ubic.basecode.ontology.providers

Interface OntologyService

All Known Implementing Classes:

AbstractOntologyMemoryBackedService, AbstractOntologyService, CellLineOntologyService, CellTypeOntologyService, ChebiOntologyService, DiseaseOntologyService, ExperimentalFactorOntologyService, FMAOntologyService, GenericOntologyService, HumanDevelopmentOntologyService, HumanPhenotypeOntologyService, MammalianPhenotypeOntologyService, MedicOntologyService, MouseDevelopmentOntologyService, NIFSTDOntologyService, ObiService, SequenceOntologyService, UberonOntologyService, UnitsOntologyService

public interface OntologyService

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	OntologyService.InferenceMode

Method Summary

Modifier and Type	Method and Description
void	cancelInitializationThread() Cancel a running initialization thread.
default Collection<OntologyIndividual>	findIndividuals(String search) Looks for any individuals that match the given search string.
Collection<OntologyIndividual>	findIndividuals(String search, boolean keepObsoletes) Looks for any individuals that match the given search string.
default Collection<OntologyResource>	findResources(String searchString) Looks for any resources (terms or individuals) that match the given search string
Collection<OntologyResource>	findResources(String search, boolean keepObsoletes) Looks for any resources (terms or individuals) that match the given search string
default Collection<OntologyTerm>	findTerm(String search) Looks for any terms that match the given search string.
Collection<OntologyTerm>	findTerm(String search, boolean keepObsoletes) Looks for any terms that match the given search string.
OntologyTerm	findUsingAlternativeId(String alternativeId) Find a term using an alternative ID.
Set<String>	getAllURIs() Obtain all the resource URIs in this ontology.
default Set<OntologyTerm>	getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties) Obtain all the children of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	getChildren(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes) Obtain all the children of a given set of terms.
OntologyService.InferenceMode	getInferenceMode() Obtain the inference mode used for this ontology.
default Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties) Obtain all the parents of a given set of terms, excluding obsolete terms.
Set<OntologyTerm>	getParents(Collection<OntologyTerm> terms, boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes) Obtain all the parents of a given set of terms.
boolean	getProcessImports()
OntologyResource	getResource(String uri) Looks through both Terms and Individuals for a OntologyResource that has a uri matching the uri given.
OntologyTerm	getTerm(String uri) Looks for a OntologyTerm that has the match in URI given
Collection<OntologyIndividual>	getTermIndividuals(String uri) Obtain all the individuals for a given term URI.
void	index(boolean force) Index the ontology for performing full-text searches.
void	initialize(boolean forceLoad, boolean forceIndexing) Initialize this ontology service.
void	initialize(InputStream stream, boolean forceIndexing) Initialize this ontology service from a stream.
boolean	isEnabled() Check if this ontology is enabled.
boolean	isInitializationThreadAlive() Check if the initialization thread is alive.
boolean	isInitializationThreadCancelled() Check if the initialization thread is cancelled.
boolean	isOntologyLoaded() Used for determining if the Ontology has finished loading into memory.
boolean	isSearchEnabled()
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
void	setInferenceMode(OntologyService.InferenceMode inferenceMode) Set the inference mode used for this ontology.
void	setProcessImports(boolean processImports)
void	setSearchEnabled(boolean searchEnabled)
void	startInitializationThread(boolean forceLoad, boolean forceIndexing) Start the initialization thread.
void	waitForInitializationThread() Wait for the initialization thread to finish.

Method Detail

getProcessImports

boolean getProcessImports()

setProcessImports

void setProcessImports(boolean processImports)

getInferenceMode

OntologyService.InferenceMode getInferenceMode()

Obtain the inference mode used for this ontology.

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()

setSearchEnabled

void setSearchEnabled(boolean searchEnabled)

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<OntologyIndividual> findIndividuals(String search)
                                                throws OntologySearchException

Looks for any individuals that match the given search string.

Obsolete terms are filtered out.

Throws:

OntologySearchException

findIndividuals

Collection<OntologyIndividual> findIndividuals(String search,
                                               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<OntologyResource> findResources(String searchString)
                                            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<OntologyResource> findResources(String search,
                                           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<OntologyTerm> findTerm(String search)
                                   throws OntologySearchException

Looks for any terms that match the given search string.

Obsolete terms are filtered out.

Throws:

OntologySearchException

findTerm

Collection<OntologyTerm> findTerm(String search,
                                  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(Collection, boolean, boolean, boolean)

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(Collection, boolean, boolean, boolean)

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:

findIndividuals(String), findTerm(String), findResources(String)

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.