biointerchange 0.1.3 → 0.2.0

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 (30) hide show
  1. data/README.md +17 -0
  2. data/VERSION +1 -1
  3. data/generators/GOxrefify.rb +41 -0
  4. data/generators/rdfxml.rb +6 -4
  5. data/lib/biointerchange/core.rb +94 -20
  6. data/lib/biointerchange/genomics/gff3_feature_set.rb +11 -3
  7. data/lib/biointerchange/genomics/gff3_pragmas.rb +3 -3
  8. data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb +217 -12
  9. data/lib/biointerchange/genomics/gff3_reader.rb +78 -20
  10. data/lib/biointerchange/genomics/gvf_reader.rb +9 -3
  11. data/lib/biointerchange/gff3o.rb +69 -55
  12. data/lib/biointerchange/goxref.rb +867 -0
  13. data/lib/biointerchange/gvf1o.rb +546 -82
  14. data/lib/biointerchange/textmining/text_mining_reader.rb +9 -0
  15. data/spec/gff3_rdfwriter_spec.rb +1 -1
  16. data/spec/gvf_rdfwriter_spec.rb +1 -1
  17. data/spec/text_mining_pdfx_xml_reader_spec.rb +3 -0
  18. data/spec/text_mining_pubannos_json_reader_spec.rb +4 -1
  19. data/supplemental/java/biointerchange/pom.xml +1 -1
  20. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java +93 -125
  21. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java +304 -205
  22. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java +4044 -4290
  23. data/supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java +3 -3
  24. data/supplemental/python/biointerchange/gff3o.py +1 -89
  25. data/supplemental/python/biointerchange/gvf1o.py +129 -147
  26. data/supplemental/python/biointerchange/sio.py +817 -46
  27. data/supplemental/python/biointerchange/sofa.py +543 -543
  28. data/supplemental/python/setup.py +1 -1
  29. data/web/ontologies.html +1 -3
  30. metadata +7 -2
@@ -2,6 +2,22 @@ module BioInterchange
2
2
 
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  class GVF1O
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4
 
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+ # Either:
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+ # Establishes the landmark (e.g. a chromosome) on which a feature is located.
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+ # (http://www.biointerchange.org/gvf1o#GVF1_0004)
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+ # Or:
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+ # Link to the landmark that establishes the coordinate system for the breakpoint.
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+ # (http://www.biointerchange.org/gvf1o#GVF1_0072)
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+ def self.seqid
12
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') ]
13
+ end
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+
15
+ # Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
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+ # (http://www.biointerchange.org/gvf1o#GVF1_0006)
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+ def self.type
18
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
19
+ end
20
+
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  # Either:
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22
  # Strand of the feature.
7
23
  # (http://www.biointerchange.org/gvf1o#GVF1_0010)
@@ -15,10 +31,14 @@ class GVF1O
15
31
  return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') ]
16
32
  end
17
33
 
18
- # Tag name/value pair attributes of a feature.
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- # (http://www.biointerchange.org/gvf1o#GVF1_0012)
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+ # Either:
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+ # Tag name/value pair attributes of a feature.
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+ # (http://www.biointerchange.org/gvf1o#GVF1_0012)
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+ # Or:
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+ # Tag name/value pair attributes that are not captured by the GVF specification.
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+ # (http://www.biointerchange.org/gvf1o#GVF1_0152)
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  def self.attributes
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- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012')
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+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') ]
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42
  end
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43
 
24
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  # Link out to the parent feature.
@@ -90,7 +110,7 @@ class GVF1O
90
110
 
91
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  # Features that are affected by this sequence alteration effect.
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  # (http://www.biointerchange.org/gvf1o#GVF1_0044)
93
- def self.feature_id
113
+ def self.feature
94
114
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
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  end
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116
 
@@ -174,10 +194,14 @@ class GVF1O
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  return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') ]
175
195
  end
176
196
 
177
- # A database cross-reference to associate a sequence alteration to its representation in another database.
178
- # (http://www.biointerchange.org/gvf1o#GVF1_0078)
197
+ # Either:
198
+ # A database cross-reference to associate a sequence alteration to its representation in another database.
199
+ # (http://www.biointerchange.org/gvf1o#GVF1_0078)
200
+ # Or:
201
+ # A database cross-reference to associate a structured pragma to a representation in another database.
202
+ # (http://www.biointerchange.org/gvf1o#GVF1_0104)
179
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  def self.dbxref
180
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078')
204
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0104') ]
181
205
  end
182
206
 
