Source code

001package org.dllearner.examples;
002
003import java.io.File;
004import java.util.ArrayList;
005import java.util.Arrays;
006import java.util.HashSet;
007import java.util.List;
008import java.util.Set;
009
010import org.apache.log4j.Level;
011import org.apache.log4j.Logger;
012import org.dllearner.algorithms.celoe.CELOE;
013import org.dllearner.algorithms.celoe.OEHeuristicRuntime;
014import org.dllearner.algorithms.el.ELLearningAlgorithm;
015import org.dllearner.core.AbstractCELA;
016import org.dllearner.core.AbstractReasonerComponent;
017import org.dllearner.core.KnowledgeSource;
018import org.dllearner.kb.OWLAPIOntology;
019import org.dllearner.learningproblems.PosNegLPStandard;
020import org.dllearner.reasoning.ClosedWorldReasoner;
021import org.dllearner.reasoning.OWLAPIReasoner;
022import org.dllearner.reasoning.ReasonerImplementation;
023import org.dllearner.refinementoperators.ELDown;
024import org.dllearner.refinementoperators.RhoDRDown;
025import org.semanticweb.elk.owlapi.ElkReasoner;
026import org.semanticweb.owlapi.apibinding.OWLManager;
027import org.dllearner.core.StringRenderer;
028import org.dllearner.core.StringRenderer.Rendering;
029import org.semanticweb.owlapi.model.IRI;
030import org.semanticweb.owlapi.model.OWLIndividual;
031import org.semanticweb.owlapi.model.OWLOntology;
032import org.semanticweb.owlapi.model.OWLOntologyManager;
033
034import uk.ac.manchester.cs.owl.owlapi.OWLNamedIndividualImpl;
035
036public class Reactome {
037    private static final Logger logger = Logger.getLogger(Reactome.class);
038    private static final String kbPathStr = "/tmp/tr.owl";
039    private static final List<String> posExampleUris = new ArrayList<>(Arrays.asList(
040            "http://www.reactome.org/biopax/48887#BiochemicalReaction670",
041            "http://www.reactome.org/biopax/48887#BiochemicalReaction1968",
042            "http://www.reactome.org/biopax/48887#BiochemicalReaction1861",
043            "http://www.reactome.org/biopax/48887#BiochemicalReaction675",
044            "http://www.reactome.org/biopax/48887#BiochemicalReaction1452",
045            "http://www.reactome.org/biopax/48887#BiochemicalReaction4648",
046            "http://www.reactome.org/biopax/48887#BiochemicalReaction1961",
047            "http://www.reactome.org/biopax/48887#BiochemicalReaction4445",
048            "http://www.reactome.org/biopax/48887#BiochemicalReaction4444",
049            "http://www.reactome.org/biopax/48887#BiochemicalReaction678",
050            "http://www.reactome.org/biopax/48887#BiochemicalReaction1966",
051            "http://www.reactome.org/biopax/48887#BiochemicalReaction672",
052            "http://www.reactome.org/biopax/48887#BiochemicalReaction4644",
053            "http://www.reactome.org/biopax/48887#BiochemicalReaction1869",
054            "http://www.reactome.org/biopax/48887#BiochemicalReaction4646",
055            "http://www.reactome.org/biopax/48887#BiochemicalReaction4640",
056            "http://www.reactome.org/biopax/48887#BiochemicalReaction4643",
057            "http://www.reactome.org/biopax/48887#BiochemicalReaction669",
058            "http://www.reactome.org/biopax/48887#BiochemicalReaction1555",
059            "http://www.reactome.org/biopax/48887#BiochemicalReaction1133",
060            "http://www.reactome.org/biopax/48887#BiochemicalReaction2583",
061            "http://www.reactome.org/biopax/48887#BiochemicalReaction1958",
062            "http://www.reactome.org/biopax/48887#BiochemicalReaction4515",
063            "http://www.reactome.org/biopax/48887#BiochemicalReaction1957",
064            "http://www.reactome.org/biopax/48887#BiochemicalReaction4513",
065            "http://www.reactome.org/biopax/48887#BiochemicalReaction4518",
066            "http://www.reactome.org/biopax/48887#BiochemicalReaction1853",
067            "http://www.reactome.org/biopax/48887#BiochemicalReaction1852",
068            "http://www.reactome.org/biopax/48887#BiochemicalReaction4456",
069            "http://www.reactome.org/biopax/48887#BiochemicalReaction4455",
070            "http://www.reactome.org/biopax/48887#BiochemicalReaction1952",
071            "http://www.reactome.org/biopax/48887#BiochemicalReaction664",
072            "http://www.reactome.org/biopax/48887#BiochemicalReaction1464",
073            "http://www.reactome.org/biopax/48887#BiochemicalReaction4454",
074            "http://www.reactome.org/biopax/48887#BiochemicalReaction1951",
075            "http://www.reactome.org/biopax/48887#BiochemicalReaction4453",
076            "http://www.reactome.org/biopax/48887#BiochemicalReaction4452",
077            "http://www.reactome.org/biopax/48887#BiochemicalReaction55",
078            "http://www.reactome.org/biopax/48887#BiochemicalReaction4451",
079            "http://www.reactome.org/biopax/48887#BiochemicalReaction4450",
080            "http://www.reactome.org/biopax/48887#BiochemicalReaction1956",
081            "http://www.reactome.org/biopax/48887#BiochemicalReaction661",
082            "http://www.reactome.org/biopax/48887#BiochemicalReaction1466",
083            "http://www.reactome.org/biopax/48887#BiochemicalReaction659",
084            "http://www.reactome.org/biopax/48887#BiochemicalReaction658",
085            "http://www.reactome.org/biopax/48887#BiochemicalReaction4457",
086            "http://www.reactome.org/biopax/48887#BiochemicalReaction1468",
087            "http://www.reactome.org/biopax/48887#BiochemicalReaction1842",
088            "http://www.reactome.org/biopax/48887#BiochemicalReaction1841",
089            "http://www.reactome.org/biopax/48887#BiochemicalReaction1114",
090            "http://www.reactome.org/biopax/48887#BiochemicalReaction1846",
091            "http://www.reactome.org/biopax/48887#BiochemicalReaction1845",
092            "http://www.reactome.org/biopax/48887#BiochemicalReaction4523",
093            "http://www.reactome.org/biopax/48887#BiochemicalReaction1849",
094            "http://www.reactome.org/biopax/48887#BiochemicalReaction1848",
095            "http://www.reactome.org/biopax/48887#BiochemicalReaction1987",
096            "http://www.reactome.org/biopax/48887#BiochemicalReaction4625",
097            "http://www.reactome.org/biopax/48887#BiochemicalReaction4624",
098            "http://www.reactome.org/biopax/48887#BiochemicalReaction1986",
099            "http://www.reactome.org/biopax/48887#BiochemicalReaction653",
100            "http://www.reactome.org/biopax/48887#BiochemicalReaction4627",
