Uses of Class
ubic.gemma.model.common.AbstractIdentifiable

Packages that use AbstractIdentifiable

Package	Description
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.association
ubic.gemma.model.blacklist
ubic.gemma.model.common
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.auditAndSecurity.eventType
ubic.gemma.model.common.description
ubic.gemma.model.common.measurement
ubic.gemma.model.common.protocol
ubic.gemma.model.common.quantitationtype
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis

Uses of AbstractIdentifiable in ubic.gemma.core.loader.expression.arrayDesign

Subclasses of AbstractIdentifiable in ubic.gemma.core.loader.expression.arrayDesign

Modifier and Type	Class	Description
class	Reporter	A "probe" (Affymetrix); for other types of arrays, there is no practical distinction between compositesequences and reporters, and all analysis would take place at the level of CompositeSequences.

Uses of AbstractIdentifiable in ubic.gemma.model.analysis

Subclasses of AbstractIdentifiable in ubic.gemma.model.analysis

Modifier and Type	Class	Description
class	Analysis	An analysis of one or more Investigations.
class	Investigation	An abstract concept of a scientific study
class	SingleExperimentAnalysis<T extends BioAssaySet>	An analysis of a single experiment or subset.

Uses of AbstractIdentifiable in ubic.gemma.model.analysis.expression

Subclasses of AbstractIdentifiable in ubic.gemma.model.analysis.expression

Modifier and Type	Class	Description
class	ExpressionAnalysis	An analysis of one or more ExpressionExperiments
class	ExpressionExperimentSet	A grouping of expression studies.

Uses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.coexpression

Subclasses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.coexpression

Modifier and Type	Class	Description
class	CoexpressionAnalysis	A coexpression analysis of one experiment.
class	SampleCoexpressionAnalysis	The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.
class	SampleCoexpressionMatrix	Holds the data of the sample coexpression matrix

Uses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.diff

Subclasses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.diff

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
class	GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.
class	GeneDifferentialExpressionMetaAnalysisResult
class	HitListSize	The number of probes meeting a given q-value threshold in the result set.
class	PvalueDistribution

Uses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.pca

Subclasses of AbstractIdentifiable in ubic.gemma.model.analysis.expression.pca

Modifier and Type	Class	Description
class	Eigenvalue
class	Eigenvector	A right singular vector (a.k.a. eigengenes)
class	PrincipalComponentAnalysis
class	ProbeLoading	Only stored for some of the probes (e.g. the top ones)

Uses of AbstractIdentifiable in ubic.gemma.model.association

Subclasses of AbstractIdentifiable in ubic.gemma.model.association

Modifier and Type	Class	Description
class	BioSequence2GeneProduct	An association between a BioSequence and a Gene Product.
class	Gene2GOAssociation
class	ReferenceAssociation	An association between a BioSequence and a GeneProduct based on external database identifiers.

Uses of AbstractIdentifiable in ubic.gemma.model.blacklist

Subclasses of AbstractIdentifiable in ubic.gemma.model.blacklist

Modifier and Type	Class	Description
class	BlacklistedEntity	Represents a blacklisted entity that should not be loaded into Gemma.
class	BlacklistedExperiment	TODO Document Me
class	BlacklistedPlatform

Uses of AbstractIdentifiable in ubic.gemma.model.common

Subclasses of AbstractIdentifiable in ubic.gemma.model.common

Modifier and Type	Class	Description
class	AbstractDescribable

Uses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	AuditEvent	An event in the life of an object.
class	AuditTrail	The trail of events (create or update) that occurred in an objects lifetime.
class	Contact	Representing a person or organization that can be contacted about, or is the source of, data in the system.
class	GroupAuthority	Authority for groups (kind of like a "user role", but for group-based authorization)
class	Person	Deprecated. not needed
class	User	A user of the software system, who is authenticated.
class	UserGroup	An organized group of researchers with an identifiable leader and group members.

Uses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity.curation

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity.curation

Modifier and Type	Class	Description
class	CurationDetails	Class encapsulating all the curation information for Curatable objects.