183
207
  # Potential source or destination of zero-length sequence alterations.
@@ -196,14 +220,125 @@ class GVF1O
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  return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') ]
197
221
  end
198
222
 
223
+ # A cross-reference to an ontology term that is associated with a feature.
224
+ # (http://www.biointerchange.org/gvf1o#GVF1_0096)
225
+ def self.ontology_term
226
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096')
227
+ end
228
+
199
229
  # Either:
200
- # ID of the landmark that establishes the coordinate system for a feature.
201
- # (http://www.biointerchange.org/gvf1o#GVF1_0004)
230
+ # Properties that are directly associated with TechnologyPlatform class instances.
231
+ # (http://www.biointerchange.org/gvf1o#GVF1_0102)
202
232
  # Or:
203
- # ID of the landmark that establishes the coordinate system for a breakpoint.
204
- # (http://www.biointerchange.org/gvf1o#GVF1_0072)
205
- def self.seqid
206
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') ]
233
+ # Properties that are directly associated with TechnologyPlatform class instances.
234
+ # (http://www.biointerchange.org/gvf1o#GVF1_0107)
235
+ def self.technologyplatform_properties
236
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') ]
237
+ end
238
+
239
+ # Properties that are directly associated with DataSource class instances.
240
+ # (http://www.biointerchange.org/gvf1o#GVF1_0103)
241
+ def self.datasource_properties
242
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103')
243
+ end
244
+
245
+ # Either:
246
+ # Properties describing structured pragma properties.
247
+ # (http://www.biointerchange.org/gvf1o#GVF1_0112)
248
+ # Or:
249
+ # Properties describing structured pragma properties.
250
+ # (http://www.biointerchange.org/gvf1o#GVF1_0113)
251
+ def self.structuredpragma_properties
252
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0113') ]
253
+ end
254
+
255
+ # Types of reads produced by the platform.
256
+ # (http://www.biointerchange.org/gvf1o#GVF1_0119)
257
+ def self.read_type
258
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0119')
259
+ end
260
+
261
+ # Datatype of this data source.
262
+ # (http://www.biointerchange.org/gvf1o#GVF1_0120)
263
+ def self.data_type
264
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0120')
265
+ end
266
+
267
+ # Technology platform that was used to derive the feature.
268
+ # (http://www.biointerchange.org/gvf1o#GVF1_0121)
269
+ def self.technology_platform
270
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0121')
271
+ end
272
+
273
+ # Data source origin of the feature.
274
+ # (http://www.biointerchange.org/gvf1o#GVF1_0122)
275
+ def self.data_source
276
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0122')
277
+ end
278
+
279
+ # Used scoring method.
280
+ # (http://www.biointerchange.org/gvf1o#GVF1_0123)
281
+ def self.score_method
282
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0123')
283
+ end
284
+
285
+ # Further information about the algorithm/methodologies used.
286
+ # (http://www.biointerchange.org/gvf1o#GVF1_0124)
287
+ def self.source_method
288
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0124')
289
+ end
290
+
291
+ # Further information about an individual's phenotype. Applies only to single individual sets.
292
+ # (http://www.biointerchange.org/gvf1o#GVF1_0125)
293
+ def self.phenotype_description
294
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0125')
295
+ end
296
+
297
+ # Either:
298
+ # Further information about the associated attribute(s).
299
+ # (http://www.biointerchange.org/gvf1o#GVF1_0126)
300
+ # Or:
301
+ # Further information about the associated attribute(s).
302
+ # (http://www.biointerchange.org/gvf1o#GVF1_0127)
303
+ # Or:
304
+ # Further information about the associated attribute(s).
305
+ # (http://www.biointerchange.org/gvf1o#GVF1_0129)
306
+ # Or:
307
+ # Further information about the associated attribute(s).
308
+ # (http://www.biointerchange.org/gvf1o#GVF1_0130)
309
+ # Or:
310
+ # Further information about the associated attribute(s).
311
+ # (http://www.biointerchange.org/gvf1o#GVF1_0131)
312
+ def self.attribute_method
313
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0126'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0127'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0129'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0130'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0131') ]
314
+ end
315
+
316
+ # Either:
317
+ # Properties about Attribute instances.
318
+ # (http://www.biointerchange.org/gvf1o#GVF1_0128)
319
+ # Or:
320
+ # Properties that are directly associated with Attribute class instances.
321
+ # (http://www.biointerchange.org/gvf1o#GVF1_0064)
322
+ def self.attribute_properties
323
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0128'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') ]
324
+ end
325
+
326
+ # Denotes the sex of the sequenced individual for single-individual sets.
327
+ # (http://www.biointerchange.org/gvf1o#GVF1_0147)
328
+ def self.sex
329
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0147')
330
+ end
331
+
332
+ # Denotes the source of genomic data (on a cell-type level).
333
+ # (http://www.biointerchange.org/gvf1o#GVF1_0148)
334
+ def self.genomic_source
335
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0148')
336
+ end
337
+
338
+ # 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.
339
+ # (http://www.biointerchange.org/gvf1o#GVF1_0150)
340
+ def self.feature_ontology
341
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150')
207
342
  end
208
343
 