101            "http://www.reactome.org/biopax/48887#BiochemicalReaction4626",
102            "http://www.reactome.org/biopax/48887#BiochemicalReaction1984",
103            "http://www.reactome.org/biopax/48887#BiochemicalReaction1983",
104            "http://www.reactome.org/biopax/48887#BiochemicalReaction1982",
105            "http://www.reactome.org/biopax/48887#BiochemicalReaction4628",
106            "http://www.reactome.org/biopax/48887#BiochemicalReaction1981",
107            "http://www.reactome.org/biopax/48887#BiochemicalReaction1435",
108            "http://www.reactome.org/biopax/48887#BiochemicalReaction1439",
109            "http://www.reactome.org/biopax/48887#BiochemicalReaction1436",
110            "http://www.reactome.org/biopax/48887#BiochemicalReaction4620",
111            "http://www.reactome.org/biopax/48887#BiochemicalReaction4521",
112            "http://www.reactome.org/biopax/48887#BiochemicalReaction4522",
113            "http://www.reactome.org/biopax/48887#BiochemicalReaction1304",
114            "http://www.reactome.org/biopax/48887#BiochemicalReaction4539",
115            "http://www.reactome.org/biopax/48887#BiochemicalReaction1307",
116            "http://www.reactome.org/biopax/48887#BiochemicalReaction1306",
117            "http://www.reactome.org/biopax/48887#BiochemicalReaction1128",
118            "http://www.reactome.org/biopax/48887#BiochemicalReaction1833",
119            "http://www.reactome.org/biopax/48887#BiochemicalReaction1300",
120            "http://www.reactome.org/biopax/48887#BiochemicalReaction1979",
121            "http://www.reactome.org/biopax/48887#BiochemicalReaction1303",
122            "http://www.reactome.org/biopax/48887#BiochemicalReaction1835",
123            "http://www.reactome.org/biopax/48887#BiochemicalReaction1834",
124            "http://www.reactome.org/biopax/48887#BiochemicalReaction1976",
125            "http://www.reactome.org/biopax/48887#BiochemicalReaction1975",
126            "http://www.reactome.org/biopax/48887#BiochemicalReaction1978",
127            "http://www.reactome.org/biopax/48887#BiochemicalReaction1972",
128            "http://www.reactome.org/biopax/48887#BiochemicalReaction2",
129            "http://www.reactome.org/biopax/48887#BiochemicalReaction4639",
130            "http://www.reactome.org/biopax/48887#BiochemicalReaction1308",
131            "http://www.reactome.org/biopax/48887#BiochemicalReaction1974",
132            "http://www.reactome.org/biopax/48887#BiochemicalReaction642",
133            "http://www.reactome.org/biopax/48887#BiochemicalReaction4437",
134            "http://www.reactome.org/biopax/48887#BiochemicalReaction638",
135            "http://www.reactome.org/biopax/48887#BiochemicalReaction4438",
136            "http://www.reactome.org/biopax/48887#BiochemicalReaction4435",
137            "http://www.reactome.org/biopax/48887#BiochemicalReaction4436",
138            "http://www.reactome.org/biopax/48887#BiochemicalReaction635",
139            "http://www.reactome.org/biopax/48887#BiochemicalReaction4631",
140            "http://www.reactome.org/biopax/48887#BiochemicalReaction1447",
141            "http://www.reactome.org/biopax/48887#BiochemicalReaction4632",
142            "http://www.reactome.org/biopax/48887#BiochemicalReaction4439",
143            "http://www.reactome.org/biopax/48887#BiochemicalReaction4630",
144            "http://www.reactome.org/biopax/48887#BiochemicalReaction538",
145            "http://www.reactome.org/biopax/48887#BiochemicalReaction5273",
146            "http://www.reactome.org/biopax/48887#BiochemicalReaction4401",
147            "http://www.reactome.org/biopax/48887#BiochemicalReaction1215",
148            "http://www.reactome.org/biopax/48887#BiochemicalReaction1213",
149            "http://www.reactome.org/biopax/48887#BiochemicalReaction572",
150            "http://www.reactome.org/biopax/48887#BiochemicalReaction4547",
151            "http://www.reactome.org/biopax/48887#BiochemicalReaction575",
152            "http://www.reactome.org/biopax/48887#BiochemicalReaction574",
153            "http://www.reactome.org/biopax/48887#BiochemicalReaction1317",
154            "http://www.reactome.org/biopax/48887#BiochemicalReaction1318",
155            "http://www.reactome.org/biopax/48887#BiochemicalReaction576",
156            "http://www.reactome.org/biopax/48887#BiochemicalReaction1315",
157            "http://www.reactome.org/biopax/48887#BiochemicalReaction1316",
158            "http://www.reactome.org/biopax/48887#BiochemicalReaction80",
159            "http://www.reactome.org/biopax/48887#BiochemicalReaction1929",
160            "http://www.reactome.org/biopax/48887#BiochemicalReaction4540",
161            "http://www.reactome.org/biopax/48887#BiochemicalReaction1310",
162            "http://www.reactome.org/biopax/48887#BiochemicalReaction4544",
163            "http://www.reactome.org/biopax/48887#BiochemicalReaction1211",
164            "http://www.reactome.org/biopax/48887#BiochemicalReaction1518",
165            "http://www.reactome.org/biopax/48887#BiochemicalReaction1517",
166            "http://www.reactome.org/biopax/48887#BiochemicalReaction4408",
167            "http://www.reactome.org/biopax/48887#BiochemicalReaction1412",
168            "http://www.reactome.org/biopax/48887#BiochemicalReaction1411",
169            "http://www.reactome.org/biopax/48887#BiochemicalReaction4412",
170            "http://www.reactome.org/biopax/48887#BiochemicalReaction5284",
171            "http://www.reactome.org/biopax/48887#BiochemicalReaction4410",
172            "http://www.reactome.org/biopax/48887#BiochemicalReaction1225",
173            "http://www.reactome.org/biopax/48887#BiochemicalReaction5280",
174            "http://www.reactome.org/biopax/48887#BiochemicalReaction1913",
175            "http://www.reactome.org/biopax/48887#BiochemicalReaction1322",
176            "http://www.reactome.org/biopax/48887#BiochemicalReaction563",
177            "http://www.reactome.org/biopax/48887#BiochemicalReaction562",
178            "http://www.reactome.org/biopax/48887#BiochemicalReaction1915",
179            "http://www.reactome.org/biopax/48887#BiochemicalReaction1916",
180            "http://www.reactome.org/biopax/48887#BiochemicalReaction568",
181            "http://www.reactome.org/biopax/48887#BiochemicalReaction1918",
182            "http://www.reactome.org/biopax/48887#BiochemicalReaction1919",
183            "http://www.reactome.org/biopax/48887#BiochemicalReaction1329",
