/*
* 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.EvaluationScripts;
import org.erasmusmc.ontology.OntologyFileLoader;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.utilities.StringUtilities;
public class RunChemicalCorpusIndexing {
// Baseline: UMLS2010ABHomologeneJochemToxV1_5.ontology (CHEMICAL voc):
// Precision: 0.6218375499334221, Recall: 0.38723051409618575
// Recall IUPAC: 0.20460358056265984
// Recall PART: 0.03260869565217391
// Recall SUM: 0.2653061224489796
// Recall TRIV: 0.7822784810126582
// Recall ABB: 0.2236024844720497
// Recall FAM: 0.1414141414141414
//BaselineUMLS2010ABHomologeneJochemToxV1_5.ontology (CHEMICAL voc && !GENE voc):
// Precision: Precision: 0.6923076923076923, Recall: 0.3805970149253731
// Recall IUPAC: 0.20460358056265984
// Recall PART: 0.03260869565217391
// Recall SUM: 0.2653061224489796
// Recall TRIV: 0.7772151898734178
// Recall ABB: 0.2111801242236025
// Recall FAM: 0.10101010101010101
public static String home = "/home/khettne/Projects/Jochem/Indexing/";
public static String ontologyFile = "/home/khettne/temp/UMLS2010ABHomologeneJochemToxV1_5.ontology";
public static String fileWithfilesToIndex = home+"files_to_index.txt";
public static String indexresultFileName = home+"index_result.txt";
public static String falsePositivePositionsFileName = home+"falsePosPositions.txt";
public static String falseNegativePositionsFileName = home+"falseNegPositions.txt";
public static String truePositivePositionsFileName = home+"truePosPositions.txt";
public static void main(String[] args) {
System.out.println("Starting script: "+StringUtilities.now());
IndexChemicalCorpus index = new IndexChemicalCorpus();
System.out.println("Processing thesaurus. "+StringUtilities.now());
OntologyFileLoader loader = new OntologyFileLoader();
OntologyStore ontology = loader.load(ontologyFile);
index.run(home, fileWithfilesToIndex, indexresultFileName, falsePositivePositionsFileName, falseNegativePositionsFileName, truePositivePositionsFileName, ontology);
System.out.println("Done! "+StringUtilities.now());
}
}