Package ubic.basecode.ontology.providers

Class MedicOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService

ubic.basecode.ontology.providers.MedicOntologyService

All Implemented Interfaces:

OntologyService

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 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()

Method Summary

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

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

loadModelFromStream

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

cancelInitializationThread, closeIndex, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getCacheName, getChildren, getInferenceMode, getLanguageLevel, getParents, getProcessImports, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadTermsInNameSpace, setAdditionalPropertyUris, 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()

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

Overrides:

getOntologyUrl in class AbstractOntologyMemoryBackedService

loadModel

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

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 AbstractOntologyMemoryBackedService