/*
* Concept profile generation tool suite
* Copyright (C) 2015 Biosemantics Group, Erasmus University Medical Center,
* Rotterdam, The Netherlands
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>
*/
package org.erasmusmc.ontology.ontologyConstructors;
import org.erasmusmc.ontology.Ontology;
import org.erasmusmc.ontology.OntologyPSFLoader;
import org.erasmusmc.ontology.ontologyutilities.GeneTermVariantGenerator;
import org.erasmusmc.ontology.ontologyutilities.OntologyCurator;
import org.erasmusmc.ontology.ontologyutilities.OntologyUtilities;
public class OCUMLSHomologeneMouseRatHuman {
public static Ontology contructOntology(){
String psfFile = "/home/public/thesauri/homologene/testThes.psf"; //testThes.psf";//120806UMLS_homologene_filtered3.psf";
String curationfile = "/home/public/Thesauri/homologene/GeneThesaurusCurationFile.txt";
System.out.println("Loading thesaurus");
OntologyPSFLoader loader = new OntologyPSFLoader();
loader.loadDefinitions = false;
loader.loadFromPSF(psfFile);
GeneTermVariantGenerator.generateVariants(loader.ontology);
OntologyCurator curator = new OntologyCurator(curationfile);
OntologyUtilities.minWordSize = 3;
curator.curateAndPrepare(loader.ontology);
loader.ontology.setName("UMLSHomologeneMouseRatHuman");
return loader.ontology;
}
}