Package ubic.gemma.core.association.phenotype

Class PhenotypeAssociationManagerServiceImpl

java.lang.Object

ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl

All Implemented Interfaces:

InitializingBean, PhenotypeAssociationManagerService

@Service
@Deprecated
public class PhenotypeAssociationManagerServiceImpl
extends Object
implements PhenotypeAssociationManagerService, InitializingBean

Deprecated.

High Level Service used to add Candidate Gene Management System capabilities

Author:

nicolas

Constructor Summary

Constructors

Constructor	Description
PhenotypeAssociationManagerServiceImpl()	Deprecated.

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()	Deprecated.
BibliographicReferenceValueObject	findBibliographicReference(String pubMedId)	Deprecated. Find all phenotypes associated to a pubmedID
Collection<GeneEvidenceValueObject>	findCandidateGenes(Collection<String> phenotypeValueUris, Taxon taxon)	Deprecated. Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypes
Set<GeneEvidenceValueObject>	findCandidateGenes(EvidenceFilter evidenceFilter, Set<String> phenotypesValuesUri)	Deprecated. Given set of phenotypes returns the genes that have all those phenotypes or children phenotypes
Map<String,Collection<? extends GeneValueObject>>	findCandidateGenesForEach(Set<String> phenotypeUris, Taxon taxon)	Deprecated.
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	findEvidenceByFilters(Long taxonId, int limit, String userName)	Deprecated. Return evidence satisfying the specified filters.
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	findEvidenceByGeneId(Long geneId)	Deprecated. Return all evidence for a specific gene id
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	findEvidenceByGeneId(Long geneId, Set<String> phenotypesValuesUri, EvidenceFilter evidenceFilter)	Deprecated. Return all evidence for a specific gene id with evidence flagged, indicating more information
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	findEvidenceByGeneNCBI(Integer geneNCBI)	Deprecated. Return all evidence for a specific gene NCBI
Collection<String>	findEvidenceOwners()	Deprecated.
Collection<CharacteristicValueObject>	findExperimentCategory()	Deprecated. Find category term that were used in the database, used to annotated Experiments
Collection<CharacteristicValueObject>	findExperimentOntologyValue(String givenQueryString)	Deprecated. for a given search string look in the database and Ontology for matches
Collection<ExternalDatabaseValueObject>	findExternalDatabasesWithEvidence()	Deprecated. Gets all External Databases that are used with evidence
Map<GeneValueObject,OntologyTerm>	findGenesForPhenotype(String phenotype, Long taxonId, boolean includeIEA)	Deprecated.
List<GeneEvidenceValueObject>	findGenesWithEvidence(String query, Long taxonId)	Deprecated. Does a Gene search (by name or symbol) for a query and return only Genes with evidence
Set<DumpsValueObject>	helpFindAllDumps()	Deprecated. Get information about external data sources from Phenocarta, including URLs and timestamps of the most recent update dates/times.
EvidenceValueObject<? extends PhenotypeAssociation>	load(Long id)	Deprecated. Load an evidence
Collection<PhenotypeValueObject>	loadAllNeurocartaPhenotypes()	Deprecated. load all the valueUri and value of phenotype present in Neurocarta
Collection<TreeCharacteristicValueObject>	loadAllPhenotypesAsTree(EvidenceFilter evidenceFilter)	Deprecated. Same as loadAllPhenotypesByTree(EvidenceFilter), but does not flatten out the tree.
Collection<SimpleTreeValueObject>	loadAllPhenotypesByTree(EvidenceFilter evidenceFilter)	Deprecated. Loads all phenotypes in the database and counts their occurrence using the database It builds the tree using parents of terms, and will return 3 trees representing Disease, HP and MP
Set<EvidenceValueObject<? extends PhenotypeAssociation>>	loadEvidenceWithExternalDatabaseName(String externalDatabaseName, int limit, int start)	Deprecated. use if we want to reimport data from a specific external Database
DiffExpressionEvidenceValueObject	loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)	Deprecated. returns an DifferentialExpressionEvidence for a geneDifferentialExpressionMetaAnalysisId if one exists (used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)
Collection<EvidenceValueObject<? extends PhenotypeAssociation>>	loadEvidenceWithoutExternalDatabaseName()	Deprecated.
Collection<ExternalDatabaseStatisticsValueObject>	loadNeurocartaStatistics()	Deprecated. find statistics on evidence used in neurocarta
ValidateEvidenceValueObject	makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, SortedSet<CharacteristicValueObject> phenotypes, Double selectionThreshold)	Deprecated. creates the DifferentialExpressionEvidences using an DiffExpressionMetaAnalysis
ValidateEvidenceValueObject	makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation> evidence)	Deprecated. Links an Evidence to a Gene
ValidateEvidenceValueObject	remove(Long id)	Deprecated. Removes an evidence
ValidateEvidenceValueObject	removeAllEvidenceFromMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)	Deprecated. Removes all the evidence that came from a specific metaAnalysis
Collection<CharacteristicValueObject>	searchInDatabaseForPhenotype(String searchQuery, int maxResults)	Deprecated. For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms
Collection<CharacteristicValueObject>	searchOntologyForPhenotypes(String searchQuery, Long geneId)	Deprecated. Giving a phenotype searchQuery, returns a selection choice to the user
ValidateEvidenceValueObject	update(EvidenceValueObject<? extends PhenotypeAssociation> modifiedEvidenceValueObject)	Deprecated. Modify an existing evidence
ValidateEvidenceValueObject	validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)	Deprecated. Validate an Evidence before we create it
void	writeAllEvidenceToFile()	Deprecated. Creates a dump of all evidence in the database that can be downloaded on the client, this is run once per month by Quartz

