Package ubic.gemma.persistence.service.association.phenotype.service

Interface PhenotypeAssociationService

All Superinterfaces:

BaseImmutableService<PhenotypeAssociation>, BaseReadOnlyService<PhenotypeAssociation>

All Known Implementing Classes:

PhenotypeAssociationServiceImpl

public interface PhenotypeAssociationService
extends BaseImmutableService<PhenotypeAssociation>

Author:

nicolas

Method Summary

Modifier and Type	Method	Description
Long	countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)
GenericExperiment	create(GenericExperiment genericExperiment)
PhenotypeAssociation	create(PhenotypeAssociation p)	Creates the given entity in the persistent storage.
Collection<GenericExperiment>	findByPubmedID(String pubmed)
Collection<CharacteristicValueObject>	findEvidenceCategoryTerms()
Collection<String>	findEvidenceOwners()
Collection<PhenotypeAssociation>	findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Collection<PhenotypeAssociation>	findEvidencesWithoutExternalDatabaseName()
Collection<ExternalDatabase>	findExternalDatabasesWithEvidence()	Gets all External Databases that are used with evidence
Map<GeneValueObject,OntologyTerm>	findGenesForPhenotype(OntologyTerm phenotype, Long taxonId, boolean includeIEA)
Collection<GeneEvidenceValueObject>	findGenesWithPhenotypes(Set<String> phenotypesValueUri, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneId(Long geneId)
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)
Collection<PhenotypeAssociation>	findPhenotypeAssociationWithIds(Collection<Long> paIds)
Collection<PhenotypeAssociation>	findPhenotypesForBibliographicReference(String pubMedId)
Set<Long>	findPrivateEvidenceId(String userName, Collection<String> groups, Long taxonId, int limit)
Map<String,Set<Integer>>	findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, String userName, Collection<String> groups, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
PhenotypeAssociation	load(Long id)	Loads object with given ID.
Collection<PhenotypeAssociation>	loadAll()	Loads all the entities of specific type.
Collection<PhenotypeValueObject>	loadAllNeurocartaPhenotypes()
Set<String>	loadAllUsedPhenotypeUris()
Collection<DifferentialExpressionEvidence>	loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, int maxResults)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnAllEvidence(String downloadFile)
Collection<ExternalDatabaseStatisticsValueObject>	loadStatisticsOnExternalDatabases(String downloadPath)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnManualCuration(String downloadFile)
void	remove(PhenotypeAssociation p)	Removes the given entity from the persistent storage.
int	removeAll()
void	removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublicationId)
void	update(PhenotypeAssociation evidence)

Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService

create, findOrCreate, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Method Detail

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(PhenotypeAssociation p)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<PhenotypeAssociation>

Parameters:

p - Using a phenotypeAssociation id removes the evidence

create

@Secured("GROUP_USER")
PhenotypeAssociation create(PhenotypeAssociation p)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<PhenotypeAssociation>

Parameters:

p - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

findGenesWithPhenotypes

Collection<GeneEvidenceValueObject> findGenesWithPhenotypes(Set<String> phenotypesValueUri,
                                                            @Nullable
                                                            Taxon taxon,
                                                            boolean showOnlyEditable,
                                                            @Nullable
                                                            Collection<Long> externalDatabaseIds)

findGenesForPhenotype

Map<GeneValueObject,OntologyTerm> findGenesForPhenotype(OntologyTerm phenotype,
                                                              Long taxonId,
                                                              boolean includeIEA)

Parameters:

phenotype - phenotype

taxonId - taxon id

includeIEA - include IEA

Returns:

map of gene value objects to ontology terms, where the term should be the most specific term relative to the phenotype that was queries (that is, it may be a child term).

create

@Secured("GROUP_USER")
GenericExperiment create(GenericExperiment genericExperiment)

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<PhenotypeAssociation>

Returns:

collection of all entities currently available in the persistent storage.

findByPubmedID

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<GenericExperiment> findByPubmedID(String pubmed)

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
PhenotypeAssociation load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<PhenotypeAssociation>

Parameters:

id - the ID of entity to be loaded.

