biointerchange 0.2.2 → 1.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (55) hide show
  1. data/Gemfile +1 -0
  2. data/README.md +269 -19
  3. data/VERSION +1 -1
  4. data/examples/bininda_emonds_mammals.new +1 -0
  5. data/examples/rdfization.rb +17 -0
  6. data/examples/tree1.new +1 -0
  7. data/examples/tree2.new +1 -0
  8. data/examples/vocabulary.rb +26 -5
  9. data/generators/javaify.rb +12 -18
  10. data/generators/make_supplement_releases.rb +2 -0
  11. data/generators/pythonify.rb +21 -8
  12. data/generators/rdfxml.rb +15 -1
  13. data/lib/biointerchange/cdao.rb +2014 -0
  14. data/lib/biointerchange/core.rb +70 -77
  15. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +16 -0
  16. data/lib/biointerchange/genomics/gff3_reader.rb +18 -4
  17. data/lib/biointerchange/genomics/gvf_reader.rb +14 -0
  18. data/lib/biointerchange/phylogenetics/cdao_rdf_ntriples.rb +108 -0
  19. data/lib/biointerchange/phylogenetics/newick_reader.rb +81 -0
  20. data/lib/biointerchange/phylogenetics/tree_set.rb +50 -0
  21. data/lib/biointerchange/registry.rb +50 -8
  22. data/lib/biointerchange/so.rb +150 -0
  23. data/lib/biointerchange/textmining/pdfx_xml_reader.rb +21 -2
  24. data/lib/biointerchange/textmining/pubannos_json_reader.rb +24 -1
  25. data/lib/biointerchange/textmining/text_mining_rdf_ntriples.rb +9 -0
  26. data/lib/biointerchange/textmining/text_mining_reader.rb +5 -5
  27. data/spec/phylogenetics_spec.rb +79 -0
  28. data/supplemental/java/biointerchange/pom.xml +1 -1
  29. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/CDAO.java +2602 -0
  30. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/FALDO.java +30 -28
  31. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +136 -104
  32. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +367 -278
  33. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4388 -3127
  34. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java +5970 -4351
  35. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +733 -544
  36. data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java +3 -1
  37. data/supplemental/python/biointerchange/cdao.py +2021 -0
  38. data/supplemental/python/biointerchange/faldo.py +37 -38
  39. data/supplemental/python/biointerchange/gff3o.py +156 -157
  40. data/supplemental/python/biointerchange/goxref.py +172 -172
  41. data/supplemental/python/biointerchange/gvf1o.py +428 -429
  42. data/supplemental/python/biointerchange/sio.py +3133 -3134
  43. data/supplemental/python/biointerchange/so.py +6626 -6527
  44. data/supplemental/python/biointerchange/sofa.py +790 -791
  45. data/supplemental/python/example.py +23 -5
  46. data/supplemental/python/setup.py +2 -2
  47. data/web/about.html +1 -0
  48. data/web/api.html +223 -15
  49. data/web/biointerchange.js +27 -6
  50. data/web/cli.html +8 -3
  51. data/web/index.html +6 -2
  52. data/web/ontologies.html +3 -0
  53. data/web/service/rdfizer.fcgi +7 -15
  54. data/web/webservices.html +6 -2
  55. metadata +30 -3
@@ -18,7 +18,7 @@ public class GFF3O {
18
18
  * (http://www.biointerchange.org/gff3o#GFF3_0004)
19
19
  */
20
20
  public static Resource seqid() {
21
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0004");
21
+ return _namespace_GFF3O("GFF3_0004");
22
22
  }
23
23
 
24
24
  /**
@@ -30,7 +30,7 @@ public class GFF3O {
30
30
  * (http://www.biointerchange.org/gff3o#GFF3_0045)
31
31
  */
32
32
  public static Set<Resource> strand() {
33
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0010"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0045") }));
33
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0010"), _namespace_GFF3O("GFF3_0045") }));
34
34
  }
35
35
 
36
36
  /**
@@ -38,7 +38,7 @@ public class GFF3O {
38
38
  * (http://www.biointerchange.org/gff3o#GFF3_0012)
39
39
  */
40
40
  public static Resource attributes() {
41
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0012");
41
+ return _namespace_GFF3O("GFF3_0012");
42
42
  }
43
43
 