184            "http://www.reactome.org/biopax/48887#BiochemicalReaction1186",
185            "http://www.reactome.org/biopax/48887#BiochemicalReaction1520",
186            "http://www.reactome.org/biopax/48887#BiochemicalReaction1523",
187            "http://www.reactome.org/biopax/48887#BiochemicalReaction1525",
188            "http://www.reactome.org/biopax/48887#BiochemicalReaction1429",
189            "http://www.reactome.org/biopax/48887#BiochemicalReaction1183",
190            "http://www.reactome.org/biopax/48887#BiochemicalReaction1321",
191            "http://www.reactome.org/biopax/48887#BiochemicalReaction1320",
192            "http://www.reactome.org/biopax/48887#BiochemicalReaction1220",
193            "http://www.reactome.org/biopax/48887#BiochemicalReaction1425",
194            "http://www.reactome.org/biopax/48887#BiochemicalReaction1221",
195            "http://www.reactome.org/biopax/48887#BiochemicalReaction1422",
196            "http://www.reactome.org/biopax/48887#BiochemicalReaction694",
197            "http://www.reactome.org/biopax/48887#BiochemicalReaction889",
198            "http://www.reactome.org/biopax/48887#BiochemicalReaction5159",
199            "http://www.reactome.org/biopax/48887#BiochemicalReaction1945",
200            "http://www.reactome.org/biopax/48887#BiochemicalReaction5156",
201            "http://www.reactome.org/biopax/48887#BiochemicalReaction1941",
202            "http://www.reactome.org/biopax/48887#BiochemicalReaction5153",
203            "http://www.reactome.org/biopax/48887#BiochemicalReaction2303",
204            "http://www.reactome.org/biopax/48887#BiochemicalReaction5152",
205            "http://www.reactome.org/biopax/48887#BiochemicalReaction1339",
206            "http://www.reactome.org/biopax/48887#BiochemicalReaction5150",
207            "http://www.reactome.org/biopax/48887#BiochemicalReaction2302",
208            "http://www.reactome.org/biopax/48887#BiochemicalReaction2308",
209            "http://www.reactome.org/biopax/48887#BiochemicalReaction1949",
210            "http://www.reactome.org/biopax/48887#BiochemicalReaction2305",
211            "http://www.reactome.org/biopax/48887#BiochemicalReaction1331",
212            "http://www.reactome.org/biopax/48887#BiochemicalReaction4565",
213            "http://www.reactome.org/biopax/48887#BiochemicalReaction4560",
214            "http://www.reactome.org/biopax/48887#BiochemicalReaction891",
215            "http://www.reactome.org/biopax/48887#BiochemicalReaction892",
216            "http://www.reactome.org/biopax/48887#BiochemicalReaction894",
217            "http://www.reactome.org/biopax/48887#BiochemicalReaction896",
218            "http://www.reactome.org/biopax/48887#BiochemicalReaction685",
219            "http://www.reactome.org/biopax/48887#BiochemicalReaction1931",
220            "http://www.reactome.org/biopax/48887#BiochemicalReaction684",
221            "http://www.reactome.org/biopax/48887#BiochemicalReaction683",
222            "http://www.reactome.org/biopax/48887#BiochemicalReaction1933",
223            "http://www.reactome.org/biopax/48887#BiochemicalReaction1934",
224            "http://www.reactome.org/biopax/48887#BiochemicalReaction688",
225            "http://www.reactome.org/biopax/48887#BiochemicalReaction2312",
226            "http://www.reactome.org/biopax/48887#BiochemicalReaction5160",
227            "http://www.reactome.org/biopax/48887#BiochemicalReaction681",
228            "http://www.reactome.org/biopax/48887#BiochemicalReaction1345",
229            "http://www.reactome.org/biopax/48887#BiochemicalReaction1937",
230            "http://www.reactome.org/biopax/48887#BiochemicalReaction1347",
231            "http://www.reactome.org/biopax/48887#BiochemicalReaction1938",
232            "http://www.reactome.org/biopax/48887#BiochemicalReaction1340",
233            "http://www.reactome.org/biopax/48887#BiochemicalReaction4576",
234            "http://www.reactome.org/biopax/48887#BiochemicalReaction1546",
235            "http://www.reactome.org/biopax/48887#BiochemicalReaction4575",
236            "http://www.reactome.org/biopax/48887#BiochemicalReaction1342",
237            "http://www.reactome.org/biopax/48887#BiochemicalReaction4574",
238            "http://www.reactome.org/biopax/48887#BiochemicalReaction1544",
239            "http://www.reactome.org/biopax/48887#BiochemicalReaction883",
240            "http://www.reactome.org/biopax/48887#BiochemicalReaction881",
241            "http://www.reactome.org/biopax/48887#BiochemicalReaction886",
242            "http://www.reactome.org/biopax/48887#BiochemicalReaction887",
243            "http://www.reactome.org/biopax/48887#BiochemicalReaction884",
244            "http://www.reactome.org/biopax/48887#BiochemicalReaction993",
245            "http://www.reactome.org/biopax/48887#BiochemicalReaction992",
246            "http://www.reactome.org/biopax/48887#BiochemicalReaction1072",
247            "http://www.reactome.org/biopax/48887#BiochemicalReaction991",
248            "http://www.reactome.org/biopax/48887#BiochemicalReaction874",
249            "http://www.reactome.org/biopax/48887#BiochemicalReaction1075",
250            "http://www.reactome.org/biopax/48887#BiochemicalReaction870",
251            "http://www.reactome.org/biopax/48887#BiochemicalReaction994",
252            "http://www.reactome.org/biopax/48887#BiochemicalReaction5630",
253            "http://www.reactome.org/biopax/48887#BiochemicalReaction4588",
254            "http://www.reactome.org/biopax/48887#BiochemicalReaction726",
255            "http://www.reactome.org/biopax/48887#BiochemicalReaction4385",
256            "http://www.reactome.org/biopax/48887#BiochemicalReaction723",
257            "http://www.reactome.org/biopax/48887#BiochemicalReaction727",
258            "http://www.reactome.org/biopax/48887#BiochemicalReaction989",
259            "http://www.reactome.org/biopax/48887#BiochemicalReaction3514",
260            "http://www.reactome.org/biopax/48887#BiochemicalReaction868",
261            "http://www.reactome.org/biopax/48887#BiochemicalReaction869",
262            "http://www.reactome.org/biopax/48887#BiochemicalReaction5045",
263            "http://www.reactome.org/biopax/48887#BiochemicalReaction867",
264            "http://www.reactome.org/biopax/48887#BiochemicalReaction324",
265            "http://www.reactome.org/biopax/48887#BiochemicalReaction865",
