Package ubic.basecode.ontology.providers

Class MedicOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

ubic.basecode.ontology.providers.MedicOntologyService

All Implemented Interfaces:

OntologyService

@Deprecated
public class MedicOntologyService
extends AbstractBaseCodeOntologyService

Deprecated.

MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a normal mesh term doesnt have

MEDIC comes from the CTD folks. See .... Unfortunately I do not know where our medic.owl file came from (PP)

Author:

Nicolas

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

Constructor Summary

Constructors

Constructor	Description
MedicOntologyService()	Deprecated.

Method Summary

Modifier and Type	Method	Description
protected String	getOntologyUrl()	Deprecated. Defines the location of the ontology eg: MGED
protected OntologyModel	loadModel(boolean processImports, OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)	Deprecated. Delegates the call as to load the model into memory or leave it on disk.

Methods inherited from class ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

getCacheName, getOntologyName, isOntologyEnabled

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, 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

Constructor Detail

MedicOntologyService

public MedicOntologyService()

Deprecated.

Method Detail

getOntologyUrl

protected String getOntologyUrl()

Deprecated.

Description copied from class: AbstractOntologyService

Defines the location of the ontology eg: MGED

Overrides:

getOntologyUrl in class AbstractBaseCodeOntologyService

loadModel

protected OntologyModel loadModel(boolean processImports,
                                  OntologyService.LanguageLevel languageLevel,
                                  OntologyService.InferenceMode inferenceMode)
                           throws IOException

Deprecated.

Description copied from class: AbstractOntologyService

Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );

Overrides:

loadModel in class AbstractOntologyService

Throws:

IOException