44
44
  /**
@@ -46,7 +46,7 @@ public class GFF3O {
46
46
  * (http://www.biointerchange.org/gff3o#GFF3_0014)
47
47
  */
48
48
  public static Resource parent() {
49
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0014");
49
+ return _namespace_GFF3O("GFF3_0014");
50
50
  }
51
51
 
52
52
  /**
@@ -54,7 +54,7 @@ public class GFF3O {
54
54
  * (http://www.biointerchange.org/gff3o#GFF3_0015)
55
55
  */
56
56
  public static Resource contains() {
57
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0015");
57
+ return _namespace_GFF3O("GFF3_0015");
58
58
  }
59
59
 
60
60
  /**
@@ -66,7 +66,7 @@ public class GFF3O {
66
66
  * (http://www.biointerchange.org/gff3o#GFF3_0050)
67
67
  */
68
68
  public static Set<Resource> region() {
69
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0021"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0050") }));
69
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0021"), _namespace_GFF3O("GFF3_0050") }));
70
70
  }
71
71
 
72
72
  /**
@@ -74,7 +74,7 @@ public class GFF3O {
74
74
  * (http://www.biointerchange.org/gff3o#GFF3_0023)
75
75
  */
76
76
  public static Resource species() {
77
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0023");
77
+ return _namespace_GFF3O("GFF3_0023");
78
78
  }
79
79
 
80
80
  /**
@@ -86,7 +86,7 @@ public class GFF3O {
86
86
  * (http://www.biointerchange.org/gff3o#GFF3_0027)
87
87
  */
88
88
  public static Set<Resource> set_properties() {
89
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0025"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0027") }));
89
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0025"), _namespace_GFF3O("GFF3_0027") }));
90
90
  }
91
91
 
92
92
  /**
@@ -98,7 +98,7 @@ public class GFF3O {
98
98
  * (http://www.biointerchange.org/gff3o#GFF3_0028)
99
99
  */
100
100
  public static Set<Resource> feature_properties() {
101
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0026"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0028") }));
101
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0026"), _namespace_GFF3O("GFF3_0028") }));
102
102
  }
103
103
 
104
104
  /**
@@ -106,7 +106,7 @@ public class GFF3O {
106
106
  * (http://www.biointerchange.org/gff3o#GFF3_0039)
107
107
  */
108
108
  public static Resource target() {
109
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0039");
109
+ return _namespace_GFF3O("GFF3_0039");
110
110
  }
111
111
 
112
112
  /**
@@ -118,7 +118,7 @@ public class GFF3O {
118
118
  * (http://www.biointerchange.org/gff3o#GFF3_0040)
119
119
  */
120
120
  public static Set<Resource> target_properties() {
121
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0044"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0040") }));
121
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0044"), _namespace_GFF3O("GFF3_0040") }));
122
122
  }
123
123
 
124
124
  /**
@@ -126,7 +126,7 @@ public class GFF3O {
126
126
  * (http://www.biointerchange.org/gff3o#GFF3_0047)
127
127
  */
128
128
  public static Resource derives_from() {
129
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0047");
129
+ return _namespace_GFF3O("GFF3_0047");
130
130
  }
131
131
 
132
132
  /**
@@ -134,7 +134,7 @@ public class GFF3O {
134
134
  * (http://www.biointerchange.org/gff3o#GFF3_0056)
135
135
  */
136
136
  public static Resource feature_ontology() {
137
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0056");
137
+ return _namespace_GFF3O("GFF3_0056");
138
138
  }
139
139
 
140
140
  /**
@@ -142,7 +142,7 @@ public class GFF3O {
142
142
  * (http://www.biointerchange.org/gff3o#GFF3_0005)
143
143
  */
144
144
  public static Resource source() {
145
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0005");
145
+ return _namespace_GFF3O("GFF3_0005");
146
146
  }
147
147
 
148
148
  /**
@@ -150,7 +150,7 @@ public class GFF3O {
150
150
  * (http://www.biointerchange.org/gff3o#GFF3_0006)
151
151
  */
152
152
  public static Resource type() {
153
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0006");
153
+ return _namespace_GFF3O("GFF3_0006");
154
154
  }
155
155
 