266            "http://www.reactome.org/biopax/48887#BiochemicalReaction3725",
267            "http://www.reactome.org/biopax/48887#BiochemicalReaction4590",
268            "http://www.reactome.org/biopax/48887#BiochemicalReaction4591",
269            "http://www.reactome.org/biopax/48887#BiochemicalReaction985",
270            "http://www.reactome.org/biopax/48887#BiochemicalReaction3726",
271            "http://www.reactome.org/biopax/48887#BiochemicalReaction3728",
272            "http://www.reactome.org/biopax/48887#BiochemicalReaction1659",
273            "http://www.reactome.org/biopax/48887#BiochemicalReaction712",
274            "http://www.reactome.org/biopax/48887#BiochemicalReaction713",
275            "http://www.reactome.org/biopax/48887#BiochemicalReaction4094",
276            "http://www.reactome.org/biopax/48887#BiochemicalReaction4097",
277            "http://www.reactome.org/biopax/48887#BiochemicalReaction5959",
278            "http://www.reactome.org/biopax/48887#BiochemicalReaction3894",
279            "http://www.reactome.org/biopax/48887#BiochemicalReaction4062",
280            "http://www.reactome.org/biopax/48887#BiochemicalReaction3893",
281            "http://www.reactome.org/biopax/48887#BiochemicalReaction747",
282            "http://www.reactome.org/biopax/48887#BiochemicalReaction745",
283            "http://www.reactome.org/biopax/48887#BiochemicalReaction746",
284            "http://www.reactome.org/biopax/48887#BiochemicalReaction847",
285            "http://www.reactome.org/biopax/48887#BiochemicalReaction4067",
286            "http://www.reactome.org/biopax/48887#BiochemicalReaction1508",
287            "http://www.reactome.org/biopax/48887#BiochemicalReaction742",
288            "http://www.reactome.org/biopax/48887#BiochemicalReaction741",
289            "http://www.reactome.org/biopax/48887#BiochemicalReaction744",
290            "http://www.reactome.org/biopax/48887#BiochemicalReaction1501",
291            "http://www.reactome.org/biopax/48887#BiochemicalReaction740",
292            "http://www.reactome.org/biopax/48887#BiochemicalReaction738",
293            "http://www.reactome.org/biopax/48887#BiochemicalReaction739",
294            "http://www.reactome.org/biopax/48887#BiochemicalReaction734",
295            "http://www.reactome.org/biopax/48887#BiochemicalReaction735",
296            "http://www.reactome.org/biopax/48887#BiochemicalReaction736",
297            "http://www.reactome.org/biopax/48887#BiochemicalReaction737",
298            "http://www.reactome.org/biopax/48887#BiochemicalReaction356",
299            "http://www.reactome.org/biopax/48887#BiochemicalReaction1772",
300            "http://www.reactome.org/biopax/48887#BiochemicalReaction5960",
301            "http://www.reactome.org/biopax/48887#BiochemicalReaction957",
302            "http://www.reactome.org/biopax/48887#BiochemicalReaction5961",
303            "http://www.reactome.org/biopax/48887#BiochemicalReaction6233",
304            "http://www.reactome.org/biopax/48887#BiochemicalReaction6236",
305            "http://www.reactome.org/biopax/48887#BiochemicalReaction6235",
306            "http://www.reactome.org/biopax/48887#BiochemicalReaction223",
307            "http://www.reactome.org/biopax/48887#BiochemicalReaction220",
308            "http://www.reactome.org/biopax/48887#BiochemicalReaction221",
309            "http://www.reactome.org/biopax/48887#BiochemicalReaction628",
310            "http://www.reactome.org/biopax/48887#BiochemicalReaction952",
311            "http://www.reactome.org/biopax/48887#BiochemicalReaction953",
312            "http://www.reactome.org/biopax/48887#BiochemicalReaction950",
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603            "http://www.reactome.org/biopax/48887#BiochemicalReaction1244",
604            "http://www.reactome.org/biopax/48887#BiochemicalReaction1241",
605            "http://www.reactome.org/biopax/48887#BiochemicalReaction2355",
606            "http://www.reactome.org/biopax/48887#BiochemicalReaction5583",
607            "http://www.reactome.org/biopax/48887#BiochemicalReaction5582",
608            "http://www.reactome.org/biopax/48887#BiochemicalReaction5388",
609            "http://www.reactome.org/biopax/48887#BiochemicalReaction5386",
610            "http://www.reactome.org/biopax/48887#BiochemicalReaction2358",
611            "http://www.reactome.org/biopax/48887#BiochemicalReaction2357",
612            "http://www.reactome.org/biopax/48887#BiochemicalReaction2639",
613            "http://www.reactome.org/biopax/48887#BiochemicalReaction2252",
614            "http://www.reactome.org/biopax/48887#BiochemicalReaction2254",
615            "http://www.reactome.org/biopax/48887#BiochemicalReaction2253",
616            "http://www.reactome.org/biopax/48887#BiochemicalReaction2246",
617            "http://www.reactome.org/biopax/48887#BiochemicalReaction1231",
618            "http://www.reactome.org/biopax/48887#BiochemicalReaction1232",
619            "http://www.reactome.org/biopax/48887#BiochemicalReaction3008",
620            "http://www.reactome.org/biopax/48887#BiochemicalReaction3006",
621            "http://www.reactome.org/biopax/48887#BiochemicalReaction3005",
622            "http://www.reactome.org/biopax/48887#BiochemicalReaction1370",
623            "http://www.reactome.org/biopax/48887#BiochemicalReaction5578",
624            "http://www.reactome.org/biopax/48887#BiochemicalReaction1372",
625            "http://www.reactome.org/biopax/48887#BiochemicalReaction1373",
626            "http://www.reactome.org/biopax/48887#BiochemicalReaction5574",
627            "http://www.reactome.org/biopax/48887#BiochemicalReaction2340",
628            "http://www.reactome.org/biopax/48887#BiochemicalReaction5573",
629            "http://www.reactome.org/biopax/48887#BiochemicalReaction3305",
630            "http://www.reactome.org/biopax/48887#BiochemicalReaction2345",
631            "http://www.reactome.org/biopax/48887#BiochemicalReaction1239",
632            "http://www.reactome.org/biopax/48887#BiochemicalReaction3004",
633            "http://www.reactome.org/biopax/48887#BiochemicalReaction3001",
634            "http://www.reactome.org/biopax/48887#BiochemicalReaction1235",
635            "http://www.reactome.org/biopax/48887#BiochemicalReaction2448",
636            "http://www.reactome.org/biopax/48887#BiochemicalReaction1234",
637            "http://www.reactome.org/biopax/48887#BiochemicalReaction2245",
