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
@@ -9,955 +9,955 @@ class GVF1O:
9
9
  def seqid(cls):
10
10
  """Either:
11
11
  Establishes the landmark (cls, e.g. a chromosome) on which a feature is located.
12
- (GVF1_0004)
12
+ (http://www.biointerchange.org/gvf1o#GVF1_0004)
13
13
  Or:
14
14
  Link to the landmark that establishes the coordinate system for the breakpoint.
15
- (GVF1_0072)
15
+ (http://www.biointerchange.org/gvf1o#GVF1_0072)
16
16
  """
17
- return [ _namespace_GVF1O('GVF1_0004'), _namespace_GVF1O('GVF1_0072') ]
17
+ return [ cls._namespace_GVF1O('GVF1_0004'), cls._namespace_GVF1O('GVF1_0072') ]
18
18
 
19
19
  @classmethod
20
20
  def strand(cls):
21
21
  """Either:
22
22
  Strand of the feature.
23
- (cls, GVF1_0010)
23
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0010)
24
24
  Or:
25
25
  Strand of the breakpoint.
26
- (GVF1_0083)
26
+ (http://www.biointerchange.org/gvf1o#GVF1_0083)
27
27
  Or:
28
28
  Strand of a target -- if applicable.
29
- (GVF1_0091)
29
+ (http://www.biointerchange.org/gvf1o#GVF1_0091)
30
30
  """
31
- return [ _namespace_GVF1O('GVF1_0010'), _namespace_GVF1O('GVF1_0083'), _namespace_GVF1O('GVF1_0091') ]
31
+ return [ cls._namespace_GVF1O('GVF1_0010'), cls._namespace_GVF1O('GVF1_0083'), cls._namespace_GVF1O('GVF1_0091') ]
32
32
 
33
33
  @classmethod
34
34
  def attributes(cls):
35
35
  """Either:
36
36
  Tag name/value pair attributes of a feature.
37
- (cls, GVF1_0012)
37
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0012)
38
38
  Or:
39
39
  Tag name/value pair attributes that are not captured by the GVF specification.
40
- (GVF1_0152)
40
+ (http://www.biointerchange.org/gvf1o#GVF1_0152)
41
41
  """
42
- return [ _namespace_GVF1O('GVF1_0012'), _namespace_GVF1O('GVF1_0152') ]
42
+ return [ cls._namespace_GVF1O('GVF1_0012'), cls._namespace_GVF1O('GVF1_0152') ]
43
43
 
44
44
  @classmethod
45
45
  def parent(cls):
46
46
  """Link out to the parent feature.
47
- (cls, GVF1_0014)
47
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0014)
48
48
  """
49
- return _namespace_GVF1O('GVF1_0014')
49
+ return cls._namespace_GVF1O('GVF1_0014')
50
50
 
51
51
  @classmethod
52
52
  def contains(cls):
53
53
  """Relationship that describes which features belong to a feature set.
54
- (cls, GVF1_0015)
54
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0015)
55
55
  """
56
- return _namespace_GVF1O('GVF1_0015')
56
+ return cls._namespace_GVF1O('GVF1_0015')
57
57
 
58
58
  @classmethod
59
59
  def region(cls):
60
60
  """Either:
61
61
  FALDO "Region" instance replacement for a feature's start, stop, strand properties.
62
- (cls, GVF1_0021)
62
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0021)
63
63
  Or:
64
64
  FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
65
- (GVF1_0079)
65
+ (http://www.biointerchange.org/gvf1o#GVF1_0079)
66
66
  Or:
67
67
  FALDO "Region" instance replacement for a target's start, stop, strand properties.
68
- (GVF1_0090)
68
+ (http://www.biointerchange.org/gvf1o#GVF1_0090)
69
69
  """
70
- return [ _namespace_GVF1O('GVF1_0021'), _namespace_GVF1O('GVF1_0079'), _namespace_GVF1O('GVF1_0090') ]
70
+ return [ cls._namespace_GVF1O('GVF1_0021'), cls._namespace_GVF1O('GVF1_0079'), cls._namespace_GVF1O('GVF1_0090') ]
71
71
 
72
72
  @classmethod
73
73
  def species(cls):
74
74
  """NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set.
75
- (GVF1_0023)
75
+ (http://www.biointerchange.org/gvf1o#GVF1_0023)
76
76
  """
77
- return _namespace_GVF1O('GVF1_0023')
77
+ return cls._namespace_GVF1O('GVF1_0023')
78
78
 
79
79
  @classmethod
80
80
  def variant(cls):
81
81
  """Specific information about the variant(cls, s) of a feature.
82
- (GVF1_0034)
82
+ (http://www.biointerchange.org/gvf1o#GVF1_0034)
83
83
  """
84
- return _namespace_GVF1O('GVF1_0034')
84
+ return cls._namespace_GVF1O('GVF1_0034')
85
85
 
86
86
  @classmethod
87
87
  def individual(cls):
88
88
  """Links to information about an individual.
89
- (cls, GVF1_0036)
89
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0036)
90
90
  """
91
- return _namespace_GVF1O('GVF1_0036')
91
+ return cls._namespace_GVF1O('GVF1_0036')
92
92
 
93
93
  @classmethod
94
94
  def zygosity(cls):
95
95
  """Zygosity of a variant.
96
- (cls, GVF1_0038)
96
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0038)
97
97
  """
98
- return _namespace_GVF1O('GVF1_0038')
98
+ return cls._namespace_GVF1O('GVF1_0038')
99
99
 
100
100
  @classmethod
101
101
  def effect(cls):
102
102
  """An effect of a particular feature variant.
103
- (cls, GVF1_0041)
103
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0041)
104
104
  """
105
- return _namespace_GVF1O('GVF1_0041')
105
+ return cls._namespace_GVF1O('GVF1_0041')
106
106
 
107
107
  @classmethod
108
108
  def sequence_variant(cls):
109
109
  """Effect of a sequence alteration on a sequence feature.
110
- (cls, GVF1_0042)
110
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0042)
111
111
  """
112
- return _namespace_GVF1O('GVF1_0042')
112
+ return cls._namespace_GVF1O('GVF1_0042')
113
113
 
114
114
  @classmethod
115
115
  def feature_type(cls):
116
116
  """A term that is describing the sequence feature that is being affected.
117
- (cls, GVF1_0043)
117
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0043)
118
118
  """
119
- return _namespace_GVF1O('GVF1_0043')
119
+ return cls._namespace_GVF1O('GVF1_0043')
120
120
 
121
121
  @classmethod
122
122
  def start_range(cls):
123
123
  """A coordinate range for ambiguous start coordinates.
124
- (cls, GVF1_0046)
124
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0046)
125
125
  """
126
- return _namespace_GVF1O('GVF1_0046')
126
+ return cls._namespace_GVF1O('GVF1_0046')
127
127
 
128
128
  @classmethod
129
129
  def end_range(cls):
130
130
  """A coordinate range for ambiguous start coordinates.
131
- (cls, GVF1_0047)
131
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0047)
132
132
  """
133
- return _namespace_GVF1O('GVF1_0047')
133
+ return cls._namespace_GVF1O('GVF1_0047')
134
134
 
135
135
  @classmethod
136
136
  def chromosome(cls):
137
137
  """Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.
138
- (cls, GVF1_0051)
138
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0051)
139
139
  """
140
- return _namespace_GVF1O('GVF1_0051')
140
+ return cls._namespace_GVF1O('GVF1_0051')
141
141
 
142
142
  @classmethod
143
143
  def genotype(cls):
144
144
  """Determines the genotype as observed in an individual.
145
- (cls, GVF1_0053)
145
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0053)
146
146
  """
147
- return _namespace_GVF1O('GVF1_0053')
147
+ return cls._namespace_GVF1O('GVF1_0053')
148
148
 
149
149
  @classmethod
150
150
  def feature_properties(cls):
151
151
  """Either:
152
152
  Properties that are directly associated with Feature class instances.
153
- (cls, GVF1_0066)
153
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0066)
154
154
  Or:
155
155
  Properties that are directly associated with Feature class instances.
156
- (GVF1_0059)
156
+ (http://www.biointerchange.org/gvf1o#GVF1_0059)
157
157
  """
158
- return [ _namespace_GVF1O('GVF1_0066'), _namespace_GVF1O('GVF1_0059') ]
158
+ return [ cls._namespace_GVF1O('GVF1_0066'), cls._namespace_GVF1O('GVF1_0059') ]
159
159
 
160
160
  @classmethod
161
161
  def sequencedindividual_properties(cls):
162
162
  """Either:
163
163
  Properties that are directly associated with SequencedIndividual class instances.
164
- (cls, GVF1_0067)
164
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0067)
165
165
  Or:
166
166
  Properties that are directly associated with SequencedIndividual class instances.
167
- (GVF1_0065)
167
+ (http://www.biointerchange.org/gvf1o#GVF1_0065)
168
168
  """
169
- return [ _namespace_GVF1O('GVF1_0067'), _namespace_GVF1O('GVF1_0065') ]
169
+ return [ cls._namespace_GVF1O('GVF1_0067'), cls._namespace_GVF1O('GVF1_0065') ]
170
170
 
171
171
  @classmethod
172
172
  def set_properties(cls):
173
173
  """Either:
174
174
  Properties that are directly associated with Set class instances.
175
- (cls, GVF1_0068)
175
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0068)
176
176
  Or:
177
177
  Properties that are directly associated with Set class instances.
178
- (GVF1_0063)
178
+ (http://www.biointerchange.org/gvf1o#GVF1_0063)
179
179
  """
180
- return [ _namespace_GVF1O('GVF1_0068'), _namespace_GVF1O('GVF1_0063') ]
180
+ return [ cls._namespace_GVF1O('GVF1_0068'), cls._namespace_GVF1O('GVF1_0063') ]
181
181
 
182
182
  @classmethod
183
183
  def variant_properties(cls):
184
184
  """Either:
185
185
  Properties that are directly associated with Variant class instances.
186
- (cls, GVF1_0069)
186
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0069)
187
187
  Or:
188
188
  Properties that are directly associated with Variant class instances.
189
- (GVF1_0060)
189
+ (http://www.biointerchange.org/gvf1o#GVF1_0060)
190
190
  """
191
- return [ _namespace_GVF1O('GVF1_0069'), _namespace_GVF1O('GVF1_0060') ]
191
+ return [ cls._namespace_GVF1O('GVF1_0069'), cls._namespace_GVF1O('GVF1_0060') ]
192
192
 
