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
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RationalRose:Tool#1
Java
RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#1
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RationalRose:Tool#1
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#1
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RationalRose:Tool#1
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RationalRose$Java:GenerateCode
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RationalRose:Tool#1
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RationalRose:Tool#1
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RationalRose$Java:ConstructorIs
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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
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RationalRose:Tool#4
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RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#4
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RationalRose$Java:GenerateFinalizer
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RationalRose:Tool#4
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#4
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RationalRose:Tool#4
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RationalRose$Java:GenerateCode
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RationalRose:Tool#4
Java
RationalRose$Java:DisableAutoSync
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RationalRose:Tool#4
Java
RationalRose$Java:ConstructorIs
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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
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RationalRose:Tool#4
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RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#4
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RationalRose$Java:GenerateFinalizer
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RationalRose:Tool#4
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#4
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RationalRose$Java:GenerateInstanceInitializer
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RationalRose:Tool#4
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RationalRose$Java:GenerateCode
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RationalRose:Tool#4
Java
RationalRose$Java:DisableAutoSync
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RationalRose:Tool#4
Java
RationalRose$Java:ConstructorIs
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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
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RationalRose:Tool#11
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RationalRose$Java:Static
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RationalRose:Tool#11
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RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#11
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RationalRose$Java:GenerateFinalizer
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RationalRose:Tool#11
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#11
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RationalRose$Java:GenerateInstanceInitializer
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RationalRose:Tool#11
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RationalRose$Java:GenerateCode
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RationalRose:Tool#11
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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
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RationalRose:Tool#12
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RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#12
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RationalRose$Java:GenerateFinalizer
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RationalRose:Tool#12
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#12
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RationalRose$Java:GenerateInstanceInitializer
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RationalRose:Tool#12
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RationalRose$Java:GenerateCode
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RationalRose$Java:ConstructorIs
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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$Java:Final
False
RationalRose:Tool#13
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RationalRose$Java:Static
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RationalRose:Tool#13
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RationalRose$Java:GenerateDefaultConstructor
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RationalRose:Tool#13
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RationalRose:Tool#13
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RationalRose$Java:GenerateStaticInitializer
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RationalRose:Tool#13
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RationalRose:Tool#13
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RationalRose$Java:ConstructorIs
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persistence
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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$Java:Static
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RationalRose$Java:GenerateDefaultConstructor
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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.
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A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength.
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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.
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The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
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The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay.
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The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array.
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The process by which an image is generated (typically scanning).
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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.
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The set of treatments undergone by this PhysicalBioAssay.
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The PhysicalBioAssay that was treated.
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The data associated with the DerivedBioAssay.
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The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc.
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The DerivedBioAssay that is produced by the sources of the BioAssayMap.
documentation
The channels captured in this image.
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The images produced by the ImageAcquisition event.
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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.
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The BioAssay associated with the value of the BioAssayDatum.
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The BioAssays for this Dimension
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The values that this BioAssay is associated with for the experiment.
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The collection of BioAssays for this Experiment.
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The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.)
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The optional channel associated with the QuantitationType.
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The association between the MeasuredBioAssay and the FeatureExtraction Event.
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The data associated with the MeasuredBioAssay.
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Specifies classes that allow tracking of changes and information on user permissions to view the data and annotation.
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A person for which the attributes are self describing.
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Permission information for an object as to ownership, write and read permissions.
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Tracks information on the contact that creates or modifies an object.
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The date of a change.
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Indicates whether an action is a creation or a modification.
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Organizations are entities like companies, universities, government agencies for which the attributes are self describing.
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Groups contacts together based on their security privileges.
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A contact is either a person or an organization.
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The organization a person belongs to.
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The people who performed the protocol.
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Information on the security for the instance of the class.
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Specifies which security groups have permission to view the associated object.
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The owner of the security rights.
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A list of Audit instances that track changes to the instance of Describable.
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The contact for creating or changing the instance referred to by the Audit.
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The containing organization (the university or business which a lab belongs to, etc.)
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The members of the Security Group.
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The roles (lab equipment sales, contractor, etc.) the contact fills.
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The providers of the Experiment, its data and annotation.
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Contact for information on the Hardware.
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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.
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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$Java:Final
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RationalRose$Java:Static
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An ordered list of quantitationTypes.
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Container of the mappings of the input BioAssay dimensions to the output BioAssay dimension.
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An ordered list of designElements. It will be realized as one of its three subclasses.
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A single cell of the quantitation, bioAssay, designElement matrix.
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The datum value.
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The output of a transformation event.
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The data associated with the MeasuredBioAssay produced by FeatureExtraction.
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Container of the mappings of the input QuantitationType dimensions to the output QuantitationType dimension.
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Container of the mappings of the input DesignElement dimensions to the output DesignElement dimension.
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A three-dimensional cube representation of the data.
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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.
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The actual values for the BioAssayCube.
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A relational, tuple representation of the data.
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An ordered list of bioAssays.
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A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.
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The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.
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A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement.
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The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.
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Specialized DesignElementDimension to hold CompositeSequences.
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Specialized DesignElementDimension to hold Reporters.