156
156
  /**
@@ -165,7 +165,7 @@ public class GFF3O {
165
165
  * (http://www.biointerchange.org/gff3o#GFF3_0054)
166
166
  */
167
167
  public static Set<Resource> start() {
168
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0007"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0042"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0054") }));
168
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0007"), _namespace_GFF3O("GFF3_0042"), _namespace_GFF3O("GFF3_0054") }));
169
169
  }
170
170
 
171
171
  /**
@@ -180,7 +180,7 @@ public class GFF3O {
180
180
  * (http://www.biointerchange.org/gff3o#GFF3_0055)
181
181
  */
182
182
  public static Set<Resource> end() {
183
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0008"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0043"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0055") }));
183
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0008"), _namespace_GFF3O("GFF3_0043"), _namespace_GFF3O("GFF3_0055") }));
184
184
  }
185
185
 
186
186
  /**
@@ -188,7 +188,7 @@ public class GFF3O {
188
188
  * (http://www.biointerchange.org/gff3o#GFF3_0009)
189
189
  */
190
190
  public static Resource score() {
191
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0009");
191
+ return _namespace_GFF3O("GFF3_0009");
192
192
  }
193
193
 
194
194
  /**
@@ -196,7 +196,7 @@ public class GFF3O {
196
196
  * (http://www.biointerchange.org/gff3o#GFF3_0011)
197
197
  */
198
198
  public static Resource phase() {
199
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0011");
199
+ return _namespace_GFF3O("GFF3_0011");
200
200
  }
201
201
 
202
202
  /**
@@ -204,7 +204,7 @@ public class GFF3O {
204
204
  * (http://www.biointerchange.org/gff3o#GFF3_0013)
205
205
  */
206
206
  public static Resource tag() {
207
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0013");
207
+ return _namespace_GFF3O("GFF3_0013");
208
208
  }
209
209
 
210
210
  /**
@@ -212,7 +212,7 @@ public class GFF3O {
212
212
  * (http://www.biointerchange.org/gff3o#GFF3_0022)
213
213
  */
214
214
  public static Resource version() {
215
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0022");
215
+ return _namespace_GFF3O("GFF3_0022");
216
216
  }
217
217
 
218
218
  /**
@@ -220,7 +220,7 @@ public class GFF3O {
220
220
  * (http://www.biointerchange.org/gff3o#GFF3_0024)
221
221
  */
222
222
  public static Resource build() {
223
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0024");
223
+ return _namespace_GFF3O("GFF3_0024");
224
224
  }
225
225
 
226
226
  /**
@@ -228,7 +228,7 @@ public class GFF3O {
228
228
  * (http://www.biointerchange.org/gff3o#GFF3_0029)
229
229
  */
230
230
  public static Resource attribute_properties() {
231
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0029");
231
+ return _namespace_GFF3O("GFF3_0029");
232
232
  }
233
233
 
234
234
  /**
@@ -236,7 +236,7 @@ public class GFF3O {
236
236
  * (http://www.biointerchange.org/gff3o#GFF3_0034)
237
237
  */
238
238
  public static Resource dbxref() {
239
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0034");
239
+ return _namespace_GFF3O("GFF3_0034");
240
240
  }
241
241
 
242
242
  /**
@@ -244,7 +244,7 @@ public class GFF3O {
244
244
  * (http://www.biointerchange.org/gff3o#GFF3_0035)
245
245
  */
246
246
  public static Resource ontology_term() {
247
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0035");
247
+ return _namespace_GFF3O("GFF3_0035");
248
248
  }
249
249
 
250
250
  /**
@@ -252,7 +252,7 @@ public class GFF3O {
252
252
  * (http://www.biointerchange.org/gff3o#GFF3_0036)
253
253
  */
254
254
  public static Resource name() {
255
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0036");
255
+ return _namespace_GFF3O("GFF3_0036");
256
256
  }
257
257
 
258
258
  /**
@@ -260,7 +260,7 @@ public class GFF3O {
260
260
  * (http://www.biointerchange.org/gff3o#GFF3_0037)
261
261
  */
262
262
  public static Resource alias() {
263
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0037");
263
+ return _namespace_GFF3O("GFF3_0037");
264
264
  }
265
265
 
266
266
  /**
@@ -268,7 +268,7 @@ public class GFF3O {
268
268
  * (http://www.biointerchange.org/gff3o#GFF3_0041)
269
269
  */
270
270
  public static Resource target_id() {
271
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0041");
271
+ return _namespace_GFF3O("GFF3_0041");
272
272
  }
273
273
 
