Interface OntologyService

  • All Known Implementing Classes:
    OntologyServiceImpl

    public interface OntologyService
    Author:
    Paul
    • Method Detail

      • findObsoleteTermUsage

        Map<String,​CharacteristicValueObject> findObsoleteTermUsage()

        Locates usages of obsolete terms in Characteristics, ignoring Gene Ontology annotations. Requires the ontologies are loaded into memory.

        Will also find terms that are no longer in an ontology we use.

        Returns:
        map of value URI to a representative characteristic using the term. The latter will contain a count of how many ocurrences there were.
      • findExperimentsCharacteristicTags

        Collection<CharacteristicValueObject> findExperimentsCharacteristicTags​(String searchQuery,
                                                                                boolean useNeuroCartaOntology)
                                                                         throws SearchException
        Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list of possible choices
        Parameters:
        searchQuery - search query
        useNeuroCartaOntology - use neurocarta ontology
        Returns:
        characteristic vos
        Throws:
        SearchException
      • findTerms

        Collection<OntologyTerm> findTerms​(String search)
                                    throws SearchException
        Given a search string will look through the loaded ontologies for terms that match the search term. If the query looks like a URI, it just retrieves the term. For other queries, this a lucene backed search, is inexact and for general terms can return a lot of results.
        Parameters:
        search - search
        Returns:
        returns a collection of ontologyTerm's
        Throws:
        SearchException
      • findTermsInexact

        Collection<CharacteristicValueObject> findTermsInexact​(String givenQueryString,
                                                               @Nullable
                                                               Taxon taxon)
                                                        throws SearchException
        Given a search string will first look through the characteristic database for any entries that have a match. If a ontologyTermURI is given it will add all the individuals from that URI that match the search term criteria to the returned list also.
        Parameters:
        taxon - Only used if we're going to search for genes or taxon is otherwise relevant; if null, restriction is not used.
        givenQueryString - query string
        Returns:
        characteristic vos
        Throws:
        SearchException
      • getCategoryTerms

        Collection<OntologyTerm> getCategoryTerms()
        Returns:
        terms which are allowed for use in the Category of a Characteristic
      • getRelationTerms

        Collection<OntologyProperty> getRelationTerms()
        Returns:
        terms allowed for the predicate (relationship) in a Characteristic
      • getDefinition

        String getDefinition​(String uri)
        Parameters:
        uri - uri
        Returns:
        the definition of the associated OntologyTerm. This requires that the ontology be loaded.
      • isObsolete

        boolean isObsolete​(String uri)
      • reindexAllOntologies

        void reindexAllOntologies()
        Recreate the search indices, for ontologies that are loaded.
      • reinitializeAndReindexAllOntologies

        void reinitializeAndReindexAllOntologies()
        Reinitialize (and reindex) all the ontologies "from scratch". This is necessary if indices are old etc. This should be admin-only.