rdfs:comment" : "Specific way in which a single gene was perturbed in a sample", - "@type" : "rdfs:Class", - "sms:displayName" : "genePerturbationType" + "sms:displayName" : "parentId", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:painStatus", + "@id" : "bts:diseaseFocus", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:notaproblem" - }, { - "@id" : "bts:occasional" - }, { - "@id" : "bts:disabling" - } ], - "rdfs:label" : "painStatus", - "rdfs:comment" : "Pain status rating.", + "schema:rangeIncludes" : [ ], + "rdfs:label" : "diseaseFocus", + "rdfs:comment" : "Disease that acts as the main topic.", "@type" : "rdfs:Class", - "sms:displayName" : "painStatus" + "sms:displayName" : "diseaseFocus" }, { "rdfs:subClassOf" : [ ], - "@id" : "bts:compoundDose", + "@id" : "bts:transplantationRecipientSpecies", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, "sms:required" : "sms:false", - "rdfs:label" : "compoundDose", - "rdfs:comment" : "A dose quantity for the treatment compound. To be used with compoundDoseUnit.", - "@type" : "rdfs:Class", - "sms:requiresDependency" : [ { - "@id" : "bts:compoundDoseUnit" + "schema:rangeIncludes" : [ { + "@id" : "bts:Human" + }, { + "@id" : "bts:Mouse" } ], - "sms:displayName" : "compoundDose" + "rdfs:label" : "transplantationRecipientSpecies", + "rdfs:comment" : "Species into which donor was grown", + "@type" : "rdfs:Class", + "sms:displayName" : "transplantationRecipientSpecies" }, { + "@id" : "bts:acknowledgementStatements", + "@type" : "rdfs:Class", + "rdfs:comment" : "Statement describing how resource use should be acknowledged.", + "rdfs:label" : "acknowledgementStatements", "rdfs:subClassOf" : [ ], - "@id" : "bts:readDepth", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:required" : "sms:false", - "sms:validationRules" : [ "int" ], - "rdfs:label" : "readDepth", - "rdfs:comment" : "If available, the coverage statistic as output from bedtools coverage or samtools stats.", - "@type" : "rdfs:Class", - "sms:displayName" : "readDepth" + "sms:displayName" : "acknowledgementStatements", + "sms:required" : "sms:false" }, { - "@id" : "bts:InChIKey", + "@id" : "bts:experimentId", "@type" : "rdfs:Class", - "rdfs:comment" : "A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). 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This template should be used when biosamples are from NF patients to provides a more valuable characterization and make additional gene-phenotype insights possible.\n", "@type" : "rdfs:Class", - "sms:displayName" : "readsMappedPercent" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:glomusTumor", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ { - "@id" : "bts:absent" + "sms:requiresDependency" : [ { + "@id" : "bts:individualID" }, { - "@id" : "bts:present" + "@id" : "bts:sex" }, { - "@id" : "bts:unknown" - } ], - "rdfs:label" : "glomusTumor", - "rdfs:comment" : "Characterization of the manifestation of Glomus tumor.", - "@type" : "rdfs:Class", - "sms:displayName" : "glomusTumor" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:studyStatus", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:true", - "schema:rangeIncludes" : [ { - "@id" : "bts:Active" + "@id" : "bts:age" }, { - 