193
193
  @classmethod
194
194
  def effect_properties(cls):
195
195
  """Either:
196
196
  Properties that are directly associated with Effect class instances.
197
- (cls, GVF1_0070)
197
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0070)
198
198
  Or:
199
199
  Properties that are directly associated with Effect class instances.
200
- (GVF1_0158)
200
+ (http://www.biointerchange.org/gvf1o#GVF1_0158)
201
201
  """
202
- return [ _namespace_GVF1O('GVF1_0070'), _namespace_GVF1O('GVF1_0158') ]
202
+ return [ cls._namespace_GVF1O('GVF1_0070'), cls._namespace_GVF1O('GVF1_0158') ]
203
203
 
204
204
  @classmethod
205
205
  def breakpoint_properties(cls):
206
206
  """Either:
207
207
  Properties that are directly associated with Breakpoint class instances.
208
- (cls, GVF1_0075)
208
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0075)
209
209
  Or:
210
210
  Properties that are directly associated with Breakpoint class instances.
211
- (GVF1_0071)
211
+ (http://www.biointerchange.org/gvf1o#GVF1_0071)
212
212
  """
213
- return [ _namespace_GVF1O('GVF1_0075'), _namespace_GVF1O('GVF1_0071') ]
213
+ return [ cls._namespace_GVF1O('GVF1_0075'), cls._namespace_GVF1O('GVF1_0071') ]
214
214
 
215
215
  @classmethod
216
216
  def dbxref(cls):
217
217
  """Either:
218
218
  A database cross-reference to associate a sequence alteration to its representation in another database.
219
- (cls, GVF1_0078)
219
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0078)
220
220
  Or:
221
221
  A database cross-reference to associate a structured pragma to a representation in another database.
222
- (GVF1_0104)
222
+ (http://www.biointerchange.org/gvf1o#GVF1_0104)
223
223
  """
224
- return [ _namespace_GVF1O('GVF1_0078'), _namespace_GVF1O('GVF1_0104') ]
224
+ return [ cls._namespace_GVF1O('GVF1_0078'), cls._namespace_GVF1O('GVF1_0104') ]
225
225
 
226
226
  @classmethod
227
227
  def breakpoint(cls):
228
228
  """Potential source or destination of zero-length sequence alterations.
229
- (cls, GVF1_0080)
229
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0080)
230
230
  """
231
- return _namespace_GVF1O('GVF1_0080')
231
+ return cls._namespace_GVF1O('GVF1_0080')
232
232
 
233
233
  @classmethod
234
234
  def target_properties(cls):
235
235
  """Either:
236
236
  Properties that are directly associated with Target class instances.
237
- (cls, GVF1_0089)
237
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0089)
238
238
  Or:
239
239
  Properties that are directly associated with Target class instances.
240
- (GVF1_0092)
240
+ (http://www.biointerchange.org/gvf1o#GVF1_0092)
241
241
  """
242
- return [ _namespace_GVF1O('GVF1_0089'), _namespace_GVF1O('GVF1_0092') ]
242
+ return [ cls._namespace_GVF1O('GVF1_0089'), cls._namespace_GVF1O('GVF1_0092') ]
243
243
 
244
244
  @classmethod
245
245
  def technologyplatform_properties(cls):
246
246
  """Either:
247
247
  Properties that are directly associated with TechnologyPlatform class instances.
248
- (cls, GVF1_0102)
248
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0102)
249
249
  Or:
250
250
  Properties that are directly associated with TechnologyPlatform class instances.
251
- (GVF1_0107)
251
+ (http://www.biointerchange.org/gvf1o#GVF1_0107)
252
252
  """
253
- return [ _namespace_GVF1O('GVF1_0102'), _namespace_GVF1O('GVF1_0107') ]
253
+ return [ cls._namespace_GVF1O('GVF1_0102'), cls._namespace_GVF1O('GVF1_0107') ]
254
254
 
255
255
  @classmethod
256
256
  def datasource_properties(cls):
257
257
  """Properties that are directly associated with DataSource class instances.
258
- (cls, GVF1_0103)
258
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0103)
259
259
  """
260
- return _namespace_GVF1O('GVF1_0103')
260
+ return cls._namespace_GVF1O('GVF1_0103')
261
261
 
262
262
  @classmethod
263
263
  def structuredpragma_properties(cls):
264
264
  """Either:
265
265
  Properties describing structured pragma properties.
266
- (cls, GVF1_0112)
266
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0112)
267
267
  Or:
268
268
  Properties describing structured pragma properties.
269
- (GVF1_0113)
269
+ (http://www.biointerchange.org/gvf1o#GVF1_0113)
270
270
  """
271
- return [ _namespace_GVF1O('GVF1_0112'), _namespace_GVF1O('GVF1_0113') ]
271
+ return [ cls._namespace_GVF1O('GVF1_0112'), cls._namespace_GVF1O('GVF1_0113') ]
272
272
 
273
273
  @classmethod
274
274
  def read_type(cls):
275
275
  """Types of reads produced by the platform.
276
- (cls, GVF1_0119)
276
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0119)
277
277
  """
278
- return _namespace_GVF1O('GVF1_0119')
278
+ return cls._namespace_GVF1O('GVF1_0119')
279
279
 
280
280
  @classmethod
281
281
  def data_type(cls):
282
282
  """Datatype of this data source.
283
- (cls, GVF1_0120)
283
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0120)
284
284
  """
285
- return _namespace_GVF1O('GVF1_0120')
285
+ return cls._namespace_GVF1O('GVF1_0120')
286
286
 
287
287
  @classmethod
288
288
  def technology_platform(cls):
289
289
  """Technology platform that was used to derive the feature.
290
- (cls, GVF1_0121)
290
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0121)
291
291
  """
292
- return _namespace_GVF1O('GVF1_0121')
292
+ return cls._namespace_GVF1O('GVF1_0121')
293
293
 
294
294
  @classmethod
295
295
  def data_source(cls):
296
296
  """Data source origin of the feature.
297
- (cls, GVF1_0122)
297
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0122)
298
298
  """
299
- return _namespace_GVF1O('GVF1_0122')
299
+ return cls._namespace_GVF1O('GVF1_0122')
300
300
 
301
301
  @classmethod
302
302
  def score_method(cls):
303
303
  """Used scoring method.
304
- (cls, GVF1_0123)
304
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0123)
305
305
  """
306
- return _namespace_GVF1O('GVF1_0123')
306
+ return cls._namespace_GVF1O('GVF1_0123')
307
307
 
308
308
  @classmethod
309
309
  def source_method(cls):
310
310
  """Further information about the algorithm/methodologies used.
311
- (cls, GVF1_0124)
311
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0124)
312
312
  """
313
- return _namespace_GVF1O('GVF1_0124')
313
+ return cls._namespace_GVF1O('GVF1_0124')
314
314
 
315
315
  @classmethod
316
316
  def phenotype_description(cls):
317
317
  """Further information about an individual's phenotype. Applies only to single individual sets.
318
- (cls, GVF1_0125)
318
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0125)
319
319
  """
320
- return _namespace_GVF1O('GVF1_0125')
320
+ return cls._namespace_GVF1O('GVF1_0125')
321
321
 
322
322
  @classmethod
323
323
  def attribute_method(cls):
324
324
  """Either:
325
325
  Further information about the associated attribute(cls, s).
326
- (GVF1_0126)
326
+ (http://www.biointerchange.org/gvf1o#GVF1_0126)
327
327
  Or:
328
328
  Further information about the associated attribute(s).
329
- (GVF1_0127)
329
+ (http://www.biointerchange.org/gvf1o#GVF1_0127)
330
330
  Or:
331
331
  Further information about the associated attribute(s).
332
- (GVF1_0129)
332
+ (http://www.biointerchange.org/gvf1o#GVF1_0129)
333
333
  Or:
334
334
  Further information about the associated attribute(s).
335
- (GVF1_0130)
335
+ (http://www.biointerchange.org/gvf1o#GVF1_0130)
336
336
  Or:
337
337
  Further information about the associated attribute(s).
338
- (GVF1_0131)
338
+ (http://www.biointerchange.org/gvf1o#GVF1_0131)
339
339
  """
340
- return [ _namespace_GVF1O('GVF1_0126'), _namespace_GVF1O('GVF1_0127'), _namespace_GVF1O('GVF1_0129'), _namespace_GVF1O('GVF1_0130'), _namespace_GVF1O('GVF1_0131') ]
340
+ return [ cls._namespace_GVF1O('GVF1_0126'), cls._namespace_GVF1O('GVF1_0127'), cls._namespace_GVF1O('GVF1_0129'), cls._namespace_GVF1O('GVF1_0130'), cls._namespace_GVF1O('GVF1_0131') ]
341
341
 
342
342
  @classmethod
343
343
  def attribute_properties(cls):
344
344
  """Either:
345
345
  Properties about Attribute instances.
346
- (cls, GVF1_0128)
346
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0128)
347
347
  Or:
348
348
  Properties that are directly associated with Attribute class instances.
349
- (GVF1_0064)
349
+ (http://www.biointerchange.org/gvf1o#GVF1_0064)
350
350
  """
351
- return [ _namespace_GVF1O('GVF1_0128'), _namespace_GVF1O('GVF1_0064') ]
351
+ return [ cls._namespace_GVF1O('GVF1_0128'), cls._namespace_GVF1O('GVF1_0064') ]
352
352
 
353
353
  @classmethod
354
354
  def sex(cls):
355
355
  """Denotes the sex of the sequenced individual for single-individual sets.
356
- (cls, GVF1_0147)
356
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0147)
357
357
  """
358
- return _namespace_GVF1O('GVF1_0147')
358
+ return cls._namespace_GVF1O('GVF1_0147')
359
359
 
360
360
  @classmethod
361
361
  def genomic_source(cls):
362
362
  """Denotes the source of genomic data (cls, on a cell-type level).
363
- (GVF1_0148)
363
+ (http://www.biointerchange.org/gvf1o#GVF1_0148)
364
364
  """
365
- return _namespace_GVF1O('GVF1_0148')
365
+ return cls._namespace_GVF1O('GVF1_0148')
366
366
 
367
367
  @classmethod
368
368
  def feature_ontology(cls):
369
369
  """Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
370
- (cls, GVF1_0150)
370
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0150)
371
371
  """
372
- return _namespace_GVF1O('GVF1_0150')
372
+ return cls._namespace_GVF1O('GVF1_0150')
373
373
 
