biointerchange 1.0.2 → 1.0.4

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Files changed (11) hide show
  1. checksums.yaml +4 -4
  2. data/VERSION +1 -1
  3. data/generators/rdfxml.rb +3 -1
  4. data/lib/biointerchange/core.rb +3 -1
  5. data/lib/biointerchange/so.rb +3001 -2200
  6. data/lib/biointerchange/sofa.rb +641 -286
  7. data/lib/biointerchange/writer.rb +4 -0
  8. data/spec/gff3_rdfwriter_spec.rb +2 -2
  9. data/spec/gvf_rdfwriter_spec.rb +2 -2
  10. data/web/ontologies.html +390 -193
  11. metadata +3 -3
data/lib/biointerchange/sofa.rb CHANGED
@@ -2,581 +2,825 @@ module BioInterchange
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2
 
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3
  class SOFA
4
4
 
5
+ # Either:
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+ # Example: amino_acid part_of polypeptide.
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+ # (http://purl.obolibrary.org/obo/part_of)
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+ # Or:
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+ # X part_of Y if X is a subregion of Y.
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+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#part_of)
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+ def self.part_of
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+ return [ RDF::URI.new('http://purl.obolibrary.org/obo/part_of'), RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#part_of') ]
13
+ end
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+
15
+ # A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
16
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to)
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17
  def self.adjacent_to
6
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:adjacent_to')
18
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to')
19
+ end
20
+
21
+ # This relationship is vague and up for discussion.
22
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with)
23
+ def self.associated_with
24
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with')
7
25
  end
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26
 
27
+ # B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
28
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature)
9
29
  def self.complete_evidence_for_feature
10
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature')
30
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature')
11
31
  end
12
32
 
33
+ # X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
34
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on)
35
+ def self.connects_on
36
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on')
37
+ end
38
+
39
+ # X contained_by Y iff X starts after start of Y and X ends before end of Y.
40
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by)
13
41
  def self.contained_by
14
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contained_by')
42
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by')
15
43
  end
16
44
 
45
+ # The inverse of contained_by.
46
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains)
17
47
  def self.contains
18
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contains')
48
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains')
19
49
  end
20
50
 
51
+ # -- No comment or description provided. --
52
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from)
21
53
  def self.derives_from
22
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:derives_from')
54
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from')
55
+ end
56
+
57
+ # X is disconnected_from Y iff it is not the case that X overlaps Y.
58
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from)
59
+ def self.disconnected_from
60
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from')
23
61
  end
24
62
 
63
+ # -- No comment or description provided. --
64
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from)
65
+ def self.edited_from
66
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from')
67
+ end
68
+
69
+ # -- No comment or description provided. --
70
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to)
71
+ def self.edited_to
72
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to')
73
+ end
74
+
75
+ # B is evidence_for_feature A, if an instance of B supports the existence of A.
76
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature)
25
77
  def self.evidence_for_feature
26
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature')
78
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature')
27
79
  end
28
80
 
81
+ # X is exemplar of Y if X is the best evidence for Y.
82
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of)
83
+ def self.exemplar_of
84
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of')
85
+ end
86
+
87
+ # Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
88
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by)
89
+ def self.finished_by
90
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by')
91
+ end
92
+
93
+ # X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
94
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes)
95
+ def self.finishes
96
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes')
97
+ end
98
+
99
+ # X gained Y if X is a variant_of X' and Y part of X but not X'.
100
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained)
101
+ def self.gained
102
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained')
103
+ end
104
+
105
+ # -- No comment or description provided. --
106
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of)
107
+ def self.genome_of
108
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of')
109
+ end
110
+
111
+ # -- No comment or description provided. --
112
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by)
113
+ def self.guided_by
114
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by')
115
+ end
116
+
117
+ # -- No comment or description provided. --
118
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides)
119
+ def self.guides
120
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides')
121
+ end
122
+
123
+ # X has_integral_part Y if and only if: X has_part Y and Y part_of X.
124
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part)
29
125
  def self.has_integral_part
30
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part')
126
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part')
31
127
  end
32
128
 
