Unisys.JCR.1 1.3.2 MAGE-OM ArrayDesign ArrayDesign version 0 1 numberOfFeatures 0 1 PhysicalArrayDesign ZoneLayout numFeaturesPerRow 0 1 numFeaturesPerCol 0 1 spacingBetweenRows 0 1 spacingBetweenCols 0 1 ZoneGroup spacingsBetweenZonesX 0 1 spacingsBetweenZonesY 0 1 zonesPerX 0 1 zonesPerY 0 1 Zone row 0 1 column 0 1 upperLeftX 0 1 upperLeftY 0 1 lowerRightX 0 1 lowerRightY 0 1 ReporterGroup FeatureGroup featureWidth 0 1 featureLength 0 1 featureHeight 0 1 DesignElementGroup CompositeGroup Design{3AC7ADC3004C} arrayDesign 1 1 0 -1 ProtocolApplications{3ADB952F007D} protocolApplications 0 -1 1 1 CompositeGroups{3B00509100C7} compositeGroups 0 -1 0 -1 DesignProviders{3ADB947901B2} designProviders 0 -1 0 -1 ReporterGroups{3B7D5DEB0219} reporterGroups 0 -1 0 -1 FeatureGroups{3B7D600601A6} featureGroups 0 -1 1 1 Groups{3ADB98E802D6} zoneGroups 0 -1 0 -1 SurfaceType{3B71A7900060} surfaceType 0 1 1 1 Layouts{3ADB9B26017D} zoneLayout 0 1 1 1 DistanceUnit{3ADC75A500E6} distanceUnit 0 1 1 1 Locations{3ADB9AF90074} zoneLocations 0 -1 1 1 DistanceUnit{3ADC75DA0056} distanceUnit 0 1 1 1 Zone{3B74603F03A9} zone 1 1 0 -1 DistanceUnit{3B6DD8610334} distanceUnit 0 1 1 1 Zone{3B799254016D} zone 0 1 0 -1 Reporters{3B1EA3210055} reporters 1 -1 0 -1 DistanceUnit{3B1C146D036A} distanceUnit 0 1 1 1 Group2Feature{3B1EA32400B4} features 1 -1 featureGroup 1 1 TechnologyType{3B72C4FF001E} technologyType 0 1 1 1 FeatureShape{3B72C550029B} featureShape 0 1 1 1 Species{3B0D1F430111} species 0 1 1 1 Types{3B71A78B022F} types 0 -1 1 1 CompositeSequences{3B1EA31E0029} compositeSequences 1 -1 0 -1 String int float Constraint-G.711 rank: 1 Constraint-G.712 rank: 4 Constraint-G.713 rank: 5 Constraint-G.714 rank: 3 Constraint-G.715 rank: 2 Constraint-G.716 rank: 6 Array Array arrayIdentifier 0 1 arrayXOrigin 0 1 arrayYOrigin 0 1 originRelativeTo 0 1 FeatureDefect ArrayGroup barcode 0 1 arraySpacingX 0 1 arraySpacingY 0 1 numArrays 0 1 orientationMark 0 1 orientationMarkPosition 0 1 width 0 1 length 0 1 ArrayManufacture manufacturingDate 0 1 tolerance 0 1 ArrayManufactureDeviation Fiducial ManufactureLIMS quality 0 1 ManufactureLIMSBiomaterial bioMaterialPlateIdentifier 0 1 bioMaterialPlateRow 0 1 bioMaterialPlateCol 0 1 PositionDelta deltaX 1 1 deltaY 1 1 ZoneDefect Arrays2ArrayGroup{3AC7AF910263} arrays 1 -1 arrayGroup 0 1 Information2Arrays{3AD289180219} information 1 1 arrays 1 -1 ArrayManufactureDeviations{3AD289BA00A9} arrayManufactureDeviations 0 -1 1 1 Array{3ADC7A13039A} array 1 1 0 1 Defects{3AD289F000CF} featureDefects 0 -1 1 1 PositionDelta{3AD28A6500EB} positionDelta 0 1 1 1 Feature{3AD28D6B01FD} feature 1 1 0 -1 DefectType{3B71ACBA0332} defectType 1 1 1 1 Fiducials{3B095E090157} fiducials 0 -1 1 1 DistanceUnit{3B6B23FC0070} distanceUnit 0 1 1 1 SubstrateType{3B745D0B031D} substrateType 0 1 1 1 ProtocolApplications{3B09486701AE} protocolApplications 0 -1 1 1 FeatureLIMS{3B1BF280005E} featureLIMSs 0 -1 1 1 ArrayManufacturers{3B1C1F8C03AA} arrayManufacturers 0 -1 0 -1 QualityControlStatistics{3B73012B0257} qualityControlStatistics 0 -1 1 1 Adjustments{3AD28A6F02C6} adjustments 0 -1 1 1 DistanceUnit{3B6B23D90110} distanceUnit 0 1 1 1 FiducialType{3B71AD7500E2} fiducialType 0 1 1 1 Position{3B73006A03B8} position 1 1 1 1 Feature{3B1BF2EF02A3} feature 1 1 0 -1 IdentifierLIMS{3B1BF75E0345} identifierLIMS 0 1 1 1 BioMaterial{3B1C107802B9} bioMaterial 0 1 0 -1 DistanceUnit{3B71B07D012E} 0 -1 distanceUnit 0 1 PositionDelta{3B74621F0218} positionDelta 0 1 1 1 DefectType{3B7460E70274} defectType 1 1 1 1 enum {top,bottom,left,right} BioMaterial BioSource BioMaterial LabeledExtract BioSample Compound isSolvent 1 1 false CompoundMeasurement BioMaterialMeasurement Treatment order 0 1 SourceContact{3B72BB590315} sourceContact 0 -1 0 -1 Treatments{3ADDDA1700C4} treatments 0 -1 1 1 BioMaterial{3B045E2D01D0} bioMaterial 1 1 0 -1 MaterialType{3B71D3C20394} materialType 1 1 1 1 Characteristics{3B72BADB0093} characteristics 0 -1 1 1 QualityControlStatistics{3B730EE201E8} qualityControlStatistics 0 -1 1 1 Labels{3B1E50BE002E} labels 1 -1 0 -1 Type{3B71D28D02DB} type 1 1 1 1 Components{3ADDDC290275} componentCompounds 0 -1 1 1 Compound{3B032237005F} compound 1 1 0 -1 MerckIndex{3B742E7D0185} merckIndex 0 1 1 1 ExternalLIMS{3D3310C202FC} externalLIMS 0 1 1 1 Labels{3B1C2D6F02F7} labels 0 -1 0 -1 Compounds{3B02A36C02AB} compoundMeasurements 0 -1 1 1 Measurement{3B02A39E0357} measurement 0 1 1 1 Sources{3ADDDB4602A1} sourceBioMaterialMeasurements 0 -1 1 1 Measurement{3B045E360179} measurement 0 1 1 1 SourceBioMaterial{3B03060A0339} sourceBioMaterialMeasurements 0 -1 1 1 Measurement{3ADDD6B8020E} actionMeasurement 0 1 1 1 Action{3B71D0C70170} action 1 1 1 1 boolean HigherLevelAnalysis BioAssayDataCluster Node NodeContents NodeValue name 0 1 value 1 1 Nodes{3B1D1A6A027F} nodes 1 -1 1 1 ClusterBioAssayData{3B1D1C3A0381} clusterBioAssayData 0 1 0 -1 AnalysisResults{3B01830B012A} analysisResults 0 -1 0 -1 Nodes{3B1D1A900284} nodes 0 -1 1 1 Contents{3B1D1AC002A1} nodeContents 0 -1 1 1 NodeValue{3BC3932200BE} nodeValue 0 -1 1 1 DesignElementDimension{3B1D1C10016E} designElementDimension 0 1 1 1 QuantitationDimension{3B1D1C1400DD} quantitationDimension 0 1 1 1 BioAssayDimension{3B1D1C170345} bioAssayDimension 0 1 1 1 Scale{3BC3944E0264} scale 0 1 1 1 DataType{3BC395590150} dataType 0 1 1 1 Type{3BC46F630192} type 1 1 1 1 any BioAssay PhysicalBioAssay DerivedBioAssay Image URI 0 1 BioAssay Channel MeasuredBioAssay BioAssayCreation FeatureExtraction Hybridization ImageAcquisition BioAssayTreatment PhysicalBioAssayData{3B0316C20184} physicalBioAssayData 0 -1 1 1 Source{3B043BD80182} physicalBioAssaySource 1 1 0 -1 Creation2Target{3B04509C003C} physicalBioAssayTarget 1 1 bioAssayCreation 0 1 Treatments{3B0455C3030A} physicalBioAssay 1 1 bioAssayTreatments 0 -1 Target{3B0455CA0093} target 1 1 1 1 Data{3B3B4CD70050} derivedBioAssayData 0 -1 1 -1 Type{3B71B63C0237} type 0 1 1 1 Target{3B6C819501ED} bioAssayMapTarget 1 1 derivedBioAssayMap 0 -1 Channels{3B043E4901EF} channels 0 -1 1 1 Images{3B1C2C1F02A4} images 0 -1 1 1 Format{3B71B7EC035B} format 1 1 1 1 Channels{3B043DDB035A} channels 0 -1 1 -1 Sources{3B1D4D7D025A} sourceBioAssays 0 -1 0 -1 BioAssay{3B01A01D0058} bioAssay 1 1 0 -1 BioAssays{3B019FB503AC} bioAssays 0 -1 0 -1 FactorValues{3B01CCB501A8} bioAssayFactorValues 0 -1 1 1 BioAssays{3B02CBD302FD} bioAssays 0 -1 0 -1 TopLevelBioAssays{3B0D291E03AE} topLevelBioAssays 0 -1 0 -1 Channel{3B1D153B0231} channel 0 1 0 -1 FeatureExtraction2Target{3B043C860359} measuredBioAssayTarget 1 1 featureExtraction 0 1 Data{3B3B4CBF01B4} 1 -1 measuredBioAssayData 0 -1 Constraint-G.720 ordered rank: 3 Constraint-G.721 ordered rank: 1 AuditAndSecurity Person lastName 0 1 firstName 0 1 midInitials 0 1 Security Audit date 1 1 action 1 1 Organization SecurityGroup Contact URI 0 1 address 0 1 phone 0 1 tollFreePhone 0 1 email 0 1 fax 0 1 Affiliation{3B04130C021B} affiliation 0 1 0 -1 Performers{3B741EB200B0} performers 0 -1 0 -1 Security{3B7170AC03D0} security 0 1 0 -1 SecurityGroups{3B0415B3034E} securityGroups 0 -1 0 -1 Owner{3B1C27E50384} owner 0 -1 0 -1 AuditTrail{3B3CFAD802D7} auditTrail 0 -1 1 1 Performer{3B0415010121} performer 0 1 0 -1 Parent{3B9BF34F0250} parent 0 1 0 -1 Members{3B0415EE0385} 0 -1 members 1 -1 Roles{3B8ABBEB027D} roles 0 -1 1 1 Providers{3B017C1A0098} providers 0 -1 0 -1 HardwareManufacturers{3B041B6E00F4} hardwareManufacturers 0 -1 0 -1 SoftwareManufacturers{3B041B930101} softwareManufacturers 0 -1 0 -1 Contacts{3B1E500F007D} contacts 0 -1 0 -1 Date enum {creation,modification} BioAssayData BioAssayData QuantitationTypeDimension BioAssayMapping DesignElementDimension BioAssayDatum value 1 1 DerivedBioAssayData MeasuredBioAssayData QuantitationTypeMapping DesignElementMapping BioDataCube cube 1 1 order 1 1 BDQ BioDataValues BioDataTuples BioAssayDimension QuantitationTypeMap Transformation DesignElementMap BioAssayMap CompositeSequenceDimension ReporterDimension FeatureDimension Sources{3B003B74010B} bioAssayDataSources 0 -1 0 -1 BioAssayDimension{3B00423D03E4} bioAssayDimension 1 1 1 1 DesignElementDimension{3B00427401BC} designElementDimension 1 1 1 1 QuantitationTypeDimension{3B00429A006C} quantitationTypeDimension 1 1 1 1 Statistics{3B1BFA8203E1} summaryStatistics 0 -1 1 1 DataValues{3B3B869A00B8} bioDataValues 0 1 1 1 BioAssayData{3B01AFE20176} bioAssayData 0 -1 0 -1 QuantitationTypes{3AC7A51B021C} quantitationTypes 0 -1 0 -1 BioAssayMapping{3B003BF202C5} bioAssayMapping 0 1 1 1 BioAssayMaps{3B02F80E0042} bioAssayMaps 1 -1 0 -1 AssayData{3B003F690071} bioAssayTupleData 0 -1 1 1 DesignElement{3B003F8A0065} designElement 1 1 0 -1 QuantitationType{3B003F92016B} quantitationType 1 1 0 -1 Target2Transformation{3B003B31012D} producerTransformation 