Uses of Class
ubic.gemma.model.common.description.BibliographicReference

Packages that use BibliographicReference

Package	Description
ubic.gemma.core.loader.crossref
ubic.gemma.core.loader.entrez.pubmed
ubic.gemma.core.search
ubic.gemma.core.search.source
ubic.gemma.model.analysis
ubic.gemma.model.common.description
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

Uses of BibliographicReference in ubic.gemma.core.loader.crossref

Methods in ubic.gemma.core.loader.crossref that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	CrossRefFetcher.retrieveByDoi(String doi)	Retrieve a BibliographicReference for the given DOI from CrossRef.

Uses of BibliographicReference in ubic.gemma.core.loader.entrez.pubmed

Methods in ubic.gemma.core.loader.entrez.pubmed that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	ExpressionExperimentBibRefFinder.locatePrimaryReference(ExpressionExperiment ee)
BibliographicReference	ExpressionExperimentBibRefFinder.locatePrimaryReference(ExpressionExperiment ee, boolean forceFromGeo)	Locate the primary reference for an experiment from GEO.
BibliographicReference	PubMedSearch.retrieve(String pubMedId)	Retrieve a single PubMed record by ID.

Methods in ubic.gemma.core.loader.entrez.pubmed that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
static Collection<BibliographicReference>	PubMedXMLParser.parse(InputStream is)
Collection<BibliographicReference>	PubMedSearch.retrieve(Collection<String> pubmedIds)	Retrieve multiple PubMed records by ID.
Collection<BibliographicReference>	PubMedSearch.searchAndRetrieve(String searchQuery, int maxResults)	Search based on terms and retrieve the PubMed records.
Collection<BibliographicReference>	PubMedSearch.searchAndRetrieveByDoi(String doi)	Retrieve PubMed records by DOI.

Methods in ubic.gemma.core.loader.entrez.pubmed with parameters of type BibliographicReference

Modifier and Type	Method	Description
static void	PubMedXMLParser.extractPublisher(BibliographicReference bibRef, Node item)
static void	PubMedXMLParser.processContributionDate(Node item, BibliographicReference bibRef)

Uses of BibliographicReference in ubic.gemma.core.search

Methods in ubic.gemma.core.search that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
default Collection<SearchResult<BibliographicReference>>	SearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)

Uses of BibliographicReference in ubic.gemma.core.search.source

Methods in ubic.gemma.core.search.source that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Collection<SearchResult<BibliographicReference>>	CompositeSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)
Collection<SearchResult<BibliographicReference>>	HibernateSearchSource.searchBibliographicReference(SearchSettings settings, SearchContext context)

Uses of BibliographicReference in ubic.gemma.model.analysis

Methods in ubic.gemma.model.analysis that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	Investigation.getPrimaryPublication()

Methods in ubic.gemma.model.analysis that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	Investigation.getOtherRelevantPublications()

Methods in ubic.gemma.model.analysis with parameters of type BibliographicReference

Modifier and Type	Method	Description
void	Investigation.setPrimaryPublication(BibliographicReference primaryPublication)

Method parameters in ubic.gemma.model.analysis with type arguments of type BibliographicReference

Modifier and Type	Method	Description
void	Investigation.setOtherRelevantPublications(Set<BibliographicReference> otherRelevantPublications)

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

Subclasses with type arguments of type BibliographicReference in ubic.gemma.model.common.description

Modifier and Type	Class	Description
class	BibliographicReferenceValueObject	represents a BibliographicReferenceValueObject when this value object is needed in core, the same value object exists in web

Methods in ubic.gemma.model.common.description that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	PublicationAssociation.getPublication()
static BibliographicReference	BibliographicReference.Factory.newInstance()

Methods in ubic.gemma.model.common.description with parameters of type BibliographicReference

Modifier and Type	Method	Description
static CitationValueObject	BibliographicReferenceValueObject.constructCitation(BibliographicReference bib)
static CitationValueObject	CitationValueObject.convert2CitationValueObject(BibliographicReference ref)
void	PublicationAssociation.setPublication(BibliographicReference publication)

Method parameters in ubic.gemma.model.common.description with type arguments of type BibliographicReference

Modifier and Type	Method	Description
static Collection<CitationValueObject>	BibliographicReferenceValueObject.constructCitations(Collection<BibliographicReference> bibs)
static List<CitationValueObject>	CitationValueObject.convert2CitationValueObjects(Collection<BibliographicReference> refs)
static List<BibliographicReferenceValueObject>	BibliographicReferenceValueObject.convert2ValueObjects(Collection<BibliographicReference> refs)	does not set related experiments field