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhenotypeAssociationManagerServiceImpl

public PhenotypeAssociationManagerServiceImpl()

Deprecated.

Method Detail

afterPropertiesSet

public void afterPropertiesSet()

Deprecated.

Specified by:

afterPropertiesSet in interface InitializingBean

findBibliographicReference

@Transactional(readOnly=true)
public BibliographicReferenceValueObject findBibliographicReference(String pubMedId)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Find all phenotypes associated to a pubmedID

Specified by:

findBibliographicReference in interface PhenotypeAssociationManagerService

Parameters:

pubMedId - pubmed id

Returns:

BibliographicReferenceValueObject

findCandidateGenes

@Transactional(readOnly=true)
public Collection<GeneEvidenceValueObject> findCandidateGenes(Collection<String> phenotypeValueUris,
                                                              Taxon taxon)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypes

Specified by:

findCandidateGenes in interface PhenotypeAssociationManagerService

Parameters:

phenotypeValueUris - the roots phenotype of the query

taxon - the name of the taxon (optional)

Returns:

A map or uris to collections of the genes found

findCandidateGenes

@Transactional(readOnly=true)
public Set<GeneEvidenceValueObject> findCandidateGenes(EvidenceFilter evidenceFilter,
                                                       Set<String> phenotypesValuesUri)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Given set of phenotypes returns the genes that have all those phenotypes or children phenotypes

Specified by:

findCandidateGenes in interface PhenotypeAssociationManagerService

Parameters:

evidenceFilter - can specify a taxon and to show modifiable evidence (optional)

phenotypesValuesUri - the roots phenotype of the query

Returns:

A collection of the genes found

findCandidateGenesForEach

@Transactional(readOnly=true)
public Map<String,Collection<? extends GeneValueObject>> findCandidateGenesForEach(Set<String> phenotypeUris,
                                                                                         Taxon taxon)

Deprecated.