0 1 derivedBioAssayDataTarget 1 1 QuantitationTypeMaps{3B1D52BC020B} quantitationTypeMaps 1 -1 0 -1 Mapping{3B1D530B0345} quantitationTypeMapping 0 1 1 1 designElementMaps{3B1D52BA0027} designElementMaps 1 -1 0 -1 Mapping{3B1D530802A0} designElementMapping 0 1 1 1 Target{3B1D4DF30097} targetQuantitationType 1 1 quantitationTypeMaps 0 -1 Sources{3B1D4DF70287} sourcesQuantitationType 0 -1 0 -1 CompositeSequences{3B003E520034} compositeSequences 0 -1 0 -1 Reporters{3B9BF7DB01D1} reporters 0 -1 0 -1 Features{3B9BF892001C} containedFeatures 0 -1 0 -1 any[][][] enum {BDQ,BQD,DBQ,DQB,QBD,QDB} Experiment Experiment ExperimentDesign ExperimentalFactor FactorValue ExperimentDesign{3B013B06031C} experimentDesign 1 1 1 1 ExperimentalFactors{3B01CC080069} experimentalFactors 0 -1 1 1 ReplicateDescription{3B6B2A63027F} replicateDescription 0 1 1 1 QualityControlDescription{3B6B2AA00273} qualityControlDescription 0 1 1 1 NormalizationDescription{3B6B2AE90083} normalizationDescription 0 1 1 1 Types{3B71A4740232} types 0 -1 1 1 Factors{3B01CCF4000E} experimentalFactor 1 1 factorValues 0 -1 Category{3B72EF1800B0} category 0 1 1 1 Annotations{3D68160A01BB} annotations 0 -1 1 1 Measurement{3B01CD9C031D} measurement 0 1 1 1 Value{3D6816DD0205} value 0 1 1 1 Protocol Protocol text 0 1 title 0 1 Parameter ParameterValue value 0 1 ProtocolApplication activityDate 1 1 Software Hardware model 0 1 make 0 1 HardwareApplication serialNumber 0 1 SoftwareApplication version 0 1 releaseDate 0 1 Parameterizable URI 0 1 ParameterizableApplication Softwares{3B041A460383} 0 -1 softwares 0 -1 Hardwares{3B041A4C03A0} 0 -1 hardwares 0 -1 Protocol{3B1EB6A8023F} protocol 1 1 0 -1 Type{3B72CBE201C8} type 0 1 1 1 Types{3B02ACEF000D} parameterTypes 0 -1 1 1 Type{3B02AD670286} parameterType 1 1 0 -1 DataType{3B72CBEC02A8} dataType 0 1 1 1 DefaultValue{3D6814E6011B} defaultValue 0 1 1 1 Values{3B02ADBC0351} parameterValues 0 -1 1 1 SoftwareApplications{3B0D1C0D00C9} softwareApplications 0 -1 1 1 HardwareApplications{3B0D1C15000C} hardwareApplications 0 -1 1 1 ProtocolApplications{3B0433370294} 1 1 protocolApplications 0 -1 Software2Hardware{3B041BB50345} hardware 0 1 softwares 0 -1 Softwares{3B041C6E0297} softwares 0 -1 0 -1 Software{3B1EB62D030B} software 1 1 0 -1 Type{3B72CBE600B5} type 0 1 1 1 Hardware{3B1EB6280155} hardware 1 1 0 -1 Type{3B72CBDF0259} type 0 1 1 1 Description Description text 0 1 URI 0 1 DatabaseEntry accession 1 1 accessionVersion 0 1 URI 0 1 Database version 0 1 URI 0 1 ExternalReference exportedFromServer 0 1 exportedFromDB 0 1 exportID 0 1 exportName 0 1 OntologyEntry category 1 1 value 1 1 description 0 1 Descriptions{3B3CFAC302C3} descriptions 0 -1 1 1 DatabaseReferences{3B0E37260016} databaseReferences 0 -1 1 1 BibliographicReferences{3B0E37280330} bibliographicReferences 0 -1 1 1 ExternalReference{3B1BD3E000F4} externalReference 0 1 1 1 Annotations{3B04110E029A} annotations 0 -1 1 1 Database{3B0417CF00D3} database 1 1 0 -1 OntologyReference{3B71A350003D} ontologyReference 0 1 1 1 Type{3B73268201E4} type 0 1 1 1 SequenceDatabases{3B71DEEA01A6} sequenceDatabases 0 -1 1 1 DataType{3B71BBA301A0} dataType 1 1 1 1 Scale{3B71BC220333} scale 1 1 1 1 Parameters{3B7836640203} parameters 1 -1 1 1 Associations{3D726252036E} associations 0 -1 1 1 OntologyEntries{3B1E97BB00F6} ontologyEntries 0 -1 1 1 PolymerType{3B71D95D00DA} polymerType 1 1 1 1 Type{3B71E0C10366} type 1 1 1 1 Species{3B71E13701C1} species 0 1 1 1 ControlType{3B72BE1C0163} controlType 0 1 1 1 FailTypes{3B72C0580120} failTypes 0 -1 1 1 WarningType{3B72C13601B5} warningType 0 1 1 1 Measurement Measurement type 1 1 absolute value 0 1 kindCV 1 1 other otherKind 0 1 Unit unitName 0 1 TimeUnit unitNameCV 1 1 DistanceUnit unitNameCV 1 1 TemperatureUnit unitNameCV 1 1 QuantityUnit unitNameCV 1 1 MassUnit unitNameCV 1 1 VolumeUnit unitNameCV 1 1 ConcentrationUnit unitNameCV 1 1 Unit{3B1C1794039C} unit 0 1 1 1 DistanceUnit{3ADB9FD70170} distanceUnit 0 1 1 1 enum {absolute,change} enum {time,distance,temperature,quantity,mass,volume,concentration,other} enum {years,months,weeks,d,h,m,s,us,other} enum {fm,pm,nm,um,mm,cm,m,other} enum {degree_C,degree_F,K} enum {mol,amol,fmol,pmol,nmol,umol,mmol,molecules,other} enum {kg,g,mg,ug,ng,pg,fg,other} enum {mL,cc,dL,L,uL,nL,pL,fL,other} enum {M,mM,uM,nM,pM,fM,mg/mL,mL/L,g/L,gram_percent,mass/volume_percent, mass/mass_percent,other} BioEvent BioEvent Map BQS BibliographicReference title 0 1 authors 0 1 publication 0 1 publisher 0 1 editor 0 1 year 0 1 volume 0 1 issue 0 1 pages 0 1 URI 0 1 BioSequence SeqFeature basis 1 1 SeqFeatureLocation strandType 1 1 BioSequence length 0 1 isApproximateLength 0 1 isCircular 0 1 sequence 0 1 SequencePosition start 0 1 end 0 1 Regions{3B0D2DA602D0} regions 0 -1 1 1 SeqFeatures{3B1C1B66021C} seqFeatures 0 -1 1 1 Subregions{3B0D2DC30032} subregions 0 -1 1 1 Coordinate{3B1E640101A1} coordinate 1 1 1 1 ImmobilizedCharacteristics{3B0D323B03A9} immobilizedCharacteristics 0 -1 0 -1 BiologicalCharacteristics{3B1C028302F7} biologicalCharacteristics 0 -1 0 -1 enum {experimental, computational,both,unknown,NA} QuantitationType StandardQuantitationType QuantitationType isBackground 1 1 SpecializedQuantitationType DerivedSignal MeasuredSignal Error PValue ExpectedValue Ratio ConfidenceIndicator PresentAbsent Failed ConfidenceIndicator2Target{3B72D9930259} targetQuantitationType 1 1 confidenceIndicators 0 3 DesignElement DesignElement Position x 1 1 y 1 1 Reporter ReporterPosition CompositePosition CompositeSequence Feature MismatchInformation startCoord 1 1 newSequence 0 1 replacedLength 1 1 FeatureInformation CompositeCompositeMap FeatureReporterMap ReporterCompositeMap FeatureLocation row 1 1 column 1 1 Position{3ADB9E4C023A} position 0 1 1 1 Reporter{3B1D3E9D0376} reporter 1 1 featureReporterMaps 0 -1 Reporter{3B1D459F0362} reporter 1 1 0 -1 Sources{3B1D3EA0028A} reporterPositionSources 1 -1 1 1 MismatchInformation{3B27F14D025C} mismatchInformation 0 -1 1 1 Sources{3B1D3EA80264} compositePositionSources 1 -1 1 1 Composite{3B1D464C0176} composite 1 1 0 -1 MismatchInformation{3B27F176021F} mismatchInformation 0 -1 1 1 CompositeSequence{3B1D3EA3013A} compositeSequence 1 1 reporterCompositeMaps 0 -1 CompositeSequence{3B1D3EA501B5} compositeSequence 1 1 compositeCompositeMaps 0 -1 Feature{3B1D3E9B002A} feature 1 1 1 1 Features2ControlFeatures{3B72C2DF01B6} controlFeatures 0 -1 controlledFeatures 0 -1 FeatureLocation{3B9E4D2B02D5} featureLocation 0 1 1 1 MismatchInformation{3B27F1970321} mismatchInformation 0 -1 1 1 Sources{3B27F0F40128} featureInformationSources 1 -1 1 1 Describable Identifiable identifier 1 1 name 0 1 Extendable NameValueType name 0 1 value 0 1 type 0 1 PropertySets{3B6B34D8038D} propertySets 0 -1 1 1 PropertySets{3B3CF8DC03DB} propertySets 0 -1 1 1 {Array?ArrayDesign}{3C3338AD02E9} {Array?AuditAndSecurity}{3C33480102EB} {Array?Description}{3C33482900AE} {Array?DesignElement}{3C33484101AD} {Array?Measurement}{3C33485F03AE} {Array?BioMaterial}{3C3348810295} {Array?Protocol}{3C33489901EF} {Array?Common}{3C3348B50254} {ArrayDesign?DesignElement}{3C3341A2014B} {ArrayDesign?AuditAndSecurity}{3C3346630368} {ArrayDesign?Description}{3C33468001D9} {ArrayDesign?Protocol}{3C33468D0390} {ArrayDesign?Measurement}{3C3346AC0038} {ArrayDesign?Common}{3C334811028A} {AuditAndSecurity?Description}{3C334650019E} {AuditAndSecurity?Common}{3C334BC80024} {BioAssay?BioAssayData}{3C3345CF0148} {BioAssay?BioMaterial}{3C3345EE0338} {BioAssay?Description}{3C334601012C} {BioAssay?Array}{3C33462E0018} {BioAssay?BioEvent}{3C334A3D02CF} {BioAssay?Common}{3C334BF60306} {BioEvent?Protocol}{3C33454D0015} {BioEvent?Common}{3C334BC2012A} {BioAssayData?Common}{3C33457D01C3} {BioAssayData?BioAssay}{3C33458B001E} {BioAssayData?QuantitationType}{3C3345960128} {BioAssayData?DesignElement}{3C33459C01A9} {BioAssayData?BioEvent}{3C334A630248} {BioSequence?Description}{3C33472F02C1} {BioSequence?Common}{3C334BB8039D} {BioMaterial?AuditAndSecurity}{3C3346CC039B} {BioMaterial?Description}{3C3346DA030F} {BioMaterial?Measurement}{3C3346E70119} {BioMaterial?Common}{3C3346FA021B} {BioMaterial?BioEvent}{3C334A320021} {Description?BQS}{3C3344D100FD} {Description?AuditAndSecurity}{3C3344E001DB} {Description?Common}{3C334BD5002D} {Protocol?Description}{3C33491F00B1} {Protocol?AuditAndSecurity}{3C33492A0360} {Protocol?Measurement}{3C33494B034A} {Protocol?Common}{3C334BBE00A2} {BQS?Common}{3C334BD00184} {Experiment?AuditAndSecurity}{3C3347B303E3} {Experiment?HigherLevelAnalysis}{3C3347BC03D2} {Experiment?BioAssayData}{3C3347C50122} {Experiment?BioAssay}{3C3347CB0080} {Experiment?Measurement}{3C3347D60090} {Experiment?Description}{3C3347DA02C7} {Experiment?Common}{3C334BED0104} {QuantitationType?BioAssay}{3C3345090176} {QuantitationType?Description}{3C3345210170} {QuantitationType?Common}{3C334BF10363} {DesignElement?BioSequence}{3C33446E023B} {DesignElement?ArrayDesign}{3C334756026D} {DesignElement?Description}{3C33476C025B} {DesignElement?Measurement}{3C33477B0071} {DesignElement?BioAssayData}{3C334A9D01A1} {DesignElement?Common}{3C334C0402AC} {HigherLevelAnalysis?Description}{3C3348E6036C} {HigherLevelAnalysis?QuantitationType}{3C3348F0023A} {HigherLevelAnalysis?BioAssayData}{3C3348F60199} {HigherLevelAnalysis?DesignElement}{3C334906023C} {HigherLevelAnalysis?Common}{3C334BE40205} {Measurement?Common}{3C334BDB03B1} {Common?Description}{3C3344360335} {Common?AuditAndSecurity}{3C33444A0081} Component