/*
* 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.MeSHheadings;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import org.erasmusmc.ids.DatabaseID;
import org.erasmusmc.ontology.Concept;
import org.erasmusmc.ontology.DefaultTypes;
import org.erasmusmc.ontology.OntologyStore;
import org.erasmusmc.ontology.Relation;
import org.erasmusmc.ontology.TermStore;
import org.erasmusmc.ontology.ontologyutilities.OntologyUtilities;
import org.erasmusmc.utilities.ReadTextFile;
import JochemBuilder.SharedCurationScripts.JochemCurator;
public class ChemicalsFromMeSHheadings {
public int generalChemicalVocID = -3000;
public String generalChemicalVocName = "CHEMICAL";
public int specificChemicalVocID = -3007;
public String specificChemicalVocName = "MESHHEADINGS";
public int umlsSemID = -103;
public String umlsSemName = "Chemical";
public static Set<Integer> chemicalSemanticTypes = JochemCurator.getAllChemicalSemanticTypes();
public static Set<Integer> undesiredChemicalSemanticTypes = JochemCurator.getUndesiredSemanticTypes();
public OntologyStore run(String filename){
OntologyStore ontology = new OntologyStore();
//Set the standard vocabulary and umls semantic type concepts
Concept generalVocabulary = new Concept(generalChemicalVocID);
generalVocabulary.setName(generalChemicalVocName);
ontology.setConcept(generalVocabulary);
Concept specificVocabulary = new Concept(specificChemicalVocID);
specificVocabulary.setName(specificChemicalVocName);
ontology.setConcept(specificVocabulary);
Concept semantictype = new Concept(umlsSemID);
semantictype.setName(umlsSemName);
ontology.setConcept(semantictype);
ReadTextFile file = new ReadTextFile(filename);
Iterator<String> iterator = file.getIterator();
boolean name = false;
List<TermStore> terms = new ArrayList<TermStore>();
boolean semanticType = false;
List<DatabaseID> databaseIds = new ArrayList<DatabaseID>();
Integer sem = 0;
List<Integer> sems = new ArrayList<Integer>();
String meshID = "";
String term = "";
String definition = "";
boolean databaseLinks = false;
String dbIdString = "";
int cui = 8000000;
int lineCount = 0;
while(iterator.hasNext()){
lineCount++;
if (lineCount % 10000 == 0)
System.out.println(lineCount);
String line = iterator.next();
if (line.startsWith("MH =")){
name = true;
} else if (line.startsWith("ENTRY =")){
name = true;
} else if (line.startsWith("ST =")){
semanticType = true;
} else if (line.startsWith("MS =")){
definition = line.substring(5).trim();
} else if (line.startsWith("RN =")){
databaseLinks = true;
}{
if (semanticType){
if (line.startsWith("ST =")){
sem = Integer.parseInt(line.substring(6));
sem = -sem;
sems.add(sem);
} else semanticType = false;
}
if (databaseLinks){
if (line.startsWith("RN =")){
dbIdString = line.substring(5).trim();
if (dbIdString.contains("|")){
String[] ids = dbIdString.split("\\|");
String dbID = ids[0].trim();
if (!dbID.equals("0") && !dbID.startsWith("EC"))
databaseIds.add(new DatabaseID("CAS", dbID));
} else {
if (!dbIdString.equals("0") && !dbIdString.startsWith("EC"))
databaseIds.add(new DatabaseID("CAS", dbIdString));
}
} else databaseLinks = false;
}
if (name){
if (line.startsWith("ENTRY =")){
term = line.substring(8).trim();
if (term.contains("|")){
String[] termString = term.split("\\|");
if (term.length()<=225)
terms.add(new TermStore(termString[0]));
} else {
if (term.length()<=225)
terms.add(new TermStore(term));
}
}else if (line.startsWith("MH =")){
term = line.substring(5).trim();
if (term.length()<=225)
terms.add(new TermStore(term));
}else{
name = false;
}
}
else if (line.startsWith("UI")){
meshID = line.substring(5);
if (terms.size() != 0 && !sems.isEmpty()){
boolean add = false;
for (Integer semtype: sems){
if (chemicalSemanticTypes.contains(semtype)
&& !undesiredChemicalSemanticTypes.contains(semtype)) add = true;
}
if (add){
Concept concept = new Concept(cui++);
// Replace double quotation mark with single if there is only one mark in the string
for (TermStore termToCheck: terms){
int i = 0;
char currentchar;
int numberOfQuotationMarks = 0;
while (i < termToCheck.text.length()){
currentchar = termToCheck.text.charAt(i);
if (currentchar =='"'){
numberOfQuotationMarks++;
}
i++;
}
if (numberOfQuotationMarks==1){
termToCheck.text = termToCheck.text.replace('"', '\'');
// System.out.println(termToCheck.text);
}
}
// Set terms and remove duplicates
concept.setTerms(terms);
OntologyUtilities.removeDuplicateTerms(terms);
//Set databaseIDs
databaseIds.add(new DatabaseID("MESH", meshID));
for (DatabaseID databaseId: databaseIds){
ontology.setDatabaseIDForConcept(concept.getID(), databaseId);
}
// Set definition. If longer than 1024 characters, then substring and add a full stop.
if (definition.length()!=0){
if (!definition.endsWith(".") && definition.length()<=1024){
definition = definition+".";
} else if (!definition.endsWith(".") && definition.length()>1024){
definition = definition.substring(0, 1023)+".";
}
concept.setDefinition(definition);
}
// Set concept
ontology.setConcept(concept);
//Set vocabularies and standard semantic type
Relation generalVocRelation = new Relation(concept.getID(), DefaultTypes.fromVocabulary, generalChemicalVocID);
ontology.setRelation(generalVocRelation);
Relation specificVocRelation = new Relation(concept.getID(), DefaultTypes.fromVocabulary, specificChemicalVocID);
ontology.setRelation(specificVocRelation);
Relation semRelation = new Relation(concept.getID(), DefaultTypes.isOfSemanticType, umlsSemID);
ontology.setRelation(semRelation);
}
}
term = "";
definition = "";
databaseIds = new ArrayList<DatabaseID>();
terms = new ArrayList<TermStore>();
sems = new ArrayList<Integer>();
}
}
}
return ontology;
}
}