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transient
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Specialized DesignElementDimension to hold Features.
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The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData.
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The BioAssays of the BioAssayData.
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The DesignElements of the BioAssayData.
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The QuantitationTypes of the BioAssayData.
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Statistics on the Quality of the BioAssayData.
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The data values of the BioAssayData.
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The collection of BioAssayDatas for this Experiment.
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The QuantitationTypes for this Dimension.
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The collection of mappings for the BioAssays.
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The maps for the BioAssays.
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The collection of BioAssayData tuples.
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The DesignElement associated with the value of the BioAssayDatum.
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The QuantitationType associated with the value of the BioAssayDatum.
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The association between the DerivedBioAssayData and the Transformation event that produced it.
documentation
The maps for the QuantitationTypes.
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The collection of mappings for the QuantitationTypes.
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The maps for the DesignElements.
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The collection of mappings for the DesignElements.
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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.
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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.
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The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
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The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
persistence
transient
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ExperimentFactors are the dependent variables of an experiment (e.g. time, glucose concentration, ...).
persistence
transient
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The value for a ExperimentalFactor
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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.
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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.
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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
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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.
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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$Java:Final
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When the protocol was applied.
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transient
documentation
Software represents the software used. Examples of Software include: feature extraction software, clustering software, etc...
RationalRose:Tool#27
Java
RationalRose$Java:Final
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RationalRose$Java:Static
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Hardware represents the hardware used. Examples of Hardware include: computers, scanners, wash stations etc...
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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.
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The use of hardware for the application of the protocol.
documentation
The applied protocols to the BioEvent.
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Associates Hardware and Software together.
documentation
Software packages this software uses, i.e. operating system, 3rd party software packages, etc.
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The underlying software.
documentation
The type of a piece of Software. Examples include: feature extractor...
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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.
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transient
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A free text description of an object.
documentation
The description.
documentation
A reference to the location and type of an outside resource.
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A reference to a record in a database.
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The identifier used to look up the record.
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The appropriate version of the accession (if applicable).
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The location of the record.
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transient
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An address to a repository.
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The version for which a DatabaseReference applies.
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The location of the Database.
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transient
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A reference to the originating source for the object.
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The originating server for the object, a network address or common name.
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Name of the database, if applicable, that the object was exported from.
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The identifier of the object at the originating source.
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The name of the object at the originating source.
persistence
transient
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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.
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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.
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The unit is a strict enumeration of types.
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The name of the unit.
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Time
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Distance
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Temperature
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Quantity
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Mass
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Volume
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Concentration
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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.
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transient
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An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
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transient
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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.
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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.
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Represents, in general, what would be a GenBank Feature Table annotation for a sequence.
documentation
How the evidence for a SeqFeature was determined.
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transient
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The location of the SeqFeature annotation.
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Indicates the direction and/or type of the SeqFeature, i.e. whether it is in the 5' or 3' direction, is double stranded, etc.
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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
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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.
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Designates the position of the Feature in its BioSequence.
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The location of the base, for nucleotides, that the SeqFeature starts.
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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.
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Superclass for the named quantitation type. Useful for mapping to those languages that can use a fly-weight for processing the subclasses.
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documentation
A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).
RationalRose:Tool#43
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Indicates whether the quantitation has been measured from the background or from the feature itself.
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User defined quantitation type.
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A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. Of type float.
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documentation
Best measure from feature extraction as to the presence and intensity of the signal. Of type float.
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Error measurement of a quantitation. Of type float.
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Measurement of the accuracy of a quantitation. Of type float.
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Indication of what value is expected of the associated standard quantitation type.
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The ratio of two or more signals, typically between two channels. Of type float.
persistence
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Indication of some measure of confidence for a standard quantitation type.
persistence
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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
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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.
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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
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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.
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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.
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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.
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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.
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A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.
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An intended position on an array.
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Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.
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Offset into the sequence that the mismatch occurs.
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The sequence that replaces the specified sequence starting at start_coord.
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Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence is less than the replacedLength.
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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.
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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.
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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.
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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.
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Specifies where a feature is located relative to a grid.
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row position in the Zone
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column position in the Zone.
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The position of the feature on the array, relative to the top, left corner.
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Associates features with their reporter.
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A reporter that comprises part of a CompositeSequence.
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Association to the reporters that compose this CompositeSequence and where those reporters occur.
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Differences in how the reporter matches its compositeSequence's sequence.
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Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.
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A source CompositeSequence that is part of a target CompositeSequence
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Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
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A map to the reporters that compose this CompositeSequence.
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A map to the compositeSequences that compose this CompositeSequence.
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The feature the FeatureInformation is supplying information for.
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Associates features with their control features.
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Location of this feature relative to a grid.
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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.
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Typically, the features on an array that are manufactured with this reporter's BioSequence.
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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.
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An Identifiable class is one that has an unambiguous reference within the scope. It also has a potentially ambiguous name.
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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.
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The potentially ambiguous common identifier.
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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.
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A tuple designed to store data, keyed by a name and type.
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The name of the key.
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The value of the name.
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The type of the key.
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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.
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Allows nested specification of name/value pairs