129
+ # -- No comment or description provided. --
130
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin)
131
+ def self.has_origin
132
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin')
133
+ end
134
+
135
+ # Inverse of part_of.
136
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part)
33
137
  def self.has_part
34
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part')
138
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part')
139
+ end
140
+
141
+ # The relationship between a feature and an attribute.
142
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality)
143
+ def self.has_quality
144
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality')
35
145
  end
36
146
 
147
+ # -- No comment or description provided. --
148
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to)
37
149
  def self.homologous_to
38
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to')
150
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to')
39
151
  end
40
152
 
153
+ # X integral_part_of Y if and only if: X part_of Y and Y has_part X.
154
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of)
41
155
  def self.integral_part_of
42
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of')
156
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of')
157
+ end
158
+
159
+ # R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
160
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of)
161
+ def self.is_consecutive_sequence_of
162
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of')
163
+ end
164
+
165
+ # X lost Y if X is a variant_of X' and Y part of X' but not X.
166
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost)
167
+ def self.lost
168
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost')
43
169
  end
44
170
 
171
+ # A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
172
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps)
173
+ def self.maximally_overlaps
174
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps')
175
+ end
176
+
177
+ # A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
178
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of)
45
179
  def self.member_of
46
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of')
180
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of')
47
181
  end
48
182
 
183
+ # A relationship between a pseudogenic feature and its functional ancestor.
184
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of)
49
185
  def self.non_functional_homolog_of
50
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of')
186
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of')
51
187
  end
52
188
 
189
+ # -- No comment or description provided. --
190
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to)
53
191
  def self.orthologous_to
54
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to')
192
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to')
55
193
  end
56
194
 
57
- def self.paralogous_to
58
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to')
195
+ # X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
196
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps)
197
+ def self.overlaps
198
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps')
59
199
  end
60
200
 
61
- def self.part_of
62
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of')
201
+ # -- No comment or description provided. --
202
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to)
203
+ def self.paralogous_to
204
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to')
63
205
  end
64
206
 
207
+ # B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
208
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature)
65
209
  def self.partial_evidence_for_feature
66
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature')
210
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature')
211
+ end
212
+
213
+ # -- No comment or description provided. --
214
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of)
215
+ def self.position_of
216
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of')
217
+ end
218
+
219
+ # Inverse of processed_into.
220
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from)
221
+ def self.processed_from
222
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from')
67
223
  end
68
224
 
225
+ # X is processed_into Y if a region X is modified to create Y.
226
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into)
227
+ def self.processed_into
228
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into')
229
+ end
230
+
231
+ # -- No comment or description provided. --
232
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from)
233
+ def self.recombined_from
234
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from')
235
+ end
236
+
237
+ # -- No comment or description provided. --
238
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to)
239
+ def self.recombined_to
240
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to')
241
+ end
242
+
243
+ # -- No comment or description provided. --
244
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of)
245
+ def self.sequence_of
246
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of')
247
+ end
248
+
249
+ # -- No comment or description provided. --
250
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to)
69
251
  def self.similar_to
70
- return RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to')
252
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to')
253
+ end
254
+
255
+ # X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
256
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by)
257
+ def self.started_by
258
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by')
259
+ end
260
+
261
+ # X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
262
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts)
263
+ def self.starts
264
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts')
265
+ end
266
+
267
+ # -- No comment or description provided. --
268
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from)
269
+ def self.trans_spliced_from
270
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from')
271
+ end
272
+
273
+ # -- No comment or description provided. --
274
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to)
275
+ def self.trans_spliced_to
276
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to')
277
+ end
278
+
279
+ # X is transcribed_from Y if X is synthesized from template Y.
280
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from)
281
+ def self.transcribed_from
282
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from')
283
+ end
284
+
285
+ # Inverse of transcribed_from.
286
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to)
287
+ def self.transcribed_to
288
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to')
289
+ end
290
+
291
+ # Inverse of translation _of.
292
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to)
293
+ def self.translates_to
294
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to')
295
+ end
296
+
297
+ # X is translation of Y if Y is translated by ribosome to create X.
298
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of)
299
+ def self.translation_of
300
+ return RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of')
301
+ end
302
+
303
+ # Either:
304
+ # A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
305
+ # (http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of)
306
+ # Or:
307
+ # A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
308
+ # (http://purl.obolibrary.org/obo/anonymous#variant_of)
309
+ def self.variant_of
310
+ return [ RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of'), RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') ]
71
311
  end
72
312
 