374
374
  @classmethod
375
375
  def target(cls):
376
376
  """Identifies the target that the features aligns to.
377
- (cls, GVF1_0155)
377
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0155)
378
378
  """
379
- return _namespace_GVF1O('GVF1_0155')
379
+ return cls._namespace_GVF1O('GVF1_0155')
380
380
 
381
381
  @classmethod
382
382
  def source(cls):
383
383
  """A free text qualifier that describes the algorithm or operating procedure that generated this feature. For example, the name of the software that generated this feature or a database name.
384
- (cls, GVF1_0005)
384
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0005)
385
385
  """
386
- return _namespace_GVF1O('GVF1_0005')
386
+ return cls._namespace_GVF1O('GVF1_0005')
387
387
 
388
388
  @classmethod
389
389
  def type(cls):
390
390
  """Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (cls, SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
391
- (GVF1_0006)
391
+ (http://www.biointerchange.org/gvf1o#GVF1_0006)
392
392
  """
393
- return _namespace_GVF1O('GVF1_0006')
393
+ return cls._namespace_GVF1O('GVF1_0006')
394
394
 
395
395
  @classmethod
396
396
  def start(cls):
397
397
  """Either:
398
398
  Start coordinate of the feature on the seqid landmark.
399
- (cls, GVF1_0007)
399
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0007)
400
400
  Or:
401
401
  A coordinate that defines the start of an ambiguous coordinate range.
402
- (GVF1_0048)
402
+ (http://www.biointerchange.org/gvf1o#GVF1_0048)
403
403
  Or:
404
404
  Start coordinate of the feature on the seqid landmark.
405
- (GVF1_0073)
405
+ (http://www.biointerchange.org/gvf1o#GVF1_0073)
406
406
  Or:
407
407
  Start coordinate of the target.
408
- (GVF1_0094)
408
+ (http://www.biointerchange.org/gvf1o#GVF1_0094)
409
409
  Or:
410
410
  Genomic start coordinate of the landmark.
411
- (GVF1_0138)
411
+ (http://www.biointerchange.org/gvf1o#GVF1_0138)
412
412
  """
413
- return [ _namespace_GVF1O('GVF1_0007'), _namespace_GVF1O('GVF1_0048'), _namespace_GVF1O('GVF1_0073'), _namespace_GVF1O('GVF1_0094'), _namespace_GVF1O('GVF1_0138') ]
413
+ return [ cls._namespace_GVF1O('GVF1_0007'), cls._namespace_GVF1O('GVF1_0048'), cls._namespace_GVF1O('GVF1_0073'), cls._namespace_GVF1O('GVF1_0094'), cls._namespace_GVF1O('GVF1_0138') ]
414
414
 
415
415
  @classmethod
416
416
  def end(cls):
417
417
  """Either:
418
418
  End coordinate of the feature on the seqid landmark.
419
- (cls, GVF1_0008)
419
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0008)
420
420
  Or:
421
421
  A coordinate that defines the end of an ambiguous coordinate range.
422
- (GVF1_0049)
422
+ (http://www.biointerchange.org/gvf1o#GVF1_0049)
423
423
  Or:
424
424
  End coordinate of the feature on the seqid landmark.
425
- (GVF1_0074)
425
+ (http://www.biointerchange.org/gvf1o#GVF1_0074)
426
426
  Or:
427
427
  End coordinate of the target.
428
- (GVF1_0095)
428
+ (http://www.biointerchange.org/gvf1o#GVF1_0095)
429
429
  Or:
430
430
  Genomic end coordinate of the landmark.
431
- (GVF1_0139)
431
+ (http://www.biointerchange.org/gvf1o#GVF1_0139)
432
432
  """
433
- return [ _namespace_GVF1O('GVF1_0008'), _namespace_GVF1O('GVF1_0049'), _namespace_GVF1O('GVF1_0074'), _namespace_GVF1O('GVF1_0095'), _namespace_GVF1O('GVF1_0139') ]
433
+ return [ cls._namespace_GVF1O('GVF1_0008'), cls._namespace_GVF1O('GVF1_0049'), cls._namespace_GVF1O('GVF1_0074'), cls._namespace_GVF1O('GVF1_0095'), cls._namespace_GVF1O('GVF1_0139') ]
434
434
 
435
435
  @classmethod
436
436
  def score(cls):
437
437
  """Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
438
- (cls, GVF1_0009)
438
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0009)
439
439
  """
440
- return _namespace_GVF1O('GVF1_0009')
440
+ return cls._namespace_GVF1O('GVF1_0009')
441
441
 
442
442
  @classmethod
443
443
  def tag(cls):
444
444
  """Either:
445
445
  Tag name of a feature attribute.
446
- (cls, GVF1_0013)
446
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0013)
447
447
  Or:
448
448
  Tag name of an user defined structured attribute.
449
- (GVF1_0154)
449
+ (http://www.biointerchange.org/gvf1o#GVF1_0154)
450
450
  """
451
- return [ _namespace_GVF1O('GVF1_0013'), _namespace_GVF1O('GVF1_0154') ]
451
+ return [ cls._namespace_GVF1O('GVF1_0013'), cls._namespace_GVF1O('GVF1_0154') ]
452
452
 
453
453
  @classmethod
454
454
  def gvf_version(cls):
455
455
  """Version of the GVF specification that defines the feature set contents.
456
- (cls, GVF1_0022)
456
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0022)
457
457
  """
458
- return _namespace_GVF1O('GVF1_0022')
458
+ return cls._namespace_GVF1O('GVF1_0022')
459
459
 
460
460
  @classmethod
461
461
  def build(cls):
462
462
  """Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
463
- (cls, GVF1_0024)
463
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0024)
464
464
  """
465
- return _namespace_GVF1O('GVF1_0024')
465
+ return cls._namespace_GVF1O('GVF1_0024')
466
466
 
467
467
  @classmethod
468
468
  def variant_seq(cls):
469
469
  """All sequence variations at a locus -- including the reference sequence when appropriate (cls, for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.
470
- (GVF1_0025)
470
+ (http://www.biointerchange.org/gvf1o#GVF1_0025)
471
471
  """
472
- return _namespace_GVF1O('GVF1_0025')
472
+ return cls._namespace_GVF1O('GVF1_0025')
473
473
 
474
474
  @classmethod
475
475
  def id(cls):
476
476
  """Either:
477
477
  A unique identifier for the feature within the feature set.
478
- (cls, GVF1_0026)
478
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0026)
479
479
  Or:
480
480
  ID that uniquely establishes the Landmark's identity within a Set.
481
- (GVF1_0137)
481
+ (http://www.biointerchange.org/gvf1o#GVF1_0137)
482
482
  """
483
- return [ _namespace_GVF1O('GVF1_0026'), _namespace_GVF1O('GVF1_0137') ]
483
+ return [ cls._namespace_GVF1O('GVF1_0026'), cls._namespace_GVF1O('GVF1_0137') ]
484
484
 
485
485
  @classmethod
486
486
  def alias(cls):
487
487
  """Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (cls, e.g. dbSNP, OMIM) which should use the dbxref property.
488
- (GVF1_0027)
488
+ (http://www.biointerchange.org/gvf1o#GVF1_0027)
489
489
  """
490
- return _namespace_GVF1O('GVF1_0027')
490
+ return cls._namespace_GVF1O('GVF1_0027')
491
491
 
492
492
  @classmethod
493
493
  def reference_seq(cls):
494
494
  """Sequence from the reference genome.
495
- (cls, GVF1_0031)
495
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0031)
496
496
  """
497
- return _namespace_GVF1O('GVF1_0031')
497
+ return cls._namespace_GVF1O('GVF1_0031')
498
498
 
499
499
  @classmethod
500
500
  def variant_reads(cls):
501
501
  """Number of reads that are supporting this variant.
502
- (cls, GVF1_0032)
502
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0032)
503
503
  """
504
- return _namespace_GVF1O('GVF1_0032')
504
+ return cls._namespace_GVF1O('GVF1_0032')
505
505
 
506
506
  @classmethod
507
507
  def total_reads(cls):
508
508
  """Total number of reads.
509
- (cls, GVF1_0037)
509
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0037)
510
510
  """
511
- return _namespace_GVF1O('GVF1_0037')
511
+ return cls._namespace_GVF1O('GVF1_0037')
512
512
 
513
513
  @classmethod
514
514
  def variant_freq(cls):
515
515
  """Frequency of a variant in a population.
516
- (cls, GVF1_0039)
516
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0039)
517
517
  """
518
- return _namespace_GVF1O('GVF1_0039')
518
+ return cls._namespace_GVF1O('GVF1_0039')
519
519
 
520
520
  @classmethod
521
521
  def feature(cls):
522
522
  """Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
523
- (cls, GVF1_0044)
523
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0044)
524
524
  """
525
- return _namespace_GVF1O('GVF1_0044')
525
+ return cls._namespace_GVF1O('GVF1_0044')
526
526
 
527
527
  @classmethod
528
528
  def phased(cls):
529
529
  """Either:
530
530
  Unclear from GVF specification.
531
- (cls, GVF1_0050)
531
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0050)
532
532
  Or:
533
533
  Indicates whether this particular is phased. Used to encode ##phased-genotypes statements.
534
- (GVF1_0101)
534
+ (http://www.biointerchange.org/gvf1o#GVF1_0101)
535
535
  """
536
- return [ _namespace_GVF1O('GVF1_0050'), _namespace_GVF1O('GVF1_0101') ]
536
+ return [ cls._namespace_GVF1O('GVF1_0050'), cls._namespace_GVF1O('GVF1_0101') ]
537
537
 
538
538
  @classmethod
539
539
  def variant_codon(cls):
540
540
  """Describes the codon that overlaps this variant.
541
- (cls, GVF1_0054)
541
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0054)
542
542
  """
543
- return _namespace_GVF1O('GVF1_0054')
543
+ return cls._namespace_GVF1O('GVF1_0054')
544
544
 
545
545
  @classmethod
546
546
  def reference_codon(cls):
547
547
  """Describes the codon from the reference sequence whose coordinates overlap with this variant.
548
- (cls, GVF1_0055)
548
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0055)
549
549
  """
550
- return _namespace_GVF1O('GVF1_0055')
550
+ return cls._namespace_GVF1O('GVF1_0055')
551
551
 
552
552
  @classmethod
553
553
  def variant_aa(cls):
554
554
  """Amino acid that overlaps with the variant.
555
- (cls, GVF1_0056)
555
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0056)
556
556
  """
557
- return _namespace_GVF1O('GVF1_0056')
557
+ return cls._namespace_GVF1O('GVF1_0056')
558
558
 
