/*
* 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 JochemBuilder.SharedCurationScripts;
import java.util.Iterator;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.OntologyFileLoader;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.TermStore;
import org.erasmusmc.ontology.ontologyutilities.HomonymAnalyzer;
import org.erasmusmc.utilities.StringUtilities;
public class ChemicalOntologyHomonymCount {
public static String ontologyFile = "/home/khettne/ChEBI/ChEBICAS_curated_110809.ontology";
public static String output = "/home/khettne/ChEBI/chebi_homonyms.txt";
public static void main(String[] args){
System.out.println("Starting script. " + StringUtilities.now());
OntologyFileLoader loader = new OntologyFileLoader();
OntologyStore ontology = new OntologyStore();
ontology = loader.load(ontologyFile);
Iterator<Concept> conceptIterator = ontology.getConceptIterator();
int lineCount = 0;
while (conceptIterator.hasNext()) {
lineCount++;
if (lineCount % 100000 == 0)
System.out.println(lineCount);
Concept concept = conceptIterator.next();
if (concept.getID() > 0) {
Iterator<TermStore> termIterator = concept.getTerms().iterator();
while (termIterator.hasNext()) {
TermStore term = termIterator.next();
term.orderSensitive = true;
term.caseSensitive = false;
term.normalised = false;
}
}
}
System.out.println("Analyzing homonyms. " + StringUtilities.now());
HomonymAnalyzer homcount = new HomonymAnalyzer();
homcount.setOntology(ontology);
homcount.countHomonyms(output);
System.out.println("Done. " + StringUtilities.now());
}
}