313
+ # -- No comment or description provided. --
314
+ # (http://purl.obolibrary.org/obo/SO_0000000)
73
315
  def self.Sequence_Ontology
74
316
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000000')
75
317
  end
76
318
 
77
- # A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. (SO:ke)
319
+ # A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
78
320
  # (http://purl.obolibrary.org/obo/SO_0000001)
79
321
  def self.region
80
322
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001')
81
323
  end
82
324
 
325
+ # -- No comment or description provided. --
326
+ # (http://purl.obolibrary.org/obo/SO_0000004)
83
327
  def self.interior_coding_exon
84
328
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004')
85
329
  end
86
330
 
87
- # The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
331
+ # The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
88
332
  # (http://purl.obolibrary.org/obo/SO_0000005)
89
333
  def self.satellite_DNA
90
334
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005')
91
335
  end
92
336
 
93
- # A region amplified by a PCR reaction. (SO:ke)
337
+ # A region amplified by a PCR reaction.
94
338
  # (http://purl.obolibrary.org/obo/SO_0000006)
95
339
  def self.PCR_product
96
340
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006')
97
341
  end
98
342
 
99
- # One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. (SO:ls)
343
+ # One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
100
344
  # (http://purl.obolibrary.org/obo/SO_0000007)
101
345
  def self.read_pair
102
346
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000007')
103
347
  end
104
348
 
105
- # A small non coding RNA sequence, present in the cytoplasm. (SO:ke)
349
+ # A small non coding RNA sequence, present in the cytoplasm.
106
350
  # (http://purl.obolibrary.org/obo/SO_0000013)
107
351
  def self.scRNA
108
352
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000013')
109
353
  end
110
354
 
111
- # A collection of match parts. (SO:ke)
355
+ # A collection of match parts.
112
356
  # (http://purl.obolibrary.org/obo/SO_0000038)
113
357
  def self.match_set
114
358
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000038')
115
359
  end
116
360
 
117
- # A part of a match, for example an hsp from blast is a match_part. (SO:ke)
361
+ # A part of a match, for example an hsp from blast is a match_part.
118
362
  # (http://purl.obolibrary.org/obo/SO_0000039)
119
363
  def self.match_part
120
364
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000039')
121
365
  end
122
366
 
123
- # A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. (SO:ke)
367
+ # A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
124
368
  # (http://purl.obolibrary.org/obo/SO_0000050)
125
369
  def self.gene_part
126
370
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000050')
127
371
  end
128
372
 
129
- # A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. (SO:ma)
373
+ # A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
130
374
  # (http://purl.obolibrary.org/obo/SO_0000057)
131
375
  def self.operator
132
376
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057')
133
377
  end
134
378
 
135
- # A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. (SO:cb)
379
+ # A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
136
380
  # (http://purl.obolibrary.org/obo/SO_0000059)
137
381
  def self.nuclease_binding_site
138
382
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059')
139
383
  end
140
384
 
141
- # A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. (http://www.sci.sdsu.edu/~smaloy/Glossary/T.html)
385
+ # A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
142
386
  # (http://purl.obolibrary.org/obo/SO_0000101)
143
387
  def self.transposable_element
144
388
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101')
145
389
  end
146
390
 
147
- # A match to an EST or cDNA sequence. (SO:ke)
391
+ # A match to an EST or cDNA sequence.
148
392
  # (http://purl.obolibrary.org/obo/SO_0000102)
149
393
  def self.expressed_sequence_match
150
394
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102')
151
395
  end
152
396
 
153
- # The end of the clone insert. (SO:ke)
397
+ # The end of the clone insert.
154
398
  # (http://purl.obolibrary.org/obo/SO_0000103)
155
399
  def self.clone_insert_end
156
400
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000103')
157
401
  end
158
402
 