559
559
  @classmethod
560
560
  def reference_aa(cls):
561
561
  """Amino acid in the reference genome that overlaps with a variant's genome coordinates.
562
- (cls, GVF1_0057)
562
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0057)
563
563
  """
564
- return _namespace_GVF1O('GVF1_0057')
564
+ return cls._namespace_GVF1O('GVF1_0057')
565
565
 
566
566
  @classmethod
567
567
  def range_properties(cls):
568
568
  """Properties that are directly associated with Range class instances.
569
- (cls, GVF1_0061)
569
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0061)
570
570
  """
571
- return _namespace_GVF1O('GVF1_0061')
571
+ return cls._namespace_GVF1O('GVF1_0061')
572
572
 
573
573
  @classmethod
574
574
  def a_context(cls):
575
575
  """Sequence context (cls, positive strand) of a feature on the 5' end.
576
- (GVF1_0076)
576
+ (http://www.biointerchange.org/gvf1o#GVF1_0076)
577
577
  """
578
- return _namespace_GVF1O('GVF1_0076')
578
+ return cls._namespace_GVF1O('GVF1_0076')
579
579
 
580
580
  @classmethod
581
581
  def gff_version(cls):
582
582
  """Version of the GFF specification that defines the feature set contents apart from GVF related definitions.
583
- (cls, GVF1_0081)
583
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0081)
584
584
  """
585
- return _namespace_GVF1O('GVF1_0081')
585
+ return cls._namespace_GVF1O('GVF1_0081')
586
586
 
587
587
  @classmethod
588
588
  def file_date(cls):
589
589
  """Creation date of the GVF file that this set stems from.
590
- (cls, GVF1_0082)
590
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0082)
591
591
  """
592
- return _namespace_GVF1O('GVF1_0082')
592
+ return cls._namespace_GVF1O('GVF1_0082')
593
593
 
594
594
  @classmethod
595
595
  def target_id(cls):
596
596
  """ID or accession of the target alignment.
597
- (cls, GVF1_0093)
597
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0093)
598
598
  """
599
- return _namespace_GVF1O('GVF1_0093')
599
+ return cls._namespace_GVF1O('GVF1_0093')
600
600
 
601
601
  @classmethod
602
602
  def ontology_term(cls):
603
603
  """A cross-reference to an ontology term that is associated with a feature.
604
- (cls, GVF1_0096)
604
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0096)
605
605
  """
606
- return _namespace_GVF1O('GVF1_0096')
606
+ return cls._namespace_GVF1O('GVF1_0096')
607
607
 
608
608
  @classmethod
609
609
  def comment(cls):
610
610
  """An arbitrary comment. Free text.
611
- (cls, GVF1_0105)
611
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0105)
612
612
  """
613
- return _namespace_GVF1O('GVF1_0105')
613
+ return cls._namespace_GVF1O('GVF1_0105')
614
614
 
615
615
  @classmethod
616
616
  def platform_class(cls):
617
617
  """Type of technology used to gather the variant data. Unrestricted range due to open specification.
618
- (cls, GVF1_0106)
618
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0106)
619
619
  """
620
- return _namespace_GVF1O('GVF1_0106')
620
+ return cls._namespace_GVF1O('GVF1_0106')
621
621
 
622
622
  @classmethod
623
623
  def platform_name(cls):
624
624
  """Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification.
625
- (cls, GVF1_0108)
625
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0108)
626
626
  """
627
- return _namespace_GVF1O('GVF1_0108')
627
+ return cls._namespace_GVF1O('GVF1_0108')
628
628
 
629
629
  @classmethod
630
630
  def read_length(cls):
631
631
  """Undocumented in GVF specification.
632
- (cls, GVF1_0132)
632
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0132)
633
633
  """
634
- return _namespace_GVF1O('GVF1_0132')
634
+ return cls._namespace_GVF1O('GVF1_0132')
635
635
 
636
636
  @classmethod
637
637
  def read_pair_span(cls):
638
638
  """Undocumented in GVF specification.
639
- (cls, GVF1_0133)
639
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0133)
640
640
  """
641
- return _namespace_GVF1O('GVF1_0133')
641
+ return cls._namespace_GVF1O('GVF1_0133')
642
642
 
643
643
  @classmethod
644
644
  def average_coverage(cls):
645
645
  """Undocumented in GVF specification.
646
- (cls, GVF1_0134)
646
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0134)
647
647
  """
648
- return _namespace_GVF1O('GVF1_0134')
648
+ return cls._namespace_GVF1O('GVF1_0134')
649
649
 
650
650
  @classmethod
651
651
  def landmark_properties(cls):
652
652
  """Properties that are directly associated with Landmark class instances.
653
- (cls, GVF1_0136)
653
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0136)
654
654
  """
655
- return _namespace_GVF1O('GVF1_0136')
655
+ return cls._namespace_GVF1O('GVF1_0136')
656
656
 
657
657
  @classmethod
658
658
  def file_version(cls):
659
659
  """Version of the GVF file that this set stems from.
660
- (cls, GVF1_0149)
660
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0149)
661
661
  """
662
- return _namespace_GVF1O('GVF1_0149')
662
+ return cls._namespace_GVF1O('GVF1_0149')
663
663
 
664
664
  @classmethod
665
665
  def structuredattribute_properties(cls):
666
666
  """Properties that are directly associated with StructuredAttribute class instances.
667
- (cls, GVF1_0153)
667
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0153)
668
668
  """
669
- return _namespace_GVF1O('GVF1_0153')
669
+ return cls._namespace_GVF1O('GVF1_0153')
670
670
 
671
671
  @classmethod
672
672
  def sequence(cls):
673
673
  """Either:
674
674
  Sequence associated with this feature, if it has been specified using a FASTA string.
675
- (cls, GVF1_0156)
675
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0156)
676
676
  Or:
677
677
  Sequence associated with this feature, if it has been specified using a FASTA string.
678
- (GVF1_0157)
678
+ (http://www.biointerchange.org/gvf1o#GVF1_0157)
679
679
  """
680
- return [ _namespace_GVF1O('GVF1_0156'), _namespace_GVF1O('GVF1_0157') ]
680
+ return [ cls._namespace_GVF1O('GVF1_0156'), cls._namespace_GVF1O('GVF1_0157') ]
681
681
 
682
682
  @classmethod
683
683
  def Set(cls):
684
684
  """Set of genomic sequence features, whose identifiers are unique within the set.
685
- (cls, GVF1_0001)
685
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0001)
686
686
  """
687
- return _namespace_GVF1O('GVF1_0001')
687
+ return cls._namespace_GVF1O('GVF1_0001')
688
688
 
689
689
  @classmethod
690
690
  def Feature(cls):
691
691
  """A genomic sequence feature.
692
- (cls, GVF1_0002)
692
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0002)
693
693
  """
694
- return _namespace_GVF1O('GVF1_0002')
694
+ return cls._namespace_GVF1O('GVF1_0002')
695
695
 
696
696
  @classmethod
697
697
  def Attribute(cls):
698
698
  """Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant.
699
- (cls, GVF1_0003)
699
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0003)
700
700
  """
701
- return _namespace_GVF1O('GVF1_0003')
701
+ return cls._namespace_GVF1O('GVF1_0003')
702
702
 
703
703
  @classmethod
704
704
  def Strand(cls):
705
705
  """Class describing a genomic strand. Instances of the class (cls, individuals) are used to denote forward-/reverse-strands, etc.
706
- (GVF1_0016)
706
+ (http://www.biointerchange.org/gvf1o#GVF1_0016)
707
707
  """
708
- return _namespace_GVF1O('GVF1_0016')
708
+ return cls._namespace_GVF1O('GVF1_0016')
709
709
 
710
710
  @classmethod
711
711
  def Variant(cls):
712
712
  """Describing specific alterations of a feature.
713
- (cls, GVF1_0033)
713
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0033)
714
714
  """
715
- return _namespace_GVF1O('GVF1_0033')
715
+ return cls._namespace_GVF1O('GVF1_0033')
716
716
 
717
717
  @classmethod
718
718
  def SequencedIndividual(cls):
719
719
  """Aggregated sequencing information for a particular individual.
720
- (cls, GVF1_0035)
720
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0035)
721
721
  """
722
- return _namespace_GVF1O('GVF1_0035')
722
+ return cls._namespace_GVF1O('GVF1_0035')
723
723
 
724
724
  @classmethod
725
725
  def Effect(cls):
726
726
  """Describing the effect of a feature variant.
727
- (cls, GVF1_0040)
727
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0040)
728
728
  """
729
- return _namespace_GVF1O('GVF1_0040')
729
+ return cls._namespace_GVF1O('GVF1_0040')
730
730
 
731
731
  @classmethod
732
732
  def Range(cls):
733
733
  """Describe ambiguity in either start or end coordinates.
734
- (cls, GVF1_0045)
734
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0045)
735
735
  """
736
- return _namespace_GVF1O('GVF1_0045')
736
+ return cls._namespace_GVF1O('GVF1_0045')
737
737
 
738
738
  @classmethod
739
739
  def Chromosome(cls):
740
740
  """An abstract representation of a chromosome to represent ploidy.
741
- (cls, GVF1_0052)
741
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0052)
742
742
  """
743
- return _namespace_GVF1O('GVF1_0052')
743
+ return cls._namespace_GVF1O('GVF1_0052')
744
744
 
745
745
  @classmethod
746
746
  def Breakpoint(cls):
747
747
  """Describes the source or destination of a zero-length sequence alteration.
748
- (cls, GVF1_0058)
748
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0058)
749
749
  """
750
- return _namespace_GVF1O('GVF1_0058')
750
+ return cls._namespace_GVF1O('GVF1_0058')
751
751
 
752
752
  @classmethod
753
753
  def Zygosity(cls):
754
754
  """Denotes the zygosity of alleles.
755
- (cls, GVF1_0084)
755
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0084)
756
756
  """
757
- return _namespace_GVF1O('GVF1_0084')
757
+ return cls._namespace_GVF1O('GVF1_0084')
758
758
 
759
759
  @classmethod
760
760
  def Target(cls):
761
761
  """Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
762
- (cls, GVF1_0088)
762
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0088)
763
763
  """
764
- return _namespace_GVF1O('GVF1_0088')
764
+ return cls._namespace_GVF1O('GVF1_0088')
765
765
 
766
766
  @classmethod
767
767
  def TechnologyPlatform(cls):
768
768
  """Details about the sequencing/microarray technology used to gather the data in a set.
769
- (cls, GVF1_0097)
769
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0097)
770
770
  """
771
- return _namespace_GVF1O('GVF1_0097')
771
+ return cls._namespace_GVF1O('GVF1_0097')
772
772
 
