Uses of Package
ubic.gemma.model.common.description

Packages that use ubic.gemma.model.common.description

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.sequence
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.crossref
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.cellxgene	This package contains classes for loading expression data from CELLxGENE.
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.model
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.util
ubic.gemma.core.ontology
ubic.gemma.core.ontology.providers	This package contains baseCode built-in ontologies and a ubic.basecode.ontology.providers.GenericOntologyService to implement your own ontologies.
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.core.tasks.maintenance
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.association
ubic.gemma.model.blacklist
ubic.gemma.model.common.description
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.association
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.biosequence
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.ranking
ubic.gemma.rest.util.args

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.analysis.expression.diff

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.analysis.sequence

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.analysis.singleCell

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.analysis.singleCell.aggregate

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.goldenpath

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.crossref

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.entrez.pubmed

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression.arrayDesign

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression.cellxgene

Class	Description
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression.geo

Class	Description
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression.geo.model

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.expression.singleCell

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.genome

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.genome.gene.ncbi

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.loader.util

Class	Description
DatabaseEntry	A reference to a record in a database.
DatabaseEntryValueObject	ValueObject for database entry
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.ontology

Class	Description
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.ontology.providers

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.search

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.search.source

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.tasks.maintenance

Class	Description
AnnotationValueObject

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.visualization

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.core.visualization.cellbrowser

Class	Description
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.analysis

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.analysis.expression

Class	Description
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.association

Class	Description
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.blacklist

Class	Description
DatabaseEntry	A reference to a record in a database.
ExternalDatabaseValueObject

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.common.description

Class	Description
AnnotationRelationBasis	How an AnnotationRelation came to be known, ranked best first.
AnnotationRelationStatus	Whether a source is stating that a relation holds, or stating that it does not.
BibliographicReference	Hibernate Search 7 indexed root.
BibliographicReferenceValueObject	represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
BibRefAnnotation	Base class for Keyword and MedicalSubjectHeading; the @Indexed annotation lives on the concrete subclasses.
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.
CitationValueObject	Represents a BibliographicReference as a citation string (which is really super light value object).
DatabaseEntry	A reference to a record in a database.
DatabaseType
ExternalDatabase
ExternalDatabaseValueObject
Keyword	Hibernate Search 7 mapping: indexed root for keyword phrases attached to a BibliographicReference.
MedicalSubjectHeading	Hibernate Search 7 mapping: indexed root for MeSH terms attached to a BibliographicReference.
PublicationAssociation	An evidenced claim about whether a BibliographicReference belongs to an Investigation — who says so, on what basis, and whether they are affirming or denying it.
PublicationAssociationRole	Which of the two publication slots on an Investigation an accepted PublicationAssociation occupies.
PublicationAssociationSource	Who asserted a PublicationAssociation — the authority behind the claim, as distinct from the evidence they gave for it.
PublicationAssociationStatus	Whether a PublicationAssociation affirms or denies the link between an experiment and a publication.
PublicationAssociationValueObject	Wire form of a PublicationAssociation: why a publication is (or is not) attached to a dataset, and on whose authority.
RelationInferenceDirection	Which end of a relation implies the other.
RelationTopicality	Whether a relation says something about the TERM, or records a parameter of an EXPERIMENT.
Value	Represents a value.
Versioned	Interface implemented by entities that are externally versioned.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.expression.arrayDesign

Class	Description
DatabaseEntry	A reference to a record in a database.
DatabaseEntryValueObject	ValueObject for database entry
Versioned	Interface implemented by entities that are externally versioned.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.expression.bioAssay

Class	Description
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.
DatabaseEntryValueObject	ValueObject for database entry

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.expression.bioAssayData

Class	Description
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.expression.biomaterial

Class	Description
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.expression.experiment

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.
CitationValueObject	Represents a BibliographicReference as a citation string (which is really super light value object).
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.genome

Class	Description
DatabaseEntry	A reference to a record in a database.
ExternalDatabase
ExternalDatabaseValueObject

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.genome.biosequence

Class	Description
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.genome.gene

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.
DatabaseEntryValueObject	ValueObject for database entry

Classes in ubic.gemma.model.common.description used by ubic.gemma.model.genome.sequenceAnalysis

Class	Description
DatabaseEntryValueObject	ValueObject for database entry
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.persister

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.
DatabaseEntry	A reference to a record in a database.
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.analysis.expression

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.association

Class	Description
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.common.description

Class	Description
AnnotationRelation	One term stands in some relation to another term: subject — predicate → object, plus where that came from.
AnnotationRelationBasis	How an AnnotationRelation came to be known, ranked best first.
AnnotationRelationStatus	Whether a source is stating that a relation holds, or stating that it does not.
BibliographicReference	Hibernate Search 7 indexed root.
BibliographicReferenceValueObject	represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.
DatabaseEntry	A reference to a record in a database.
DatabaseEntryValueObject	ValueObject for database entry
ExternalDatabase
PublicationAssociation	An evidenced claim about whether a BibliographicReference belongs to an Investigation — who says so, on what basis, and whether they are affirming or denying it.
PublicationAssociationRole	Which of the two publication slots on an Investigation an accepted PublicationAssociation occupies.
PublicationAssociationSource	Who asserted a PublicationAssociation — the authority behind the claim, as distinct from the evidence they gave for it.
PublicationAssociationStatus	Whether a PublicationAssociation affirms or denies the link between an experiment and a publication.
RelationInferenceDirection	Which end of a relation implies the other.
RelationTopicality	Whether a relation says something about the TERM, or records a parameter of an EXPERIMENT.

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.expression.biomaterial

Class	Description
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.expression.experiment

Class	Description
AnnotationValueObject
BibliographicReference	Hibernate Search 7 indexed root.
Category	Represents a category.
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.genome

Class	Description
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.genome.biosequence

Class	Description
DatabaseEntry	A reference to a record in a database.

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.genome.gene

Class	Description
AnnotationValueObject
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.service.genome.sequenceAnalysis

Class	Description
AnnotationValueObject

Classes in ubic.gemma.model.common.description used by ubic.gemma.persistence.util

Class	Description
BibliographicReference	Hibernate Search 7 indexed root.
Characteristic	Instances of this are used to describe other entities.
DatabaseEntry	A reference to a record in a database.
ExternalDatabase

Classes in ubic.gemma.model.common.description used by ubic.gemma.rest

Class	Description
AnnotationValueObject
Characteristic	Instances of this are used to describe other entities.
CharacteristicValueObject	Value object representation of a Characteristic.
DatasetPublicationValueObject	A publication as it appears in the context of one dataset: the reference, plus the evidenced claim that ties it to (or rules it out for) that dataset.
ExternalDatabaseValueObject
Versioned	Interface implemented by entities that are externally versioned.

Classes in ubic.gemma.model.common.description used by ubic.gemma.rest.ranking

Class	Description
CharacteristicValueObject	Value object representation of a Characteristic.

Classes in ubic.gemma.model.common.description used by ubic.gemma.rest.util.args

Class	Description
AnnotationValueObject
DatabaseEntry	A reference to a record in a database.
DatasetPublicationValueObject	A publication as it appears in the context of one dataset: the reference, plus the evidenced claim that ties it to (or rules it out for) that dataset.