View Array ArrayDesign AuditAndSecurity BioAssay BioEvent BioAssayData BioSequence BioMaterial Description Protocol BQS Experiment QuantitationType DesignElement HigherLevelAnalysis Measurement Common documentation Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, short (~20-100mer) nucleotide sequences onto the features. Reporters can be grouped together into CompositeSequences, typically representing a gene or one or more splice variants in gene expression experiments. There are then two distinct ways that DesignElements are grouped. The one described in the ArrayDesign package by FeatureGroup, ReporterGroup and CompositeGroup is by technology type, that is, one might want to segregate the controls to a Group and all the non-controls to another. Or if PCR Product and Oligos are both used on an array they would likely be in different groups. The grouping described in the DesignElement package by the mappings relates the Features to the Reporter, the Reporters to CompositeSequence, and at higher levels, CompositeSequences to CompositeSequence. persistence transient documentation Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features. RationalRose:Tool#1 Java RationalRose$Java:Final False RationalRose:Tool#1 Java RationalRose$Java:Static False RationalRose:Tool#1 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#1 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#1 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#1 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#1 Java RationalRose$Java:GenerateCode True RationalRose:Tool#1 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#1 Java RationalRose$Java:ConstructorIs public documentation The version of this design. documentation The number of features for this array persistence transient documentation A design that is expected to be used to manufacture physical arrays. persistence transient documentation Specifies the layout of features in a rectangular grid. documentation The number of features from left to right. documentation The number of features from top to bottom of the grid. documentation Spacing between the rows. documentation Spacing between the columns. persistence transient documentation Specifies a repeating area on an array. This is useful for printing when the same pattern is repeated in a regular fashion. documentation Spacing between zones, if applicable. documentation Spacing between zones, if applicable. documentation The number of zones on the x-axis. documentation The number of zones on the y-axis. persistence transient documentation Specifies the location of a zone on an array. documentation row position in the ZoneGroup documentation column position in the ZoneGroup. documentation Boundary vertical upper left position relative to (0,0). documentation Boundary horizontal upper left position relative to (0,0). documentation Boundary vertical lower right position relative to (0,0). documentation Boundary horizontal lower right position relative to (0,0). persistence transient documentation Allows specification of the type of Reporter Design Element. RationalRose:Tool#4 Java RationalRose$Java:Final False RationalRose:Tool#4 Java RationalRose$Java:Static False RationalRose:Tool#4 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#4 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#4 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#4 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#4 Java RationalRose$Java:GenerateCode True RationalRose:Tool#4 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#4 Java RationalRose$Java:ConstructorIs public persistence transient documentation A collection of like features. documentation The width of the feature. documentation The length of the feature. documentation The height of the feature. persistence transient documentation The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained. RationalRose:Tool#4 Java RationalRose$Java:Final False RationalRose:Tool#4 Java RationalRose$Java:Static False RationalRose:Tool#4 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#4 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#4 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#4 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#4 Java RationalRose$Java:GenerateCode True RationalRose:Tool#4 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#4 Java RationalRose$Java:ConstructorIs public persistence transient documentation Allows specification of the type of Composite Design Element. documentation The association of a physical array with its array design. documentation Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array. documentation The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types. documentation The primary contact for information on the array design documentation The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types. documentation The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types. documentation In the case where the array design is specified by one or more zones, allows specifying where those zones are located. documentation The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc. documentation Describes the rectangular layout of features in the array design. documentation Unit of the ZoneLayout attributes. documentation Describes the location of different zones within the array design. documentation Unit for the ZoneGroup attributes. documentation Reference to the Zone that was misprinted. documentation Unit for the Zone attributes. documentation A reference to the zone this feature is in. documentation The reporters that belong to this group. documentation The unit for the feature measures. documentation The features that belong to this group. documentation The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography. documentation The expected shape of the feature on the array: circular, oval, square, etc. documentation The organism from which the biosequences of this group are from. documentation The specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo. documentation The compositeSequences that belong to this group. documentation Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters. persistence transient documentation The physical substrate along with its features and their annotation documentation An identifying string, e.g. a barcode. documentation This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial. documentation This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial. documentation What the array origin is relative to, e.g. upper left corner, fiducial, etc. persistence transient documentation Stores the defect information for a feature. RationalRose:Tool#11 Java RationalRose$Java:Final False RationalRose:Tool#11 Java RationalRose$Java:Static False RationalRose:Tool#11 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#11 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#11 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#11 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#11 Java RationalRose$Java:GenerateCode True RationalRose:Tool#11 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#11 Java RationalRose$Java:ConstructorIs public persistence transient documentation An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes. documentation Identifier for the ArrayGroup. documentation If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay. documentation If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay. documentation This attribute defines the number of arrays on a chip or a slide. documentation For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc. documentation One of top, bottom, left or right. documentation The width of the platform documentation The length of the platform. persistence transient documentation Describes the process by which arrays are produced. RationalRose:Tool#12 Java RationalRose$Java:Final False RationalRose:Tool#12 Java RationalRose$Java:Static False RationalRose:Tool#12 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#12 