diff --git a/GF.jsonld b/GF.jsonld index f22f2f0..35d310d 100644 --- a/GF.jsonld +++ b/GF.jsonld @@ -472,12 +472,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -633,12 +655,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -702,12 +746,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -730,8 +796,6 @@ "@id" : "bts:SingleNucleusBuffer" }, { "@id" : "bts:TranspositionReaction" - }, { - "@id" : "bts:ScATACseqLibraryLayout" }, { "@id" : "bts:NucleusIdentifier" }, { @@ -872,12 +936,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -900,8 +986,6 @@ "@id" : "bts:SingleNucleusBuffer" }, { "@id" : "bts:TranspositionReaction" - }, { - "@id" : "bts:ScATACseqLibraryLayout" }, { "@id" : "bts:NucleusIdentifier" }, { @@ -956,7 +1040,7 @@ "sms:required" : "sms:false", "sms:requiresComponent" : "", "rdfs:label" : "Sequencing", - "rdfs:comment" : "TBD", + "rdfs:comment" : "Base template for some type of sequencing data, for which below properties are relevant/in common.", "@type" : "rdfs:Class", "sms:requiresDependency" : [ { "@id" : "bts:Component" @@ -976,12 +1060,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" } ], @@ -1017,12 +1123,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -1043,10 +1171,10 @@ "@id" : "bts:EndBias" }, { "@id" : "bts:ScRNAseqWorkflowType" - }, { - "@id" : "bts:WorkflowVersion" }, { "@id" : "bts:ScRNAseqWorkflowParametersDescription" + }, { + "@id" : "bts:WorkflowVersion" }, { "@id" : "bts:WorkflowLink" }, { @@ -1113,12 +1241,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -1170,12 +1320,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -1198,8 +1370,6 @@ "@id" : "bts:SingleNucleusBuffer" }, { "@id" : "bts:TranspositionReaction" - }, { - "@id" : "bts:ScATACseqLibraryLayout" }, { "@id" : "bts:NucleusIdentifier" }, { @@ -1286,12 +1456,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -1669,6 +1861,71 @@ "@id" : "bts:DaystoDeath" } ], "sms:displayName" : "Dead" + }, { + "rdfs:subClassOf" : [ { + "@id" : "bts:Sequencing" + } ], + "@id" : "bts:BulkDNA-seqLevel1", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:requiresComponent" : "", + "rdfs:label" : "BulkDNA-seqLevel1", + "rdfs:comment" : "TBD", + "@type" : "rdfs:Class", + "sms:requiresDependency" : [ { + "@id" : "bts:Component" + }, { + "@id" : "bts:Filename" + }, { + "@id" : "bts:FileFormat" + }, { + "@id" : "bts:ParticipantID" + }, { + "@id" : "bts:SampleID" + }, { + "@id" : "bts:DetailedSampleID" + }, { + "@id" : "bts:SequencingPlatform" + }, { + "@id" : "bts:NucleicAcidSource" + }, { + "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" + }, { + "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" + }, { + "@id" : "bts:Read1" + }, { + "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" + }, { + "@id" : "bts:TechnicalReplicateGroup" + }, { + "@id" : "bts:TargetCaptureKit" + } ], + "sms:displayName" : "BulkDNA-seqLevel1" }, { "rdfs:subClassOf" : [ { "@id" : "bts:Patient" @@ -1853,12 +2110,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -1967,12 +2246,34 @@ "@id" : "bts:NucleicAcidSource" }, { "@id" : "bts:LibraryConstructionMethod" + }, { + "@id" : "bts:LibrarySelectionMethod" + }, { + "@id" : "bts:LibraryLayout" + }, { + "@id" : "bts:LibraryPreparationKitName" + }, { + "@id" : "bts:LibraryPreparationKitVendor" + }, { + "@id" : "bts:LibraryPreparationKitVersion" }, { "@id" : "bts:ReadIndicator" + }, { + "@id" : "bts:ReadLength" }, { "@id" : "bts:Read1" }, { "@id" : "bts:Read2" + }, { + "@id" : "bts:TargetDepth" + }, { + "@id" : "bts:AdapterName" + }, { + "@id" : "bts:AdapterSequence" + }, { + "@id" : "bts:BatchID" + }, { + "@id" : "bts:LaneNumber" }, { "@id" : "bts:TechnicalReplicateGroup" }, { @@ -2824,6 +3125,17 @@ }, "sms:displayName" : "DissociationMethodEnum", "sms:required" : "sms:false" + }, { + "@id" : "bts:LibraryLayoutEnum", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LibraryLayoutEnum", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryLayoutEnum", + "sms:required" : "sms:false" }, { "@id" : "bts:BreastCancerAllredEstrogenReceptorScoreEnum", "@type" : "rdfs:Class", @@ -3231,6 +3543,17 @@ }, "sms:displayName" : "AdjacentSampleIDs", "sms:required" : "sms:false" + }, { + "@id" : "bts:AdapterSequence", + "@type" : "rdfs:Class", + "rdfs:comment" : "Base sequence of the sequencing adapter. String", + "rdfs:label" : "AdapterSequence", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AdapterSequence", + "sms:required" : "sms:false" }, { "@id" : "bts:DaystoDeath", "@type" : "rdfs:Class", @@ -3419,6 +3742,26 @@ "rdfs:comment" : "Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.", "@type" : "rdfs:Class", "sms:displayName" : "BreastBiopsyProcedureFindingType" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:LibraryLayout", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "schema:rangeIncludes" : [ { + "@id" : "bts:PairedEnd" + }, { + "@id" : "bts:SingleRead" + }, { + "@id" : "bts:Mid-length" + }, { + "@id" : "bts:LongRead" + } ], + "rdfs:label" : "LibraryLayout", + "rdfs:comment" : "Sequencing read type", + "@type" : "rdfs:Class", + "sms:displayName" : "LibraryLayout" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:SpecimenLaterality", @@ -4198,6 +4541,17 @@ "rdfs:comment" : "Genomic coverage", "@type" : "rdfs:Class", "sms:displayName" : "GenomicCoverageType" + }, { + "@id" : "bts:TargetDepth", + "@type" : "rdfs:Class", + "rdfs:comment" : "Targeted read depth prior to sequencing. Integer", + "rdfs:label" : "TargetDepth", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TargetDepth", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:PixelType", @@ -4800,6 +5154,17 @@ }, "sms:displayName" : "Filename", "sms:required" : "sms:false" + }, { + "@id" : "bts:AdapterName", + "@type" : "rdfs:Class", + "rdfs:comment" : "Name of the sequencing adapter. String", + "rdfs:label" : "AdapterName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "AdapterName", + "sms:required" : "sms:false" }, { "@id" : "bts:CountryofBirth", "@type" : "rdfs:Class", @@ -6822,6 +7187,34 @@ }, "sms:displayName" : "PhysicalSizeZ", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:LibrarySelectionMethod", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:true", + "schema:rangeIncludes" : [ { + "@id" : "bts:hybridselection" + }, { + "@id" : "bts:PCR" + }, { + "@id" : "bts:affinityenrichment" + }, { + "@id" : "bts:poly-Tenrichment" + }, { + "@id" : "bts:random" + }, { + "@id" : "bts:rRNAdepletion" + }, { + "@id" : "bts:miRNAsizefractionation" + }, { + "@id" : "bts:other" + } ], + "rdfs:label" : "LibrarySelectionMethod", + "rdfs:comment" : "How RNA molecules are isolated", + "@type" : "rdfs:Class", + "sms:displayName" : "LibrarySelectionMethod" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:CountryofResidence", @@ -7745,6 +8138,17 @@ "rdfs:comment" : "The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.", "@type" : "rdfs:Class", "sms:displayName" : "MolecularAnalysisMethod" + }, { + "@id" : "bts:LaneNumber", + "@type" : "rdfs:Class", + "rdfs:comment" : "Basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer", + "rdfs:label" : "LaneNumber", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LaneNumber", + "sms:required" : "sms:false" }, { "@id" : "bts:ParticipantID", "@type" : "rdfs:Class", @@ -7833,6 +8237,18 @@ }, "sms:displayName" : "AcquisitionMethodOtherSpecify", "sms:required" : "sms:false" + }, { + "rdfs:subClassOf" : [ ], + "@id" : "bts:ReadLength", + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:required" : "sms:false", + "sms:validationRules" : [ "num" ], + "rdfs:label" : "ReadLength", + "rdfs:comment" : "Length of the sequencing reads. Can be integer, null", + "@type" : "rdfs:Class", + "sms:displayName" : "ReadLength" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:WellIndex", @@ -8049,6 +8465,17 @@ "rdfs:comment" : "Nuclei isolation buffer", "@type" : "rdfs:Class", "sms:displayName" : "SingleNucleusBuffer" + }, { + "@id" : "bts:LibraryPreparationKitVendor", + "@type" : "rdfs:Class", + "rdfs:comment" : "Vendor of Library Preparation Kit. String", + "rdfs:label" : "LibraryPreparationKitVendor", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryPreparationKitVendor", + "sms:required" : "sms:false" }, { "@id" : "bts:LensNA", "@type" : "rdfs:Class", @@ -9247,6 +9674,17 @@ }, "sms:displayName" : "Objective", "sms:required" : "sms:false" + }, { + "@id" : "bts:BatchID", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "BatchID", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "BatchID", + "sms:required" : "sms:false" }, { "rdfs:subClassOf" : [ ], "@id" : "bts:VascularInvasionType", @@ -10083,6 +10521,17 @@ }, "sms:displayName" : "TargetName", "sms:required" : "sms:false" + }, { + "@id" : "bts:TargetCaptureKit", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "TargetCaptureKit", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "TargetCaptureKit", + "sms:required" : "sms:true" }, { "@id" : "bts:SecondExon", "@type" : "rdfs:Class", @@ -10131,18 +10580,6 @@ }, "sms:displayName" : "BloodTestNormalRangeUpper", "sms:required" : "sms:false" - }, { - "rdfs:subClassOf" : [ ], - "@id" : "bts:ScATACseqLibraryLayout", - "schema:isPartOf" : { - "@id" : "http://schema.biothings.io/" - }, - "sms:required" : "sms:false", - "schema:rangeIncludes" : [ ], - "rdfs:label" : "ScATACseqLibraryLayout", - "rdfs:comment" : "Sequencing read type", - "@type" : "rdfs:Class", - "sms:displayName" : "ScATACseqLibraryLayout" }, { "@id" : "bts:Immunosuppression", "@type" : "rdfs:Class", @@ -10575,6 +11012,17 @@ }, "sms:displayName" : "FOVnumber", "sms:required" : "sms:false" + }, { + "@id" : "bts:LibraryPreparationKitName", + "@type" : "rdfs:Class", + "rdfs:comment" : "Name of Library Preparation Kit. String", + "rdfs:label" : "LibraryPreparationKitName", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryPreparationKitName", + "sms:required" : "sms:false" }, { "@id" : "bts:ChannelMetadataFilename", "@type" : "rdfs:Class", @@ -10952,6 +11400,17 @@ "rdfs:comment" : "The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.", "@type" : "rdfs:Class", "sms:displayName" : "RelationshipPrimaryDiagnosis" + }, { + "@id" : "bts:LibraryPreparationKitVersion", + "@type" : "rdfs:Class", + "rdfs:comment" : "Version of Library Preparation Kit. String", + "rdfs:label" : "LibraryPreparationKitVersion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "LibraryPreparationKitVersion", + "sms:required" : "sms:true" }, { "@id" : "bts:AppliedHardTrimming", "@type" : "rdfs:Class", @@ -12870,6 +13329,17 @@ }, "sms:displayName" : "vcf", "sms:required" : "sms:false" + }, { + "@id" : "bts:random", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "random", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "random", + "sms:required" : "sms:false" }, { "@id" : "bts:CD25", "@type" : "rdfs:Class", @@ -14498,6 +14968,17 @@ }, "sms:displayName" : "Karyotype", "sms:required" : "sms:false" + }, { + "@id" : "bts:SingleRead", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "SingleRead", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Single Read", + "sms:required" : "sms:false" }, { "@id" : "bts:bgzip", "@type" : "rdfs:Class", @@ -16962,6 +17443,17 @@ }, "sms:displayName" : "Bile duct