Specified by:

findCandidateGenesForEach in interface PhenotypeAssociationManagerService

Parameters:

phenotypeUris - URIs

taxon - taxon

Returns:

For each phenotypeUri, find the genes that are associated with it. Different from findCandidateGenes which finds genes associated with all the phenotypes together.

findEvidenceByFilters

@Transactional(readOnly=true)
public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByFilters(Long taxonId,
                                                                                             int limit,
                                                                                             String userName)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Return evidence satisfying the specified filters. If the current user has not logged in, empty container is returned.

Specified by:

findEvidenceByFilters in interface PhenotypeAssociationManagerService

Parameters:

taxonId - taxon id

limit - number of evidence value objects to return

userName - user name

Returns:

evidence satisfying the specified filters

findEvidenceByGeneId

@Transactional(readOnly=true)
public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByGeneId(Long geneId)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Return all evidence for a specific gene id

Specified by:

findEvidenceByGeneId in interface PhenotypeAssociationManagerService

Parameters:

geneId - The Evidence id

Returns:

The Gene we are interested in

findEvidenceByGeneId

@Transactional(readOnly=true)
public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByGeneId(Long geneId,
                                                                                            Set<String> phenotypesValuesUri,
                                                                                            EvidenceFilter evidenceFilter)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Return all evidence for a specific gene id with evidence flagged, indicating more information

Specified by:

findEvidenceByGeneId in interface PhenotypeAssociationManagerService

Parameters:

geneId - The Evidence id

phenotypesValuesUri - the chosen phenotypes

evidenceFilter - can specify a taxon and to show modifiable evidence (optional)

Returns:

The Gene we are interested in

findEvidenceByGeneNCBI

@Transactional(readOnly=true)
public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByGeneNCBI(Integer geneNCBI)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Return all evidence for a specific gene NCBI

Specified by:

findEvidenceByGeneNCBI in interface PhenotypeAssociationManagerService

Parameters:

geneNCBI - The Evidence id

Returns:

The Gene we are interested in

findEvidenceOwners

@Transactional(readOnly=true)
public Collection<String> findEvidenceOwners()

Deprecated.

Specified by:

findEvidenceOwners in interface PhenotypeAssociationManagerService

Returns:

the list of the owners that have evidence in the system

findExperimentCategory

@Transactional(readOnly=true)
public Collection<CharacteristicValueObject> findExperimentCategory()

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Find category term that were used in the database, used to annotated Experiments

Specified by:

findExperimentCategory in interface PhenotypeAssociationManagerService

Returns:

the terms found

findExperimentOntologyValue

@Transactional(readOnly=true)
public Collection<CharacteristicValueObject> findExperimentOntologyValue(String givenQueryString)
                                                                  throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

for a given search string look in the database and Ontology for matches

Specified by:

findExperimentOntologyValue in interface PhenotypeAssociationManagerService

Parameters:

givenQueryString - the search query

Returns:

the terms found

Throws:

SearchException

findExternalDatabasesWithEvidence

@Transactional(readOnly=true)
public Collection<ExternalDatabaseValueObject> findExternalDatabasesWithEvidence()

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Gets all External Databases that are used with evidence

Specified by:

findExternalDatabasesWithEvidence in interface PhenotypeAssociationManagerService

Returns:

the externalDatabases

findGenesForPhenotype

@Transactional(readOnly=true)
public Map<GeneValueObject,OntologyTerm> findGenesForPhenotype(String phenotype,
                                                                     Long taxonId,
                                                                     boolean includeIEA)

Deprecated.