274
274
  /**
@@ -276,7 +276,7 @@ public class GFF3O {
276
276
  * (http://www.biointerchange.org/gff3o#GFF3_0046)
277
277
  */
278
278
  public static Resource gap() {
279
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0046");
279
+ return _namespace_GFF3O("GFF3_0046");
280
280
  }
281
281
 
282
282
  /**
@@ -284,7 +284,7 @@ public class GFF3O {
284
284
  * (http://www.biointerchange.org/gff3o#GFF3_0048)
285
285
  */
286
286
  public static Resource note() {
287
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0048");
287
+ return _namespace_GFF3O("GFF3_0048");
288
288
  }
289
289
 
290
290
  /**
@@ -292,7 +292,7 @@ public class GFF3O {
292
292
  * (http://www.biointerchange.org/gff3o#GFF3_0049)
293
293
  */
294
294
  public static Resource is_circular() {
295
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0049");
295
+ return _namespace_GFF3O("GFF3_0049");
296
296
  }
297
297
 
298
298
  /**
@@ -300,7 +300,7 @@ public class GFF3O {
300
300
  * (http://www.biointerchange.org/gff3o#GFF3_0052)
301
301
  */
302
302
  public static Resource landmark_properties() {
303
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0052");
303
+ return _namespace_GFF3O("GFF3_0052");
304
304
  }
305
305
 
306
306
  /**
@@ -308,7 +308,7 @@ public class GFF3O {
308
308
  * (http://www.biointerchange.org/gff3o#GFF3_0053)
309
309
  */
310
310
  public static Resource id() {
311
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0053");
311
+ return _namespace_GFF3O("GFF3_0053");
312
312
  }
313
313
 
314
314
  /**
@@ -320,7 +320,7 @@ public class GFF3O {
320
320
  * (http://www.biointerchange.org/gff3o#GFF3_0058)
321
321
  */
322
322
  public static Set<Resource> sequence() {
323
- return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0057"), _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0058") }));
323
+ return new HashSet<Resource>(Arrays.asList(new Resource[] { _namespace_GFF3O("GFF3_0057"), _namespace_GFF3O("GFF3_0058") }));
324
324
  }
325
325
 
326
326
  /**
@@ -328,7 +328,7 @@ public class GFF3O {
328
328
  * (http://www.biointerchange.org/gff3o#GFF3_0001)
329
329
  */
330
330
  public static Resource Set() {
331
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0001");
331
+ return _namespace_GFF3O("GFF3_0001");
332
332
  }
333
333
 
334
334
  /**
@@ -336,7 +336,7 @@ public class GFF3O {
336
336
  * (http://www.biointerchange.org/gff3o#GFF3_0002)
337
337
  */
338
338
  public static Resource Feature() {
339
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0002");
339
+ return _namespace_GFF3O("GFF3_0002");
340
340
  }
341
341
 
342
342
  /**
@@ -344,7 +344,7 @@ public class GFF3O {
344
344
  * (http://www.biointerchange.org/gff3o#GFF3_0003)
345
345
  */
346
346
  public static Resource Attribute() {
347
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0003");
347
+ return _namespace_GFF3O("GFF3_0003");
348
348
  }
349
349
 
350
350
  /**
@@ -352,7 +352,7 @@ public class GFF3O {
352
352
  * (http://www.biointerchange.org/gff3o#GFF3_0016)
353
353
  */
354
354
  public static Resource Strand() {
355
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0016");
355
+ return _namespace_GFF3O("GFF3_0016");
356
356
  }
357
357
 
358
358
  /**
@@ -360,7 +360,7 @@ public class GFF3O {
360
360
  * (http://www.biointerchange.org/gff3o#GFF3_0038)
361
361
  */
362
362
  public static Resource Target() {
363
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0038");
363
+ return _namespace_GFF3O("GFF3_0038");
364
364
  }
365
365
 
366
366
  /**
@@ -368,7 +368,7 @@ public class GFF3O {
368
368
  * (http://www.biointerchange.org/gff3o#GFF3_0051)
369
369
  */
370
370
  public static Resource Landmark() {
371
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0051");
371
+ return _namespace_GFF3O("GFF3_0051");
372
372
  }
373
373
 