773
773
  @classmethod
774
774
  def DataSource(cls):
775
775
  """Provides information about the source of the data. For example, it can link out to actual sequences associated with the Feature individuals in a Set.
776
- (cls, GVF1_0098)
776
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0098)
777
777
  """
778
- return _namespace_GVF1O('GVF1_0098')
778
+ return cls._namespace_GVF1O('GVF1_0098')
779
779
 
780
780
  @classmethod
781
781
  def Method(cls):
782
782
  """Information about the used scoring algorithm or method.
783
- (cls, GVF1_0099)
783
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0099)
784
784
  """
785
- return _namespace_GVF1O('GVF1_0099')
785
+ return cls._namespace_GVF1O('GVF1_0099')
786
786
 
787
787
  @classmethod
788
788
  def PhenotypeDescription(cls):
789
789
  """Additional information about an individual's phenotype.
790
- (cls, GVF1_0100)
790
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0100)
791
791
  """
792
- return _namespace_GVF1O('GVF1_0100')
792
+ return cls._namespace_GVF1O('GVF1_0100')
793
793
 
794
794
  @classmethod
795
795
  def ReadType(cls):
796
796
  """Type of reads obtained for a given technology platform.
797
- (cls, GVF1_0109)
797
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0109)
798
798
  """
799
- return _namespace_GVF1O('GVF1_0109')
799
+ return cls._namespace_GVF1O('GVF1_0109')
800
800
 
801
801
  @classmethod
802
802
  def DataType(cls):
803
803
  """Determines the datatype of a variant sequence.
804
- (cls, GVF1_0114)
804
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0114)
805
805
  """
806
- return _namespace_GVF1O('GVF1_0114')
806
+ return cls._namespace_GVF1O('GVF1_0114')
807
807
 
808
808
  @classmethod
809
809
  def Landmark(cls):
810
810
  """A landmark that establishes the coordinate system for features.
811
- (cls, GVF1_0135)
811
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0135)
812
812
  """
813
- return _namespace_GVF1O('GVF1_0135')
813
+ return cls._namespace_GVF1O('GVF1_0135')
814
814
 
815
815
  @classmethod
816
816
  def Sex(cls):
817
817
  """For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (cls, real-life) individuals.
818
- (GVF1_0140)
818
+ (http://www.biointerchange.org/gvf1o#GVF1_0140)
819
819
  """
820
- return _namespace_GVF1O('GVF1_0140')
820
+ return cls._namespace_GVF1O('GVF1_0140')
821
821
 
822
822
  @classmethod
823
823
  def GenomicSource(cls):
824
824
  """An enumerated class for determining the genomic source (cls, cell type) of sequenced data.
825
- (GVF1_0141)
825
+ (http://www.biointerchange.org/gvf1o#GVF1_0141)
826
826
  """
827
- return _namespace_GVF1O('GVF1_0141')
827
+ return cls._namespace_GVF1O('GVF1_0141')
828
828
 
829
829
  @classmethod
830
830
  def StructuredAttribute(cls):
831
831
  """Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification.
832
- (cls, GVF1_0151)
832
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0151)
833
833
  """
834
- return _namespace_GVF1O('GVF1_0151')
834
+ return cls._namespace_GVF1O('GVF1_0151')
835
835
 
836
836
  @classmethod
837
837
  def Positive(cls):
838
838
  """Location on the positive (cls, forward) strand.
839
- (GVF1_0017)
839
+ (http://www.biointerchange.org/gvf1o#GVF1_0017)
840
840
  """
841
- return _namespace_GVF1O('GVF1_0017')
841
+ return cls._namespace_GVF1O('GVF1_0017')
842
842
 
843
843
  @classmethod
844
844
  def Negative(cls):
845
845
  """Location on the negative (cls, reverse) strand.
846
- (GVF1_0018)
846
+ (http://www.biointerchange.org/gvf1o#GVF1_0018)
847
847
  """
848
- return _namespace_GVF1O('GVF1_0018')
848
+ return cls._namespace_GVF1O('GVF1_0018')
849
849
 
850
850
  @classmethod
851
851
  def UnknownStrand(cls):
852
852
  """Strand was not determined, which leaves it open whether the location is on the positive (cls, forward) or negative (reverse) strand.
853
- (GVF1_0019)
853
+ (http://www.biointerchange.org/gvf1o#GVF1_0019)
854
854
  """
855
- return _namespace_GVF1O('GVF1_0019')
855
+ return cls._namespace_GVF1O('GVF1_0019')
856
856
 
857
857
  @classmethod
858
858
  def NotStranded(cls):
859
859
  """Strand is not applicable.
860
- (cls, GVF1_0020)
860
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0020)
861
861
  """
862
- return _namespace_GVF1O('GVF1_0020')
862
+ return cls._namespace_GVF1O('GVF1_0020')
863
863
 
864
864
  @classmethod
865
865
  def Heterozygous(cls):
866
866
  """Denotes heterozygous alleles.
867
- (cls, GVF1_0085)
867
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0085)
868
868
  """
869
- return _namespace_GVF1O('GVF1_0085')
869
+ return cls._namespace_GVF1O('GVF1_0085')
870
870
 
871
871
  @classmethod
872
872
  def Homozygous(cls):
873
873
  """Denotes homozygous alleles.
874
- (cls, GVF1_0086)
874
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0086)
875
875
  """
876
- return _namespace_GVF1O('GVF1_0086')
876
+ return cls._namespace_GVF1O('GVF1_0086')
877
877
 
878
878
  @classmethod
879
879
  def Hemizygous(cls):
880
880
  """Denotes hemizygous alleles.
881
- (cls, GVF1_0087)
881
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0087)
882
882
  """
883
- return _namespace_GVF1O('GVF1_0087')
883
+ return cls._namespace_GVF1O('GVF1_0087')
884
884
 
885
885
  @classmethod
886
886
  def Fragment(cls):
887
887
  """Denotes reads that are fragments.
888
- (cls, GVF1_0110)
888
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0110)
889
889
  """
890
- return _namespace_GVF1O('GVF1_0110')
890
+ return cls._namespace_GVF1O('GVF1_0110')
891
891
 
892
892
  @classmethod
893
893
  def Pair(cls):
894
894
  """Denotes reads that are pairs.
895
- (cls, GVF1_0111)
895
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0111)
896
896
  """
897
- return _namespace_GVF1O('GVF1_0111')
897
+ return cls._namespace_GVF1O('GVF1_0111')
898
898
 
899
899
  @classmethod
900
900
  def DNASequence(cls):
901
901
  """Denotes a DNA sequence.
902
- (cls, GVF1_0115)
902
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0115)
903
903
  """
904
- return _namespace_GVF1O('GVF1_0115')
904
+ return cls._namespace_GVF1O('GVF1_0115')
905
905
 
906
906
  @classmethod
907
907
  def RNASequence(cls):
908
908
  """Denotes an RNA sequence.
909
- (cls, GVF1_0116)
909
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0116)
910
910
  """
911
- return _namespace_GVF1O('GVF1_0116')
911
+ return cls._namespace_GVF1O('GVF1_0116')
912
912
 
913
913
  @classmethod
914
914
  def DNAMicroarray(cls):
915
915
  """Denotes a DNA microarray probe.
916
- (cls, GVF1_0117)
916
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0117)
917
917
  """
918
- return _namespace_GVF1O('GVF1_0117')
918
+ return cls._namespace_GVF1O('GVF1_0117')
919
919
 
920
920
  @classmethod
921
921
  def ArrayComparativeGenomicHybridization(cls):
922
922
  """Denotes an array-comparative genomic hybridization.
923
- (cls, GVF1_0118)
923
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0118)
924
924
  """
925
- return _namespace_GVF1O('GVF1_0118')
925
+ return cls._namespace_GVF1O('GVF1_0118')
926
926
 
927
927
  @classmethod
928
928
  def Female(cls):
929
929
  """Denotes that a Set contains features of a female.
930
- (cls, GVF1_0142)
930
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0142)
931
931
  """
932
- return _namespace_GVF1O('GVF1_0142')
932
+ return cls._namespace_GVF1O('GVF1_0142')
933
933
 
934
934
  @classmethod
935
935
  def Male(cls):
936
936
  """Denotes that a Set contains features of a male.
937
- (cls, GVF1_0143)
937
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0143)
938
938
  """
939
- return _namespace_GVF1O('GVF1_0143')
939
+ return cls._namespace_GVF1O('GVF1_0143')
940
940
 
941
941
  @classmethod
942
942
  def Prenatal(cls):
943
943
  """Denotes that a set contains features of prenatal cells.
944
- (cls, GVF1_0144)
944
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0144)
945
945
  """
946
- return _namespace_GVF1O('GVF1_0144')
946
+ return cls._namespace_GVF1O('GVF1_0144')
947
947
 
948
948
  @classmethod
949
949
  def Germline(cls):
950
950
  """Denotes that a set contains features of germline cells.
951
- (cls, GVF1_0145)
951
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0145)
952
952
  """
953
- return _namespace_GVF1O('GVF1_0145')
953
+ return cls._namespace_GVF1O('GVF1_0145')
954
954
 
955
955
  @classmethod
956
956
  def Somatic(cls):
957
957
  """Denotes that a set contains features of somatic cells.
958
- (cls, GVF1_0146)
958
+ (cls, http://www.biointerchange.org/gvf1o#GVF1_0146)
959
959
  """
960
- return _namespace_GVF1O('GVF1_0146')
960
+ return cls._namespace_GVF1O('GVF1_0146')
961
961
 
962
962
  @classmethod
963
963
  def is_object_property(cls, uri):
@@ -965,111 +965,111 @@ class GVF1O:
965
965
 