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#12 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#12 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#12 Java RationalRose$Java:GenerateCode True RationalRose:Tool#12 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#12 Java RationalRose$Java:ConstructorIs public documentation The date the arrays were manufactured documentation The allowable error of a feature printed to its intended position. persistence transient documentation Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g. a tip failed to print several spots). persistence transient documentation A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid. persistence transient documentation Information on the physical production of arrays within the laboratory. documentation A brief description of the quality of the array manufacture process. persistence transient documentation Stores the location from which a biomaterial was obtained. documentation The plate from which a biomaterial was obtained. documentation The plate row from which a biomaterial was obtained. Specified by a letter. documentation The plate column from which a biomaterial was obtained. Specified by a number. persistence transient documentation The delta the feature was actually printed on the array from the position specified for the feature in the array design. documentation Deviation from the y coordinate of this feature's position. documentation Deviation from the y coordinate of this feature's position. persistence transient documentation Stores the defect information for a zone. documentation Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide. documentation Association between the manufactured array and the information on that manufacture. documentation Association to classes to describe deviations from the ArrayDesign. documentation The array used in the BioAssayCreation event. documentation Description on features who are manufactured in a different location than specified in the ArrayDesign. documentation How the feature deviates in position from the ArrayDesign. documentation The feature that was manufactured defectively. documentation Indicates the type of defect (e.g. a missing feature or a moved feature). documentation Association to the marks on the Array for alignment for the scanner. documentation The unit of the measurement attributes. documentation Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays. documentation The protocols followed in the manufacturing of the arrays. documentation Information on the manufacture of the features. documentation The person or organization to contact for information concerning the ArrayManufacture. documentation Information on the quality of the ArrayManufacture. documentation Descriptions of how a Zone has been printed differently than specified in the ArrayDesign. documentation The units the fiducial is measured in. documentation A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark). documentation The position, relative to the upper left corner, of the fiducial documentation The feature whose LIMS information is being described. documentation Association to a LIMS data source for further information on the manufacturing process. documentation The BioMaterial used for the feature. documentation The unit for the attributes. documentation How the zone deviates in position from the ArrayDesign. documentation Indicates the type of defect (e.g. a missing zone or a moved zone). documentation The classes in this package describe how a BioSource is treated to obtain the BioMaterial (typically a LabeledExtract) that is used by a BioAssayCreation in combination with an Array to produce a PhysicalBioAssay. A set of treatments are typically linear in time but can form a Directed Acyclic Graph. persistence transient documentation The BioSource is the original source material before any treatment events. It is also a top node of the directed acyclic graph generated by treatments. The association to OntologyEntry allows enumeration of a BioSource's inherent properties. persistence transient documentation BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)). RationalRose:Tool#13 Java RationalRose$Java:Final False RationalRose:Tool#13 Java RationalRose$Java:Static False RationalRose:Tool#13 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#13 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#13 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#13 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#13 Java RationalRose$Java:GenerateCode True RationalRose:Tool#13 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#13 Java RationalRose$Java:ConstructorIs public persistence transient documentation LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties). persistence transient documentation BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract. persistence transient documentation A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media. documentation A Compound may be a special case Solvent. persistence transient documentation A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound. persistence transient documentation A BioMaterialMeasurement is a pairing of a source BioMaterial and an amount (Measurement) of that BioMaterial. persistence transient documentation The process by which a biomaterial is created (from source biomaterials). Treatments have an order and an action. documentation The chronological order in which a treatment occurred (in relation to other treatments). More than one treatment can have the same chronological order indicating that they happened (or were caused to happen) simultaneously. documentation The BioSource's source is the provider of the biological material (a cell line, strain, etc...). This could be the ATTC (American Tissue Type Collection). documentation This association is one way from BioMaterial to Treatment. From this a BioMaterial can discover the amount and type of BioMaterial that was part of the treatment that produced it. documentation A source BioMaterial for a treatment. documentation The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc. documentation Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc. documentation Measures of the quality of the BioMaterial. documentation Compound used to label the extract. documentation The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract. documentation The Compounds and their amounts used to create this Compound. documentation A Compound to be used to create another Compound. documentation The Merck Index of this Compound. documentation Reference to an entry in an external LIMS data source. documentation The compound used to label the extract. documentation The compounds and their amounts used in the treatment. documentation The amount of the Compound. documentation The BioMaterials and the amounts used in the treatment documentation The amount of the BioMaterial. documentation The BioSample and its amount used in the BioAssayCreation event. documentation Measures events like duration, centrifuge speed, etc. documentation The event that occurred (e.g. grow, wait, add, etc...). The actions should be a recommended vocabulary documentation Describes the results of performing analysis on the result of the BioAssayData from an Experiment. persistence transient documentation A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes. persistence transient documentation An individual component of a clustering. May contain other nodes. persistence transient documentation The contents of a node for any or all of the three Dimensions. If a node only contained genes just the DesignElementDimension would be defined. persistence transient documentation A value associated with the Node that can rank it in relation to the other nodes produced by the clustering algorithm. documentation The name for this value. documentation The value for this NodeValue. documentation The nodes of the cluster. documentation The BioAssayData whose values were used by the cluster algorithm. documentation The results of analyzing the data, typically with a clustering algorithm. documentation Nested nodes of the BioAssayDataCluster. documentation The contents of the node, expressed as either a one, two or three dimensional object. documentation Values or measurements for this node that may be produced by the clustering algorithm. Typical are distance values for the nodes. documentation The relevant DesignElements for this NodeContents from the BioAssayData. documentation The relevant QuantitationTypes for this NodeContents from the BioAssayData. documentation The relevant BioAssays for this NodeContents from the BioAssayData. documentation The scale (linear, log10, ln, etc.) of the value. documentation The data type of the any element. documentation The type of value, distance, etc. documentation Provides classes that contain information and annotation on the event of joining an Array with a BioMaterial preparation, the acquisition of images and the extraction of data on a per feature basis from those images. The derived classes of BioAssay represent the base PhysicalBioAssays which lead to the production of Images, the MeasuredBioAssay which is associated with the set of quantitations produced by FeatureExtraction, and DerivedBioAssay (see BioAssayData package) which groups together BioAssays that have been analyzed together to produce further refinement of the quantitations. The design of this package and the related BioAssayData package was driven by the following query considerations and the desire to return as little data as necessary to satisfy a query. Often, the first set of queries for experiments below the Experiment level will want to discover the why of an experiment and this is captured in the BioAssay class through its FactorValue, BioEvent and Description associations. This separates it from the data but allows an overview of the experiment hierarchy. The BioAssayData class association to BioDataValues is optional only to allow queries on them to discover the how of the experiment through the association to the transformation and mappings of the three BioAssayData dimensions and the protocols used. Once a researcher, for instance, has narrowed down the experiments of interest then the actual data, represented by the BioDataValues, can be downloaded. Because these data can be in the hundreds of megabytes to gigabytes range, it was considered desirable to be able to return information and annotation on the experiment without the data. persistence transient documentation A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event). persistence transient documentation A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays. persistence transient documentation An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay). RationalRose:Tool#17 Java RationalRose$Java:Final False RationalRose:Tool#17 Java RationalRose$Java:Static False RationalRose:Tool#17 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#17 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#17 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#17 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#17 Java RationalRose$Java:GenerateCode True RationalRose:Tool#17 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#17 Java RationalRose$Java:ConstructorIs public documentation The file location in which an image may be found. persistence transient documentation An abstract class which represents both physical and computational groupings of arrays and biomaterials. RationalRose:Tool#17 Java RationalRose$Java:Final False RationalRose:Tool#17 Java RationalRose$Java:Static False RationalRose:Tool#17 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#17 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#17 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#17 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#17 Java RationalRose$Java:GenerateCode True RationalRose:Tool#17 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#17 Java RationalRose$Java:ConstructorIs public persistence transient documentation A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength. persistence transient documentation A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. Often uses images which are referenced through the physical bioAssay. persistence transient documentation The process by which an array and one or more biomaterials are combined to create a bioAssayCreation. persistence transient documentation The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay. persistence transient documentation The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array. persistence transient documentation The process by which an image is generated (typically scanning). persistence transient documentation The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...). documentation The Images associated with this PhysicalBioAssay by ImageAcquisition. documentation The PhysicalBioAssay used in the FeatureExtraction event. documentation The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event. documentation The set of treatments undergone by this PhysicalBioAssay. documentation The PhysicalBioAssay that was treated. documentation The data associated with the DerivedBioAssay. documentation The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc. documentation The DerivedBioAssay that is produced by the sources of the BioAssayMap. documentation The channels captured in this image. documentation The images produced by the ImageAcquisition event. documentation The file format of the image typically a TIF or a JPEG. documentation Channels can be non-null for all subclasses. For instance, collapsing across replicate features will create a DerivedBioAssay that will potentially reference channels. documentation The sources of the BioAssayMap that are used to produce a target DerivedBioAssay. documentation The BioAssay associated with the value of the BioAssayDatum. documentation The BioAssays for this Dimension documentation The values that this BioAssay is associated with for the experiment. documentation The collection of BioAssays for this Experiment. documentation The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.) documentation The optional channel associated with the QuantitationType. documentation The association between the MeasuredBioAssay and the FeatureExtraction Event. documentation The data associated with the MeasuredBioAssay. documentation Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation. persistence transient documentation A person for which the attributes are self describing. persistence transient documentation Permission information for an object as to ownership, write and read permissions. persistence transient documentation Tracks information on the contact that creates or modifies an object. documentation The date of a change. documentation Indicates whether an action is a creation or a modification. persistence transient documentation Organizations are entities like companies, universities, government agencies for which the attributes are self describing. persistence transient documentation Groups contacts together based on their security privileges. persistence transient documentation A contact is either a person or an organization. documentation The organization a person belongs to. documentation The people who performed the protocol. documentation Information on the security for the instance of the class. documentation Specifies which security groups have permission to view the associated object. documentation The owner of the security rights. documentation A list of Audit instances that track changes to the instance of Describable. documentation The contact for creating or changing the instance referred to by the Audit. documentation The containing organization (the university or business which a lab belongs to, etc.) documentation The members of the Security Group. documentation The roles (lab equipment sales, contractor, etc.) the contact fills. documentation The providers of the Experiment, its data and annotation. documentation Contact for information on the Hardware. documentation Contact for information on the software. documentation Information on the contacts for the database documentation The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired. persistence transient documentation Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data. RationalRose:Tool#23 Java RationalRose$Java:Final False RationalRose:Tool#23 Java RationalRose$Java:Static False RationalRose:Tool#23 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#23 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#23 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#23 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#23 Java RationalRose$Java:GenerateCode True RationalRose:Tool#23 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#23 Java RationalRose$Java:ConstructorIs public persistence transient documentation An ordered list of quantitationTypes. persistence transient documentation Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension. persistence transient documentation An ordered list of designElements. It will be realized as one of its three subclasses. persistence transient documentation A single cell of the quantitation, bioAssay, designElement matrix. documentation The datum value. persistence transient documentation The output of