Package ubic.gemma.core.association.phenotype

Interface PhenotypeAssoOntologyHelper

    • Method Detail

      • getOntologyServices

        Collection<OntologyService> getOntologyServices()
        Deprecated.
        Returns the ontology services this helper is using.

      • characteristicValueObject2Characteristic

        Characteristic characteristicValueObject2Characteristic​(CharacteristicValueObject characteristicValueObject)
        Deprecated.
        CharacteristicValueObject to Characteristic with no valueUri given
        Parameters:
        characteristicValueObject - characteristic VO
        Returns:
        vocab characteristic

      • findOntologyTermByUri

        @Nullable
OntologyTerm findOntologyTermByUri​(String valueUri)
        Deprecated.
        For a valueUri return the OntologyTerm found
        Parameters:
        valueUri - value uri
        Returns:
        ontology term

      • findPhenotypesInOntology

        Set<CharacteristicValueObject> findPhenotypesInOntology​(String searchQuery)
                                                 throws SearchException
        Deprecated.
        search the disease,hp and mp ontology for a searchQuery and return an ordered set of CharacteristicVO
        Parameters:
        searchQuery - query
        Returns:
        characteristic VOs
        Throws:
        SearchException

      • valueUri2Characteristic

        @Nullable
Characteristic valueUri2Characteristic​(String valueUri)
        Deprecated.
        Helper method. For a valueUri return the Characteristic (represents a phenotype)
        Parameters:
        valueUri - value uri
        Returns:
        Characteristic