Constructors in ubic.gemma.model.common.description with parameters of type BibliographicReference

Modifier	Constructor	Description
	BibliographicReferenceValueObject(BibliographicReference ref)	does not set related experiments field
	DatasetPublicationValueObject(BibliographicReference ref, PublicationAssociation association)

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

Methods in ubic.gemma.model.expression.experiment that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	ExpressionExperiment.getPrimaryPublication()

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	ExpressionExperiment.getOtherRelevantPublications()

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

Methods in ubic.gemma.model.genome.gene that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
Set<BibliographicReference>	GeneSet.getLiteratureSources()

Method parameters in ubic.gemma.model.genome.gene with type arguments of type BibliographicReference

Modifier and Type	Method	Description
void	GeneSet.setLiteratureSources(Set<BibliographicReference> literatureSources)

Uses of BibliographicReference in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	CommonPersister.persistBibliographicReference(BibliographicReference reference, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.

Methods in ubic.gemma.persistence.persister with parameters of type BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	CommonPersister.persistBibliographicReference(BibliographicReference reference, Map<String, ExternalDatabase> externalDbCache)	Phase 3 persister-retirement scaffold: takes a per-call Map<String, ExternalDatabase>.

Uses of BibliographicReference in ubic.gemma.persistence.service.common.description

Subclasses with type arguments of type BibliographicReference in ubic.gemma.persistence.service.common.description

Modifier and Type	Class	Description
class	BibliographicReferenceDaoImpl
class	BibliographicReferenceServiceImpl	Implementation of BibliographicReferenceService.

Subinterfaces with type arguments of type BibliographicReference in ubic.gemma.persistence.service.common.description

Modifier and Type	Interface	Description
interface	BibliographicReferenceDao
interface	BibliographicReferenceDao
interface	BibliographicReferenceService
interface	BibliographicReferenceService

Methods in ubic.gemma.persistence.service.common.description that return BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	BibliographicReferenceService.create(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.find(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.find(BibliographicReference bibliographicReference)	check to see if the object already exists
BibliographicReference	BibliographicReferenceDao.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceDao.findByExternalId(DatabaseEntry externalId)	Find by the external database id, such as for PubMed
BibliographicReference	BibliographicReferenceDaoImpl.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceDaoImpl.findByExternalId(DatabaseEntry externalId)
BibliographicReference	BibliographicReferenceReadService.findByExternalId(String id)	Get a reference by the unqualified external id.
BibliographicReference	BibliographicReferenceReadService.findByExternalId(String id, String databaseName)	Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
BibliographicReference	BibliographicReferenceReadService.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceReadServiceImpl.findByExternalId(String id)
BibliographicReference	BibliographicReferenceReadServiceImpl.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceReadServiceImpl.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceService.findByExternalId(String id)	Get a reference by the unqualified external id.
BibliographicReference	BibliographicReferenceService.findByExternalId(String id, String databaseName)	Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
BibliographicReference	BibliographicReferenceService.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(String id)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(String id, String databaseName)
BibliographicReference	BibliographicReferenceServiceImpl.findByExternalId(DatabaseEntry accession)
BibliographicReference	BibliographicReferenceService.findOrCreate(BibliographicReference BibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.findOrCreate(BibliographicReference ref)	Find an existing BibliographicReference by its pubAccession, or create a new one.
BibliographicReference	BibliographicReferenceService.findOrCreateByDoi(String doi)	Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.
BibliographicReference	BibliographicReferenceServiceImpl.findOrCreateByDoi(String doi)
BibliographicReference	BibliographicReferenceService.findOrCreateByPubMedId(String pubMedId)	Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.
BibliographicReference	BibliographicReferenceServiceImpl.findOrCreateByPubMedId(String pubMedId)
BibliographicReference	PublicationAssertion.getPublication()
BibliographicReference	BibliographicReferenceService.refresh(String pubMedId)
BibliographicReference	BibliographicReferenceServiceImpl.refresh(String pubMedId)
BibliographicReference	BibliographicReferenceService.save(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDao.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceReadService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceReadServiceImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.thaw(BibliographicReference bibliographicReference)

Methods in ubic.gemma.persistence.service.common.description that return types with arguments of type BibliographicReference