209
344
  # 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.
@@ -212,12 +347,6 @@ class GVF1O
212
347
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005')
213
348
  end
214
349
 
215
- # Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
216
- # (http://www.biointerchange.org/gvf1o#GVF1_0006)
217
- def self.type
218
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
219
- end
220
-
221
350
  # Either:
222
351
  # Start coordinate of the feature on the seqid landmark.
223
352
  # (http://www.biointerchange.org/gvf1o#GVF1_0007)
@@ -230,8 +359,11 @@ class GVF1O
230
359
  # Or:
231
360
  # Start coordinate of the target.
232
361
  # (http://www.biointerchange.org/gvf1o#GVF1_0094)
362
+ # Or:
363
+ # Genomic start coordinate of the landmark.
364
+ # (http://www.biointerchange.org/gvf1o#GVF1_0138)
233
365
  def self.start
234
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') ]
366
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0138') ]
235
367
  end
236
368
 
237
369
  # Either:
@@ -246,8 +378,11 @@ class GVF1O
246
378
  # Or:
247
379
  # End coordinate of the target.
248
380
  # (http://www.biointerchange.org/gvf1o#GVF1_0095)
381
+ # Or:
382
+ # Genomic end coordinate of the landmark.
383
+ # (http://www.biointerchange.org/gvf1o#GVF1_0139)
249
384
  def self.end
250
- return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') ]
385
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0139') ]
251
386
  end
252
387
 
253
388
  # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
@@ -256,10 +391,14 @@ class GVF1O
256
391
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009')
257
392
  end
258
393
 
259
- # Tag name of a feature attribute.
260
- # (http://www.biointerchange.org/gvf1o#GVF1_0013)
394
+ # Either:
395
+ # Tag name of a feature attribute.
396
+ # (http://www.biointerchange.org/gvf1o#GVF1_0013)
397
+ # Or:
398
+ # Tag name of an user defined structured attribute.
399
+ # (http://www.biointerchange.org/gvf1o#GVF1_0154)
261
400
  def self.tag
262
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013')
401
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0154') ]
263
402
  end
264
403
 
265
404
  # Version of the GVF specification that defines the feature set contents.
@@ -280,10 +419,14 @@ class GVF1O
280
419
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025')
281
420
  end
282
421
 
283
- # A unique identifier for the feature within the feature set.
284
- # (http://www.biointerchange.org/gvf1o#GVF1_0026)
422
+ # Either:
423
+ # A unique identifier for the feature within the feature set.
424
+ # (http://www.biointerchange.org/gvf1o#GVF1_0026)
425
+ # Or:
426
+ # ID that uniquely establishes the Landmark's identity within a Set.
427
+ # (http://www.biointerchange.org/gvf1o#GVF1_0137)
285
428
  def self.id
286
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026')
429
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0137') ]
287
430
  end
288
431
 