966
966
  uri -- URI that is tested for being an object property
967
967
  """
968
- if uri == _namespace_GVF1O('GVF1_0004'):
968
+ if uri == cls._namespace_GVF1O('GVF1_0004'):
969
969
  return True
970
- if uri == _namespace_GVF1O('GVF1_0010'):
970
+ if uri == cls._namespace_GVF1O('GVF1_0010'):
971
971
  return True
972
- if uri == _namespace_GVF1O('GVF1_0012'):
972
+ if uri == cls._namespace_GVF1O('GVF1_0012'):
973
973
  return True
974
- if uri == _namespace_GVF1O('GVF1_0014'):
974
+ if uri == cls._namespace_GVF1O('GVF1_0014'):
975
975
  return True
976
- if uri == _namespace_GVF1O('GVF1_0015'):
976
+ if uri == cls._namespace_GVF1O('GVF1_0015'):
977
977
  return True
978
- if uri == _namespace_GVF1O('GVF1_0021'):
978
+ if uri == cls._namespace_GVF1O('GVF1_0021'):
979
979
  return True
980
- if uri == _namespace_GVF1O('GVF1_0023'):
980
+ if uri == cls._namespace_GVF1O('GVF1_0023'):
981
981
  return True
982
- if uri == _namespace_GVF1O('GVF1_0034'):
982
+ if uri == cls._namespace_GVF1O('GVF1_0034'):
983
983
  return True
984
- if uri == _namespace_GVF1O('GVF1_0036'):
984
+ if uri == cls._namespace_GVF1O('GVF1_0036'):
985
985
  return True
986
- if uri == _namespace_GVF1O('GVF1_0038'):
986
+ if uri == cls._namespace_GVF1O('GVF1_0038'):
987
987
  return True
988
- if uri == _namespace_GVF1O('GVF1_0041'):
988
+ if uri == cls._namespace_GVF1O('GVF1_0041'):
989
989
  return True
990
- if uri == _namespace_GVF1O('GVF1_0042'):
990
+ if uri == cls._namespace_GVF1O('GVF1_0042'):
991
991
  return True
992
- if uri == _namespace_GVF1O('GVF1_0043'):
992
+ if uri == cls._namespace_GVF1O('GVF1_0043'):
993
993
  return True
994
- if uri == _namespace_GVF1O('GVF1_0046'):
994
+ if uri == cls._namespace_GVF1O('GVF1_0046'):
995
995
  return True
996
- if uri == _namespace_GVF1O('GVF1_0047'):
996
+ if uri == cls._namespace_GVF1O('GVF1_0047'):
997
997
  return True
998
- if uri == _namespace_GVF1O('GVF1_0051'):
998
+ if uri == cls._namespace_GVF1O('GVF1_0051'):
999
999
  return True
1000
- if uri == _namespace_GVF1O('GVF1_0053'):
1000
+ if uri == cls._namespace_GVF1O('GVF1_0053'):
1001
1001
  return True
1002
- if uri == _namespace_GVF1O('GVF1_0066'):
1002
+ if uri == cls._namespace_GVF1O('GVF1_0066'):
1003
1003
  return True
1004
- if uri == _namespace_GVF1O('GVF1_0067'):
1004
+ if uri == cls._namespace_GVF1O('GVF1_0067'):
1005
1005
  return True
1006
- if uri == _namespace_GVF1O('GVF1_0068'):
1006
+ if uri == cls._namespace_GVF1O('GVF1_0068'):
1007
1007
  return True
1008
- if uri == _namespace_GVF1O('GVF1_0069'):
1008
+ if uri == cls._namespace_GVF1O('GVF1_0069'):
1009
1009
  return True
1010
- if uri == _namespace_GVF1O('GVF1_0070'):
1010
+ if uri == cls._namespace_GVF1O('GVF1_0070'):
1011
1011
  return True
1012
- if uri == _namespace_GVF1O('GVF1_0072'):
1012
+ if uri == cls._namespace_GVF1O('GVF1_0072'):
1013
1013
  return True
1014
- if uri == _namespace_GVF1O('GVF1_0075'):
1014
+ if uri == cls._namespace_GVF1O('GVF1_0075'):
1015
1015
  return True
1016
- if uri == _namespace_GVF1O('GVF1_0078'):
1016
+ if uri == cls._namespace_GVF1O('GVF1_0078'):
1017
1017
  return True
1018
- if uri == _namespace_GVF1O('GVF1_0079'):
1018
+ if uri == cls._namespace_GVF1O('GVF1_0079'):
1019
1019
  return True
1020
- if uri == _namespace_GVF1O('GVF1_0080'):
1020
+ if uri == cls._namespace_GVF1O('GVF1_0080'):
1021
1021
  return True
1022
- if uri == _namespace_GVF1O('GVF1_0083'):
1022
+ if uri == cls._namespace_GVF1O('GVF1_0083'):
1023
1023
  return True
1024
- if uri == _namespace_GVF1O('GVF1_0089'):
1024
+ if uri == cls._namespace_GVF1O('GVF1_0089'):
1025
1025
  return True
1026
- if uri == _namespace_GVF1O('GVF1_0090'):
1026
+ if uri == cls._namespace_GVF1O('GVF1_0090'):
1027
1027
  return True
1028
- if uri == _namespace_GVF1O('GVF1_0091'):
1028
+ if uri == cls._namespace_GVF1O('GVF1_0091'):
1029
1029
  return True
1030
- if uri == _namespace_GVF1O('GVF1_0102'):
1030
+ if uri == cls._namespace_GVF1O('GVF1_0102'):
1031
1031
  return True
1032
- if uri == _namespace_GVF1O('GVF1_0103'):
1032
+ if uri == cls._namespace_GVF1O('GVF1_0103'):
1033
1033
  return True
1034
- if uri == _namespace_GVF1O('GVF1_0104'):
1034
+ if uri == cls._namespace_GVF1O('GVF1_0104'):
1035
1035
  return True
1036
- if uri == _namespace_GVF1O('GVF1_0112'):
1036
+ if uri == cls._namespace_GVF1O('GVF1_0112'):
1037
1037
  return True
1038
- if uri == _namespace_GVF1O('GVF1_0119'):
1038
+ if uri == cls._namespace_GVF1O('GVF1_0119'):
1039
1039
  return True
1040
- if uri == _namespace_GVF1O('GVF1_0120'):
1040
+ if uri == cls._namespace_GVF1O('GVF1_0120'):
1041
1041
  return True
1042
- if uri == _namespace_GVF1O('GVF1_0121'):
1042
+ if uri == cls._namespace_GVF1O('GVF1_0121'):
1043
1043
  return True
1044
- if uri == _namespace_GVF1O('GVF1_0122'):
1044
+ if uri == cls._namespace_GVF1O('GVF1_0122'):
1045
1045
  return True
1046
- if uri == _namespace_GVF1O('GVF1_0123'):
1046
+ if uri == cls._namespace_GVF1O('GVF1_0123'):
1047
1047
  return True
1048
- if uri == _namespace_GVF1O('GVF1_0124'):
1048
+ if uri == cls._namespace_GVF1O('GVF1_0124'):
1049
1049
  return True
1050
- if uri == _namespace_GVF1O('GVF1_0125'):
1050
+ if uri == cls._namespace_GVF1O('GVF1_0125'):
1051
1051
  return True
1052
- if uri == _namespace_GVF1O('GVF1_0126'):
1052
+ if uri == cls._namespace_GVF1O('GVF1_0126'):
1053
1053
  return True
1054
- if uri == _namespace_GVF1O('GVF1_0127'):
1054
+ if uri == cls._namespace_GVF1O('GVF1_0127'):
1055
1055
  return True
1056
- if uri == _namespace_GVF1O('GVF1_0128'):
1056
+ if uri == cls._namespace_GVF1O('GVF1_0128'):
1057
1057
  return True
1058
- if uri == _namespace_GVF1O('GVF1_0129'):
1058
+ if uri == cls._namespace_GVF1O('GVF1_0129'):
1059
1059
  return True
1060
- if uri == _namespace_GVF1O('GVF1_0130'):
1060
+ if uri == cls._namespace_GVF1O('GVF1_0130'):
1061
1061
  return True
1062
- if uri == _namespace_GVF1O('GVF1_0131'):
1062
+ if uri == cls._namespace_GVF1O('GVF1_0131'):
1063
1063
  return True
1064
- if uri == _namespace_GVF1O('GVF1_0147'):
1064
+ if uri == cls._namespace_GVF1O('GVF1_0147'):
1065
1065
  return True
1066
- if uri == _namespace_GVF1O('GVF1_0148'):
1066
+ if uri == cls._namespace_GVF1O('GVF1_0148'):
1067
1067
  return True
1068
- if uri == _namespace_GVF1O('GVF1_0150'):
1068
+ if uri == cls._namespace_GVF1O('GVF1_0150'):
1069
1069
  return True
1070
- if uri == _namespace_GVF1O('GVF1_0152'):
1070
+ if uri == cls._namespace_GVF1O('GVF1_0152'):
1071
1071
  return True
1072
- if uri == _namespace_GVF1O('GVF1_0155'):
1072
+ if uri == cls._namespace_GVF1O('GVF1_0155'):
1073
1073
  return True
1074
1074
  return False
1075
1075
 
