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Uses of HasAuditTrail in org.biomage.Array |
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Classes in org.biomage.Array that implement HasAuditTrail | |
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class |
Array
The physical substrate along with its features and their annotation |
class |
ArrayGroup
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. |
class |
ArrayManufacture
Describes the process by which arrays are produced. |
class |
Fiducial
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. |
class |
ManufactureLIMS
Information on the physical production of arrays within the laboratory. |
class |
ManufactureLIMSBiomaterial
Stores the location from which a biomaterial was obtained. |
Uses of HasAuditTrail in org.biomage.ArrayDesign |
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Classes in org.biomage.ArrayDesign that implement HasAuditTrail | |
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class |
ArrayDesign
Describes the design of an gene expression layout. |
class |
CompositeGroup
Allows specification of the type of Composite Design Element. |
class |
DesignElementGroup
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained. |
class |
FeatureGroup
A collection of like features. |
class |
PhysicalArrayDesign
A design that is expected to be used to manufacture physical arrays. |
class |
ReporterGroup
Allows specification of the type of Reporter Design Element. |
class |
Zone
Specifies the location of a zone on an array. |
Uses of HasAuditTrail in org.biomage.AuditAndSecurity |
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Classes in org.biomage.AuditAndSecurity that implement HasAuditTrail | |
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class |
Audit
Tracks information on the contact that creates or modifies an object. |
class |
Contact
A contact is either a person or an organization. |
class |
Organization
Organizations are entities like companies, universities, government agencies for which the attributes are self describing. |
class |
Person
A person for which the attributes are self describing. |
class |
Security
Permission information for an object as to ownership, write and read permissions. |
class |
SecurityGroup
Groups contacts together based on their security privileges. |
class |
User
A user for which the attributes are self describing. |
Uses of HasAuditTrail in org.biomage.BioAssay |
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Classes in org.biomage.BioAssay that implement HasAuditTrail | |
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class |
BioAssay
An abstract class which represents both physical and computational groupings of arrays and biomaterials. |
class |
BioAssayCreation
The process by which an array and one or more biomaterials are combined to create a bioAssayCreation. |
class |
BioAssayTreatment
The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...). |
class |
Channel
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength. |
class |
DerivedBioAssay
A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays. |
class |
FeatureExtraction
The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay. |
class |
Hybridization
The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array. |
class |
Image
An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay). |
class |
ImageAcquisition
The process by which an image is generated (typically scanning). |
class |
MeasuredBioAssay
A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. |
class |
PhysicalBioAssay
A bioAssay created by the bioAssayCreation event (e.g. |
Uses of HasAuditTrail in org.biomage.BioAssayData |
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Classes in org.biomage.BioAssayData that implement HasAuditTrail | |
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BioAssayData
Represents the dataset created when the BioAssays are created. |
class |
BioAssayDimension
An ordered list of bioAssays. |
class |
BioAssayMap
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays. |
class |
CompositeSequenceDimension
Specialized DesignElementDimension to hold CompositeSequences. |
class |
DerivedBioAssayData
The output of a transformation event. |
class |
DesignElementDimension
An ordered list of designElements. |
class |
DesignElementMap
A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement. |
class |
FeatureDimension
Specialized DesignElementDimension to hold Features. |
class |
MeasuredBioAssayData
The data associated with the MeasuredBioAssay produced by FeatureExtraction. |
class |
QuantitationTypeDimension
An ordered list of quantitationTypes. |
class |
QuantitationTypeMap
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType. |
class |
ReporterDimension
Specialized DesignElementDimension to hold Reporters. |
class |
Transformation
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. |
Uses of HasAuditTrail in org.biomage.BioEvent |
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Classes in org.biomage.BioEvent that implement HasAuditTrail | |
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class |
BioEvent
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis). |
class |
Map
A Map is the description of how sources are transformed into a target. |
Uses of HasAuditTrail in org.biomage.BioMaterial |
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Classes in org.biomage.BioMaterial that implement HasAuditTrail | |
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class |
BioMaterial
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... |
class |
BioSample
BioSamples are products of treatments that are of interest. |
class |
BioSource
The BioSource is the original source material before any treatment events. |
class |
Compound
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). |