638            "http://www.reactome.org/biopax/48887#BiochemicalReaction2948",
639            "http://www.reactome.org/biopax/48887#BiochemicalReaction2946",
640            "http://www.reactome.org/biopax/48887#BiochemicalReaction2851",
641            "http://www.reactome.org/biopax/48887#BiochemicalReaction2944",
642            "http://www.reactome.org/biopax/48887#BiochemicalReaction2651",
643            "http://www.reactome.org/biopax/48887#BiochemicalReaction2942",
644            "http://www.reactome.org/biopax/48887#BiochemicalReaction2858",
645            "http://www.reactome.org/biopax/48887#BiochemicalReaction2650",
646            "http://www.reactome.org/biopax/48887#BiochemicalReaction2940",
647            "http://www.reactome.org/biopax/48887#BiochemicalReaction4612",
648            "http://www.reactome.org/biopax/48887#BiochemicalReaction4616",
649            "http://www.reactome.org/biopax/48887#BiochemicalReaction5221",
650            "http://www.reactome.org/biopax/48887#BiochemicalReaction4617",
651            "http://www.reactome.org/biopax/48887#BiochemicalReaction3359",
652            "http://www.reactome.org/biopax/48887#BiochemicalReaction5490",
653            "http://www.reactome.org/biopax/48887#BiochemicalReaction5491",
654            "http://www.reactome.org/biopax/48887#BiochemicalReaction5492",
655            "http://www.reactome.org/biopax/48887#BiochemicalReaction5493",
656            "http://www.reactome.org/biopax/48887#BiochemicalReaction2958",
657            "http://www.reactome.org/biopax/48887#BiochemicalReaction1290",
658            "http://www.reactome.org/biopax/48887#BiochemicalReaction2954",
659            "http://www.reactome.org/biopax/48887#BiochemicalReaction2842",
660            "http://www.reactome.org/biopax/48887#BiochemicalReaction1295",
661            "http://www.reactome.org/biopax/48887#BiochemicalReaction1294",
662            "http://www.reactome.org/biopax/48887#BiochemicalReaction2843",
663            "http://www.reactome.org/biopax/48887#BiochemicalReaction5494",
664            "http://www.reactome.org/biopax/48887#BiochemicalReaction2951",
665            "http://www.reactome.org/biopax/48887#BiochemicalReaction2845",
666            "http://www.reactome.org/biopax/48887#BiochemicalReaction1299",
667            "http://www.reactome.org/biopax/48887#BiochemicalReaction2952",
668            "http://www.reactome.org/biopax/48887#BiochemicalReaction3221",
669            "http://www.reactome.org/biopax/48887#BiochemicalReaction3228",
670            "http://www.reactome.org/biopax/48887#BiochemicalReaction1495",
671            "http://www.reactome.org/biopax/48887#BiochemicalReaction2649",
672            "http://www.reactome.org/biopax/48887#BiochemicalReaction5312",
673            "http://www.reactome.org/biopax/48887#BiochemicalReaction1280",
674            "http://www.reactome.org/biopax/48887#BiochemicalReaction3929",
675            "http://www.reactome.org/biopax/48887#BiochemicalReaction3923",
676            "http://www.reactome.org/biopax/48887#BiochemicalReaction3922",
677            "http://www.reactome.org/biopax/48887#BiochemicalReaction2493",
678            "http://www.reactome.org/biopax/48887#BiochemicalReaction3234",
679            "http://www.reactome.org/biopax/48887#BiochemicalReaction3924",
680            "http://www.reactome.org/biopax/48887#BiochemicalReaction1285",
681            "http://www.reactome.org/biopax/48887#BiochemicalReaction1284",
682            "http://www.reactome.org/biopax/48887#BiochemicalReaction2873",
683            "http://www.reactome.org/biopax/48887#BiochemicalReaction1282",
684            "http://www.reactome.org/biopax/48887#BiochemicalReaction1281",
685            "http://www.reactome.org/biopax/48887#BiochemicalReaction3237",
686            "http://www.reactome.org/biopax/48887#BiochemicalReaction1482",
687            "http://www.reactome.org/biopax/48887#BiochemicalReaction3239",
688            "http://www.reactome.org/biopax/48887#BiochemicalReaction2536",
689            "http://www.reactome.org/biopax/48887#BiochemicalReaction2936",
690            "http://www.reactome.org/biopax/48887#BiochemicalReaction2938",
691            "http://www.reactome.org/biopax/48887#BiochemicalReaction3918",
692            "http://www.reactome.org/biopax/48887#BiochemicalReaction3245",
693            "http://www.reactome.org/biopax/48887#BiochemicalReaction2661",
694            "http://www.reactome.org/biopax/48887#BiochemicalReaction3913",
695            "http://www.reactome.org/biopax/48887#BiochemicalReaction3246",
696            "http://www.reactome.org/biopax/48887#BiochemicalReaction2483",
697            "http://www.reactome.org/biopax/48887#BiochemicalReaction2868",
698            "http://www.reactome.org/biopax/48887#BiochemicalReaction1277",
699            "http://www.reactome.org/biopax/48887#BiochemicalReaction3243",
700            "http://www.reactome.org/biopax/48887#BiochemicalReaction3244",
701            "http://www.reactome.org/biopax/48887#BiochemicalReaction2932",
702            "http://www.reactome.org/biopax/48887#BiochemicalReaction3241",
703            "http://www.reactome.org/biopax/48887#BiochemicalReaction2485",
704            "http://www.reactome.org/biopax/48887#BiochemicalReaction2484",
705            "http://www.reactome.org/biopax/48887#BiochemicalReaction3242",
706            "http://www.reactome.org/biopax/48887#BiochemicalReaction2934",
707            "http://www.reactome.org/biopax/48887#BiochemicalReaction3240",
708            "http://www.reactome.org/biopax/48887#BiochemicalReaction1472",
709            "http://www.reactome.org/biopax/48887#BiochemicalReaction2529",
710            "http://www.reactome.org/biopax/48887#BiochemicalReaction2861",
711            "http://www.reactome.org/biopax/48887#BiochemicalReaction3249",
712            "http://www.reactome.org/biopax/48887#BiochemicalReaction1470",
713            "http://www.reactome.org/biopax/48887#BiochemicalReaction3247",
714            "http://www.reactome.org/biopax/48887#BiochemicalReaction5334",
715            "http://www.reactome.org/biopax/48887#BiochemicalReaction2525"
716    ));
717    private static final List<String> negExampleUris = new ArrayList<>(Arrays.asList(
718            "http://www.reactome.org/biopax/48887#BiochemicalReaction2588",
719            "http://www.reactome.org/biopax/48887#BiochemicalReaction2582",
720            "http://www.reactome.org/biopax/48887#BiochemicalReaction2580",
721            "http://www.reactome.org/biopax/48887#BiochemicalReaction2585",
