1 /*
2 * The Gemma21 project
3 *
4 * Copyright (c) 2007-2019 University of British Columbia
5 *
6 * Licensed under the Apache License, Version 2.0 (the "License");
7 * you may not use this file except in compliance with the License.
8 * You may obtain a copy of the License at
9 *
10 * http://www.apache.org/licenses/LICENSE-2.0
11 *
12 * Unless required by applicable law or agreed to in writing, software
13 * distributed under the License is distributed on an "AS IS" BASIS,
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 * See the License for the specific language governing permissions and
16 * limitations under the License.
17 *
18 */
19 package ubic.basecode.ontology.providers;
20
21 import ubic.basecode.ontology.jena.ClasspathOntologyService;
22 import ubic.basecode.util.Configuration;
23
24 /**
25 * MEDIC ONTOLOGY USED BY PHENOCARTA, its represents MESH terms as a tree so with can use the parent structure that a
26 * normal mesh term doesnt have
27 * <p>
28 * MEDIC comes from the CTD folks. See <a href="http://ctd.mdibl.org/voc.go?type=disease">...</a>. Unfortunately I do not know where our
29 * medic.owl file came from (PP)
30 *
31 * @author Nicolas
32 */
33 @Deprecated
34 public class MedicOntologyService extends AbstractDelegatingOntologyService {
35
36 /**
37 * FIXME this shouldn't be hard-coded like this, we should load it like any other ontology service.
38 */
39 private static final String MEDIC_ONTOLOGY_FILE = "/data/loader/ontology/medic.owl.gz";
40
41 public MedicOntologyService() {
42 super( new ClasspathOntologyService( "Medic Ontology", MEDIC_ONTOLOGY_FILE,
43 Boolean.TRUE.equals( Configuration.getBoolean( "load.medicOntology" ) ), "medicOntology" ) );
44 }
45 }