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| Uses of Identifiable in gov.nih.nci.mageom.domain.Array |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Array | |
|---|---|
interface |
Array
The physical substrate along with its features and their annotation |
interface |
ArrayGroup
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. |
interface |
ArrayManufacture
Describes the process by which arrays are produced. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Array.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.Array.impl that implement Identifiable | |
|---|---|
class |
ArrayGroupImpl
An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. |
class |
ArrayImpl
The physical substrate along with its features and their annotation |
class |
ArrayManufactureImpl
Describes the process by which arrays are produced. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign | |
|---|---|
interface |
ArrayDesign
Describes the design of an gene expression layout. |
interface |
CompositeGroup
Allows specification of the type of Composite Design Element. |
interface |
DesignElementGroup
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained. |
interface |
FeatureGroup
A collection of like features. |
interface |
PhysicalArrayDesign
A design that is expected to be used to manufacture physical arrays. |
interface |
ReporterGroup
Allows specification of the type of Reporter Design Element. |
interface |
Zone
Specifies the location of a zone on an array. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.ArrayDesign.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.ArrayDesign.impl that implement Identifiable | |
|---|---|
class |
ArrayDesignImpl
Describes the design of an gene expression layout. |
class |
CompositeGroupImpl
Allows specification of the type of Composite Design Element. |
class |
DesignElementGroupImpl
The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained. |
class |
FeatureGroupImpl
A collection of like features. |
class |
PhysicalArrayDesignImpl
A design that is expected to be used to manufacture physical arrays. |
class |
ReporterGroupImpl
Allows specification of the type of Reporter Design Element. |
class |
ZoneImpl
Specifies the location of a zone on an array. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity | |
|---|---|
interface |
Contact
A contact is either a person or an organization. |
interface |
Organization
Organizations are entities like companies, universities, government agencies for which the attributes are self describing. |
interface |
Person
A person for which the attributes are self describing. |
interface |
Security
Permission information for an object as to ownership, write and read permissions. |
interface |
SecurityGroup
Groups contacts together based on their security privileges. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.AuditAndSecurity.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.AuditAndSecurity.impl that implement Identifiable | |
|---|---|
class |
ContactImpl
A contact is either a person or an organization. |
class |
OrganizationImpl
Organizations are entities like companies, universities, government agencies for which the attributes are self describing. |
class |
PersonImpl
A person for which the attributes are self describing. |
class |
SecurityGroupImpl
Groups contacts together based on their security privileges. |
class |
SecurityImpl
Permission information for an object as to ownership, write and read permissions. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssay |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioAssay | |
|---|---|
interface |
BioAssay
An abstract class which represents both physical and computational groupings of arrays and biomaterials. |
interface |
BioAssayCreation
The process by which an array and one or more biomaterials are combined to create a bioAssayCreation. |
interface |
BioAssayTreatment
The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...). |
interface |
Channel
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength. |
interface |
DerivedBioAssay
A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays. |
interface |
FeatureExtraction
The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay. |
interface |
Hybridization
The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array. |
interface |
Image
An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay). |
interface |
ImageAcquisition
The process by which an image is generated (typically scanning). |
interface |
MeasuredBioAssay
A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. |
interface |
PhysicalBioAssay
A bioAssay created by the bioAssayCreation event (e.g. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssay.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.BioAssay.impl that implement Identifiable | |
|---|---|
class |
BioAssayCreationImpl
The process by which an array and one or more biomaterials are combined to create a bioAssayCreation. |
class |
BioAssayImpl
An abstract class which represents both physical and computational groupings of arrays and biomaterials. |
class |
BioAssayTreatmentImpl
The event which records the process by which PhysicalBioAssays are processed (typically washing, blocking, etc...). |
class |
ChannelImpl
A channel represents an independent acquisition scheme for the ImageAcquisition event, typically a wavelength. |
class |
DerivedBioAssayImpl
A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays. |
class |
FeatureExtractionImpl
The process by which data is extracted from an image producing a measuredBioAssayData and a measuredBioAssay. |
class |
HybridizationImpl
The archetypal bioAssayCreation event, whereby biomaterials are hybridized to an array. |
class |
ImageAcquisitionImpl
The process by which an image is generated (typically scanning). |
class |
ImageImpl
An image is created by an imageAcquisition event, typically by scanning the hybridized array (the PhysicalBioAssay). |
class |
MeasuredBioAssayImpl
A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. |
