Package ubic.gemma.core.association.phenotype

Interface PhenotypeAssociationManagerService

  • All Known Implementing Classes:
    PhenotypeAssociationManagerServiceImpl
    @Deprecated
public interface PhenotypeAssociationManagerService
    Deprecated.
    High Level Service used to add Candidate Gene Management System capabilities. (Most of these methods are not secured, but the underlying calls are)
    Author:
    paul

    • Method Detail

      • findBibliographicReference

        BibliographicReferenceValueObject findBibliographicReference​(String pubMedId)
        Deprecated.
        Find all phenotypes associated to a pubmedID
        Parameters:
        pubMedId - pubmed id
        Returns:
        BibliographicReferenceValueObject

      • findCandidateGenes

        Collection<GeneEvidenceValueObject> findCandidateGenes​(Collection<String> phenotypesValuesUris,
                                                       Taxon taxon)
        Deprecated.
        Given an set of phenotypes returns the genes that have all those phenotypes or children phenotypes
        Parameters:
        phenotypesValuesUris - 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

        Set<GeneEvidenceValueObject> findCandidateGenes​(EvidenceFilter evidenceFilter,
                                                Set<String> phenotypesValuesUri)
        Deprecated.
        Given set of phenotypes returns the genes that have all those phenotypes or children phenotypes
        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

        Map<String,​Collection<? extends GeneValueObject>> findCandidateGenesForEach​(Set<String> phenotypeUris,
                                                                                  Taxon taxon)
        Deprecated.
        Parameters:
        taxon - taxon
        phenotypeUris - URIs
        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

        Collection<EvidenceValueObject<? extends PhenotypeAssociation>> findEvidenceByFilters​(Long taxonId,
                                                                                      int limit,
                                                                                      String userName)
        Deprecated.
        Return evidence satisfying the specified filters. If the current user has not logged in, empty container is returned.
        Parameters:
        taxonId - taxon id
        limit - number of evidence value objects to return
        userName - user name
        Returns:
        evidence satisfying the specified filters

      • findEvidenceByGeneId

        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
        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

      • findEvidenceOwners

        Collection<String> findEvidenceOwners()
        Deprecated.
        Returns:
        the list of the owners that have evidence in the system

      • findExperimentCategory

        Collection<CharacteristicValueObject> findExperimentCategory()
        Deprecated.
        Find category term that were used in the database, used to annotated Experiments
        Returns:
        the terms found

      • findExternalDatabasesWithEvidence

        Collection<ExternalDatabaseValueObject> findExternalDatabasesWithEvidence()
        Deprecated.
        Gets all External Databases that are used with evidence
        Returns:
        the externalDatabases

      • findGenesWithEvidence

        List<GeneEvidenceValueObject> findGenesWithEvidence​(String query,
                                                    Long taxonId)
                                             throws SearchException
        Deprecated.
        Does a Gene search (by name or symbol) for a query and return only Genes with evidence
        Parameters:
        query - query
        taxonId - can be null to not constrain by taxon
        Returns:
        list of Genes
        Throws:
        SearchException

      • loadAllNeurocartaPhenotypes

        Collection<PhenotypeValueObject> loadAllNeurocartaPhenotypes()
        Deprecated.
        load all the valueUri and value of phenotype present in Neurocarta
        Returns:
        the valueUri of the phenotypes

      • loadAllPhenotypesByTree

        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
        Parameters:
        evidenceFilter - filter
        Returns:
        A collection of the phenotypes with the gene occurrence

      • loadAllPhenotypesAsTree

        Collection<TreeCharacteristicValueObject> loadAllPhenotypesAsTree​(EvidenceFilter evidenceFilter)
        Deprecated.
        Same as loadAllPhenotypesByTree(EvidenceFilter), but does not flatten out the tree.
        Parameters:
        evidenceFilter - evidence filter
        Returns:
        a tree set of phenotypes

      • helpFindAllDumps

        Set<DumpsValueObject> helpFindAllDumps()
        Deprecated.
        Get information about external data sources from Phenocarta, including URLs and timestamps of the most recent update dates/times.
        Returns:
        A collection of objects with information about external data sources in Phenocarta

      • loadEvidenceWithExternalDatabaseName

        Set<EvidenceValueObject<? extends PhenotypeAssociation>> loadEvidenceWithExternalDatabaseName​(String externalDatabaseName,
                                                                                              int limit,
                                                                                              int start)
        Deprecated.
        use if we want to reimport data from a specific external Database
        Parameters:
        limit - limit
        start - offset
        externalDatabaseName - database name
        Returns:
        evidence VOs

      • loadEvidenceWithGeneDifferentialExpressionMetaAnalysis

        DiffExpressionEvidenceValueObject loadEvidenceWithGeneDifferentialExpressionMetaAnalysis​(Long geneDifferentialExpressionMetaAnalysisId)
        Deprecated.
        returns an DifferentialExpressionEvidence for a geneDifferentialExpressionMetaAnalysisId if one exists (used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)
        Parameters:
        geneDifferentialExpressionMetaAnalysisId - id of the GeneDifferentialExpressionMetaAnalysis
        Returns:
        DifferentialExpressionEvidence if an differentialExpressionEvidence exists for that id returns it

      • makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis

        ValidateEvidenceValueObject makeDifferentialExpressionEvidencesFromDiffExpressionMetaAnalysis​(Long geneDifferentialExpressionMetaAnalysisId,
                                                                                              SortedSet<CharacteristicValueObject> phenotypes,
                                                                                              Double thresholdChosen)
        Deprecated.
        creates the DifferentialExpressionEvidences using an DiffExpressionMetaAnalysis
        Parameters:
        geneDifferentialExpressionMetaAnalysisId - id of the DiffExpressionMetaAnalysis
        phenotypes - phenotypes chosen
        thresholdChosen - threshold chosen to keep certain results
        Returns:
        ValidateEvidenceValueObject flags of information to show user messages

      • remove

        ValidateEvidenceValueObject remove​(Long id)
        Deprecated.
        Removes an evidence
        Parameters:
        id - The Evidence database id
        Returns:
        validate evidence VO

      • removeAllEvidenceFromMetaAnalysis

        ValidateEvidenceValueObject removeAllEvidenceFromMetaAnalysis​(Long geneDifferentialExpressionMetaAnalysisId)
        Deprecated.
        Removes all the evidence that came from a specific metaAnalysis
        Parameters:
        geneDifferentialExpressionMetaAnalysisId - the geneDifferentialExpressionMetaAnalysis Id
        Returns:
        ValidateEvidenceValueObject flags of information to show user messages

      • searchInDatabaseForPhenotype

        Collection<CharacteristicValueObject> searchInDatabaseForPhenotype​(String searchQuery,
                                                                   int maxResults)
                                                            throws SearchException
        Deprecated.
        For a given search string find all Ontology terms related, and then count their gene occurrence by taxon, including ontology children terms
        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

        Collection<CharacteristicValueObject> searchOntologyForPhenotypes​(String searchQuery,
                                                                  Long geneId)
                                                           throws SearchException
        Deprecated.
        Giving a phenotype searchQuery, returns a selection choice to the user
        Parameters:
        searchQuery - query typed by the user
        geneId - the id of the chosen gene
        Returns:
        list of choices returned
        Throws:
        SearchException

      • writeAllEvidenceToFile

        @Secured("GROUP_AGENT")
void writeAllEvidenceToFile()
                     throws IOException
        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
        Throws:
        IOException - when there are IO problems