722            "http://www.reactome.org/biopax/48887#BiochemicalReaction1950",
723            "http://www.reactome.org/biopax/48887#BiochemicalReaction1008",
724            "http://www.reactome.org/biopax/48887#BiochemicalReaction1009",
725            "http://www.reactome.org/biopax/48887#BiochemicalReaction1955",
726            "http://www.reactome.org/biopax/48887#BiochemicalReaction2567",
727            "http://www.reactome.org/biopax/48887#BiochemicalReaction2568",
728            "http://www.reactome.org/biopax/48887#BiochemicalReaction2565",
729            "http://www.reactome.org/biopax/48887#BiochemicalReaction2566",
730            "http://www.reactome.org/biopax/48887#BiochemicalReaction1989",
731            "http://www.reactome.org/biopax/48887#BiochemicalReaction1016",
732            "http://www.reactome.org/biopax/48887#BiochemicalReaction1017",
733            "http://www.reactome.org/biopax/48887#BiochemicalReaction1012",
734            "http://www.reactome.org/biopax/48887#BiochemicalReaction1010",
735            "http://www.reactome.org/biopax/48887#BiochemicalReaction2563",
736            "http://www.reactome.org/biopax/48887#BiochemicalReaction2561",
737            "http://www.reactome.org/biopax/48887#BiochemicalReaction2560",
738            "http://www.reactome.org/biopax/48887#BiochemicalReaction2576",
739            "http://www.reactome.org/biopax/48887#BiochemicalReaction2578",
740            "http://www.reactome.org/biopax/48887#BiochemicalReaction2579",
741            "http://www.reactome.org/biopax/48887#BiochemicalReaction1",
742            "http://www.reactome.org/biopax/48887#BiochemicalReaction1028",
743            "http://www.reactome.org/biopax/48887#BiochemicalReaction1022",
744            "http://www.reactome.org/biopax/48887#BiochemicalReaction1020",
745            "http://www.reactome.org/biopax/48887#BiochemicalReaction2573",
746            "http://www.reactome.org/biopax/48887#BiochemicalReaction2572",
747            "http://www.reactome.org/biopax/48887#BiochemicalReaction2575",
748            "http://www.reactome.org/biopax/48887#BiochemicalReaction2574",
749            "http://www.reactome.org/biopax/48887#BiochemicalReaction2571",
750            "http://www.reactome.org/biopax/48887#BiochemicalReaction2570",
751            "http://www.reactome.org/biopax/48887#BiochemicalReaction1039",
752            "http://www.reactome.org/biopax/48887#BiochemicalReaction1922",
753            "http://www.reactome.org/biopax/48887#BiochemicalReaction1923",
754            "http://www.reactome.org/biopax/48887#BiochemicalReaction1924",
755            "http://www.reactome.org/biopax/48887#BiochemicalReaction1925",
756            "http://www.reactome.org/biopax/48887#BiochemicalReaction1030",
757            "http://www.reactome.org/biopax/48887#BiochemicalReaction1047",
758            "http://www.reactome.org/biopax/48887#BiochemicalReaction1914",
759            "http://www.reactome.org/biopax/48887#BiochemicalReaction1917",
760            "http://www.reactome.org/biopax/48887#BiochemicalReaction1041",
761            "http://www.reactome.org/biopax/48887#BiochemicalReaction1944",
762            "http://www.reactome.org/biopax/48887#BiochemicalReaction1948",
763            "http://www.reactome.org/biopax/48887#BiochemicalReaction879",
764            "http://www.reactome.org/biopax/48887#BiochemicalReaction878",
765            "http://www.reactome.org/biopax/48887#BiochemicalReaction1936",
766            "http://www.reactome.org/biopax/48887#BiochemicalReaction1066",
767            "http://www.reactome.org/biopax/48887#BiochemicalReaction1068",
768            "http://www.reactome.org/biopax/48887#BiochemicalReaction875",
769            "http://www.reactome.org/biopax/48887#BiochemicalReaction1078",
770            "http://www.reactome.org/biopax/48887#BiochemicalReaction860",
771            "http://www.reactome.org/biopax/48887#BiochemicalReaction859",
772            "http://www.reactome.org/biopax/48887#BiochemicalReaction850",
773            "http://www.reactome.org/biopax/48887#BiochemicalReaction852",
774            "http://www.reactome.org/biopax/48887#BiochemicalReaction851",
775            "http://www.reactome.org/biopax/48887#BiochemicalReaction4883",
776            "http://www.reactome.org/biopax/48887#BiochemicalReaction4884",
777            "http://www.reactome.org/biopax/48887#BiochemicalReaction1995",
778            "http://www.reactome.org/biopax/48887#BiochemicalReaction818",
779            "http://www.reactome.org/biopax/48887#BiochemicalReaction1993",
780            "http://www.reactome.org/biopax/48887#BiochemicalReaction817",
781            "http://www.reactome.org/biopax/48887#BiochemicalReaction812",
782            "http://www.reactome.org/biopax/48887#BiochemicalReaction814",
783            "http://www.reactome.org/biopax/48887#BiochemicalReaction813",
784            "http://www.reactome.org/biopax/48887#BiochemicalReaction4870",
785            "http://www.reactome.org/biopax/48887#BiochemicalReaction4874",
786            "http://www.reactome.org/biopax/48887#BiochemicalReaction4873",
787            "http://www.reactome.org/biopax/48887#BiochemicalReaction4872",
788            "http://www.reactome.org/biopax/48887#BiochemicalReaction4871",
789            "http://www.reactome.org/biopax/48887#BiochemicalReaction804",
790            "http://www.reactome.org/biopax/48887#BiochemicalReaction4877",
791            "http://www.reactome.org/biopax/48887#BiochemicalReaction4878",
792            "http://www.reactome.org/biopax/48887#BiochemicalReaction4875",
793            "http://www.reactome.org/biopax/48887#BiochemicalReaction809",
794            "http://www.reactome.org/biopax/48887#BiochemicalReaction4876",
795            "http://www.reactome.org/biopax/48887#BiochemicalReaction4861",
796            "http://www.reactome.org/biopax/48887#BiochemicalReaction4860",
797            "http://www.reactome.org/biopax/48887#BiochemicalReaction4863",
798            "http://www.reactome.org/biopax/48887#BiochemicalReaction4862",
799            "http://www.reactome.org/biopax/48887#BiochemicalReaction4864",
800            "http://www.reactome.org/biopax/48887#BiochemicalReaction4865",
801            "http://www.reactome.org/biopax/48887#BiochemicalReaction4866",
802            "http://www.reactome.org/biopax/48887#BiochemicalReaction4867",
803            "http://www.reactome.org/biopax/48887#BiochemicalReaction4868",
