ubic.basecode.ontology.providers

Class MedicOntologyService

java.lang.Object

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService

ubic.basecode.ontology.providers.MedicOntologyService

public class MedicOntologyService
extends AbstractOntologyMemoryBackedService

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 http://ctd.mdibl.org/voc.go?type=disease. Unfortunately I do not know where our medic.owl file came from (PP)

Author:

Nicolas

Nested Class Summary

Nested classes/interfaces inherited from class ubic.basecode.ontology.providers.AbstractOntologyService

AbstractOntologyService.OntologyInitializationThread

Field Summary

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

cacheReady, index, indexReady, individuals, initializationThread, isInitialized, log, model, modelReady, terms

Constructor Summary

Constructors

Constructor and Description
MedicOntologyService() Warning, this constructor initializes the ontology no matter what

Method Summary

Modifier and Type	Method and Description
protected String	getOntologyName() The simple name of the ontology.
protected String	getOntologyUrl() Defines the location of the ontology eg: http://mged.sourceforge.net/ontologies/MGEDOntology.owl
void	loadMedicOntologyFromFile() Warning, this uses a method intended only for tests.

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

loadModel, loadTermsInNameSpace

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

addTerms, closeIndex, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAllURIs, getModel, getResource, getTerm, getTermIndividuals, index, isEnabled, isInitializationThreadAlive, isOntologyLoaded, loadTermsInNameSpace, startInitializationThread

Methods inherited from class java.lang.Object

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

Constructor Detail

MedicOntologyService

public MedicOntologyService()

Warning, this constructor initializes the ontology no matter what

Method Detail

getOntologyName

protected String getOntologyName()

Description copied from class: AbstractOntologyService

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

Specified by:

getOntologyName in class AbstractOntologyService

Returns:

getOntologyUrl

protected String getOntologyUrl()

Description copied from class: AbstractOntologyService

Defines the location of the ontology eg: http://mged.sourceforge.net/ontologies/MGEDOntology.owl

Specified by:

getOntologyUrl in class AbstractOntologyService

Returns:

loadMedicOntologyFromFile

public void loadMedicOntologyFromFile()

Warning, this uses a method intended only for tests.