Specified by:

findGenesForPhenotype in interface PhenotypeAssociationManagerService

findGenesWithEvidence

@Transactional(readOnly=true)
public List<GeneEvidenceValueObject> findGenesWithEvidence(String query,
                                                           Long taxonId)
                                                    throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Does a Gene search (by name or symbol) for a query and return only Genes with evidence

Specified by:

findGenesWithEvidence in interface PhenotypeAssociationManagerService

Parameters:

query - query

taxonId - can be null to not constrain by taxon

Returns:

list of Genes

Throws:

SearchException

load

@Transactional(readOnly=true)
public EvidenceValueObject<? extends PhenotypeAssociation> load(Long id)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Load an evidence

Specified by:

load in interface PhenotypeAssociationManagerService

Parameters:

id - The Evidence database id

Returns:

phenotype associations

loadAllNeurocartaPhenotypes

@Transactional(readOnly=true)
public Collection<PhenotypeValueObject> loadAllNeurocartaPhenotypes()

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

load all the valueUri and value of phenotype present in Neurocarta

Specified by:

loadAllNeurocartaPhenotypes in interface PhenotypeAssociationManagerService

Returns:

the valueUri of the phenotypes

loadAllPhenotypesByTree

@Transactional(readOnly=true)
public Collection<SimpleTreeValueObject> loadAllPhenotypesByTree(EvidenceFilter evidenceFilter)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Loads all phenotypes in the database and counts their occurrence using the database It builds the tree using parents of terms, and will return 3 trees representing Disease, HP and MP

Specified by:

loadAllPhenotypesByTree in interface PhenotypeAssociationManagerService

Parameters:

evidenceFilter - filter

Returns:

A collection of the phenotypes with the gene occurrence

loadAllPhenotypesAsTree

@Transactional(readOnly=true)
public Collection<TreeCharacteristicValueObject> loadAllPhenotypesAsTree(EvidenceFilter evidenceFilter)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Same as loadAllPhenotypesByTree(EvidenceFilter), but does not flatten out the tree.

Specified by:

loadAllPhenotypesAsTree in interface PhenotypeAssociationManagerService

Parameters:

evidenceFilter - evidence filter

Returns:

a tree set of phenotypes

helpFindAllDumps

@Transactional(readOnly=true)
public Set<DumpsValueObject> helpFindAllDumps()

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Get information about external data sources from Phenocarta, including URLs and timestamps of the most recent update dates/times.

Specified by:

helpFindAllDumps in interface PhenotypeAssociationManagerService

Returns:

A collection of objects with information about external data sources in Phenocarta

loadEvidenceWithExternalDatabaseName

@Transactional(readOnly=true)
public Set<EvidenceValueObject<? extends PhenotypeAssociation>> loadEvidenceWithExternalDatabaseName(String externalDatabaseName,
                                                                                                     int limit,
                                                                                                     int start)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

use if we want to reimport data from a specific external Database

Specified by:

loadEvidenceWithExternalDatabaseName in interface PhenotypeAssociationManagerService

Parameters:

externalDatabaseName - database name

limit - limit

start - offset

Returns:

evidence VOs

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis

@Transactional(readOnly=true)
public DiffExpressionEvidenceValueObject loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

returns an DifferentialExpressionEvidence for a geneDifferentialExpressionMetaAnalysisId if one exists (used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)

Specified by:

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis in interface PhenotypeAssociationManagerService

Parameters:

geneDifferentialExpressionMetaAnalysisId - id of the GeneDifferentialExpressionMetaAnalysis

Returns:

DifferentialExpressionEvidence if an differentialExpressionEvidence exists for that id returns it

loadEvidenceWithoutExternalDatabaseName

@Transactional(readOnly=true)
public Collection<EvidenceValueObject<? extends PhenotypeAssociation>> loadEvidenceWithoutExternalDatabaseName()

Deprecated.

