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

Interface PhenotypeAssociationDao

All Superinterfaces:

BaseDao<PhenotypeAssociation>

All Known Implementing Classes:

PhenotypeAssociationDaoImpl

public interface PhenotypeAssociationDao
extends BaseDao<PhenotypeAssociation>

Author:

nicolas

Method Summary

Modifier and Type	Method	Description
Long	countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)
Collection<CharacteristicValueObject>	findEvidenceCategoryTerms()
Collection<String>	findEvidenceOwners()
Collection<PhenotypeAssociation>	findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)
Collection<PhenotypeAssociation>	findEvidencesWithoutExternalDatabaseName()
Collection<ExternalDatabase>	findExternalDatabasesWithEvidence()
Map<GeneValueObject,OntologyTerm>	findGenesForPhenotype(OntologyTerm term, Long taxon, 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> ids)
Collection<PhenotypeAssociation>	findPhenotypesForBibliographicReference(String pubMedID)
Set<Long>	findPrivateEvidenceId(Long taxonId, int limit)
Map<String,Set<Integer>>	findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Map<String,Set<Integer>>	findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)
Collection<PhenotypeValueObject>	loadAllNeurocartaPhenotypes()
Set<String>	loadAllPhenotypesUri()
Collection<DifferentialExpressionEvidence>	loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, int maxResults)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnAllEvidence(String filePath)
Collection<ExternalDatabaseStatisticsValueObject>	loadStatisticsOnExternalDatabases(String folderPath)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnManualCuration(String filePath)
int	removeAll()
void	removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublicationId)	remove a PhenotypeAssociationPublication

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

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Method Detail

countEvidenceWithGeneDifferentialExpressionMetaAnalysis

Long countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)

Parameters:

geneDifferentialExpressionMetaAnalysisId - id

Returns:

count of the evidence that from neurocarta that came from a specific MetaAnalysis

findEvidenceCategoryTerms

Collection<CharacteristicValueObject> findEvidenceCategoryTerms()

Returns:

category terms currently used in the database by evidence

findEvidenceOwners

Collection<String> findEvidenceOwners()

Returns:

the list of the owners that have evidence in the system

findEvidencesWithExternalDatabaseName

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

Parameters:

limit - limit

externalDatabaseName - external database name

start - start

Returns:

all evidences from a specific external database

findEvidencesWithoutExternalDatabaseName

Collection<PhenotypeAssociation> findEvidencesWithoutExternalDatabaseName()

Returns:

all evidence that doesn't come from an external course

findExternalDatabasesWithEvidence

Collection<ExternalDatabase> findExternalDatabasesWithEvidence()

Returns:

all External Databases that are used with evidence

findGenesForPhenotype

Map<GeneValueObject,OntologyTerm> findGenesForPhenotype(OntologyTerm term,
                                                              Long taxon,
                                                              boolean includeIEA)

Parameters:

taxon - taxon

term - term

includeIEA - if false, electronic annotations will be omitted

Returns:

map of gene value objects to the exact phenotype the gene was annotated to. (gives no indication of 'bag of terms')

findGenesWithPhenotypes

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

Parameters:

taxon - taxon

externalDatabaseIds - external db ids

phenotypesValueUri - phenotype value uri

showOnlyEditable - show only editable

Returns:

Genes link to a phenotype

findPhenotypeAssociationForGeneId

Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneId(Long geneId)

Parameters:

geneId - gene id

Returns:

all PhenotypeAssociation for a specific gene id

findPhenotypeAssociationForGeneIdAndDatabases

Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneIdAndDatabases(Long geneId,
                                                                               @Nullable
                                                                               Collection<Long> externalDatabaseIds)

Parameters:

externalDatabaseIds - external db ids

geneId - gene id

Returns:

all PhenotypeAssociation for a specific gene id and external Databases ids

findPhenotypeAssociationForGeneNCBI

Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)

Parameters:

geneNCBI - gene ncbi id

Returns:

all PhenotypeAssociation for a specific NCBI id

findPhenotypeAssociationForGeneNCBI

Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI,
                                                                     Set<String> phenotype)

Parameters:

geneNCBI - gene ncbi id

phenotype - phenotype

Returns:

all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri

findPhenotypeAssociationWithIds

Collection<PhenotypeAssociation> findPhenotypeAssociationWithIds(Collection<Long> ids)

Parameters:

ids - ids

Returns:

PhenotypeAssociations satisfying the given filters: ids, taxonId and limit

findPhenotypesForBibliographicReference

Collection<PhenotypeAssociation> findPhenotypesForBibliographicReference(String pubMedID)

Parameters:

pubMedID - pumbed id

Returns:

PhenotypeAssociations associated with a BibliographicReference

findPrivateEvidenceId

Set<Long> findPrivateEvidenceId(@Nullable
                                Long taxonId,
                                int limit)

Parameters:

limit - limit

taxonId - taxon id

Returns:

private evidence id that the user can modify or owns

findPrivatePhenotypesGenesAssociations

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

Parameters:

externalDatabaseIds - external db ids

taxon - taxon

noElectronicAnnotation - no electronic annotation

showOnlyEditable - show only editable

valuesUri - value uris

Returns:

ll private phenotypes associated with genes on a specific taxon and containing the valuesUri

findPublicPhenotypesGenesAssociations

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

Parameters:

showOnlyEditable - show only editable

noElectronicAnnotation - no electronic annotation

taxon - taxon

externalDatabaseIds - external database ids

valuesUri - values uri

Returns:

all public phenotypes associated with genes on a specific taxon and containing the valuesUri

loadAllNeurocartaPhenotypes

Collection<PhenotypeValueObject> loadAllNeurocartaPhenotypes()

Returns:

all phenotypes in Neurocarta

loadAllPhenotypesUri

Set<String> loadAllPhenotypesUri()

Returns:

all valueURI of Phenotype in the database

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis

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

Parameters:

maxResults - max results

geneDifferentialExpressionMetaAnalysisId - ids

Returns:

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

loadStatisticsOnAllEvidence

ExternalDatabaseStatisticsValueObject loadStatisticsOnAllEvidence(String filePath)

Parameters:

filePath - path

Returns:

statistics all evidences

loadStatisticsOnExternalDatabases

Collection<ExternalDatabaseStatisticsValueObject> loadStatisticsOnExternalDatabases(String folderPath)

Parameters:

folderPath - path

Returns:

all external databases statistics used in neurocarta

loadStatisticsOnManualCuration

ExternalDatabaseStatisticsValueObject loadStatisticsOnManualCuration(String filePath)

Parameters:

filePath - path

Returns:

statistics for a neurocarta manual curation (numGene, numPhenotypes, etc.)

removePhenotypePublication

void removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublicationId)

remove a PhenotypeAssociationPublication

Parameters:

phenotypeAssociationPublicationId - id

removeAll

int removeAll()