Modifier and Type	Method	Description
List<BibliographicReference>	BibliographicReferenceDaoImpl.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceDaoImpl.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceReadService.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceReadService.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceReadServiceImpl.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceReadServiceImpl.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceService.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceService.browse(int start, int limit, String orderField, boolean descending)
List<BibliographicReference>	BibliographicReferenceServiceImpl.browse(int start, int limit)
List<BibliographicReference>	BibliographicReferenceServiceImpl.browse(int start, int limit, String orderField, boolean descending)
Collection<BibliographicReference>	BibliographicReferenceService.create(Collection<BibliographicReference> entities)
List<BibliographicReference>	BibliographicReferenceDao.findAllByExternalId(String id, String databaseName)	Find ALL references sharing an external id, ordered by id ascending.
List<BibliographicReference>	BibliographicReferenceDaoImpl.findAllByExternalId(String id, String databaseName)
List<BibliographicReference>	BibliographicReferenceReadService.findAllByExternalId(String id, String databaseName)	Retrieve ALL references sharing an identifier (accession + database name), ordered by id ascending.
List<BibliographicReference>	BibliographicReferenceReadServiceImpl.findAllByExternalId(String id, String databaseName)
LinkedHashMap<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceDao.getRelatedExperiments(int offset, int limit)	Get a slice of the references that are linked to experiments.
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)	Get the related experiments for the given references.
LinkedHashMap<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceDaoImpl.getRelatedExperiments(int offset, int limit)
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceReadService.getRelatedExperiments(int offset, int limit)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceReadServiceImpl.getRelatedExperiments(int offset, int limit)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceService.getRelatedExperiments(int offset, int limit)	Return all the BibRefs that are linked to ExpressionExperiments.
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	BibliographicReferenceServiceImpl.getRelatedExperiments(int offset, int limit)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Collection<BibliographicReference>	BibliographicReferenceService.save(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceDao.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceDaoImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceReadService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceReadServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)

Methods in ubic.gemma.persistence.service.common.description with parameters of type BibliographicReference

Modifier and Type	Method	Description
BibliographicReference	BibliographicReferenceService.create(BibliographicReference bibliographicReference)
protected BibliographicReferenceValueObject	BibliographicReferenceDaoImpl.doLoadValueObject(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDaoImpl.find(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.find(BibliographicReference bibliographicReference)	check to see if the object already exists
PublicationAssociation	PublicationAssociationService.find(Investigation investigation, BibliographicReference publication)	The assertion held for this exact pair, or null if the pair has never been ruled on.
PublicationAssociation	PublicationAssociationServiceImpl.find(Investigation investigation, BibliographicReference publication)
PublicationAssociation	PublicationAssociationService.findBlockingRejection(Investigation investigation, BibliographicReference publication, PublicationAssociationSource source)	The standing rejection that would refuse an attempt by source to accept publication for investigation, or null if the write is allowed.
PublicationAssociation	PublicationAssociationServiceImpl.findBlockingRejection(Investigation investigation, BibliographicReference publication, PublicationAssociationSource source)
PublicationAssociation	PublicationAssociationDao.findByInvestigationAndPublication(Investigation investigation, BibliographicReference publication)	The assertion held for this exact pair, or null if none.
PublicationAssociation	PublicationAssociationDaoImpl.findByInvestigationAndPublication(Investigation investigation, BibliographicReference publication)
BibliographicReference	BibliographicReferenceService.findOrCreate(BibliographicReference BibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.findOrCreate(BibliographicReference ref)	Find an existing BibliographicReference by its pubAccession, or create a new one.
List<PublicationAssociation>	PublicationAssociationService.findRejections(BibliographicReference publication)	Every rejection of this publication across all datasets: who ruled it out, where, and why.
List<PublicationAssociation>	PublicationAssociationServiceImpl.findRejections(BibliographicReference publication)
List<PublicationAssociation>	PublicationAssociationDao.findRejectionsByPublication(BibliographicReference publication)	Every investigation-side rejection of this publication, across all datasets.
List<PublicationAssociation>	PublicationAssociationDaoImpl.findRejectionsByPublication(BibliographicReference publication)
BibliographicReferenceValueObject	BibliographicReferenceServiceImpl.loadValueObject(BibliographicReference entity)
int	PublicationAssociationDao.rebindPublication(BibliographicReference from, BibliographicReference to)	Move every assertion about from onto to, for the duplicate-reference merge.
int	PublicationAssociationDaoImpl.rebindPublication(BibliographicReference from, BibliographicReference to)
int	PublicationAssociationService.rebindPublication(BibliographicReference from, BibliographicReference to)	Move every assertion about from onto to, for the duplicate-reference merge.
int	PublicationAssociationServiceImpl.rebindPublication(BibliographicReference from, BibliographicReference to)
void	BibliographicReferenceService.remove(BibliographicReference BibliographicReference)
BibliographicReference	BibliographicReferenceService.save(BibliographicReference entity)
BibliographicReference	BibliographicReferenceDao.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceDaoImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceReadService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceReadServiceImpl.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceService.thaw(BibliographicReference bibliographicReference)
BibliographicReference	BibliographicReferenceServiceImpl.thaw(BibliographicReference bibliographicReference)
void	BibliographicReferenceService.update(BibliographicReference entity)