class |
LabeledExtract
LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties). |
class |
Treatment
The process by which a biomaterial is created (from source biomaterials). |
Uses of HasAuditTrail in org.biomage.BioSequence |
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Classes in org.biomage.BioSequence that implement HasAuditTrail | |
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class |
BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence. |
class |
SeqFeature
Represents, in general, what would be a GenBank Feature Table annotation for a sequence. |
Uses of HasAuditTrail in org.biomage.BQS |
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Classes in org.biomage.BQS that implement HasAuditTrail | |
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class |
BibliographicReference
Attributes for the most common criteria and association with OntologyEntry allows criteria to be specified for searching for a Bibliographic reference. |
Uses of HasAuditTrail in org.biomage.Common |
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Classes in org.biomage.Common that implement HasAuditTrail | |
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class |
Describable
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. |
class |
Identifiable
An Identifiable class is one that has an unambiguous reference within the scope. |
Uses of HasAuditTrail in org.biomage.Description |
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Classes in org.biomage.Description that implement HasAuditTrail | |
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class |
Database
An address to a repository. |
class |
Description
A free text description of an object. |
Uses of HasAuditTrail in org.biomage.DesignElement |
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Classes in org.biomage.DesignElement that implement HasAuditTrail | |
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class |
CompositeCompositeMap
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. |
class |
CompositeSequence
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence. |
class |
DesignElement
An element of an array. |
class |
Feature
An intended position on an array. |
class |
FeatureReporterMap
A FeatureReporterMap is the description of how source features are transformed into a target reporter. |
class |
Reporter
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. |
class |
ReporterCompositeMap
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. |
Uses of HasAuditTrail in org.biomage.Experiment |
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Classes in org.biomage.Experiment that implement HasAuditTrail | |
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class |
Experiment
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign. |
class |
ExperimentalFactor
ExperimentFactors are the dependent variables of an experiment (e.g. |
class |
ExperimentDesign
The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain. |
class |
FactorValue
The value for a ExperimentalFactor |
Uses of HasAuditTrail in org.biomage.HigherLevelAnalysis |
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Classes in org.biomage.HigherLevelAnalysis that implement HasAuditTrail | |
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class |
BioAssayDataCluster
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes. |
class |
Node
An individual component of a clustering. |
class |
NodeContents
The contents of a node for any or all of the three Dimensions. |
Uses of HasAuditTrail in org.biomage.Protocol |
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Classes in org.biomage.Protocol that implement HasAuditTrail | |
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class |
Hardware
Hardware represents the hardware used. |
class |
HardwareApplication
The use of a piece of hardware with the requisite Parameters and ParameterValues. |
class |
Parameter
A Parameter is a replaceable value in a Parameterizable class. |
class |
Parameterizable
The Parameterizable interface encapsulates the association of Parameters with ParameterValues. |
class |
ParameterizableApplication
The interface that is the use of a Parameterizable class. |
class |
Protocol
A Protocol is a parameterizable description of a method. |
class |
ProtocolApplication
The use of a protocol with the requisite Parameters and ParameterValues. |
class |
Software
Software represents the software used. |
class |
SoftwareApplication
The use of a piece of software with the requisite Parameters and ParameterValues. |
Uses of HasAuditTrail in org.biomage.QuantitationType |
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Classes in org.biomage.QuantitationType that implement HasAuditTrail | |
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class |
ConfidenceIndicator
Indication of some measure of confidence for a standard quantitation type. |
class |
DerivedSignal
A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. |
class |
Error
Error measurement of a quantitation. |
class |
ExpectedValue
Indication of what value is expected of the associated standard quantitation type. |
class |
Failed
Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay. |
class |
MeasuredSignal
Best measure from feature extraction as to the presence and intensity of the signal. |
class |
PresentAbsent
Indicates relative presence or absence. |
class |
PValue
Measurement of the accuracy of a quantitation. |
class |
QuantitationType
A method for calculating a single datum of the matrix (e.g. |
class |
Ratio
The ratio of two or more signals, typically between two channels. |
class |
SpecializedQuantitationType
User defined quantitation type. |
class |
StandardQuantitationType
Superclass for the named quantitation type. |
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