374
374
  /**
@@ -376,7 +376,7 @@ public class GFF3O {
376
376
  * (http://www.biointerchange.org/gff3o#GFF3_0017)
377
377
  */
378
378
  public static Resource Positive() {
379
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0017");
379
+ return _namespace_GFF3O("GFF3_0017");
380
380
  }
381
381
 
382
382
  /**
@@ -384,7 +384,7 @@ public class GFF3O {
384
384
  * (http://www.biointerchange.org/gff3o#GFF3_0018)
385
385
  */
386
386
  public static Resource Negative() {
387
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0018");
387
+ return _namespace_GFF3O("GFF3_0018");
388
388
  }
389
389
 
390
390
  /**
@@ -392,7 +392,7 @@ public class GFF3O {
392
392
  * (http://www.biointerchange.org/gff3o#GFF3_0019)
393
393
  */
394
394
  public static Resource UnknownStrand() {
395
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0019");
395
+ return _namespace_GFF3O("GFF3_0019");
396
396
  }
397
397
 
398
398
  /**
@@ -400,7 +400,7 @@ public class GFF3O {
400
400
  * (http://www.biointerchange.org/gff3o#GFF3_0020)
401
401
  */
402
402
  public static Resource NotStranded() {
403
- return _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0020");
403
+ return _namespace_GFF3O("GFF3_0020");
404
404
  }
405
405
 