a transformation event. persistence transient documentation The data associated with the MeasuredBioAssay produced by FeatureExtraction. persistence transient documentation Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension. persistence transient documentation Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension. persistence transient documentation A three-dimensional cube representation of the data. documentation Three dimension array, indexed by the three dimensions to provide the data for the BioAssayData. documentation The order to expect the dimension. The enumeration uses the first letter of the three dimensions to represent the six possible orderings. persistence transient documentation The actual values for the BioAssayCube. persistence transient documentation A relational, tuple representation of the data. persistence transient documentation An ordered list of bioAssays. persistence transient documentation A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType. persistence transient documentation The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions. persistence transient documentation A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement. persistence transient documentation The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays. persistence transient documentation Specialized DesignElementDimension to hold CompositeSequences. persistence transient documentation Specialized DesignElementDimension to hold Reporters. persistence transient documentation Specialized DesignElementDimension to hold Features. documentation The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData. documentation The BioAssays of the BioAssayData. documentation The DesignElements of the BioAssayData. documentation The QuantitationTypes of the BioAssayData. documentation Statistics on the Quality of the BioAssayData. documentation The data values of the BioAssayData. documentation The collection of BioAssayDatas for this Experiment. documentation The QuantitationTypes for this Dimension. documentation The collection of mappings for the BioAssays. documentation The maps for the BioAssays. documentation The collection of BioAssayData tuples. documentation The DesignElement associated with the value of the BioAssayDatum. documentation The QuantitationType associated with the value of the BioAssayDatum. documentation The association between the DerivedBioAssayData and the Transformation event that produced it. documentation The maps for the QuantitationTypes. documentation The collection of mappings for the QuantitationTypes. documentation The maps for the DesignElements. documentation The collection of mappings for the DesignElements. documentation The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol. documentation The QuantitationType sources for values for the transformation. documentation The CompositeSequences for this Dimension. documentation The reporters for this dimension. documentation The features for this dimension. documentation Represents the container for a hierarchical grouping of BioAssays. Can have the end results of Clustering Analysis specified and, through the ExperimentDesign, a description and annotation of the overall design of the experiment and what it was to show. persistence transient documentation The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign. persistence transient documentation The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain. persistence transient documentation ExperimentFactors are the dependent variables of an experiment (e.g. time, glucose concentration, ...). persistence transient documentation The value for a ExperimentalFactor documentation The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays. documentation The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays. documentation Description of the replicate strategy of the Experiment. documentation Description of the quality control aspects of the Experiment. documentation Description of the normalization strategy of the Experiment. documentation Classification of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc. documentation The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor. documentation The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols). documentation Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #. documentation The measured value for this factor. documentation Allows a more complex value to be specified for a FactorValue than a simple Measurement. documentation Provides a relatively immutable class, Protocol, that can describe a generic laboratory procedure or analysis algorithm, for example, and an instance class, ProtocolApplication, which can describe the actual application of a protocol. The ProtocolApplication provides values for the replaceable parameters of the Protocol and, through the Description association of Describable, any variation from the Protocol. persistence transient documentation A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters. documentation The text description of the Protocol. documentation The title of the Protocol persistence transient documentation A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures. persistence transient documentation The value of a Parameter. documentation The value of the parameter. Will have the datatype of its associated Parameter. persistence transient documentation The use of a protocol with the requisite Parameters and ParameterValues. RationalRose:Tool#27 Java RationalRose$Java:Final False RationalRose:Tool#27 Java RationalRose$Java:Static False RationalRose:Tool#27 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#27 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#27 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateCode True RationalRose:Tool#27 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#27 Java RationalRose$Java:ConstructorIs public documentation When the protocol was applied. persistence transient documentation Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc... RationalRose:Tool#27 Java RationalRose$Java:Final False RationalRose:Tool#27 Java RationalRose$Java:Static False RationalRose:Tool#27 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#27 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#27 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateCode True RationalRose:Tool#27 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#27 Java RationalRose$Java:ConstructorIs public persistence transient documentation Hardware represents the hardware used. Examples of Hardware include: computers, scanners, wash stations etc... RationalRose:Tool#27 Java RationalRose$Java:Final False RationalRose:Tool#27 Java RationalRose$Java:Static False RationalRose:Tool#27 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#27 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#27 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#27 Java RationalRose$Java:GenerateCode True RationalRose:Tool#27 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#27 Java RationalRose$Java:ConstructorIs public documentation The model (number) of a piece of hardware. documentation The make of the Hardware (its manufacturer). persistence transient documentation The use of a piece of hardware with the requisite Parameters and ParameterValues. documentation Manufacturer's identifier for the Hardware. persistence transient documentation The use of a piece of software with the requisite Parameters and ParameterValues. documentation The version of the software. documentation When the software was released. persistence transient documentation The Parameterizable interface encapsulates the association of Parameters with ParameterValues. documentation Where an instantiated Parameterizable is located. persistence transient documentation The interface that is the use of a Parameterizable class. documentation Software used by this Protocol. documentation Hardware used by this protocol. documentation The protocol that is being used. documentation The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc... documentation The description of the parameters for the Parameterizable class instance. documentation The parameter this value is for. documentation The type of data generated by the parameter i.e. Boolean, float, etc... documentation Allows the optional specification of a default values and the unit for the Parameter documentation The parameter values for this Parameterizable Application. documentation The use of software for the application of the protocol. documentation The use of hardware for the application of the protocol. documentation The applied protocols to the BioEvent. documentation Associates Hardware and Software