@@ -1079,125 +1079,125 @@ class GVF1O:
1079
1079
 
1080
1080
  uri -- URI that is tested for being a datatype property
1081
1081
  """
1082
- if uri == _namespace_GVF1O('GVF1_0005'):
1082
+ if uri == cls._namespace_GVF1O('GVF1_0005'):
1083
1083
  return True
1084
- if uri == _namespace_GVF1O('GVF1_0006'):
1084
+ if uri == cls._namespace_GVF1O('GVF1_0006'):
1085
1085
  return True
1086
- if uri == _namespace_GVF1O('GVF1_0007'):
1086
+ if uri == cls._namespace_GVF1O('GVF1_0007'):
1087
1087
  return True
1088
- if uri == _namespace_GVF1O('GVF1_0008'):
1088
+ if uri == cls._namespace_GVF1O('GVF1_0008'):
1089
1089
  return True
1090
- if uri == _namespace_GVF1O('GVF1_0009'):
1090
+ if uri == cls._namespace_GVF1O('GVF1_0009'):
1091
1091
  return True
1092
- if uri == _namespace_GVF1O('GVF1_0013'):
1092
+ if uri == cls._namespace_GVF1O('GVF1_0013'):
1093
1093
  return True
1094
- if uri == _namespace_GVF1O('GVF1_0022'):
1094
+ if uri == cls._namespace_GVF1O('GVF1_0022'):
1095
1095
  return True
1096
- if uri == _namespace_GVF1O('GVF1_0024'):
1096
+ if uri == cls._namespace_GVF1O('GVF1_0024'):
1097
1097
  return True
1098
- if uri == _namespace_GVF1O('GVF1_0025'):
1098
+ if uri == cls._namespace_GVF1O('GVF1_0025'):
1099
1099
  return True
1100
- if uri == _namespace_GVF1O('GVF1_0026'):
1100
+ if uri == cls._namespace_GVF1O('GVF1_0026'):
1101
1101
  return True
1102
- if uri == _namespace_GVF1O('GVF1_0027'):
1102
+ if uri == cls._namespace_GVF1O('GVF1_0027'):
1103
1103
  return True
1104
- if uri == _namespace_GVF1O('GVF1_0031'):
1104
+ if uri == cls._namespace_GVF1O('GVF1_0031'):
1105
1105
  return True
1106
- if uri == _namespace_GVF1O('GVF1_0032'):
1106
+ if uri == cls._namespace_GVF1O('GVF1_0032'):
1107
1107
  return True
1108
- if uri == _namespace_GVF1O('GVF1_0037'):
1108
+ if uri == cls._namespace_GVF1O('GVF1_0037'):
1109
1109
  return True
1110
- if uri == _namespace_GVF1O('GVF1_0039'):
1110
+ if uri == cls._namespace_GVF1O('GVF1_0039'):
1111
1111
  return True
1112
- if uri == _namespace_GVF1O('GVF1_0044'):
1112
+ if uri == cls._namespace_GVF1O('GVF1_0044'):
1113
1113
  return True
1114
- if uri == _namespace_GVF1O('GVF1_0048'):
1114
+ if uri == cls._namespace_GVF1O('GVF1_0048'):
1115
1115
  return True
1116
- if uri == _namespace_GVF1O('GVF1_0049'):
1116
+ if uri == cls._namespace_GVF1O('GVF1_0049'):
1117
1117
  return True
1118
- if uri == _namespace_GVF1O('GVF1_0050'):
1118
+ if uri == cls._namespace_GVF1O('GVF1_0050'):
1119
1119
  return True
1120
- if uri == _namespace_GVF1O('GVF1_0054'):
1120
+ if uri == cls._namespace_GVF1O('GVF1_0054'):
1121
1121
  return True
1122
- if uri == _namespace_GVF1O('GVF1_0055'):
1122
+ if uri == cls._namespace_GVF1O('GVF1_0055'):
1123
1123
  return True
1124
- if uri == _namespace_GVF1O('GVF1_0056'):
1124
+ if uri == cls._namespace_GVF1O('GVF1_0056'):
1125
1125
  return True
1126
- if uri == _namespace_GVF1O('GVF1_0057'):
1126
+ if uri == cls._namespace_GVF1O('GVF1_0057'):
1127
1127
  return True
1128
- if uri == _namespace_GVF1O('GVF1_0059'):
1128
+ if uri == cls._namespace_GVF1O('GVF1_0059'):
1129
1129
  return True
1130
- if uri == _namespace_GVF1O('GVF1_0060'):
1130
+ if uri == cls._namespace_GVF1O('GVF1_0060'):
1131
1131
  return True
1132
- if uri == _namespace_GVF1O('GVF1_0061'):
1132
+ if uri == cls._namespace_GVF1O('GVF1_0061'):
1133
1133
  return True
1134
- if uri == _namespace_GVF1O('GVF1_0063'):
1134
+ if uri == cls._namespace_GVF1O('GVF1_0063'):
1135
1135
  return True
1136
- if uri == _namespace_GVF1O('GVF1_0064'):
1136
+ if uri == cls._namespace_GVF1O('GVF1_0064'):
1137
1137
  return True
1138
- if uri == _namespace_GVF1O('GVF1_0065'):
1138
+ if uri == cls._namespace_GVF1O('GVF1_0065'):
1139
1139
  return True
1140
- if uri == _namespace_GVF1O('GVF1_0071'):
1140
+ if uri == cls._namespace_GVF1O('GVF1_0071'):
1141
1141
  return True
1142
- if uri == _namespace_GVF1O('GVF1_0073'):
1142
+ if uri == cls._namespace_GVF1O('GVF1_0073'):
1143
1143
  return True
1144
- if uri == _namespace_GVF1O('GVF1_0074'):
1144
+ if uri == cls._namespace_GVF1O('GVF1_0074'):
1145
1145
  return True
1146
- if uri == _namespace_GVF1O('GVF1_0076'):
1146
+ if uri == cls._namespace_GVF1O('GVF1_0076'):
1147
1147
  return True
1148
- if uri == _namespace_GVF1O('GVF1_0077'):
1148
+ if uri == cls._namespace_GVF1O('GVF1_0077'):
1149
1149
  return True
1150
- if uri == _namespace_GVF1O('GVF1_0081'):
1150
+ if uri == cls._namespace_GVF1O('GVF1_0081'):
1151
1151
  return True
1152
- if uri == _namespace_GVF1O('GVF1_0082'):
1152
+ if uri == cls._namespace_GVF1O('GVF1_0082'):
1153
1153
  return True
1154
- if uri == _namespace_GVF1O('GVF1_0092'):
1154
+ if uri == cls._namespace_GVF1O('GVF1_0092'):
1155
1155
  return True
1156
- if uri == _namespace_GVF1O('GVF1_0093'):
1156
+ if uri == cls._namespace_GVF1O('GVF1_0093'):
1157
1157
  return True
1158
- if uri == _namespace_GVF1O('GVF1_0094'):
1158
+ if uri == cls._namespace_GVF1O('GVF1_0094'):
1159
1159
  return True
1160
- if uri == _namespace_GVF1O('GVF1_0095'):
1160
+ if uri == cls._namespace_GVF1O('GVF1_0095'):
1161
1161
  return True
1162
- if uri == _namespace_GVF1O('GVF1_0096'):
1162
+ if uri == cls._namespace_GVF1O('GVF1_0096'):
1163
1163
  return True
1164
- if uri == _namespace_GVF1O('GVF1_0101'):
1164
+ if uri == cls._namespace_GVF1O('GVF1_0101'):
1165
1165
  return True
1166
- if uri == _namespace_GVF1O('GVF1_0105'):
1166
+ if uri == cls._namespace_GVF1O('GVF1_0105'):
1167
1167
  return True
1168
- if uri == _namespace_GVF1O('GVF1_0106'):
1168
+ if uri == cls._namespace_GVF1O('GVF1_0106'):
1169
1169
  return True
1170
- if uri == _namespace_GVF1O('GVF1_0107'):
1170
+ if uri == cls._namespace_GVF1O('GVF1_0107'):
1171
1171
  return True
1172
- if uri == _namespace_GVF1O('GVF1_0108'):
1172
+ if uri == cls._namespace_GVF1O('GVF1_0108'):
1173
1173
  return True
1174
- if uri == _namespace_GVF1O('GVF1_0113'):
1174
+ if uri == cls._namespace_GVF1O('GVF1_0113'):
1175
1175
  return True
1176
- if uri == _namespace_GVF1O('GVF1_0132'):
1176
+ if uri == cls._namespace_GVF1O('GVF1_0132'):
1177
1177
  return True
1178
- if uri == _namespace_GVF1O('GVF1_0133'):
1178
+ if uri == cls._namespace_GVF1O('GVF1_0133'):
1179
1179
  return True
1180
- if uri == _namespace_GVF1O('GVF1_0134'):
1180
+ if uri == cls._namespace_GVF1O('GVF1_0134'):
1181
1181
  return True
1182
- if uri == _namespace_GVF1O('GVF1_0136'):
1182
+ if uri == cls._namespace_GVF1O('GVF1_0136'):
1183
1183
  return True
1184
- if uri == _namespace_GVF1O('GVF1_0137'):
1184
+ if uri == cls._namespace_GVF1O('GVF1_0137'):
1185
1185
  return True
1186
- if uri == _namespace_GVF1O('GVF1_0138'):
1186
+ if uri == cls._namespace_GVF1O('GVF1_0138'):
1187
1187
  return True
1188
- if uri == _namespace_GVF1O('GVF1_0139'):
1188
+ if uri == cls._namespace_GVF1O('GVF1_0139'):
1189
1189
  return True
1190
- if uri == _namespace_GVF1O('GVF1_0149'):
1190
+ if uri == cls._namespace_GVF1O('GVF1_0149'):
1191
1191
  return True
1192
- if uri == _namespace_GVF1O('GVF1_0153'):
1192
+ if uri == cls._namespace_GVF1O('GVF1_0153'):
1193
1193
  return True
1194
- if uri == _namespace_GVF1O('GVF1_0154'):
1194
+ if uri == cls._namespace_GVF1O('GVF1_0154'):
1195
1195
  return True
1196
- if uri == _namespace_GVF1O('GVF1_0156'):
1196
+ if uri == cls._namespace_GVF1O('GVF1_0156'):
1197
1197
  return True
1198
- if uri == _namespace_GVF1O('GVF1_0157'):
1198
+ if uri == cls._namespace_GVF1O('GVF1_0157'):
1199
1199
  return True
1200
- if uri == _namespace_GVF1O('GVF1_0158'):
1200
+ if uri == cls._namespace_GVF1O('GVF1_0158'):
1201
1201
  return True
1202
1202
  return False
1203
1203
 