406
406
  /**
@@ -409,49 +409,49 @@ public class GFF3O {
409
409
  * @param uri URI that is tested for being an object property
410
410
  */
411
411
  public static boolean isObjectProperty(Resource uri) {
412
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0004")) {
412
+ if (uri.equals(_namespace_GFF3O("GFF3_0004"))) {
413
413
  return true;
414
414
  }
415
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0010")) {
415
+ if (uri.equals(_namespace_GFF3O("GFF3_0010"))) {
416
416
  return true;
417
417
  }
418
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0012")) {
418
+ if (uri.equals(_namespace_GFF3O("GFF3_0012"))) {
419
419
  return true;
420
420
  }
421
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0014")) {
421
+ if (uri.equals(_namespace_GFF3O("GFF3_0014"))) {
422
422
  return true;
423
423
  }
424
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0015")) {
424
+ if (uri.equals(_namespace_GFF3O("GFF3_0015"))) {
425
425
  return true;
426
426
  }
427
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0021")) {
427
+ if (uri.equals(_namespace_GFF3O("GFF3_0021"))) {
428
428
  return true;
429
429
  }
430
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0023")) {
430
+ if (uri.equals(_namespace_GFF3O("GFF3_0023"))) {
431
431
  return true;
432
432
  }
433
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0025")) {
433
+ if (uri.equals(_namespace_GFF3O("GFF3_0025"))) {
434
434
  return true;
435
435
  }
436
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0026")) {
436
+ if (uri.equals(_namespace_GFF3O("GFF3_0026"))) {
437
437
  return true;
438
438
  }
439
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0039")) {
439
+ if (uri.equals(_namespace_GFF3O("GFF3_0039"))) {
440
440
  return true;
441
441
  }
442
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0044")) {
442
+ if (uri.equals(_namespace_GFF3O("GFF3_0044"))) {
443
443
  return true;
444
444
  }
445
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0045")) {
445
+ if (uri.equals(_namespace_GFF3O("GFF3_0045"))) {
446
446
  return true;
447
447
  }
448
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0047")) {
448
+ if (uri.equals(_namespace_GFF3O("GFF3_0047"))) {
449
449
  return true;
450
450
  }
451
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0050")) {
451
+ if (uri.equals(_namespace_GFF3O("GFF3_0050"))) {
452
452
  return true;
453
453
  }
454
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0056")) {
454
+ if (uri.equals(_namespace_GFF3O("GFF3_0056"))) {
455
455
  return true;
456
456
  }
457
457
  return false;
@@ -463,91 +463,91 @@ public class GFF3O {
463
463
  * @param uri URI that is tested for being a datatype property
464
464
  */
465
465
  public static boolean isDatatypeProperty(Resource uri) {
466
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0005")) {
466
+ if (uri.equals(_namespace_GFF3O("GFF3_0005"))) {
467
467
  return true;
468
468
  }
469
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0006")) {
469
+ if (uri.equals(_namespace_GFF3O("GFF3_0006"))) {
470
470
  return true;
471
471
  }
472
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0007")) {
472
+ if (uri.equals(_namespace_GFF3O("GFF3_0007"))) {
473
473
  return true;
474
474
  }
475
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0008")) {
475
+ if (uri.equals(_namespace_GFF3O("GFF3_0008"))) {
476
476
  return true;
477
477
  }
478
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0009")) {
478
+ if (uri.equals(_namespace_GFF3O("GFF3_0009"))) {
479
479
  return true;
480
480
  }
481
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0011")) {
481
+ if (uri.equals(_namespace_GFF3O("GFF3_0011"))) {
482
482
  return true;
483
483
  }
484
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0013")) {
484
+ if (uri.equals(_namespace_GFF3O("GFF3_0013"))) {
485
485
  return true;
486
486
  }
487
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0022")) {
487
+ if (uri.equals(_namespace_GFF3O("GFF3_0022"))) {
488
488
  return true;
489
489
  }
490
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0024")) {
490
+ if (uri.equals(_namespace_GFF3O("GFF3_0024"))) {
491
491
  return true;
492
492
  }
493
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0027")) {
493
+ if (uri.equals(_namespace_GFF3O("GFF3_0027"))) {
494
494
  return true;
495
495
  }
496
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0028")) {
496
+ if (uri.equals(_namespace_GFF3O("GFF3_0028"))) {
497
497
  return true;
498
498
  }
499
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0029")) {
499
+ if (uri.equals(_namespace_GFF3O("GFF3_0029"))) {
500
500
  return true;
501
501
  }
502
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0034")) {
502
+ if (uri.equals(_namespace_GFF3O("GFF3_0034"))) {
503
503
  return true;
504
504
  }
505
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0035")) {
505
+ if (uri.equals(_namespace_GFF3O("GFF3_0035"))) {
506
506
  return true;
507
507
  }
508
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0036")) {
508
+ if (uri.equals(_namespace_GFF3O("GFF3_0036"))) {
509
509
  return true;
510
510
  }
511
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0037")) {
511
+ if (uri.equals(_namespace_GFF3O("GFF3_0037"))) {
512
512
  return true;
513
513
  }
514
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0040")) {
514
+ if (uri.equals(_namespace_GFF3O("GFF3_0040"))) {
515
515
  return true;
516
516
  }
517
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0041")) {
517
+ if (uri.equals(_namespace_GFF3O("GFF3_0041"))) {
518
518
  return true;
519
519
  }
520
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0042")) {
520
+ if (uri.equals(_namespace_GFF3O("GFF3_0042"))) {
521
521
  return true;
522
522
  }
523
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0043")) {
523
+ if (uri.equals(_namespace_GFF3O("GFF3_0043"))) {
524
524
  return true;
525
525
  }
526
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0046")) {
526
+ if (uri.equals(_namespace_GFF3O("GFF3_0046"))) {
527
527
  return true;
528
528
  }
529
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0048")) {
529
+ if (uri.equals(_namespace_GFF3O("GFF3_0048"))) {
530
530
  return true;
531
531
  }
532
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0049")) {
532
+ if (uri.equals(_namespace_GFF3O("GFF3_0049"))) {
533
533
  return true;
534
534
  }
535
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0052")) {
535
+ if (uri.equals(_namespace_GFF3O("GFF3_0052"))) {
536
536
  return true;
537
537
  }
538
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0053")) {
538
+ if (uri.equals(_namespace_GFF3O("GFF3_0053"))) {
539
539
  return true;
540
540
  }
541
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0054")) {
541
+ if (uri.equals(_namespace_GFF3O("GFF3_0054"))) {
542
542
  return true;
543
543
  }
544
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0055")) {
544
+ if (uri.equals(_namespace_GFF3O("GFF3_0055"))) {
545
545
  return true;
546
546
  }
547
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0057")) {
547
+ if (uri.equals(_namespace_GFF3O("GFF3_0057"))) {
548
548
  return true;
549
549
  }
550
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0058")) {
550
+ if (uri.equals(_namespace_GFF3O("GFF3_0058"))) {
551
551
  return true;
552
552
  }
553
553
  return false;
@@ -559,22 +559,22 @@ public class GFF3O {
559
559
  * @param uri URI that is tested for being a class
560
560
  */
561
561
  public static boolean isClass(Resource uri) {
562
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0001")) {
562
+ if (uri.equals(_namespace_GFF3O("GFF3_0001"))) {
563
563
  return true;
564
564
  }
565
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0002")) {
565
+ if (uri.equals(_namespace_GFF3O("GFF3_0002"))) {
566
566
  return true;
567
567
  }
568
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0003")) {
568
+ if (uri.equals(_namespace_GFF3O("GFF3_0003"))) {
569
569
  return true;
570
570
  }
571
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0016")) {
571
+ if (uri.equals(_namespace_GFF3O("GFF3_0016"))) {
572
572
  return true;
573
573
  }
574
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0038")) {
574
+ if (uri.equals(_namespace_GFF3O("GFF3_0038"))) {
575
575
  return true;
576
576
  }
577
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0051")) {
577
+ if (uri.equals(_namespace_GFF3O("GFF3_0051"))) {
578
578
  return true;
579
579
  }
580
580
  return false;
@@ -586,16 +586,16 @@ public class GFF3O {
586
586
  * @param uri URI that is tested for being a named individual
587
587
  */
588
588
  public static boolean isNamedIndividual(Resource uri) {
589
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0017")) {
589
+ if (uri.equals(_namespace_GFF3O("GFF3_0017"))) {
590
590
  return true;
591
591
  }
592
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0018")) {
592
+ if (uri.equals(_namespace_GFF3O("GFF3_0018"))) {
593
593
  return true;
594
594
  }
595
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0019")) {
595
+ if (uri.equals(_namespace_GFF3O("GFF3_0019"))) {
596
596
  return true;
597
597
  }
598
- if (uri == _namespace_GFF3O("http://www.biointerchange.org/gff3o#GFF3_0020")) {
598
+ if (uri.equals(_namespace_GFF3O("GFF3_0020"))) {
599
599
  return true;
600
600
  }
601
601
  return false;
@@ -619,7 +619,7 @@ public class GFF3O {
619
619
  */
620
620
  public static boolean hasParent(Resource uri, Resource parent) {
621
621
  if (__parent_properties.containsKey(uri)) {
622
- if (__parent_properties.get(uri) == parent) {
622
+ if (__parent_properties.get(uri).equals(parent)) {
623
623
  return true;
624
624
  }
625
625
  return hasParent((Resource)__parent_properties.get(uri), parent);
@@ -628,11 +628,7 @@ public class GFF3O {
628
628
  }
629
629
 