804            "http://www.reactome.org/biopax/48887#BiochemicalReaction4869",
805            "http://www.reactome.org/biopax/48887#BiochemicalReaction4845",
806            "http://www.reactome.org/biopax/48887#BiochemicalReaction4844",
807            "http://www.reactome.org/biopax/48887#BiochemicalReaction4842",
808            "http://www.reactome.org/biopax/48887#BiochemicalReaction4849",
809            "http://www.reactome.org/biopax/48887#BiochemicalReaction4847",
810            "http://www.reactome.org/biopax/48887#BiochemicalReaction4846",
811            "http://www.reactome.org/biopax/48887#BiochemicalReaction3392",
812            "http://www.reactome.org/biopax/48887#BiochemicalReaction3398",
813            "http://www.reactome.org/biopax/48887#BiochemicalReaction4031",
814            "http://www.reactome.org/biopax/48887#BiochemicalReaction4840",
815            "http://www.reactome.org/biopax/48887#BiochemicalReaction4841",
816            "http://www.reactome.org/biopax/48887#BiochemicalReaction3393",
817            "http://www.reactome.org/biopax/48887#BiochemicalReaction4029",
818            "http://www.reactome.org/biopax/48887#BiochemicalReaction4854",
819            "http://www.reactome.org/biopax/48887#BiochemicalReaction4853",
820            "http://www.reactome.org/biopax/48887#BiochemicalReaction4855",
821            "http://www.reactome.org/biopax/48887#BiochemicalReaction4858",
822            "http://www.reactome.org/biopax/48887#BiochemicalReaction4859",
823            "http://www.reactome.org/biopax/48887#BiochemicalReaction4850",
824            "http://www.reactome.org/biopax/48887#BiochemicalReaction4851",
825            "http://www.reactome.org/biopax/48887#BiochemicalReaction4852",
826            "http://www.reactome.org/biopax/48887#BiochemicalReaction4027",
827            "http://www.reactome.org/biopax/48887#BiochemicalReaction4827",
828            "http://www.reactome.org/biopax/48887#BiochemicalReaction5507",
829            "http://www.reactome.org/biopax/48887#BiochemicalReaction4826",
830            "http://www.reactome.org/biopax/48887#BiochemicalReaction4825",
831            "http://www.reactome.org/biopax/48887#BiochemicalReaction5508",
832            "http://www.reactome.org/biopax/48887#BiochemicalReaction5509",
833            "http://www.reactome.org/biopax/48887#BiochemicalReaction4823",
834            "http://www.reactome.org/biopax/48887#BiochemicalReaction5502",
835            "http://www.reactome.org/biopax/48887#BiochemicalReaction5503",
836            "http://www.reactome.org/biopax/48887#BiochemicalReaction4822",
837            "http://www.reactome.org/biopax/48887#BiochemicalReaction5504",
838            "http://www.reactome.org/biopax/48887#BiochemicalReaction4821",
839            "http://www.reactome.org/biopax/48887#BiochemicalReaction5505",
840            "http://www.reactome.org/biopax/48887#BiochemicalReaction4820",
841            "http://www.reactome.org/biopax/48887#BiochemicalReaction4829",
842            "http://www.reactome.org/biopax/48887#BiochemicalReaction4828",
843            "http://www.reactome.org/biopax/48887#BiochemicalReaction4052",
844            "http://www.reactome.org/biopax/48887#BiochemicalReaction4050",
845            "http://www.reactome.org/biopax/48887#BiochemicalReaction5501",
846            "http://www.reactome.org/biopax/48887#BiochemicalReaction5500",
847            "http://www.reactome.org/biopax/48887#BiochemicalReaction4053",
848            "http://www.reactome.org/biopax/48887#BiochemicalReaction4054",
849            "http://www.reactome.org/biopax/48887#BiochemicalReaction4836",
850            "http://www.reactome.org/biopax/48887#BiochemicalReaction4835",
851            "http://www.reactome.org/biopax/48887#BiochemicalReaction4838",
852            "http://www.reactome.org/biopax/48887#BiochemicalReaction4837",
853            "http://www.reactome.org/biopax/48887#BiochemicalReaction4832",
854            "http://www.reactome.org/biopax/48887#BiochemicalReaction4831",
855            "http://www.reactome.org/biopax/48887#BiochemicalReaction4834",
856            "http://www.reactome.org/biopax/48887#BiochemicalReaction4839",
857            "http://www.reactome.org/biopax/48887#BiochemicalReaction4046",
858            "http://www.reactome.org/biopax/48887#BiochemicalReaction4047",
859            "http://www.reactome.org/biopax/48887#BiochemicalReaction4830",
860            "http://www.reactome.org/biopax/48887#BiochemicalReaction3387",
861            "http://www.reactome.org/biopax/48887#BiochemicalReaction3389",
862            "http://www.reactome.org/biopax/48887#BiochemicalReaction4808",
863            "http://www.reactome.org/biopax/48887#BiochemicalReaction4809",
864            "http://www.reactome.org/biopax/48887#BiochemicalReaction4806",
865            "http://www.reactome.org/biopax/48887#BiochemicalReaction4807",
866            "http://www.reactome.org/biopax/48887#BiochemicalReaction5525",
867            "http://www.reactome.org/biopax/48887#BiochemicalReaction5527",
868            "http://www.reactome.org/biopax/48887#BiochemicalReaction5526",
869            "http://www.reactome.org/biopax/48887#BiochemicalReaction5529",
870            "http://www.reactome.org/biopax/48887#BiochemicalReaction4804",
871            "http://www.reactome.org/biopax/48887#BiochemicalReaction4805",
872            "http://www.reactome.org/biopax/48887#BiochemicalReaction5528",
873            "http://www.reactome.org/biopax/48887#BiochemicalReaction4802",
874            "http://www.reactome.org/biopax/48887#BiochemicalReaction4803",
875            "http://www.reactome.org/biopax/48887#BiochemicalReaction4810",
876            "http://www.reactome.org/biopax/48887#BiochemicalReaction4811",
877            "http://www.reactome.org/biopax/48887#BiochemicalReaction4812",
878            "http://www.reactome.org/biopax/48887#BiochemicalReaction5512",
879            "http://www.reactome.org/biopax/48887#BiochemicalReaction5510",
880            "http://www.reactome.org/biopax/48887#BiochemicalReaction5547",
881            "http://www.reactome.org/biopax/48887#BiochemicalReaction5546",
882            "http://www.reactome.org/biopax/48887#BiochemicalReaction5549",
883            "http://www.reactome.org/biopax/48887#BiochemicalReaction5548",
884            "http://www.reactome.org/biopax/48887#BiochemicalReaction5543",
885            "http://www.reactome.org/biopax/48887#BiochemicalReaction5544",
886            "http://www.reactome.org/biopax/48887#BiochemicalReaction5545",