Uses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity.eventType

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.auditAndSecurity.eventType

Modifier and Type	Class	Description
class	AlignmentBasedGeneMappingEvent	Signifies a mapping based on sequence alignment performed by the system.
class	AnalysisSuitabilityEvent	Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.
class	AnnotationBasedGeneMappingEvent	To signify the array design was mapped from an external source, not by our own sequence analysis.
class	AnnotationEvent
class	ArrayDesignAnalysisEvent	An event involving the analysis of an ArrayDesign
class	ArrayDesignGeneMappingEvent	The mapping of probes to genes for an ArrayDesign
class	ArrayDesignMergeEvent
class	ArrayDesignProbeRenamingEvent	Signifies that the probes were renamed from their original values.
class	ArrayDesignRepeatAnalysisEvent
class	ArrayDesignSequenceAnalysisEvent	The sequence alignment analysis of an ArrayDesign
class	ArrayDesignSequenceRemoveEvent	Used to indicate that all associations that this array design has with BioSequences have been removed.
class	ArrayDesignSequenceUpdateEvent	The updating of the sequences associated with an ArrayDesign
class	ArrayDesignSubsumeCheckEvent
class	AuditEventType
class	AutomatedAnnotationEvent	Deprecated. this event type was used by the auto-tagger, which has been removed.
class	BatchCorrectionEvent
class	BatchInformationEvent	Abstract class for events related to batch information.
class	BatchInformationFetchingEvent	Indicates that batch information was successfully obtained.
class	BatchInformationMissingEvent	Indicate that batch information has been looked for and was missing.
class	BatchProblemsUpdateEvent	Event that tracks when batch effects or problems are detected.
class	BioMaterialMappingUpdate	Indicates that the biomaterial to bioassay mapping of the expression experiment was modified.
class	CellLevelCharacteristicsAddedEvent	Event emitted when a cell-level characteristics is removed.
class	CellLevelCharacteristicsEvent	Event emitted when a cell-level characteristics is modified (either added or removed).
class	CellLevelCharacteristicsRemovedEvent	Event emitted when a cell-level characteristics is removed.
class	CellTypeAssignmentAddedEvent	Event emitted when a CellTypeAssignmentEvent is added.
class	CellTypeAssignmentEvent	Event emitted when a cell type assignment is modified (either added or removed).
class	CellTypeAssignmentRemovedEvent	Event emitted when a CellTypeAssignmentEvent is removed.
class	CommentedEvent	An event indicating a comment was added to the auditable.
class	CurationDetailsEvent	Event types that can change CurationDetails of Curatable objects.
class	CurationNoteUpdateEvent	Indicates that previous validation is being invalidated
class	DataAddedEvent	Indicates that a data type (for a specific QuantitationType, possibly new) was added.
class	DataRemovedEvent	Indicates that a data type (for a specific QuantitationType, possibly new) was removed.
class	DataReplacedEvent	Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the system.
class	DifferentialExpressionAnalysisEvent	Indicates the experiment was the subject of a differential expression analysis.
class	DifferentialExpressionSuitabilityEvent	Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.
class	DoesNotNeedAttentionEvent	An event that occurs when a curator has validated the entity and indicated that it is "approved".
class	ExperimentalDesignUpdatedEvent	Describes an event that involved a change of assignment of factor value to bio material, or other changes in the experimental design.
class	ExpressionExperimentAnalysisEvent	An event involving an ExpressionExperiment
class	ExpressionExperimentPlatformSwitchEvent	The event that this experiment has had its array design switched (typically to a 'merged' one.
class	ExpressionExperimentUpdateFromGEOEvent	Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.
class	ExpressionExperimentVectorMergeEvent	Indicates that the "Vector merging" has been done on the associated experiment.
class	FactorValueNeedsAttentionEvent	Indicates that a factor value needs attention.
class	FailedBatchInformationFetchingEvent	Indicates that the attempt to get batch information failed due to an error.
class	FailedBatchInformationMissingEvent	Deprecated. use BatchInformationMissingEvent
class	FailedDataReplacedEvent	Represents a failed data replace.
class	FailedDifferentialExpressionAnalysisEvent
class	FailedLinkAnalysisEvent
class	FailedMeanVarianceUpdateEvent
class	FailedMissingValueAnalysisEvent
class	FailedPCAAnalysisEvent
class	FailedProcessedVectorComputationEvent
class	FailedSampleCorrelationAnalysisEvent
class	GeeqEvent
class	LinkAnalysisEvent	Computing coexpression links for an expression experiment
class	MakePrivateEvent	Indicate that an entity has been made private.
class	MakePublicEvent	Indicate that an entity has been made public.
class	ManualAnnotationEvent
class	MeanVarianceUpdateEvent
class	MissingValueAnalysisEvent	Computing missing values for an expression experiment
class	NeedsAttentionAlteringEvent	Base class for events altering CurationDetails.getNeedsAttention().
class	NeedsAttentionEvent	Indicates that previous validation is being invalidated
class	NotTroubledStatusFlagEvent	This event type resets the trouble flag of curation details of a curatable object.
class	OutlierAnalysisEvent
class	OutlierFoundAnalysisEvent
class	OutliersNotFoundAnalysisEvent
class	PCAAnalysisEvent
class	PermissionChangeEvent	Represents a change in permissions of an Auditable entity.
class	ProcessedVectorComputationEvent	Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an Expression Experiment
class	RankComputationEvent	Deprecated.
class	ReleaseDetailsUpdateEvent	Event triggered when the release details of a Versioned entity are updated.
class	ResetSuitabilityForDifferentialExpressionAnalysisEvent	Used to indicate that the suitability status of an experiment is the default.
class	SampleCorrelationAnalysisEvent
class	SampleRemovalEvent	Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).
class	SampleRemovalReversionEvent	Indicates that samples that were previously removed have been "put back", e.g. un-marked as an outlier.
class	SingleBatchDeterminationEvent	Indicates that we got batch information, but there was (as far as we can tell) just one batch.
class	SingleCellSubSetsCreatedEvent	Emitted when a collection of ExpressionExperimentSubSet for holding aggregated single-cell data is created.
class	SingletonBatchInvalidEvent	Indiates that there was at least one batch with only one sample.
class	TooSmallDatasetLinkAnalysisEvent	Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skipped
class	TroubledStatusFlagAlteringEvent	Base class for events that alter the CurationDetails.getTroubled() flag.
class	TroubledStatusFlagEvent	Sets the trouble flag of curation details of any Curatable object.
class	UninformativeFASTQHeadersForBatchingEvent	Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of invalid formatting or lack of information.
class	UnsuitableForDifferentialExpressionAnalysisEvent	Indicates that the associated Experiment is NOT suitable for differential expression analysis.
class	VersionedEvent	Base class for events relating to a Versioned entity.