630
630
  private static Resource _namespace_GFF3O(String accession) {
631
- if (isClass(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#" + accession))) {
632
- return ResourceFactory.createResource("http://www.biointerchange.org/gff3o#" + accession);
633
- } else {
634
- return ResourceFactory.createProperty("http://www.biointerchange.org/gff3o#" + accession);
635
- }
631
+ return ResourceFactory.createResource("http://www.biointerchange.org/gff3o#" + accession);
636
632
  }
637
633
 
638
634
 
@@ -641,6 +637,42 @@ public class GFF3O {
641
637
  private static Map<Resource, Resource> _init___parent_properties() {
642
638
  Map<Resource, Resource> map = new HashMap<Resource, Resource>();
643
639
 
640
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0004"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
641
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0010"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
642
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0012"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
643
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0014"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
644
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0015"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
645
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0021"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
646
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0023"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
647
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0039"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
648
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0045"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0044"));
649
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0047"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0026"));
650
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0050"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0044"));
651
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0056"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0025"));
652
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0005"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
653
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0006"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
654
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0007"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
655
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0008"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
656
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0009"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
657
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0011"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
658
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0013"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0029"));
659
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0022"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0027"));
660
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0024"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0027"));
661
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0034"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
662
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0035"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
663
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0036"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
664
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0037"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
665
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0041"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
666
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0042"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
667
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0043"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0040"));
668
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0046"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
669
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0048"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
670
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0049"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
671
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0053"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
672
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0054"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
673
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0055"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
674
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0057"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0028"));
675
+ map.put(ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0058"), ResourceFactory.createResource("http://www.biointerchange.org/gff3o#GFF3_0052"));
644
676
 
645
677
  return map;
646
678
  }