Uses of Class
org.biomage.Common.Describable

Packages that use Describable
gov.nih.nci.caarray.services.util   
gov.nih.nci.caarray.services.vocab   
org.biomage.Array   
org.biomage.ArrayDesign   
org.biomage.AuditAndSecurity   
org.biomage.BioAssay   
org.biomage.BioAssayData   
org.biomage.BioEvent   
org.biomage.BioMaterial   
org.biomage.BioSequence   
org.biomage.BQS   
org.biomage.Common   
org.biomage.Description   
org.biomage.DesignElement   
org.biomage.Experiment   
org.biomage.HigherLevelAnalysis   
org.biomage.Protocol   
org.biomage.QuantitationType   
 

Uses of Describable in gov.nih.nci.caarray.services.util
 

Methods in gov.nih.nci.caarray.services.util with parameters of type Describable
static void DBUtils.resetAttributes(Describable obj)
          Resets the ID and identifying attributes including audit trail, property set, and security typically useful for duplication
 

Uses of Describable in gov.nih.nci.caarray.services.vocab
 

Methods in gov.nih.nci.caarray.services.vocab with parameters of type Describable
 void VocabManagerDB.addOrSyncAnnotations(Describable describable)
          Adds or synchronizes the vocabularies that represent the annotations of the specified Describable object.
 

Uses of Describable in org.biomage.Array
 

Subclasses of Describable in org.biomage.Array
 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 Describable in org.biomage.ArrayDesign
 

Subclasses of Describable in org.biomage.ArrayDesign
 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 Describable in org.biomage.AuditAndSecurity
 

Subclasses of Describable in org.biomage.AuditAndSecurity
 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 Describable in org.biomage.BioAssay
 

Subclasses of Describable in org.biomage.BioAssay
 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 Describable in org.biomage.BioAssayData
 

Subclasses of Describable in org.biomage.BioAssayData
 class 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 Describable in org.biomage.BioEvent
 

Subclasses of Describable in org.biomage.BioEvent
 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 Describable in org.biomage.BioMaterial
 

Subclasses of Describable in org.biomage.BioMaterial
 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 Describable in org.biomage.BioSequence
 

Subclasses of Describable in org.biomage.BioSequence
 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 Describable in org.biomage.BQS
 

Subclasses of Describable in org.biomage.BQS
 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 Describable in org.biomage.Common
 

Subclasses of Describable in org.biomage.Common
 class Identifiable
          An Identifiable class is one that has an unambiguous reference within the scope.
 

Uses of Describable in org.biomage.Description
 

Subclasses of Describable in org.biomage.Description
 class Database
          An address to a repository.
 class Description
          A free text description of an object.
 

Uses of Describable in org.biomage.DesignElement
 

Subclasses of Describable in org.biomage.DesignElement
 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 Describable in org.biomage.Experiment
 

Subclasses of Describable in org.biomage.Experiment
 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 Describable in org.biomage.HigherLevelAnalysis
 

Subclasses of Describable in org.biomage.HigherLevelAnalysis
 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 Describable in org.biomage.Protocol
 

Subclasses of Describable in org.biomage.Protocol
 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 Describable in org.biomage.QuantitationType
 

Subclasses of Describable in org.biomage.QuantitationType
 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.