Method parameters in ubic.gemma.persistence.service.common.description with type arguments of type BibliographicReference

Modifier and Type	Method	Description
Collection<BibliographicReference>	BibliographicReferenceService.create(Collection<BibliographicReference> entities)
List<PublicationAssociation>	PublicationAssociationDao.findByInvestigationAndPublications(Investigation investigation, Collection<BibliographicReference> publications)	Assertions for the investigation whose publication is one of publications, in one query.
List<PublicationAssociation>	PublicationAssociationDaoImpl.findByInvestigationAndPublications(Investigation investigation, Collection<BibliographicReference> publications)
Map<Long, PublicationAssociation>	PublicationAssociationService.findByPublications(Investigation investigation, Collection<BibliographicReference> publications)	Assertions for the investigation covering publications, in one query, keyed by publication id — the read path's way to decorate a dataset's publication list without a query per row.
Map<Long, PublicationAssociation>	PublicationAssociationServiceImpl.findByPublications(Investigation investigation, Collection<BibliographicReference> publications)
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDao.getRelatedExperiments(Collection<BibliographicReference> records)	Get the related experiments for the given references.
LinkedHashMap<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceDaoImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceReadServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceService.getRelatedExperiments(Collection<BibliographicReference> records)
Map<BibliographicReference, Collection<ExpressionExperiment>>	BibliographicReferenceServiceImpl.getRelatedExperiments(Collection<BibliographicReference> records)
void	BibliographicReferenceService.remove(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceService.save(Collection<BibliographicReference> entities)
Collection<BibliographicReference>	BibliographicReferenceDao.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceDaoImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceReadService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceReadServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceService.thaw(Collection<BibliographicReference> bibliographicReferences)
Collection<BibliographicReference>	BibliographicReferenceServiceImpl.thaw(Collection<BibliographicReference> bibliographicReferences)
void	BibliographicReferenceService.update(Collection<BibliographicReference> entities)

Constructors in ubic.gemma.persistence.service.common.description with parameters of type BibliographicReference

Modifier	Constructor	Description
	PublicationAssertion(BibliographicReference publication, PublicationAssociationSource source)	A claim with a reference and an authority but no stated basis — what the pre-evidence write path amounts to, and what the plain three-argument ExpressionExperimentService.updatePublications(ExpressionExperiment, BibliographicReference, Collection) produces for its callers.
	PublicationAssertion(BibliographicReference publication, PublicationAssociationSource source, String evidence, String supportingEvidence, GOEvidenceCode evidenceCode, Double confidence, String assertedBy)

Uses of BibliographicReference in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type BibliographicReference

Modifier and Type	Method	Description
Collection<ExpressionExperiment>	ExpressionExperimentDao.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentDaoImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentReadService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentReadServiceImpl.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentService.findByBibliographicReference(BibliographicReference bibRef)
Collection<ExpressionExperiment>	ExpressionExperimentServiceImpl.findByBibliographicReference(BibliographicReference bibRef)
void	ExpressionExperimentService.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace the publications associated with ee: set (or clear) its primary publication and replace its other-relevant-publication set in one shot (idempotent set semantics).
void	ExpressionExperimentServiceImpl.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace an EE's primary + other-relevant publications, recording every one as a bare curator assertion.

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type BibliographicReference

Modifier and Type	Method	Description
void	ExpressionExperimentService.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace the publications associated with ee: set (or clear) its primary publication and replace its other-relevant-publication set in one shot (idempotent set semantics).
void	ExpressionExperimentServiceImpl.updatePublications(ExpressionExperiment ee, BibliographicReference primaryPublication, Collection<BibliographicReference> otherRelevantPublications)	Replace an EE's primary + other-relevant publications, recording every one as a bare curator assertion.

Uses of BibliographicReference in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type BibliographicReference

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(BibliographicReference bibliographicReference)
static void	Thaws.thawBibliographicReference(BibliographicReference br)