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"@id" : "bts:NanoFCM" + "@id" : "bts:Filename" }, { - "@id" : "bts:Illuminah650" + "@id" : "bts:fileFormat" }, { - "@id" : "bts:BGISEQ-500" + "@id" : "bts:resourceType" }, { - "@id" : "bts:PacBioSequelIISystem" + "@id" : "bts:dataType" }, { - "@id" : "bts:PromegaGloMaxDiscover" + "@id" : "bts:dataSubtype" }, { - "@id" : "bts:BionanoIrys" + "@id" : "bts:assay" }, { - "@id" : "bts:LeicaAperioAT2" + "@id" : "bts:individualID" }, { - "@id" : "bts:LeicaS9Stereomicroscope" + "@id" : "bts:species" }, { - "@id" : "bts:PhilipsAchieva3T" + "@id" : "bts:sex" }, { - "@id" : "bts:ZenoElectronicWalkway" + "@id" : "bts:age" }, { - "@id" : "bts:BDFACSCalibur" + "@id" : "bts:ageUnit" }, { - "@id" : "bts:Pannoramic250Flash" + "@id" : "bts:diagnosis" }, { - "@id" : "bts:Scale" + "@id" : "bts:nf1Genotype" }, { - "@id" : "bts:Caliper" + "@id" : "bts:nf2Genotype" }, { - "@id" : "bts:TOOsonixSystemONE-M" + "@id" : "bts:tumorType" }, { - "@id" : "bts:MGIT-series" + "@id" : "bts:modelSystemName" }, { - "@id" : "bts:VarioskanLUX" + "@id" : "bts:organ" }, { - "@id" : "bts:Panorama1.0T" + "@id" : "bts:comments" }, { - "@id" : "bts:OxfordNanopore" + "@id" : "bts:platform" }, { - "@id" : "bts:OtherPlatform" + "@id" : "bts:cellType" }, { - "@id" : "bts:NotApplicable" + "@id" : "bts:auxiliaryAsset" } ], - "rdfs:label" : "platform", - "rdfs:comment" : "A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.", - "@type" : "rdfs:Class", - "sms:displayName" : "platform" + "sms:displayName" : "FlowCytometryTemplate" }, { - "@id" : "bts:studyLeads", - "@type" : "rdfs:Class", - "rdfs:comment" : "Individuals with lead roles in a study.", - "rdfs:label" : "studyLeads", - "rdfs:subClassOf" : [ ], + "rdfs:subClassOf" : [ { + "@id" : "bts:Template" + } ], + "@id" : "bts:WorkflowReport", "schema:isPartOf" : { "@id" : "http://schema.biothings.io/" }, - "sms:displayName" : "studyLeads", - "sms:required" : "sms:true" + "sms:required" : "sms:false", + "sms:requiresComponent" : null, + "rdfs:label" : "WorkflowReport", + "rdfs:comment" : "Template used for miscellaneous workflow reports and accessory files", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:resourceType" + }, { + "@id" : "bts:assay" + }, { + "@id" : "bts:fileFormat" + }, { + "@id" : "bts:relatedDataset" + }, { + "@id" : "bts:workflow" + }, { + "@id" : "bts:workflowLink" + } ], + "sms:displayName" : "WorkflowReport" }, { "@id" : "bts:autograft", "@type" : "rdfs:Class", @@ -23375,6 +23377,17 @@ }, "sms:displayName" : "TrimGalore", "sms:required" : "sms:false" + }, { + "@id" : "bts:IlluminaRibo-ZeroPlus", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "IlluminaRibo-ZeroPlus", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Illumina Ribo-Zero Plus", + "sms:required" : "sms:false" }, { "@id" : "bts:hTERTNF1ipn02.32λ", "@type" : "rdfs:Class", diff --git a/modules/Assay/Parameter.yaml b/modules/Assay/Parameter.yaml index 49eaa1c0..d2a7d7c6 100644 --- a/modules/Assay/Parameter.yaml +++ b/modules/Assay/Parameter.yaml @@ -78,6 +78,8 @@ enums: Illumina Tn5 Transposase: description: Tn5 simultaneously fragments DNA, preferentially inserts into open chromatin sites, and adds sequencing primers (a process known as tagmentation). source: https://www.illumina.com/techniques/multiomics/epigenetics/atac-seq-chromatin-accessibility.html + Illumina Ribo-Zero Plus: + source: https://www.illumina.com/products/by-type/accessory-products/ribo-zero-plus-rrna-depletion.html KAPA HyperPrep Kit PCR-free: description: KAPA HyperPrep Kits offer a streamlined library preparation protocol that combines several enzymatic steps and eliminates bead cleanups to significantly reduce library preparation time and improve consistency. source: https://sequencing.roche.com/en/products-solutions/products/sample-preparation/dna-reagents/library-preparation/kapa-hyperprep/ordering.html