289
432
  # Secondary name of a feature, which can be HGVS/ISCN nomenclature names, but not cross-references to databases (e.g. dbSNP, OMIM) which should use the dbxref property.
@@ -292,18 +435,6 @@ class GVF1O
292
435
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027')
293
436
  end
294
437
 
295
- # Name of an external database. For example, "dbSNP" or "OMIM".
296
- # (http://www.biointerchange.org/gvf1o#GVF1_0029)
297
- def self.name
298
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029')
299
- end
300
-
301
- # External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
302
- # (http://www.biointerchange.org/gvf1o#GVF1_0030)
303
- def self.xref
304
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030')
305
- end
306
-
307
438
  # Sequence from the reference genome.
308
439
  # (http://www.biointerchange.org/gvf1o#GVF1_0031)
309
440
  def self.reference_seq
@@ -328,10 +459,14 @@ class GVF1O
328
459
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039')
329
460
  end
330
461
 
331
- # Unclear from GVF specification.
332
- # (http://www.biointerchange.org/gvf1o#GVF1_0050)
462
+ # Either:
463
+ # Unclear from GVF specification.
464
+ # (http://www.biointerchange.org/gvf1o#GVF1_0050)
465
+ # Or:
466
+ # Indicates whether this particular is phased. Used to encode ##phased-genotypes statements.
467
+ # (http://www.biointerchange.org/gvf1o#GVF1_0101)
333
468
  def self.phased
334
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050')
469
+ return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0101') ]
335
470
  end
336
471
 
337
472
  # Describes the codon that overlaps this variant.
@@ -364,18 +499,6 @@ class GVF1O
364
499
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061')
365
500
  end
366
501
 
367
- # Properties that are directly associated with DBXRef class instances.
368
- # (http://www.biointerchange.org/gvf1o#GVF1_0062)
369
- def self.dbxref_properties
370
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062')
371
- end
372
-
373
- # Properties that are directly associated with Attribute class instances.
374
- # (http://www.biointerchange.org/gvf1o#GVF1_0064)
375
- def self.attribute_properties
376
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064')
377
- end
378
-
379
502
  # Sequence context (positive strand) of a feature on the 5' end.
380
503
  # (http://www.biointerchange.org/gvf1o#GVF1_0076)
381
504
  def self.a_context
@@ -400,6 +523,60 @@ class GVF1O
400
523
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093')
401
524
  end
402
525
 
526
+ # An arbitrary comment. Free text.
527
+ # (http://www.biointerchange.org/gvf1o#GVF1_0105)
528
+ def self.comment
529
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0105')
530
+ end
531
+
532
+ # Type of technology used to gather the variant data. Unrestricted range due to open specification.
533
+ # (http://www.biointerchange.org/gvf1o#GVF1_0106)
534
+ def self.platform_class
535
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0106')
536
+ end
537
+
538
+ # Sequencer or other machine used to collect the variant data. Unrestricted range due to open specification.
539
+ # (http://www.biointerchange.org/gvf1o#GVF1_0108)
540
+ def self.platform_name
541
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0108')
542
+ end
543
+
544
+ # Undocumented in GVF specification.
545
+ # (http://www.biointerchange.org/gvf1o#GVF1_0132)
546
+ def self.read_length
547
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0132')
548
+ end
549
+
550
+ # Undocumented in GVF specification.
551
+ # (http://www.biointerchange.org/gvf1o#GVF1_0133)
552
+ def self.read_pair_span
553
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0133')
554
+ end
555
+
556
+ # Undocumented in GVF specification.
557
+ # (http://www.biointerchange.org/gvf1o#GVF1_0134)
558
+ def self.average_coverage
559
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0134')
560
+ end
561
+
562
+ # Properties that are directly associated with Landmark class instances.
563
+ # (http://www.biointerchange.org/gvf1o#GVF1_0136)
564
+ def self.landmark_properties
565
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136')
566
+ end
567
+
568
+ # Version of the GVF file that this set stems from.
569
+ # (http://www.biointerchange.org/gvf1o#GVF1_0149)
570
+ def self.file_version
571
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0149')
572
+ end
573
+
574
+ # Properties that are directly associated with StructuredAttribute class instances.
575
+ # (http://www.biointerchange.org/gvf1o#GVF1_0153)
576
+ def self.structuredattribute_properties
577
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0153')
578
+ end
579
+
403
580
  # Set of genomic sequence features, whose identifiers are unique within the set.
404
581
  # (http://www.biointerchange.org/gvf1o#GVF1_0001)
405
582
  def self.Set
@@ -412,6 +589,8 @@ class GVF1O
412
589
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0002')
413
590
  end
414
591
 
