Package ubic.basecode.ontology.providers

Interface OntologyService

All Superinterfaces:
AutoCloseable
All Known Implementing Classes:
AbstractBaseCodeOntologyService, AbstractDelegatingOntologyService, AbstractOntologyService, CellLineOntologyService, CellTypeOntologyService, ChebiOntologyService, ClasspathOntologyService, DiseaseOntologyService, ExperimentalFactorOntologyService, FMAOntologyService, GenericOntologyService, HumanDevelopmentOntologyService, HumanPhenotypeOntologyService, MammalianPhenotypeOntologyService, MedicOntologyService, MouseDevelopmentOntologyService, NIFSTDOntologyService, ObiService, SequenceOntologyService, TdbOntologyService, UberonOntologyService, UnitsOntologyService, UrlOntologyService
public interface OntologyService extends AutoCloseable

  • Method Details

    • getName

      @Nullable String getName()
      Obtain the name of this ontology if available.

    • getDescription

      @Nullable String getDescription()
      Obtain a description of this ontology if available.

    • getProcessImports

      boolean getProcessImports()
      Check if this ontology will process imports.

      If disabled, ontologies imported by this ontology will not be loaded.

    • setProcessImports

      void setProcessImports(boolean processImports)
      Allow of forbid this ontology to process imports.

      Changes are applicable only if the service is re-initialized.

    • getLanguageLevel

      OntologyService.LanguageLevel getLanguageLevel()
      Obtain the OWL language level supported by this ontology.

      The default is to use OntologyService.LanguageLevel.FULL.

    • setLanguageLevel

      void setLanguageLevel(OntologyService.LanguageLevel languageLevel)
      Set the OWL language level supported by this ontology.

      Changes are applicable only if the service is re-initialized.

    • getInferenceMode

      OntologyService.InferenceMode getInferenceMode()
      Obtain the inference mode used for this ontology.

      The default is OntologyService.InferenceMode.TRANSITIVE.

    • setInferenceMode

      void setInferenceMode(OntologyService.InferenceMode inferenceMode)
      Set the inference mode used for this ontology.

      Changes are applicable only if the service is re-initialized.

    • isSearchEnabled

      boolean isSearchEnabled()
      Check if this ontology has full-text search enabled.

      This is necessary for finding term using full-text queries. If enabled, an index will be generated in during initialization by initialize(boolean, boolean).

      Search is enabled by default.

      See Also:

    • setSearchEnabled

      void setSearchEnabled(boolean searchEnabled)
      Enable or disable search for this ontology.

      Changes are only applicable if the service is re-initialized.

    • getExcludedWordsFromStemming

      Set<String> getExcludedWordsFromStemming()
      Obtain the words that should be excluded from stemming.

      By default, all words are subject to stemming. The exact implementation of stemming depends on the actual search implementation.

    • setExcludedWordsFromStemming

      void setExcludedWordsFromStemming(Set<String> excludedWordsFromStemming)
      Set words that should be excluded from stemming when searching.

    • getAdditionalPropertyUris

      Set<String> getAdditionalPropertyUris()
      Obtain the URIs used as additional properties when inferring parents and children.

      The default is to use part of, proper part of and all of their sub-properties if inference is enabled.

      See Also:

    • setAdditionalPropertyUris

      void setAdditionalPropertyUris(Set<String> additionalPropertyUris)
      Set the URIs to be used as additional properties when inferring parents and children.

      Changes are applicable only if the service is re-initialized.

    • initialize

      void initialize(boolean forceLoad, boolean forceIndexing)
      Initialize this ontology service.
      Parameters:
      forceLoad - Force loading of ontology, even if it is already loaded
      forceIndexing - If forceLoad is also true, indexing will be performed. If you know the index is up-to-date, there's no need to do it again. Normally indexing is only done if there is no index, or if the ontology has changed since last loaded.

    • initialize

      void initialize(InputStream stream, boolean forceIndexing)
      Initialize this ontology service from a stream.

      Note that when this method of initialization is used, the ontology cache is not created on-disk.

    • findIndividuals

      default Collection<OntologySearchResult<OntologyIndividual>> findIndividuals(String search, int maxResults) throws OntologySearchException
      Looks for any individuals that match the given search string.

      Obsolete terms are filtered out.

      Throws:
      OntologySearchException

    • findIndividuals

      Collection<OntologySearchResult<OntologyIndividual>> findIndividuals(String search, int maxResults, boolean keepObsoletes) throws OntologySearchException
      Looks for any individuals that match the given search string.
      Parameters:
      search - search query
      keepObsoletes - retain obsolete terms
      Throws:
      OntologySearchException

    • findResources

      default Collection<OntologySearchResult<OntologyResource>> findResources(String searchString, int maxResults) throws OntologySearchException
      Looks for any resources (terms or individuals) that match the given search string

      Obsolete terms are filtered out.