Returns:

the entity with matching ID, or null if the entity does not exist or if the passed ID was null

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(PhenotypeAssociation evidence)

loadAllUsedPhenotypeUris

Set<String> loadAllUsedPhenotypeUris()

Returns:

load all valueURI of Phenotype in the database

findPhenotypesForBibliographicReference

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypesForBibliographicReference(String pubMedId)

findPhenotypeAssociationWithIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypeAssociationWithIds(Collection<Long> paIds)

findPhenotypeAssociationForGeneId

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneId(Long geneId)

findPhenotypeAssociationForGeneIdAndDatabases

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneIdAndDatabases(Long geneId,
                                                                               @Nullable
                                                                               Collection<Long> externalDatabaseIds)

findPhenotypeAssociationForGeneNCBI

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)

findPhenotypeAssociationForGeneNCBI

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI,
                                                                     Set<String> phenotype)

findEvidenceCategoryTerms

Collection<CharacteristicValueObject> findEvidenceCategoryTerms()

findEvidencesWithExternalDatabaseName

Collection<PhenotypeAssociation> findEvidencesWithExternalDatabaseName(String externalDatabaseName,
                                                                       int limit,
                                                                       int start)

findEvidencesWithoutExternalDatabaseName

@Secured("GROUP_AGENT")
Collection<PhenotypeAssociation> findEvidencesWithoutExternalDatabaseName()

findPublicPhenotypesGenesAssociations

Map<String,Set<Integer>> findPublicPhenotypesGenesAssociations(@Nullable
                                                                     Taxon taxon,
                                                                     @Nullable
                                                                     Set<String> valuesUri,
                                                                     @Nullable
                                                                     String userName,
                                                                     @Nullable
                                                                     Collection<String> groups,
                                                                     boolean showOnlyEditable,
                                                                     @Nullable
                                                                     Collection<Long> externalDatabaseIds,
                                                                     boolean noElectronicAnnotation)

findPrivateEvidenceId

Set<Long> findPrivateEvidenceId(@Nullable
                                String userName,
                                @Nullable
                                Collection<String> groups,
                                Long taxonId,
                                int limit)

findPrivatePhenotypesGenesAssociations

Map<String,Set<Integer>> findPrivatePhenotypesGenesAssociations(@Nullable
                                                                      Taxon taxon,
                                                                      @Nullable
                                                                      Set<String> valuesUri,
                                                                      @Nullable
                                                                      String userName,
                                                                      @Nullable
                                                                      Collection<String> groups,
                                                                      boolean showOnlyEditable,
                                                                      @Nullable
                                                                      Collection<Long> externalDatabaseIds,
                                                                      boolean noElectronicAnnotation)

findEvidenceOwners

Collection<String> findEvidenceOwners()

loadStatisticsOnExternalDatabases

Collection<ExternalDatabaseStatisticsValueObject> loadStatisticsOnExternalDatabases(String downloadPath)

loadStatisticsOnManualCuration

ExternalDatabaseStatisticsValueObject loadStatisticsOnManualCuration(String downloadFile)

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis

Collection<DifferentialExpressionEvidence> loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId,
                                                                                                  int maxResults)

Parameters:

geneDifferentialExpressionMetaAnalysisId - id

maxResults - max results

Returns:

a Collection for a geneDifferentialExpressionMetaAnalysisId if one exists (can be used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)

countEvidenceWithGeneDifferentialExpressionMetaAnalysis

Long countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)

loadAllNeurocartaPhenotypes

Collection<PhenotypeValueObject> loadAllNeurocartaPhenotypes()

findExternalDatabasesWithEvidence

Collection<ExternalDatabase> findExternalDatabasesWithEvidence()

Gets all External Databases that are used with evidence

Returns:

Collection the externalDatabases

loadStatisticsOnAllEvidence

ExternalDatabaseStatisticsValueObject loadStatisticsOnAllEvidence(String downloadFile)

removePhenotypePublication

void removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublicationId)

removeAll

@Secured("GROUP_ADMIN")
int removeAll()