/*
* 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.HMDB;
import org.erasmusmc.ontology.OntologyFileLoader;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.ontologyutilities.OntologyCurator;
import org.erasmusmc.utilities.StringUtilities;
import JochemBuilder.SharedCurationScripts.CasperForJochem;
import JochemBuilder.SharedCurationScripts.CurateUsingManualCurationFile;
import JochemBuilder.SharedCurationScripts.RemoveDictAndCompanyNamesAtEndOfTerm;
import JochemBuilder.SharedCurationScripts.RewriteFurther;
import JochemBuilder.SharedCurationScripts.SaveOnlyCASandInchiEntries;
public class HMDBImport {
public static String date = "110809";
public static String home = "/home/khettne/Projects/Jochem";
public static String hmdbImportFile = home+"/HMDB/metabocards.txt";
public static String hmdbDictionariesLog = home+"/HMDB/HMDB_dictionaries_"+date+".log";
public static String hmdbRewriteLog = home+"/HMDB/HMDBCAS_casperFiltered_"+date+".log";
public static String hmdbLowerCaseLog = home+"/HMDB/HMDBCAS_lowerCase_"+date+".log";
public static String termsToRemove = "hmdbTermsToRemove.txt";
public static String hmdbCuratedOntologyPath = home+"/HMDB/HMDBCAS_curated_"+date+".ontology";
public static String hmdbCuratedLog = home+"/HMDB/HMDBCAS_curated_"+date+".log";
public static void main(String[] args) {
OntologyStore ontology = new OntologyStore();
OntologyFileLoader loader = new OntologyFileLoader();
//Make unprocessed thesaurus
ChemicalsFromHMDB hmbd = new ChemicalsFromHMDB();
ontology = hmbd.run(hmdbImportFile);
RemoveDictAndCompanyNamesAtEndOfTerm remove = new RemoveDictAndCompanyNamesAtEndOfTerm();
ontology = remove.run(ontology, hmdbDictionariesLog);
// CAS and InChI
SaveOnlyCASandInchiEntries make = new SaveOnlyCASandInchiEntries();
ontology = make.run(ontology);
// Rewrite
CasperForJochem casper = new CasperForJochem();
ontology = casper.run(ontology, hmdbRewriteLog);
// Make some entries lower case and filter further
RewriteFurther rewrite = new RewriteFurther();
ontology = rewrite.run(ontology, hmdbLowerCaseLog);
//Remove terms based on medline frequency
CurateUsingManualCurationFile curate = new CurateUsingManualCurationFile();
ontology = curate.run(ontology, hmdbCuratedLog,termsToRemove);
// Set default flags and save ontology
OntologyCurator curator = new OntologyCurator();
curator.curateAndPrepare(ontology);
loader.save(ontology,hmdbCuratedOntologyPath);
System.out.println("Done! " + StringUtilities.now());
}
}