      Returns:
      results, or an empty collection if the results are empty OR the ontology is not available to be searched.
      Throws:
      OntologySearchException

    • findResources

      Collection<OntologySearchResult<OntologyResource>> findResources(String search, int maxResults, boolean keepObsoletes) throws OntologySearchException
      Looks for any resources (terms or individuals) that match the given search string
      Parameters:
      search - search query
      keepObsoletes - retain obsolete terms
      Throws:
      OntologySearchException

    • findTerm

      default Collection<OntologySearchResult<OntologyTerm>> findTerm(String search, int maxResults) throws OntologySearchException
      Looks for any terms that match the given search string.

      Obsolete terms are filtered out.

      Throws:
      OntologySearchException

    • findTerm

      Collection<OntologySearchResult<OntologyTerm>> findTerm(String search, int maxResults, boolean keepObsoletes) throws OntologySearchException
      Looks for any terms that match the given search string.
      Parameters:
      search - search query
      keepObsoletes - retain obsolete terms
      Throws:
      OntologySearchException

    • findUsingAlternativeId

      @Nullable OntologyTerm findUsingAlternativeId(String alternativeId)
      Find a term using an alternative ID.

    • getAllURIs

      Set<String> getAllURIs()
      Obtain all the resource URIs in this ontology.

    • getResource

      @Nullable OntologyResource getResource(String uri)
      Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given. If no OntologyTerm is found only then will ontologyIndividuals be searched. returns null if nothing is found.

    • getTerm

      @Nullable OntologyTerm getTerm(String uri)
      Looks for a OntologyTerm that has the match in URI given

    • getTermIndividuals

      Collection<OntologyIndividual> getTermIndividuals(String uri)
      Obtain all the individuals for a given term URI.

    • getParents

      default Set<OntologyTerm> getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)
      Obtain all the parents of a given set of terms, excluding obsolete terms.
      See Also:

    • getParents

      Set<OntologyTerm> getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
      Obtain all the parents of a given set of terms.
      Parameters:
      terms - set of terms whose parents are retrieved
      direct - only retain direct parents
      includeAdditionalProperties - also include parents matched via additional properties
      keepObsoletes - retain obsolete terms
      Returns:
      a set of parent terms

    • getChildren

      default Set<OntologyTerm> getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties)
      Obtain all the children of a given set of terms, excluding obsolete terms.
      See Also:

    • getChildren

      Set<OntologyTerm> getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
      Obtain all the children of a given set of terms.
      Parameters:
      terms - set of terms whose children are retrieved
      direct - only retain direct children
      includeAdditionalProperties - also include children matched via additional properties
      keepObsoletes - retain obsolete terms
      Returns:
      a set of child terms

    • isEnabled

      boolean isEnabled()
      Check if this ontology is enabled.

    • isOntologyLoaded

      boolean isOntologyLoaded()
      Used for determining if the Ontology has finished loading into memory. Although calls like getParents, getChildren will still work (its much faster once the ontologies have been preloaded into memory.)

    • startInitializationThread

      void startInitializationThread(boolean forceLoad, boolean forceIndexing)
      Start the initialization thread.

      If the initialization thread is already running, this method does nothing. If the initialization thread previously completed, the ontology will be reinitialized.

      Parameters:
      forceLoad - Force loading of ontology, even if it is already loaded
      forceIndexing - If forceLoad is also true, indexing will be performed. If you know the index is up to date, there's no need to do it again. Normally indexing is only done if there is no index, or if the ontology has changed since last loaded.

    • isInitializationThreadAlive

      boolean isInitializationThreadAlive()
      Check if the initialization thread is alive.

    • isInitializationThreadCancelled

      boolean isInitializationThreadCancelled()
      Check if the initialization thread is cancelled.

    • cancelInitializationThread

      void cancelInitializationThread()
      Cancel a running initialization thread.

    • waitForInitializationThread

      void waitForInitializationThread() throws InterruptedException
      Wait for the initialization thread to finish.
      Throws:
      InterruptedException

    • index

      void index(boolean force)
      Index the ontology for performing full-text searches.
      Parameters:
      force - if true, perform indexing even if an index already exists
      See Also:

    • loadTermsInNameSpace

      @Deprecated void loadTermsInNameSpace(InputStream is, boolean forceIndex)
      Deprecated.
      use initialize(InputStream, boolean) instead and possibly cancelInitializationThread() prior to get any running initialization thread out of the way
      For testing! Overrides normal way of loading the ontology. This does not index the ontology unless 'force' is true (if there is an existing index, it will be used)
      Parameters:
      is - input stream from which the ontology model is loaded
      forceIndex - initialize the index. Otherwise it will only be initialized if it doesn't exist.