adenoma", "sms:required" : "sms:false" + }, { + "@id" : "bts:poly-Tenrichment", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "poly-Tenrichment", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "poly-T enrichment", + "sms:required" : "sms:false" }, { "@id" : "bts:Overlappinglesionofbladder", "@type" : "rdfs:Class", @@ -19635,6 +20127,17 @@ }, "sms:displayName" : "mm", "sms:required" : "sms:false" + }, { + "@id" : "bts:affinityenrichment", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "affinityenrichment", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "affinity enrichment", + "sms:required" : "sms:false" }, { "@id" : "bts:CranialnerveNOS", "@type" : "rdfs:Class", @@ -24684,6 +25187,17 @@ }, "sms:displayName" : "Floor of mouth NOS", "sms:required" : "sms:false" + }, { + "@id" : "bts:PairedEnd", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PairedEnd", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Paired End", + "sms:required" : "sms:false" }, { "@id" : "bts:LymphaticleukemicNOS", "@type" : "rdfs:Class", @@ -24772,6 +25286,17 @@ }, "sms:displayName" : "Illumina Genome Analyzer IIx", "sms:required" : "sms:false" + }, { + "@id" : "bts:LongRead", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "LongRead", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Long Read", + "sms:required" : "sms:false" }, { "@id" : "bts:Bodyofpenis", "@type" : "rdfs:Class", @@ -26796,6 +27321,17 @@ }, "sms:displayName" : "Burkitt tumor", "sms:required" : "sms:false" + }, { + "@id" : "bts:rRNAdepletion", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "rRNAdepletion", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "rRNA depletion", + "sms:required" : "sms:false" }, { "@id" : "bts:H1", "@type" : "rdfs:Class", @@ -28193,6 +28729,17 @@ }, "sms:displayName" : "CDKN2A mutation", "sms:required" : "sms:false" + }, { + "@id" : "bts:PCR", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "PCR", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "PCR", + "sms:required" : "sms:false" }, { "@id" : "bts:Peripheralnervesandautonomicnervoussystemofabdomen", "@type" : "rdfs:Class", @@ -28666,6 +29213,17 @@ }, "sms:displayName" : "chr13", "sms:required" : "sms:false" + }, { + "@id" : "bts:other", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "other", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "other", + "sms:required" : "sms:false" }, { "@id" : "bts:OrbitNOS", "@type" : "rdfs:Class", @@ -30888,6 +31446,17 @@ }, "sms:displayName" : "Submandibular gland", "sms:required" : "sms:false" + }, { + "@id" : "bts:hybridselection", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "hybridselection", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "hybrid selection", + "sms:required" : "sms:false" }, { "@id" : "bts:PigmentednevusNOS", "@type" : "rdfs:Class", @@ -32263,6 +32832,17 @@ }, "sms:displayName" : "Familial gastrointestinal stromal tumor", "sms:required" : "sms:false" + }, { + "@id" : "bts:Mid-length", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "Mid-length", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "Mid-length", + "sms:required" : "sms:false" }, { "@id" : "bts:H2A.Z", "@type" : "rdfs:Class", @@ -32824,6 +33404,17 @@ }, "sms:displayName" : "Grenada", "sms:required" : "sms:false" + }, { + "@id" : "bts:miRNAsizefractionation", + "@type" : "rdfs:Class", + "rdfs:comment" : "TBD", + "rdfs:label" : "miRNAsizefractionation", + "rdfs:subClassOf" : [ ], + "schema:isPartOf" : { + "@id" : "http://schema.biothings.io/" + }, + "sms:displayName" : "miRNA size fractionation", + "sms:required" : "sms:false" }, { "@id" : "bts:Niue", "@type" : "rdfs:Class", diff --git a/modules/classes/sequencing.yaml b/modules/classes/sequencing.yaml index 24a28c6..3ab6eb5 100644 --- a/modules/classes/sequencing.yaml +++ b/modules/classes/sequencing.yaml @@ -1,6 +1,8 @@ classes: Sequencing: + abstract: true + description: Base template for some type of sequencing data, for which below properties are relevant/in common. annotations: requiresComponent: '' required: false @@ -14,9 +16,20 @@ classes: - SequencingPlatform - NucleicAcidSource - LibraryConstructionMethod + - LibrarySelectionMethod + - LibraryLayout + - LibraryPreparationKitName + - LibraryPreparationKitVendor + - LibraryPreparationKitVersion - ReadIndicator + - ReadLength - Read1 - Read2 + - TargetDepth + - AdapterName + - AdapterSequence + - BatchID + - LaneNumber - TechnicalReplicateGroup SingleCellSequencing: @@ -54,8 +67,8 @@ classes: required: false slots: - ScRNAseqWorkflowType - - WorkflowVersion - ScRNAseqWorkflowParametersDescription + - WorkflowVersion - WorkflowLink - GenomicReference - GenomicReferenceURL @@ -107,7 +120,6 @@ classes: slots: - SingleNucleusBuffer - TranspositionReaction - - ScATACseqLibraryLayout - NucleusIdentifier - NucleiBarcodeLength - NucleiBarcodeRead @@ -120,6 +132,16 @@ classes: - MedianPercentageofMitochondrialReadsperNucleus - TotalReads + + BulkDNA-seqLevel1: + is_a: Sequencing + annotations: + requiresComponent: '' + required: false + slots: + - TargetCaptureKit + + BulkMethylation-seqLevel1: is_a: Sequencing annotations: @@ -127,8 +149,10 @@ classes: required: false slots: - GenomicCoverageType - - + + +# These are not templates, schematic-specific way of adding specific dependencies + CEL-seq2: is_a: ScRNA-seqLevel1 annotations: diff --git a/modules/enums/Sequencing.yaml b/modules/enums/Sequencing.yaml index 86bfe6e..d8a2018 100644 --- a/modules/enums/Sequencing.yaml +++ b/modules/enums/Sequencing.yaml @@ -1,74 +1,80 @@ enums: NucleicAcidSourceEnum: permissible_values: - Single Cell: null - Bulk Whole Cell: null - Single Nucleus: null - Bulk Nuclei: null + Single Cell: + Bulk Whole Cell: + Single Nucleus: + Bulk Nuclei: LibraryConstructionMethodEnum: permissible_values: - 10xV3: null - inDropsV2: null - 10xV1.1: null - 10xV3.1: null - Drop-seq: null - 10xV2: null - 10xV1.0: null - Smart-seq2: null - Smart-SeqV4: null - sci-ATAC-seq: null - inDropsV3: null - CEL-seq2: null - TruDrop: null + 10xV3: + inDropsV2: + 10xV1.1: + 10xV3.1: + Drop-seq: + 10xV2: + 10xV1.0: + Smart-seq2: + Smart-SeqV4: + sci-ATAC-seq: + inDropsV3: + CEL-seq2: + TruDrop: + LibraryLayoutEnum: + permissible_values: + Paired End: + Single Read: + Mid-length: + Long Read: SingleCellIsolationMethodEnum: permissible_values: - Microfluidics Chip: null - Droplets: null - FACS: null - Plates: null - 10x: null - Nuclei Isolation: null + Microfluidics Chip: + Droplets: + FACS: + Plates: + 10x: + Nuclei Isolation: DissociationMethodEnum: permissible_values: - Not Applicable: null - gentleMACS: null - Dounce: null - Enzymatic Digestion: null + Not Applicable: + gentleMACS: + Dounce: + Enzymatic Digestion: SpikeInEnum: permissible_values: - ERCC: null - Other Spike In: null - No Spike In: null - PhiX: null + ERCC: + Other Spike In: + No Spike In: + PhiX: ReverseTranscriptionPrimerEnum: permissible_values: - Feature barcoding: null - Oligo-dT: null - Poly-dT: null - Random: null + Feature barcoding: + Oligo-dT: + Poly-dT: + Random: EndBiasEnum: permissible_values: - 3 Prime: null - 5 Prime: null - Full Length Transcript: null + 3 Prime: + 5 Prime: + Full Length Transcript: SingleNucleusBufferEnum: permissible_values: - 10x: null - NIB: null - Omni: null + 10x: + NIB: + Omni: TranspositionReactionEnum: permissible_values: - Tn5: null - EZ-Tn5: null - Tn5-059: null - Nextera Tn5: null - Diagenode-unloaded Apex-Bio: null - Diagenode-loaded Apex-Bio: null - In-House: null + Tn5: + EZ-Tn5: + Tn5-059: + Nextera Tn5: + Diagenode-unloaded Apex-Bio: + Diagenode-loaded Apex-Bio: + In-House: ReadEnum: permissible_values: - Cell Barcode and DNA Insert: null - Sample Index and DNA Insert: null - DNA Insert: null - Sample Index: null - Cell Barcode: null + Cell Barcode and DNA Insert: + Sample Index and DNA Insert: + DNA Insert: + Sample Index: + Cell Barcode: diff --git a/modules/slots.yaml b/modules/slots.yaml index b2c48c0..8555e7e 100644 --- a/modules/slots.yaml +++ b/modules/slots.yaml @@ -9,6 +9,14 @@ slots: required: false description: A custom acquisition method [Text - max length 100 characters] annotations: + AdapterName: + title: Adapter Name + required: false + description: Name of the sequencing adapter. String + AdapterSequence: + title: Adapter Sequence + required: false + description: Base sequence of the sequencing adapter. String AdjacentBiospecimenIDs: title: Adjacent Biospecimen IDs required: false @@ -118,6 +126,11 @@ slots: required: false description: TBD annotations: + BatchID: + title: Batch ID, for sequencing or other experimental run context. + required: false + description: TBD + annotations: BIRADSMammographyBreastDensityCategory: title: BIRADS Mammography Breast Density Category required: false @@ -846,6 +859,11 @@ slots: description: The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease. annotations: range: LaboratoryTestEnum + LaneNumber: + title: Lane Number + required: false + description: Basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer + annotations: Laterality: title: Sample Laterality required: false @@ -863,6 +881,38 @@ slots: description: 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] annotations: range: LibraryConstructionMethodEnum + LibraryLayout: + title: Library Layout + required: false + description: Sequencing read type + annotations: + range: LibraryLayoutEnum + LibraryPreparationKitName: + title: Library Preparation Kit Name + required: false + description: Name of Library Preparation Kit. String + LibraryPreparationKitVendor: + title: Library Preparation Kit Vendor + required: false + description: Vendor of Library Preparation Kit. String + LibraryPreparationKitVersion: + title: Library Preparation Kit Version + required: true + description: Version of Library Preparation Kit. String + LibrarySelectionMethod: + title: Library Selection Method + required: true + description: How RNA molecules are isolated + annotations: + enum_range: + - hybrid selection + - PCR + - affinity enrichment + - poly-T enrichment + - random + - rRNA depletion + - miRNA size fractionation + - other LinkedDatasets: title: Linked Datasets required: false @@ -1302,6 +1352,12 @@ slots: required: false description: TBD annotations: + ReadLength: + title: Read Length + required: false + description: Length of the sequencing reads. Can be integer, null + annotations: + validationRules: 'num' RelationshipAgeatDiagnosis: title: Relationship Age at Diagnosis required: false @@ -1372,12 +1428,6 @@ slots: description: A yes/no indicator to ask if intransit metastases or satellite lesions are present. annotations: range: SatelliteMetastasisPresentIndicatorEnum - ScATACseqLibraryLayout: - title: scATACseq Library Layout - required: false - description: Sequencing read type - annotations: - range: ScATACseqLibraryLayoutEnum ScRNAseqWorkflowParametersDescription: title: scRNAseq Workflow Parameters Description required: false @@ -1560,6 +1610,15 @@ slots: required: false description: TBD annotations: + TargetCaptureKit: + title: Uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version + required: true + description: TBD + annotations: + TargetDepth: + title: Target Depth + required: false + description: Targeted read depth prior to sequencing. Integer TargetName: title: Target Name required: false