592
+ # Representation of attribute tag/value pairs that are not covered by specific classes such as Effect or Variant.
593
+ # (http://www.biointerchange.org/gvf1o#GVF1_0003)
415
594
  def self.Attribute
416
595
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0003')
417
596
  end
@@ -422,12 +601,6 @@ class GVF1O
422
601
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0016')
423
602
  end
424
603
 
425
- # A class describing relationships between features and external databases.
426
- # (http://www.biointerchange.org/gvf1o#GVF1_0028)
427
- def self.DBXRef
428
- return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0028')
429
- end
430
-
431
604
  # Describing specific alterations of a feature.
432
605
  # (http://www.biointerchange.org/gvf1o#GVF1_0033)
433
606
  def self.Variant
@@ -476,6 +649,66 @@ class GVF1O
476
649
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088')
477
650
  end
478
651
 
652
+ # Details about the sequencing/microarray technology used to gather the data in a set.
653
+ # (http://www.biointerchange.org/gvf1o#GVF1_0097)
654
+ def self.TechnologyPlatform
655
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0097')
656
+ end
657
+
658
+ # 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.
659
+ # (http://www.biointerchange.org/gvf1o#GVF1_0098)
660
+ def self.DataSource
661
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0098')
662
+ end
663
+
664
+ # Information about the used scoring algorithm or method.
665
+ # (http://www.biointerchange.org/gvf1o#GVF1_0099)
666
+ def self.Method
667
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0099')
668
+ end
669
+
670
+ # Additional information about an individual's phenotype.
671
+ # (http://www.biointerchange.org/gvf1o#GVF1_0100)
672
+ def self.PhenotypeDescription
673
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0100')
674
+ end
675
+
676
+ # Type of reads obtained for a given technology platform.
677
+ # (http://www.biointerchange.org/gvf1o#GVF1_0109)
678
+ def self.ReadType
679
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0109')
680
+ end
681
+
682
+ # Determines the datatype of a variant sequence.
683
+ # (http://www.biointerchange.org/gvf1o#GVF1_0114)
684
+ def self.DataType
685
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0114')
686
+ end
687
+
688
+ # A landmark that establishes the coordinate system for features.
689
+ # (http://www.biointerchange.org/gvf1o#GVF1_0135)
690
+ def self.Landmark
691
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0135')
692
+ end
693
+
694
+ # For single individual sets, the Sex class' OWL-individuals can be used to specify the sex of the sequenced (real-life) individuals.
695
+ # (http://www.biointerchange.org/gvf1o#GVF1_0140)
696
+ def self.Sex
697
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0140')
698
+ end
699
+
700
+ # An enumerated class for determining the genomic source (cell type) of sequenced data.
701
+ # (http://www.biointerchange.org/gvf1o#GVF1_0141)
702
+ def self.GenomicSource
703
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0141')
704
+ end
705
+
706
+ # Representation of attribute tag/value pairs that are specific to particular structured attributes, but which are not covered by the GVF specification.
707
+ # (http://www.biointerchange.org/gvf1o#GVF1_0151)
708
+ def self.StructuredAttribute
709
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0151')
710
+ end
711
+
479
712
  # Location on the positive (forward) strand.
480
713
  # (http://www.biointerchange.org/gvf1o#GVF1_0017)
481
714
  def self.Positive
@@ -518,10 +751,82 @@ class GVF1O
518
751
  return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087')
519
752
  end
520
753
 