together. documentation Software packages this software uses, i.e. operating system, 3rd party software packages, etc. documentation The underlying software. documentation The type of a piece of Software. Examples include: feature extractor... documentation The underlying hardware. documentation The type of a piece of Hardware. Examples include: scanner, wash station... documentation The classes in this package allow a variety of references to third party annotation and direct annotation by the experimenter. persistence transient documentation A free text description of an object. documentation The description. documentation A reference to the location and type of an outside resource. persistence transient documentation A reference to a record in a database. documentation The identifier used to look up the record. documentation The appropriate version of the accession (if applicable). documentation The location of the record. persistence transient documentation An address to a repository. documentation The version for which a DatabaseReference applies. documentation The location of the Database. persistence transient documentation A reference to the originating source for the object. documentation The originating server for the object, a network address or common name. documentation Name of the database, if applicable, that the object was exported from. documentation The identifier of the object at the originating source. documentation The name of the object at the originating source. persistence transient documentation A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI. documentation The category to which this entry belongs. documentation The value for this entry in this category. documentation The description of the meaning for this entry. documentation Free hand text descriptions. Makes available the associations of Description to an instance of Describable. documentation References to entries in databases. documentation References to existing literature. documentation Specifies where the described instance was originally obtained from. documentation Allows specification of ontology entries related to the instance being described. documentation Reference to the database where the DataEntry instance can be found. documentation Many ontology entries will not yet have formalized ontologies. In those cases, they will not have a database reference to the ontology. In the future it is highly encouraged that these ontologies be developed and ontologyEntry be subclassed from DatabaseReference. documentation The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD). documentation References an entry in a species database, like GenBank, UniGene, etc. documentation The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.} documentation Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER} documentation Criteria that can be used to look up the reference in a repository. documentation Allows an instance of an OntologyEntry to be further qualified. documentation Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc. documentation A choice of protein, RNA, or DNA. documentation The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc. documentation The organism from which this sequence was obtained. documentation If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.) documentation If at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.) documentation Similar to failType but indicates a warning rather than a failure. documentation The classes of this package provide utility information on the quantities of other classes to each other. persistence transient documentation A Measurement is a quantity with a unit. documentation The type of measurement, for instance if the measurement is five feet, it can be either absolute (five feet tall) or change (five feet further along). documentation The value of the measurement. kindCV (and otherKind) determine with Unit the datatype of value. documentation One of the enumeration values to determine the controlled vocabulary of the value. documentation Name of the controlled vocabulary if it isn't one of the Unit subclasses. persistence transient documentation The unit is a strict enumeration of types. documentation The name of the unit. persistence transient documentation Time persistence transient documentation Distance persistence transient documentation Temperature persistence transient documentation Quantity persistence transient documentation Mass persistence transient documentation Volume persistence transient documentation Concentration documentation The Unit associated with the Measurement. documentation The units of the x, y positions. documentation An abstract class representing an event that takes sources of some type to produce a target of some type. Each of the realized subclasses determines the type of the sources and the target. The association to a protocol application allows specification of how the event was performed. persistence transient documentation An abstract class to capture the concept of an event (either in the laboratory or a computational analysis). persistence transient documentation A Map is the description of how sources are transformed into a target. Provides an abstarct base class that separates the mapping BioEvents from the transforming. documentation Allows a reference to an article, book or other publication to be specified for searching repositories. persistence transient documentation Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference. documentation Describes a known gene or sequence. BioAssays typically seek to identify what BioSequences are expressed in a BioMaterial after treatments, the expression level measured from the association between the BioMaterial and the Array. The Array's Features typically provide known locations for this association to occur. Most often, the Reporter and CompositeSequence are known and the presence or absence of a particular BioSequence in the BioMaterial is based on whether there as been an association to the DesignElement targeted for it. Some other experiments may not know the DesignElement's target but can discover it with known properties of the BioSequences in the BioMaterial. persistence transient documentation Represents, in general, what would be a GenBank Feature Table annotation for a sequence. documentation How the evidence for a SeqFeature was determined. persistence transient documentation The location of the SeqFeature annotation. documentation Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' direction, is double stranded, etc. persistence transient documentation A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence. documentation The number of residues in the biosequence. documentation If length not positively known will be true documentation Indicates if the BioSequence is circular in nature. documentation The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G. The attribute is optional and instead of specified here, can be found through the DatabaseEntry. persistence transient documentation Designates the position of the Feature in its BioSequence. documentation The location of the base, for nucleotides, that the SeqFeature starts. documentation The location of the base, for nucleotides, that the SeqFeature ends. documentation Association to classes that describe the location with the sequence of the SeqFeature. documentation Association to annotations for subsequences. Corresponds to the GenBank Frame Table. documentation Regions within the SeqFeature. documentation At which base pairs or amino acid this SeqFeature begins and ends. documentation The sequence annotation on the BioMaterial this reporter represents. Typically the sequences will be an Oligo Sequence, Clone or PCR Primer. documentation The annotation on the BioSequence this CompositeSequence represents. Typically the sequences will be a Genes, Exons, or SpliceVariants. documentation This Package defines the classes for quantitations, such as measured and derived signal, error, and pvalue. The subclasses of StandardQuantitationType will be the best fit from FeatureExtraction or Transformation Protocol for the values obtained. Other values can be specified using SpecializedQuantitationType. persistence transient documentation Superclass for the named quantitation type. Useful for mapping to those languages that can use a fly-weight for processing the subclasses. persistence transient documentation A method for calculating a single datum of the matrix (e.g. raw intensity, background, error). RationalRose:Tool#43 Java RationalRose$Java:Final False RationalRose:Tool#43 Java RationalRose$Java:Static False RationalRose:Tool#43 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#43 