class |
PhysicalBioAssayImpl
A bioAssay created by the bioAssayCreation event (e.g. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssayData |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioAssayData | |
|---|---|
interface |
BioAssayData
Represents the dataset created when the BioAssays are created. |
interface |
BioAssayDimension
An ordered list of bioAssays. |
interface |
BioAssayMap
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays. |
interface |
CompositeSequenceDimension
Specialized DesignElementDimension to hold CompositeSequences. |
interface |
DerivedBioAssayData
The output of a transformation event. |
interface |
DesignElementDimension
An ordered list of designElements. |
interface |
DesignElementMap
A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement. |
interface |
FeatureDimension
Specialized DesignElementDimension to hold Features. |
interface |
MeasuredBioAssayData
The data associated with the MeasuredBioAssay produced by FeatureExtraction. |
interface |
QuantitationTypeDimension
An ordered list of quantitationTypes. |
interface |
QuantitationTypeMap
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType. |
interface |
ReporterDimension
Specialized DesignElementDimension to hold Reporters. |
interface |
Transformation
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioAssayData.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.BioAssayData.impl that implement Identifiable | |
|---|---|
class |
BioAssayDataImpl
Represents the dataset created when the BioAssays are created. |
class |
BioAssayDimensionImpl
An ordered list of bioAssays. |
class |
BioAssayMapImpl
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays. |
class |
CompositeSequenceDimensionImpl
Specialized DesignElementDimension to hold CompositeSequences. |
class |
DerivedBioAssayDataImpl
The output of a transformation event. |
class |
DesignElementDimensionImpl
An ordered list of designElements. |
class |
DesignElementMapImpl
A DesignElementMap is the description of how source DesignElements are transformed into a target DesignElement. |
class |
FeatureDimensionImpl
Specialized DesignElementDimension to hold Features. |
class |
MeasuredBioAssayDataImpl
The data associated with the MeasuredBioAssay produced by FeatureExtraction. |
class |
QuantitationTypeDimensionImpl
An ordered list of quantitationTypes. |
class |
QuantitationTypeMapImpl
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType. |
class |
ReporterDimensionImpl
Specialized DesignElementDimension to hold Reporters. |
class |
TransformationImpl
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioEvent |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioEvent | |
|---|---|
interface |
BioEvent
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis). |
interface |
Map
A Map is the description of how sources are transformed into a target. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioEvent.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.BioEvent.impl that implement Identifiable | |
|---|---|
class |
BioEventImpl
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis). |
class |
MapImpl
A Map is the description of how sources are transformed into a target. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioMaterial |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioMaterial | |
|---|---|
interface |
BioMaterial
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... |
interface |
BioSample
BioSamples are products of treatments that are of interest. |
interface |
BioSource
The BioSource is the original source material before any treatment events. |
interface |
Compound
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). |
interface |
LabeledExtract
LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties). |
interface |
Treatment
The process by which a biomaterial is created (from source biomaterials). |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioMaterial.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.BioMaterial.impl that implement Identifiable | |
|---|---|
class |
BioMaterialImpl
BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... |
class |
BioSampleImpl
BioSamples are products of treatments that are of interest. |
class |
BioSourceImpl
The BioSource is the original source material before any treatment events. |
class |
CompoundImpl
A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). |
class |
LabeledExtractImpl
LabeledExtracts are special BioSamples that have Compounds which are detectable (these are often fluorescent or reactive moieties). |
class |
TreatmentImpl
The process by which a biomaterial is created (from source biomaterials). |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioSequence |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.BioSequence | |
|---|---|
interface |
BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.BioSequence.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.BioSequence.impl that implement Identifiable | |
|---|---|
class |
BioSequenceImpl
A BioSequence is a representation of a DNA, RNA, or protein sequence. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Description |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Description | |
|---|---|
interface |
Database
An address to a repository. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Description.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.Description.impl that implement Identifiable | |
|---|---|
class |
DatabaseImpl
An address to a repository. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.DesignElement |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.DesignElement | |
|---|---|
interface |
CompositeCompositeMap
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. |
interface |
CompositeSequence
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence. |
interface |
DesignElement
An element of an array. |
interface |
Feature
An intended position on an array. |
interface |
FeatureReporterMap