754
+ # Denotes reads that are fragments.
755
+ # (http://www.biointerchange.org/gvf1o#GVF1_0110)
756
+ def self.Fragment
757
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0110')
758
+ end
759
+
760
+ # Denotes reads that are pairs.
761
+ # (http://www.biointerchange.org/gvf1o#GVF1_0111)
762
+ def self.Pair
763
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0111')
764
+ end
765
+
766
+ # Denotes a DNA sequence.
767
+ # (http://www.biointerchange.org/gvf1o#GVF1_0115)
768
+ def self.DNASequence
769
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0115')
770
+ end
771
+
772
+ # Denotes an RNA sequence.
773
+ # (http://www.biointerchange.org/gvf1o#GVF1_0116)
774
+ def self.RNASequence
775
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0116')
776
+ end
777
+
778
+ # Denotes a DNA microarray probe.
779
+ # (http://www.biointerchange.org/gvf1o#GVF1_0117)
780
+ def self.DNAMicroarray
781
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0117')
782
+ end
783
+
784
+ # Denotes an array-comparative genomic hybridization.
785
+ # (http://www.biointerchange.org/gvf1o#GVF1_0118)
786
+ def self.ArrayComparativeGenomicHybridization
787
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0118')
788
+ end
789
+
790
+ # Denotes that a Set contains features of a female.
791
+ # (http://www.biointerchange.org/gvf1o#GVF1_0142)
792
+ def self.Female
793
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0142')
794
+ end
795
+
796
+ # Denotes that a Set contains features of a male.
797
+ # (http://www.biointerchange.org/gvf1o#GVF1_0143)
798
+ def self.Male
799
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0143')
800
+ end
801
+
802
+ # Denotes that a set contains features of prenatal cells.
803
+ # (http://www.biointerchange.org/gvf1o#GVF1_0144)
804
+ def self.Prenatal
805
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0144')
806
+ end
807
+
808
+ # Denotes that a set contains features of germline cells.
809
+ # (http://www.biointerchange.org/gvf1o#GVF1_0145)
810
+ def self.Germline
811
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0145')
812
+ end
813
+
814
+ # Denotes that a set contains features of somatic cells.
815
+ # (http://www.biointerchange.org/gvf1o#GVF1_0146)
816
+ def self.Somatic
817
+ return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0146')
818
+ end
819
+
521
820
  # Determines whether the given URI is an object property.
522
821
  #
523
822
  # +uri+:: URI that is tested for being an object property
524
823
  def self.is_object_property?(uri)
824
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') then
825
+ return true
826
+ end
827
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
828
+ return true
829
+ end
525
830
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') then
526
831
  return true
527
832
  end
@@ -588,6 +893,9 @@ class GVF1O
588
893
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') then
589
894
  return true
590
895
  end
896
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') then
897
+ return true
898
+ end
591
899
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') then
592
900
  return true
593
901
  end
@@ -612,6 +920,72 @@ class GVF1O
612
920
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') then
613
921
  return true
614
922
  end
923
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') then
924
+ return true
925
+ end
926
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') then
927
+ return true
928
+ end
929
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103') then
930
+ return true
931
+ end
932
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0104') then
933
+ return true
934
+ end
935
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') then
936
+ return true
937
+ end
938
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0119') then
939
+ return true
940
+ end
941
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0120') then
942
+ return true
943
+ end
944
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0121') then
945
+ return true
946
+ end
947
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0122') then
948
+ return true
949
+ end
950
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0123') then
951
+ return true
952
+ end
953
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0124') then
954
+ return true
955
+ end
956
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0125') then
957
+ return true
958
+ end
959
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0126') then
960
+ return true
961
+ end
962
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0127') then
963
+ return true
964
+ end
965
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0128') then
966
+ return true
967
+ end
968
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0129') then
969
+ return true
970
+ end
971
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0130') then
972
+ return true
973
+ end
974
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0131') then
975
+ return true
976
+ end
977
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0147') then
978
+ return true
979
+ end
980
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0148') then
981
+ return true
982
+ end
983
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150') then
984
+ return true
985
+ end
986
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') then
987
+ return true
988
+ end
615
989
  return false
616
990
  end
617
991
 