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#43 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#43 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#43 Java RationalRose$Java:GenerateCode True RationalRose:Tool#43 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#43 Java RationalRose$Java:ConstructorIs public documentation Indicates whether the quantitation has been measured from the background or from the feature itself. persistence transient documentation User defined quantitation type. persistence transient documentation A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. Of type float. persistence transient documentation Best measure from feature extraction as to the presence and intensity of the signal. Of type float. persistence transient documentation Error measurement of a quantitation. Of type float. persistence transient documentation Measurement of the accuracy of a quantitation. Of type float. persistence transient documentation Indication of what value is expected of the associated standard quantitation type. persistence transient documentation The ratio of two or more signals, typically between two channels. Of type float. persistence transient documentation Indication of some measure of confidence for a standard quantitation type. persistence transient documentation Indicates relative presence or absence. From the enumeration AbsoluteCallTypeEnum {Present | Absent | Marginal | No call} or ComparisonCallTypeEnum {Increase I Marginal Increase | Decrease | Marginal Decrease | No change | No Call | Unknown }, as specified by the dataType. persistence transient documentation Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay. Of type boolean. documentation The association between a ConfidenceIndicator and the QuantitationType its is an indicator for. documentation The classes of this package are the contained classes of the ArrayDesign and describe through the DesignElements what is intended to be at each location of the Array. The Feature describes an intended location on the Array, the Reporter the Oligo, Clone, PCR Product that is on a Feature and the CompositeSequence which combines Reporters or CompositeSequences into what the child DesignElements are meant to represent biologically, e.g. a Gene, Exon, SpliceVariant, etc. persistence transient documentation An element of an array. This is generally of type feature but can be specified as reporters or compositeSequence for arrays that are abstracted from a physical array. persistence transient documentation Specifies a position on an array. documentation The horizontal distance from the upper left corner of the array. documentation The vertical distance from the upper left corner of the array. persistence transient documentation A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. The derived data from the measured data of its Features represents the presence or absence of the biosequence or biosequences it is reporting on in the BioAssay. Reporters are Identifiable and several Features on the same array can be mapped to the same reporter as can Features from a different ArrayDesign. The granularity of the Reporters independence is dependent on the technology and the intent of the ArrayDesign. Oligos using mature technologies can in general be assumed to be safely replicated on many features where as with PCR Products there might be the desire for quality assurence to make reporters one to one with features and use the mappings to CompositeSequences for replication purposes. persistence transient documentation The location in the composite target's sequence to which a source reporter maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial. persistence transient documentation The location in the compositeSequence target's sequence to which a source compositeSequence maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial. persistence transient documentation A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence. RationalRose:Tool#44 Java RationalRose$Java:Final False RationalRose:Tool#44 Java RationalRose$Java:Static False RationalRose:Tool#44 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#44 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#44 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#44 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#44 Java RationalRose$Java:GenerateCode True RationalRose:Tool#44 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#44 Java RationalRose$Java:ConstructorIs public persistence transient documentation An intended position on an array. RationalRose:Tool#44 Java RationalRose$Java:Final False RationalRose:Tool#44 Java RationalRose$Java:Static False RationalRose:Tool#44 Java RationalRose$Java:GenerateDefaultConstructor True RationalRose:Tool#44 Java RationalRose$Java:GenerateFinalizer False RationalRose:Tool#44 Java RationalRose$Java:GenerateStaticInitializer False RationalRose:Tool#44 Java RationalRose$Java:GenerateInstanceInitializer False RationalRose:Tool#44 Java RationalRose$Java:GenerateCode True RationalRose:Tool#44 Java RationalRose$Java:DisableAutoSync False RationalRose:Tool#44 Java RationalRose$Java:ConstructorIs public persistence transient documentation Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence. documentation Offset into the sequence that the mismatch occurs. documentation The sequence that replaces the specified sequence starting at start_coord. documentation Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence is less than the replacedLength. persistence transient documentation As part of the map information, allows the association of one or more differences in the BioMaterial on a feature from the BioMaterial of the Reporter. Useful for control purposes such as in Affymetrix probe pairs. persistence transient documentation A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene. persistence transient documentation A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter. persistence transient documentation A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence. persistence transient documentation Specifies where a feature is located relative to a grid. documentation row position in the Zone documentation column position in the Zone. documentation The position of the feature on the array, relative to the top, left corner. documentation Associates features with their reporter. documentation A reporter that comprises part of a CompositeSequence. documentation Association to the reporters that compose this CompositeSequence and where those reporters occur. documentation Differences in how the reporter matches its compositeSequence's sequence. documentation Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur. documentation A source CompositeSequence that is part of a target CompositeSequence documentation Differences in how the contained compositeSequence matches its target compositeSequence's sequence. documentation A map to the reporters that compose this CompositeSequence. documentation A map to the compositeSequences that compose this CompositeSequence. documentation The feature the FeatureInformation is supplying information for. documentation Associates features with their control features. documentation Location of this feature relative to a grid. documentation Differences in how the feature matches the reporter's sequence, typical examples is the Affymetrix probe pair where one of the features is printed with a mismatch to the other feature's perfect match. documentation Typically, the features on an array that are manufactured with this reporter's BioSequence. persistence transient documentation Abstract class that allows subclasses to inherit the association to Description, for detailed annotations such as Ontology entries and Database references, the association to Audit, for tracking changes, and the association to Security for indicating permissions. persistence transient documentation An Identifiable class is one that has an unambiguous reference within the scope. It also has a potentially ambiguous name. documentation An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. documentation The potentially ambiguous common identifier. persistence transient documentation Abstract class that specifies for subclasses an association to NameValueTypes. These can be used, for instance, to specify proprietary properties and in-house processing hints. persistence transient documentation A tuple designed to store data, keyed by a name and type. documentation The name of the key. documentation The value of the name. documentation The type of the key. documentation Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper. documentation Allows nested specification of name/value pairs