/*
* 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.dataimport.genes;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.erasmusmc.ids.DatabaseID;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.OntologyPSFLoader;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.TermStore;
import org.erasmusmc.utilities.ReadTextFile;
/**
* Imports genes from an SGD tab delimited file (registry.genenames.tab) into an ontology structure
* @author Schuemie
*
*/
public class SGDGeneImport {
public static void main(String[] args){
new SGDGeneImport();
}
private int cui = 2300000;
public SGDGeneImport(){
OntologyStore ontology = new OntologyStore();
ReadTextFile sgdFile = new ReadTextFile("/data/Saccharomyces Genome Database/registry.genenames.tab");
Iterator<String> iterator = sgdFile.getIterator();
while (iterator.hasNext()){
addToOntology(iterator.next(), ontology);
}
OntologyPSFLoader loader = new OntologyPSFLoader();
loader.ontology = ontology;
loader.saveToPSF("/home/public/Thesauri/GenesNonHuman/SGD_june2007.psf");
}
private void addToOntology(String line, OntologyStore ontology) {
Concept concept = new Concept(cui);
String[] cols = line.split("\t");
List<TermStore> terms = new ArrayList<TermStore>();
terms.add(newTerm(cols[0]));
if (!cols[1].equals("")){
String[] synonyms = cols[1].split("\\|");
for (String synonym : synonyms)
terms.add(newTerm(synonym));
}
String OLN = cols[5];
if (!OLN.equals("")){
terms.add(newTerm(OLN));
ontology.setDatabaseIDForConcept(cui, new DatabaseID("OLN", OLN));
}
ontology.setDatabaseIDForConcept(cui, new DatabaseID("SGD", cols[6]));
concept.setTerms(terms);
ontology.setConcept(concept);
cui++;
}
private TermStore newTerm(String term) {
TermStore result = new TermStore(term);
result.caseSensitive = true;
result.normalised = false;
result.orderSensitive = true;
return result;
}
}