A FeatureReporterMap is the description of how source features are transformed into a target reporter. |
interface |
Reporter
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. |
interface |
ReporterCompositeMap
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.DesignElement.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.DesignElement.impl that implement Identifiable | |
|---|---|
class |
CompositeCompositeMapImpl
A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. |
class |
CompositeSequenceImpl
A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence. |
class |
DesignElementImpl
An element of an array. |
class |
FeatureImpl
An intended position on an array. |
class |
FeatureReporterMapImpl
A FeatureReporterMap is the description of how source features are transformed into a target reporter. |
class |
ReporterCompositeMapImpl
A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. |
class |
ReporterImpl
A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Experiment |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Experiment | |
|---|---|
interface |
Experiment
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign. |
interface |
ExperimentalFactor
ExperimentFactors are the dependent variables of an experiment (e.g. |
interface |
FactorValue
The value for a ExperimentalFactor |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Experiment.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.Experiment.impl that implement Identifiable | |
|---|---|
class |
ExperimentalFactorImpl
ExperimentFactors are the dependent variables of an experiment (e.g. |
class |
ExperimentImpl
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign. |
class |
FactorValueImpl
The value for a ExperimentalFactor |
| Uses of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis | |
|---|---|
interface |
BioAssayDataCluster
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.HigherLevelAnalysis.impl that implement Identifiable | |
|---|---|
class |
BioAssayDataClusterImpl
A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.impl that implement Identifiable | |
|---|---|
class |
IdentifiableImpl
An Identifiable class is one that has an unambiguous reference within the scope. |
| Methods in gov.nih.nci.mageom.domain.impl that return Identifiable | |
|---|---|
Identifiable[] |
IdentifiableImpl.searchIdentifiables(IdentifiableSearchCriteria criteria)
Returns an array of Identifiable objects that
satisfy the given IdentifiableSearchCriteria. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Protocol |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.Protocol | |
|---|---|
interface |
Hardware
Hardware represents the hardware used. |
interface |
Parameter
A Parameter is a replaceable value in a Parameterizable class. |
interface |
Parameterizable
The Parameterizable interface encapsulates the association of Parameters with ParameterValues. |
interface |
Protocol
A Protocol is a parameterizable description of a method. |
interface |
Software
Software represents the software used. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.Protocol.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.Protocol.impl that implement Identifiable | |
|---|---|
class |
HardwareImpl
Hardware represents the hardware used. |
class |
ParameterImpl
A Parameter is a replaceable value in a Parameterizable class. |
class |
ParameterizableImpl
The Parameterizable interface encapsulates the association of Parameters with ParameterValues. |
class |
ProtocolImpl
A Protocol is a parameterizable description of a method. |
class |
SoftwareImpl
Software represents the software used. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.QuantitationType |
|---|
| Subinterfaces of Identifiable in gov.nih.nci.mageom.domain.QuantitationType | |
|---|---|
interface |
ConfidenceIndicator
Indication of some measure of confidence for a standard quantitation type. |
interface |
DerivedSignal
A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. |
interface |
Error
Error measurement of a quantitation. |
interface |
ExpectedValue
Indication of what value is expected of the associated standard quantitation type. |
interface |
Failed
Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay. |
interface |
MeasuredSignal
Best measure from feature extraction as to the presence and intensity of the signal. |
interface |
PresentAbsent
Indicates relative presence or absence. |
interface |
PValue
Measurement of the accuracy of a quantitation. |
interface |
QuantitationType
A method for calculating a single datum of the matrix (e.g. |
interface |
Ratio
The ratio of two or more signals, typically between two channels. |
interface |
SpecializedQuantitationType
User defined quantitation type. |
interface |
StandardQuantitationType
Superclass for the named quantitation type. |
| Uses of Identifiable in gov.nih.nci.mageom.domain.QuantitationType.impl |
|---|
| Classes in gov.nih.nci.mageom.domain.QuantitationType.impl that implement Identifiable | |
|---|---|
class |
ConfidenceIndicatorImpl
Indication of some measure of confidence for a standard quantitation type. |
class |
DerivedSignalImpl
A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. |
class |
ErrorImpl
Error measurement of a quantitation. |
class |
ExpectedValueImpl
Indication of what value is expected of the associated standard quantitation type. |
class |
FailedImpl
Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay. |
class |
MeasuredSignalImpl
Best measure from feature extraction as to the presence and intensity of the signal. |
class |
PresentAbsentImpl
Indicates relative presence or absence. |
class |
PValueImpl
Measurement of the accuracy of a quantitation. |
class |
QuantitationTypeImpl
A method for calculating a single datum of the matrix (e.g. |
class |
RatioImpl
The ratio of two or more signals, typically between two channels. |
class |
SpecializedQuantitationTypeImpl
User defined quantitation type. |
class |
StandardQuantitationTypeImpl
Superclass for the named quantitation type. |
|
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