Uses of AbstractIdentifiable in ubic.gemma.model.common.description

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.description

Modifier and Type	Class	Description
class	BibliographicReference
class	BibRefAnnotation
class	Characteristic	Instances of this are used to describe other entities.
class	DatabaseEntry	A reference to a record in a database.
class	ExternalDatabase
class	Keyword
class	MedicalSubjectHeading

Uses of AbstractIdentifiable in ubic.gemma.model.common.measurement

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.measurement

Modifier and Type	Class	Description
class	Measurement
class	Unit

Uses of AbstractIdentifiable in ubic.gemma.model.common.protocol

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.protocol

Modifier and Type	Class	Description
class	Protocol

Uses of AbstractIdentifiable in ubic.gemma.model.common.quantitationtype

Subclasses of AbstractIdentifiable in ubic.gemma.model.common.quantitationtype

Modifier and Type	Class	Description
class	QuantitationType

Uses of AbstractIdentifiable in ubic.gemma.model.expression.arrayDesign

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.arrayDesign

Modifier and Type	Class	Description
class	AlternateName
class	ArrayDesign	Represents an assembly of design elements that are assayed all at once.

Uses of AbstractIdentifiable in ubic.gemma.model.expression.bioAssay

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.bioAssay

Modifier and Type	Class	Description
class	BioAssay	Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).

Uses of AbstractIdentifiable in ubic.gemma.model.expression.bioAssayData

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	BioAssayDimension	Stores the order of BioAssays referred to in DataVectors.
class	BulkExpressionDataVector	A data vector storing bulk expression data.
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	DataVector	An abstract class representing a one-dimensional vector of data about some aspect of an ExpressionExperiment.
class	DesignElementDataVector	Data vector associated to a CompositeSequence.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.
class	MeanVarianceRelation
class	ProcessedExpressionDataVector	Represents the processed data that is used for actual analyses.
class	RawExpressionDataVector	Data for one design element, across one or more bioassays, for a single quantitation type.
class	SingleCellDimension	Represents a single-cell dimension, holding shared information for a set of SingleCellExpressionDataVector.
class	SingleCellExpressionDataVector	An expression data vector that contains data at the resolution of individual cells.

Uses of AbstractIdentifiable in ubic.gemma.model.expression.biomaterial

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.biomaterial

Modifier and Type	Class	Description
class	BioMaterial	In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...
class	Compound
class	Treatment

Uses of AbstractIdentifiable in ubic.gemma.model.expression.designElement

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.designElement

Modifier and Type	Class	Description
class	CompositeSequence	A "Probe set" (Affymetrix) or a "Probe" (other types of arrays).

Uses of AbstractIdentifiable in ubic.gemma.model.expression.experiment

Subclasses of AbstractIdentifiable in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	BioAssaySet	Represents a set of BioAssays.
class	ExperimentalDesign
class	ExperimentalFactor	ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
class	ExpressionExperiment
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment
class	FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
class	Geeq	Represents quality information about a data set.
class	Statement	A special kind of characteristic that act as a statement.

Uses of AbstractIdentifiable in ubic.gemma.model.genome

Subclasses of AbstractIdentifiable in ubic.gemma.model.genome

Modifier and Type	Class	Description
class	Chromosome	Immutable representation of a chromosome
class	ChromosomeFeature	Some part of a chromosome
class	ChromosomeLocation
class	Gene	Represents a functionally transcribed unit in the genome, recognized by other databases (NCBI, Ensembl).
class	PhysicalLocation
class	Taxon

Uses of AbstractIdentifiable in ubic.gemma.model.genome.biosequence

Subclasses of AbstractIdentifiable in ubic.gemma.model.genome.biosequence

Modifier and Type	Class	Description
class	BioSequence	The sequence of a biological polymer such as a protein or DNA.

Uses of AbstractIdentifiable in ubic.gemma.model.genome.gene

Subclasses of AbstractIdentifiable in ubic.gemma.model.genome.gene

Modifier and Type	Class	Description
class	GeneAlias
class	GeneProduct
class	GeneSet	A grouping of genes that share a common relationship
class	GeneSetMember
class	Multifunctionality

Uses of AbstractIdentifiable in ubic.gemma.model.genome.sequenceAnalysis

Subclasses of AbstractIdentifiable in ubic.gemma.model.genome.sequenceAnalysis

Modifier and Type	Class	Description
class	AnnotationAssociation	An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis.
class	BlatAssociation
class	BlatResult	Represents the result of a BLAT search.
class	SequenceSimilaritySearchResult