Package ubic.basecode.ontology.providers

Class AbstractBaseCodeOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

All Implemented Interfaces:

OntologyService

Direct Known Subclasses:

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

public abstract class AbstractBaseCodeOntologyService
extends AbstractOntologyService

Base class for all ontologies built-in to the baseCode project.

The ontologies that subclass this will honor settings in the basecode.properties file for loading and locating the ontology.

Author:

poirigui

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.basecode.ontology.providers.OntologyService

OntologyService.InferenceMode, OntologyService.LanguageLevel

Field Summary

Fields inherited from class ubic.basecode.ontology.jena.AbstractOntologyService

log

Method Summary

Modifier and Type	Method	Description
String	getCacheName()	A name for caching this ontology, or null to disable caching.
protected String	getOntologyName()	The simple getOntologyName() of the ontology.
protected String	getOntologyUrl()	Defines the location of the ontology eg: MGED
protected boolean	isOntologyEnabled()	Indicate if this ontology is enabled.

Methods inherited from class ubic.basecode.ontology.jena.AbstractOntologyService

cancelInitializationThread, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getChildren, getDescription, getExcludedWordsFromStemming, getInferenceMode, getLanguageLevel, getName, getParents, getProcessImports, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadModel, loadModelFromStream, loadTermsInNameSpace, setAdditionalPropertyUris, setExcludedWordsFromStemming, setInferenceMode, setLanguageLevel, setProcessImports, setSearchEnabled, startInitializationThread, toString, waitForInitializationThread

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.basecode.ontology.providers.OntologyService

findIndividuals, findResources, findTerm, getChildren, getParents

Method Detail

getOntologyName

protected String getOntologyName()

Description copied from class: AbstractOntologyService

The simple getOntologyName() of the ontology. Used for indexing purposes. (ie this will determine the getOntologyName() of the underlying index for searching the ontology)

Specified by:

getOntologyName in class AbstractOntologyService

getOntologyUrl

protected String getOntologyUrl()

Description copied from class: AbstractOntologyService

Defines the location of the ontology eg: MGED

Specified by:

getOntologyUrl in class AbstractOntologyService

isOntologyEnabled

protected boolean isOntologyEnabled()

Description copied from class: AbstractOntologyService

Indicate if this ontology is enabled.

Specified by:

isOntologyEnabled in class AbstractOntologyService

getCacheName

@Nullable
public String getCacheName()

Description copied from class: AbstractOntologyService

A name for caching this ontology, or null to disable caching.

Note that if null is returned, the ontology will not have full-text search capabilities.

Specified by:

getCacheName in class AbstractOntologyService