@@ -619,15 +993,9 @@ class GVF1O
619
993
  #
620
994
  # +uri+:: URI that is tested for being a datatype property
621
995
  def self.is_datatype_property?(uri)
622
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') then
623
- return true
624
- end
625
996
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') then
626
997
  return true
627
998
  end
628
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
629
- return true
630
- end
631
999
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') then
632
1000
  return true
633
1001
  end
@@ -655,12 +1023,6 @@ class GVF1O
655
1023
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') then
656
1024
  return true
657
1025
  end
658
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029') then
659
- return true
660
- end
661
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') then
662
- return true
663
- end
664
1026
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') then
665
1027
  return true
666
1028
  end
@@ -703,9 +1065,6 @@ class GVF1O
703
1065
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') then
704
1066
  return true
705
1067
  end
706
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') then
707
- return true
708
- end
709
1068
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') then
710
1069
  return true
711
1070
  end
@@ -718,9 +1077,6 @@ class GVF1O
718
1077
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') then
719
1078
  return true
720
1079
  end
721
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') then
722
- return true
723
- end
724
1080
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') then
725
1081
  return true
726
1082
  end
@@ -751,6 +1107,54 @@ class GVF1O
751
1107
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') then
752
1108
  return true
753
1109
  end
1110
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0101') then
1111
+ return true
1112
+ end
1113
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0105') then
1114
+ return true
1115
+ end
1116
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0106') then
1117
+ return true
1118
+ end
1119
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0107') then
1120
+ return true
1121
+ end
1122
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0108') then
1123
+ return true
1124
+ end
1125
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0113') then
1126
+ return true
1127
+ end
1128
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0132') then
1129
+ return true
1130
+ end
1131
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0133') then
1132
+ return true
1133
+ end
1134
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0134') then
1135
+ return true
1136
+ end
1137
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0136') then
1138
+ return true
1139
+ end
1140
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0137') then
1141
+ return true
1142
+ end
1143
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0138') then
1144
+ return true
1145
+ end
1146
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0139') then
1147
+ return true
1148
+ end
1149
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0149') then
1150
+ return true
1151
+ end
1152
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0153') then
1153
+ return true
1154
+ end
1155
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0154') then
1156
+ return true
1157
+ end
754
1158
  return false
755
1159
  end
756
1160
 
@@ -770,9 +1174,6 @@ class GVF1O
770
1174
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0016') then
771
1175
  return true
772
1176
  end
773
- if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0028') then
774
- return true
775
- end
776
1177
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0033') then
777
1178
  return true
778
1179
  end
@@ -797,6 +1198,36 @@ class GVF1O
797
1198
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') then
798
1199
  return true
799
1200
  end
1201
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0097') then
1202
+ return true
1203
+ end
1204
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0098') then
1205
+ return true
1206
+ end
1207
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0099') then
1208
+ return true
1209
+ end
1210
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0100') then
1211
+ return true
1212
+ end
1213
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0109') then
1214
+ return true
1215
+ end
1216
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0114') then
1217
+ return true
1218
+ end
1219
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0135') then
1220
+ return true
1221
+ end
1222
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0140') then
1223
+ return true
1224
+ end
1225
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0141') then
1226
+ return true
1227
+ end
1228
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0151') then
1229
+ return true
1230
+ end
800
1231
  return false
801
1232
  end
802
1233
 
@@ -825,6 +1256,39 @@ class GVF1O
825
1256
  if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087') then
826
1257
  return true
827
1258
  end
1259
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0110') then
1260
+ return true
1261
+ end
1262
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0111') then
1263
+ return true
1264
+ end
1265
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0115') then
1266
+ return true
1267
+ end
1268
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0116') then
1269
+ return true
1270
+ end
1271
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0117') then
1272
+ return true
1273
+ end
1274
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0118') then
1275
+ return true
1276
+ end
1277
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0142') then
1278
+ return true
1279
+ end
1280
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0143') then
1281
+ return true
1282
+ end
1283
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0144') then
1284
+ return true
1285
+ end
1286
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0145') then
1287
+ return true
1288
+ end
1289
+ if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0146') then
1290
+ return true
1291
+ end
828
1292
  return false
829
1293
  end
830
1294
 
@@ -851,7 +1315,7 @@ class GVF1O
851
1315
  end
852
1316
 
853
1317
  private
854
- @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') => RDF::URI.new('http://www.w3.org/2002/07/owl#Thing') }
1318
+ @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0104') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0119') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0120') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0103') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0121') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0122') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0123') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0124') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0125') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0126') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0127') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0129') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0128') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0130') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0131') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0147') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0148') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0112') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') => 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855
1319
 
856
1320
  end
857
1321