MedicOntologyService (baseCode 1.1.16 API)

java.lang.Object
- ubic.basecode.ontology.jena.AbstractOntologyService
- - ubic.basecode.ontology.providers.MedicOntologyService

All Implemented Interfaces:

OntologyService
```
public class MedicOntologyService
extends AbstractOntologyService
```
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

Field Summary
- Fields inherited from class ubic.basecode.ontology.jena.AbstractOntologyService
  log

Constructor Summary

Constructors
Constructor Description

MedicOntologyService()

Method Summary

All Methods Instance Methods Concrete Methods
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 com.hp.hpl.jena.ontology.OntModel`	`loadModel()`	Delegates the call as to load the model into memory or leave it on disk.
`protected com.hp.hpl.jena.ontology.OntModel`	`loadModelFromStream(InputStream stream)`	Load a model from a given input stream.

Methods inherited from class ubic.basecode.ontology.jena.AbstractOntologyService
cancelInitializationThread, closeIndex, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAllURIs, getCacheName, getChildren, getParents, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, loadTermsInNameSpace, 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
    
    Specified by:
    
    getOntologyUrl in class AbstractOntologyService
  - loadModel
```
protected com.hp.hpl.jena.ontology.OntModel loadModel()
```
    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 );
    
    Specified by:
    
    loadModel in class AbstractOntologyService
  - loadModelFromStream
```
protected com.hp.hpl.jena.ontology.OntModel loadModelFromStream(InputStream stream)
```
    Description copied from class: AbstractOntologyService
    
    Load a model from a given input stream.
    
    Specified by:
    
    loadModelFromStream in class AbstractOntologyService