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

Packages that use AbstractDescribable

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.blacklist
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.description
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

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

Subclasses of AbstractDescribable 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 AbstractDescribable in ubic.gemma.model.analysis

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

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

Subclasses of AbstractDescribable 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.

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

Subclasses of AbstractDescribable 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.

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

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

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

Uses of AbstractDescribable in ubic.gemma.model.blacklist

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

Subclasses of AbstractDescribable 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	Contact	Representing a person or organization that can be contacted about, or is the source of, data in the system.
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 AbstractDescribable in ubic.gemma.model.common.description

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

Modifier and Type	Class	Description
class	BibliographicReference
class	Characteristic	Instances of this are used to describe other entities.
class	ExternalDatabase

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

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

Modifier and Type	Class	Description
class	Protocol

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

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

Modifier and Type	Class	Description
class	QuantitationType

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

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

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

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

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

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

Modifier and Type	Class	Description
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.

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

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

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

Subclasses of AbstractDescribable 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	Statement	A special kind of characteristic that act as a statement.

Uses of AbstractDescribable in ubic.gemma.model.genome

Subclasses of AbstractDescribable in ubic.gemma.model.genome

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

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

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

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

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