@@ -1207,49 +1207,49 @@ class GVF1O:
1207
1207
 
1208
1208
  uri -- URI that is tested for being a class
1209
1209
  """
1210
- if uri == _namespace_GVF1O('GVF1_0001'):
1210
+ if uri == cls._namespace_GVF1O('GVF1_0001'):
1211
1211
  return True
1212
- if uri == _namespace_GVF1O('GVF1_0002'):
1212
+ if uri == cls._namespace_GVF1O('GVF1_0002'):
1213
1213
  return True
1214
- if uri == _namespace_GVF1O('GVF1_0003'):
1214
+ if uri == cls._namespace_GVF1O('GVF1_0003'):
1215
1215
  return True
1216
- if uri == _namespace_GVF1O('GVF1_0016'):
1216
+ if uri == cls._namespace_GVF1O('GVF1_0016'):
1217
1217
  return True
1218
- if uri == _namespace_GVF1O('GVF1_0033'):
1218
+ if uri == cls._namespace_GVF1O('GVF1_0033'):
1219
1219
  return True
1220
- if uri == _namespace_GVF1O('GVF1_0035'):
1220
+ if uri == cls._namespace_GVF1O('GVF1_0035'):
1221
1221
  return True
1222
- if uri == _namespace_GVF1O('GVF1_0040'):
1222
+ if uri == cls._namespace_GVF1O('GVF1_0040'):
1223
1223
  return True
1224
- if uri == _namespace_GVF1O('GVF1_0045'):
1224
+ if uri == cls._namespace_GVF1O('GVF1_0045'):
1225
1225
  return True
1226
- if uri == _namespace_GVF1O('GVF1_0052'):
1226
+ if uri == cls._namespace_GVF1O('GVF1_0052'):
1227
1227
  return True
1228
- if uri == _namespace_GVF1O('GVF1_0058'):
1228
+ if uri == cls._namespace_GVF1O('GVF1_0058'):
1229
1229
  return True
1230
- if uri == _namespace_GVF1O('GVF1_0084'):
1230
+ if uri == cls._namespace_GVF1O('GVF1_0084'):
1231
1231
  return True
1232
- if uri == _namespace_GVF1O('GVF1_0088'):
1232
+ if uri == cls._namespace_GVF1O('GVF1_0088'):
1233
1233
  return True
1234
- if uri == _namespace_GVF1O('GVF1_0097'):
1234
+ if uri == cls._namespace_GVF1O('GVF1_0097'):
1235
1235
  return True
1236
- if uri == _namespace_GVF1O('GVF1_0098'):
1236
+ if uri == cls._namespace_GVF1O('GVF1_0098'):
1237
1237
  return True
1238
- if uri == _namespace_GVF1O('GVF1_0099'):
1238
+ if uri == cls._namespace_GVF1O('GVF1_0099'):
1239
1239
  return True
1240
- if uri == _namespace_GVF1O('GVF1_0100'):
1240
+ if uri == cls._namespace_GVF1O('GVF1_0100'):
1241
1241
  return True
1242
- if uri == _namespace_GVF1O('GVF1_0109'):
1242
+ if uri == cls._namespace_GVF1O('GVF1_0109'):
1243
1243
  return True
1244
- if uri == _namespace_GVF1O('GVF1_0114'):
1244
+ if uri == cls._namespace_GVF1O('GVF1_0114'):
1245
1245
  return True
1246
- if uri == _namespace_GVF1O('GVF1_0135'):
1246
+ if uri == cls._namespace_GVF1O('GVF1_0135'):
1247
1247
  return True
1248
- if uri == _namespace_GVF1O('GVF1_0140'):
1248
+ if uri == cls._namespace_GVF1O('GVF1_0140'):
1249
1249
  return True
1250
- if uri == _namespace_GVF1O('GVF1_0141'):
1250
+ if uri == cls._namespace_GVF1O('GVF1_0141'):
1251
1251
  return True
1252
- if uri == _namespace_GVF1O('GVF1_0151'):
1252
+ if uri == cls._namespace_GVF1O('GVF1_0151'):
1253
1253
  return True
1254
1254
  return False
1255
1255
 
@@ -1259,41 +1259,41 @@ class GVF1O:
1259
1259
 
1260
1260
  uri -- URI that is tested for being a named individual
1261
1261
  """
1262
- if uri == _namespace_GVF1O('GVF1_0017'):
1262
+ if uri == cls._namespace_GVF1O('GVF1_0017'):
1263
1263
  return True
1264
- if uri == _namespace_GVF1O('GVF1_0018'):
1264
+ if uri == cls._namespace_GVF1O('GVF1_0018'):
1265
1265
  return True
1266
- if uri == _namespace_GVF1O('GVF1_0019'):
1266
+ if uri == cls._namespace_GVF1O('GVF1_0019'):
1267
1267
  return True
1268
- if uri == _namespace_GVF1O('GVF1_0020'):
1268
+ if uri == cls._namespace_GVF1O('GVF1_0020'):
1269
1269
  return True
1270
- if uri == _namespace_GVF1O('GVF1_0085'):
1270
+ if uri == cls._namespace_GVF1O('GVF1_0085'):
1271
1271
  return True
1272
- if uri == _namespace_GVF1O('GVF1_0086'):
1272
+ if uri == cls._namespace_GVF1O('GVF1_0086'):
1273
1273
  return True
1274
- if uri == _namespace_GVF1O('GVF1_0087'):
1274
+ if uri == cls._namespace_GVF1O('GVF1_0087'):
1275
1275
  return True
1276
- if uri == _namespace_GVF1O('GVF1_0110'):
1276
+ if uri == cls._namespace_GVF1O('GVF1_0110'):
1277
1277
  return True
1278
- if uri == _namespace_GVF1O('GVF1_0111'):
1278
+ if uri == cls._namespace_GVF1O('GVF1_0111'):
1279
1279
  return True
1280
- if uri == _namespace_GVF1O('GVF1_0115'):
1280
+ if uri == cls._namespace_GVF1O('GVF1_0115'):
1281
1281
  return True
1282
- if uri == _namespace_GVF1O('GVF1_0116'):
1282
+ if uri == cls._namespace_GVF1O('GVF1_0116'):
1283
1283
  return True
1284
- if uri == _namespace_GVF1O('GVF1_0117'):
1284
+ if uri == cls._namespace_GVF1O('GVF1_0117'):
1285
1285
  return True
1286
- if uri == _namespace_GVF1O('GVF1_0118'):
1286
+ if uri == cls._namespace_GVF1O('GVF1_0118'):
1287
1287
  return True
1288
- if uri == _namespace_GVF1O('GVF1_0142'):
1288
+ if uri == cls._namespace_GVF1O('GVF1_0142'):
1289
1289
  return True
1290
- if uri == _namespace_GVF1O('GVF1_0143'):
1290
+ if uri == cls._namespace_GVF1O('GVF1_0143'):
1291
1291
  return True
1292
- if uri == _namespace_GVF1O('GVF1_0144'):
1292
+ if uri == cls._namespace_GVF1O('GVF1_0144'):
1293
1293
  return True
1294
- if uri == _namespace_GVF1O('GVF1_0145'):
1294
+ if uri == cls._namespace_GVF1O('GVF1_0145'):
1295
1295
  return True
1296
- if uri == _namespace_GVF1O('GVF1_0146'):
1296
+ if uri == cls._namespace_GVF1O('GVF1_0146'):
1297
1297
  return True
1298
1298
  return False
1299
1299
 
@@ -1319,11 +1319,10 @@ class GVF1O:
1319
1319
  return cls.has_parent(cls.__parent_properties[uri], parent)
1320
1320
  return False
1321
1321
 
1322
- __namespace_GVF1O = Namespace('http://www.biointerchange.org/gvf1o#')
1323
-
1324
- def _namespace_GVF1O(accession):
1325
- return __namespace_GVF1O[accession]
1322
+ @classmethod
1323
+ def _namespace_GVF1O(cls, accession):
1324
+ return Namespace('http://www.biointerchange.org/gvf1o#')[accession]
1326
1325
 
1327
- __parent_properties = { _namespace_GVF1O('GVF1_0004') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0010') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0012') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0014') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0015') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0021') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0023') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0034') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0036') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0038') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0041') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0042') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0043') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0046') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0047') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0051') : _namespace_GVF1O('GVF1_0067') , _namespace_GVF1O('GVF1_0053') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0072') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0078') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0079') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0080') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0083') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0090') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0091') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0102') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0103') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0104') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0119') : _namespace_GVF1O('GVF1_0102') , _namespace_GVF1O('GVF1_0120') : _namespace_GVF1O('GVF1_0103') , _namespace_GVF1O('GVF1_0121') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0122') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0123') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0124') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0125') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0126') : _namespace_GVF1O('GVF1_0070') , _namespace_GVF1O('GVF1_0127') : _namespace_GVF1O('GVF1_0075') , _namespace_GVF1O('GVF1_0129') : _namespace_GVF1O('GVF1_0128') , _namespace_GVF1O('GVF1_0130') : _namespace_GVF1O('GVF1_0089') , _namespace_GVF1O('GVF1_0131') : _namespace_GVF1O('GVF1_0069') , _namespace_GVF1O('GVF1_0147') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0148') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0150') : _namespace_GVF1O('GVF1_0068') , _namespace_GVF1O('GVF1_0152') : _namespace_GVF1O('GVF1_0112') , _namespace_GVF1O('GVF1_0155') : _namespace_GVF1O('GVF1_0066') , _namespace_GVF1O('GVF1_0005') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0006') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0007') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0008') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0009') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0013') : _namespace_GVF1O('GVF1_0064') , _namespace_GVF1O('GVF1_0022') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0024') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0025') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0026') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0027') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0031') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0032') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0037') : _namespace_GVF1O('GVF1_0065') , _namespace_GVF1O('GVF1_0039') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0044') : _namespace_GVF1O('GVF1_0158') , _namespace_GVF1O('GVF1_0048') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0049') : _namespace_GVF1O('GVF1_0061') , _namespace_GVF1O('GVF1_0050') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0054') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0055') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0056') : _namespace_GVF1O('GVF1_0060') , _namespace_GVF1O('GVF1_0057') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0073') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0074') : _namespace_GVF1O('GVF1_0071') , _namespace_GVF1O('GVF1_0076') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0077') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0081') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0082') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0093') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0094') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0095') : _namespace_GVF1O('GVF1_0092') , _namespace_GVF1O('GVF1_0096') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0101') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0105') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0106') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0107') : _namespace_GVF1O('GVF1_0113') , _namespace_GVF1O('GVF1_0108') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0132') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0133') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0134') : _namespace_GVF1O('GVF1_0107') , _namespace_GVF1O('GVF1_0137') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0138') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0139') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0149') : _namespace_GVF1O('GVF1_0063') , _namespace_GVF1O('GVF1_0154') : _namespace_GVF1O('GVF1_0153') , _namespace_GVF1O('GVF1_0156') : _namespace_GVF1O('GVF1_0059') , _namespace_GVF1O('GVF1_0157') : _namespace_GVF1O('GVF1_0136') , _namespace_GVF1O('GVF1_0088') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') , _namespace_GVF1O('GVF1_0151') : _namespace_GVF1O('http://www.w3.org/2002/07/owl#Thing') }
1326
+ __parent_properties = { Namespace('http://www.biointerchange.org/gvf1o#GVF1_0004') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0010') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0012') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0014') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0015') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0021') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0023') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0034') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0036') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0038') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0041') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0042') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0043') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0046') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0047') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0051') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0067') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0053') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0072') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0078') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0079') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0080') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0083') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0090') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0089') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0091') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0089') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0102') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0103') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0104') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0119') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0102') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0120') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0103') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0121') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0122') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0123') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0124') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0125') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0126') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0070') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0127') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0075') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0129') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0128') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0130') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0089') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0131') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0069') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0147') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0148') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0150') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0068') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0152') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0112') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0155') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0066') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0005') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0006') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0007') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0008') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0009') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0013') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0064') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0022') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0063') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0024') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0063') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0025') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0060') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0026') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0027') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , Namespace('http://www.biointerchange.org/gvf1o#GVF1_0031') : Namespace('http://www.biointerchange.org/gvf1o#GVF1_0059') , 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