Specified by:

loadEvidenceWithoutExternalDatabaseName in interface PhenotypeAssociationManagerService

Returns:

find all evidence that doesn't come from an external source

loadNeurocartaStatistics

@Transactional(readOnly=true)
public Collection<ExternalDatabaseStatisticsValueObject> loadNeurocartaStatistics()

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

find statistics on evidence used in neurocarta

Specified by:

loadNeurocartaStatistics in interface PhenotypeAssociationManagerService

Returns:

statistics for each external database

makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis

@Transactional
public ValidateEvidenceValueObject makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId,
                                                                                                     SortedSet<CharacteristicValueObject> phenotypes,
                                                                                                     Double selectionThreshold)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

creates the DifferentialExpressionEvidences using an DiffExpressionMetaAnalysis

Specified by:

makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis in interface PhenotypeAssociationManagerService

Parameters:

geneDifferentialExpressionMetaAnalysisId - id of the DiffExpressionMetaAnalysis

phenotypes - phenotypes chosen

selectionThreshold - threshold chosen to keep certain results

Returns:

ValidateEvidenceValueObject flags of information to show user messages

makeEvidence

@Transactional
public ValidateEvidenceValueObject makeEvidence(EvidenceValueObject<? extends PhenotypeAssociation> evidence)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Links an Evidence to a Gene

Specified by:

makeEvidence in interface PhenotypeAssociationManagerService

Parameters:

evidence - The evidence

Returns:

Status of the operation

remove

@Transactional
public ValidateEvidenceValueObject remove(Long id)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Removes an evidence

Specified by:

remove in interface PhenotypeAssociationManagerService

Parameters:

id - The Evidence database id

Returns:

validate evidence VO

removeAllEvidenceFromMetaAnalysis

@Transactional
public ValidateEvidenceValueObject removeAllEvidenceFromMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Removes all the evidence that came from a specific metaAnalysis

Specified by:

removeAllEvidenceFromMetaAnalysis in interface PhenotypeAssociationManagerService

Parameters:

geneDifferentialExpressionMetaAnalysisId - the geneDifferentialExpressionMetaAnalysis Id

Returns:

ValidateEvidenceValueObject flags of information to show user messages

searchInDatabaseForPhenotype

@Transactional(readOnly=true)
public Collection<CharacteristicValueObject> searchInDatabaseForPhenotype(String searchQuery,
                                                                          int maxResults)
                                                                   throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms

Specified by:

searchInDatabaseForPhenotype in interface PhenotypeAssociationManagerService

Parameters:

searchQuery - the query search that was type by the user

maxResults - maximum number of results to return or -1 to return all

Returns:

the terms found in the database with taxon and gene occurrence

Throws:

SearchException

searchOntologyForPhenotypes

@Transactional(readOnly=true)
public Collection<CharacteristicValueObject> searchOntologyForPhenotypes(String searchQuery,
                                                                         Long geneId)
                                                                  throws SearchException

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Giving a phenotype searchQuery, returns a selection choice to the user

Specified by:

searchOntologyForPhenotypes in interface PhenotypeAssociationManagerService

Parameters:

searchQuery - query typed by the user

geneId - the id of the chosen gene

Returns:

list of choices returned

Throws:

SearchException

update

@Transactional
public ValidateEvidenceValueObject update(EvidenceValueObject<? extends PhenotypeAssociation> modifiedEvidenceValueObject)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Modify an existing evidence

Specified by:

update in interface PhenotypeAssociationManagerService

Parameters:

modifiedEvidenceValueObject - the evidence with modified fields

Returns:

Status of the operation

validateEvidence

@Transactional(readOnly=true)
public ValidateEvidenceValueObject validateEvidence(EvidenceValueObject<PhenotypeAssociation> evidence)

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Validate an Evidence before we create it

Specified by:

validateEvidence in interface PhenotypeAssociationManagerService

Parameters:

evidence - The evidence

Returns:

ValidateEvidenceValueObject flags of information to show user messages

writeAllEvidenceToFile

@Transactional(readOnly=true)
public void writeAllEvidenceToFile()
                            throws IOException

Deprecated.

Description copied from interface: PhenotypeAssociationManagerService

Creates a dump of all evidence in the database that can be downloaded on the client, this is run once per month by Quartz

Specified by:

writeAllEvidenceToFile in interface PhenotypeAssociationManagerService

Throws:

IOException - when there are IO problems