887            "http://www.reactome.org/biopax/48887#BiochemicalReaction5533",
888            "http://www.reactome.org/biopax/48887#BiochemicalReaction5531",
889            "http://www.reactome.org/biopax/48887#BiochemicalReaction5530",
890            "http://www.reactome.org/biopax/48887#BiochemicalReaction4001",
891            "http://www.reactome.org/biopax/48887#BiochemicalReaction5563",
892            "http://www.reactome.org/biopax/48887#BiochemicalReaction5562",
893            "http://www.reactome.org/biopax/48887#BiochemicalReaction5561",
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3147            "http://www.reactome.org/biopax/48887#BiochemicalReaction2397",
3148            "http://www.reactome.org/biopax/48887#BiochemicalReaction2395",
3149            "http://www.reactome.org/biopax/48887#BiochemicalReaction2394",
3150            "http://www.reactome.org/biopax/48887#BiochemicalReaction1287",
3151            "http://www.reactome.org/biopax/48887#BiochemicalReaction2390",
3152            "http://www.reactome.org/biopax/48887#BiochemicalReaction2386",
3153            "http://www.reactome.org/biopax/48887#BiochemicalReaction2385",
3154            "http://www.reactome.org/biopax/48887#BiochemicalReaction2388",
3155            "http://www.reactome.org/biopax/48887#BiochemicalReaction2382",
3156            "http://www.reactome.org/biopax/48887#BiochemicalReaction2381",
3157            "http://www.reactome.org/biopax/48887#BiochemicalReaction2384",
3158            "http://www.reactome.org/biopax/48887#BiochemicalReaction2380",
3159            "http://www.reactome.org/biopax/48887#BiochemicalReaction1273"
3160    ));
3161
3162    public static void main(String[] args) throws Exception {
3163        setUp();
3164        logger.debug("Starting...");
3165        
3166        logger.debug("creating positive and negative examples...");
3167        Set<OWLIndividual> posExamples = makeIndividuals(posExampleUris);
3168        Set<OWLIndividual> negExamples = makeIndividuals(negExampleUris);
3169        logger.debug("finished creating positive and negative examples");
3170        
3171        logger.debug("reading ontology...");
3172        OWLOntologyManager man = OWLManager.createOWLOntologyManager();
3173        OWLOntology ontology = man.loadOntologyFromOntologyDocument(new File(kbPathStr));
3174        logger.debug("read " + ontology.getAxiomCount() + " axioms");
3175        logger.debug("finished reading the ontology");
3176
3177        logger.debug("initializing knowledge source...");
3178        KnowledgeSource ks = new OWLAPIOntology(ontology);
3179        ks.init();
3180        logger.debug("finished initializing knowledge source");
3181        
3182        logger.debug("initializing reasoner...");
3183        OWLAPIReasoner baseReasoner = new OWLAPIReasoner(ks);
3184        baseReasoner.setReasonerImplementation(ReasonerImplementation.ELK);
3185        baseReasoner.setUseFallbackReasoner(true);
3186        baseReasoner.init();
3187        Logger.getLogger(ElkReasoner.class).setLevel(Level.OFF);
3188        logger.debug("finished initializing reasoner");
3189        
3190        logger.debug("initializing reasoner component...");
3191        ClosedWorldReasoner cwReasoner = new ClosedWorldReasoner(ks);
3192        cwReasoner.setReasonerComponent(baseReasoner);
3193        cwReasoner.setHandlePunning(false);
3194        cwReasoner.setUseMaterializationCaching(false);
3195        cwReasoner.setMaterializeExistentialRestrictions(true);
3196        cwReasoner.init();
3197        logger.debug("finished initializing reasoner component");
3198        
3199//        AbstractReasonerComponent rc = baseReasoner;
3200        AbstractReasonerComponent rc = cwReasoner;
3201        
3202        logger.debug("initializing learning problem...");
3203        PosNegLPStandard lp = new PosNegLPStandard(rc);
3204        lp.setPositiveExamples(posExamples);
3205        lp.setNegativeExamples(negExamples);
3206        lp.init();
3207        logger.debug("finished initializing learning problem");
3208
3209        logger.debug("initializing learning algorithm...");
3210        AbstractCELA la;
3211        
3212        OEHeuristicRuntime heuristic = new OEHeuristicRuntime();
3213        heuristic.setExpansionPenaltyFactor(0.1);
3214        
3215        CELOE celoe = new CELOE(lp, rc);
3216        celoe.setHeuristic(heuristic);
3217        celoe.setMaxExecutionTimeInSeconds(300);
3218        celoe.setNoisePercentage(50);
3219        celoe.setMaxNrOfResults(10);
3220        celoe.setWriteSearchTree(true);
3221        celoe.setReplaceSearchTree(true);
3222        
3223        ELLearningAlgorithm elLa = new ELLearningAlgorithm(lp, rc);
3224
3225        elLa.setNoisePercentage(1.0);
3226        la = elLa; // celoe;
3227//        Description startClass = new NamedClass("http://dl-learner.org/smallis/Allelic_info");
3228        logger.debug("finished initializing learning algorithm");
3229        logger.debug("initializing operator...");
3230        RhoDRDown op = new RhoDRDown();
3231        op.setUseHasValueConstructor(true);
3232        op.setInstanceBasedDisjoints(true);
3233        op.setUseNegation(false);
3234//        op.setStartClass(new NamedClass("http://dl-learner.org/smallis/Allelic_info"));
3235        op.setUseHasValueConstructor(false);
3236        op.setReasoner(rc);
3237        op.setSubHierarchy(rc.getClassHierarchy());
3238        op.setObjectPropertyHierarchy(rc.getObjectPropertyHierarchy());
3239        op.setDataPropertyHierarchy(rc.getDatatypePropertyHierarchy());
3240        op.init();
3241        logger.debug("finished initializing operator");
3242        if(la instanceof CELOE)
3243                ((CELOE) la).setOperator(op);
3244
3245        la.init();
3246        la.start();
3247
3248        logger.debug("Finished");
3249    }
3250    
3251    private static void setUp() {
3252        logger.setLevel(Level.DEBUG);
3253        Logger.getLogger(AbstractReasonerComponent.class).setLevel(Level.OFF);
3254        Logger.getLogger(ELDown.class).setLevel(Level.TRACE);
3255        StringRenderer.setRenderer(Rendering.DL_SYNTAX);
3256    }
3257    
3258    private static Set<OWLIndividual> makeIndividuals(List<String> uris) {
3259        Set<OWLIndividual> individuals = new HashSet<>();
3260        for (String uri : uris) {
3261            individuals.add(new OWLNamedIndividualImpl(IRI.create(uri)));
3262        }
3263        
3264        return individuals;
3265    }
3266}