159
- # A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. (SO:ma)
403
+ # A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
160
404
  # (http://purl.obolibrary.org/obo/SO_0000104)
161
405
  def self.polypeptide
162
406
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000104')
163
407
  end
164
408
 
165
- # A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. (SO:ke)
409
+ # A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
166
410
  # (http://purl.obolibrary.org/obo/SO_0000109)
167
411
  def self.sequence_variant_obs
168
412
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000109')
169
413
  end
170
414
 
171
- # An extent of biological sequence. (SO:ke)
415
+ # Any extent of continuous biological sequence.
172
416
  # (http://purl.obolibrary.org/obo/SO_0000110)
173
417
  def self.sequence_feature
174
418
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110')
175
419
  end
176
420
 
177
- # An oligo to which new deoxyribonucleotides can be added by DNA polymerase. (SO:ke)
421
+ # An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
178
422
  # (http://purl.obolibrary.org/obo/SO_0000112)
179
423
  def self.primer
180
424
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112')
181
425
  end
182
426
 
183
- # A viral sequence which has integrated into a host genome. (SO:ke)
427
+ # A viral sequence which has integrated into a host genome.
184
428
  # (http://purl.obolibrary.org/obo/SO_0000113)
185
429
  def self.proviral_region
186
430
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113')
187
431
  end
188
432
 
189
- # A methylated deoxy-cytosine. (SO:ke)
433
+ # A methylated deoxy-cytosine.
190
434
  # (http://purl.obolibrary.org/obo/SO_0000114)
191
- def self.methylated_C
435
+ def self.methylated_cytosine
192
436
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114')
193
437
  end
194
438
 
195
- # A primary transcript that, at least in part, encodes one or more proteins. (SO:ke)
439
+ # A primary transcript that, at least in part, encodes one or more proteins.
196
440
  # (http://purl.obolibrary.org/obo/SO_0000120)
197
441
  def self.protein_coding_primary_transcript
198
442
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120')
199
443
  end
200
444
 
201
- # Region in mRNA where ribosome assembles. (SO:ke)
445
+ # Region in mRNA where ribosome assembles.
202
446
  # (http://purl.obolibrary.org/obo/SO_0000139)
203
447
  def self.ribosome_entry_site
204
448
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139')
205
449
  end
206
450
 
207
- # A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. (SO:as)
451
+ # A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
208
452
  # (http://purl.obolibrary.org/obo/SO_0000140)
209
453
  def self.attenuator
210
454
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000140')
211
455
  end
212
456
 
213
- # The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
457
+ # The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
214
458
  # (http://purl.obolibrary.org/obo/SO_0000141)
215
459
  def self.terminator
216
460
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000141')
217
461
  end
218
462
 
219
- # A region of known length which may be used to manufacture a longer region. (SO:ke)
463
+ # A region of known length which may be used to manufacture a longer region.
220
464
  # (http://purl.obolibrary.org/obo/SO_0000143)
221
465
  def self.assembly_component
222
466
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143')
223
467
  end
224
468
 
225
- # A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. (SO:ke)
469
+ # A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
226
470
  # (http://purl.obolibrary.org/obo/SO_0000147)
227
471
  def self.exon
228
472
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147')
229
473
  end
230
474
 
231
- # One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. (SO:ls)
475
+ # One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
232
476
  # (http://purl.obolibrary.org/obo/SO_0000148)
233
477
  def self.supercontig
234
478
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000148')
235
479
  end
236
480
 
237
- # A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. (SO:ls)
481
+ # A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
238
482
  # (http://purl.obolibrary.org/obo/SO_0000149)
239
483
  def self.contig
240
484
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000149')
241
485
  end
242
486
 
243
- # A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. (SO:rd)
487
+ # A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
244
488
  # (http://purl.obolibrary.org/obo/SO_0000150)
245
489
  def self.read
246
490
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000150')
247
491
  end
248
492
 
249
- # A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. (SO:ke)
493
+ # A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
250
494
  # (http://purl.obolibrary.org/obo/SO_0000151)
251
495
  def self.clone
252
496
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151')
253
497
  end
254
498
 
255
- # The point at which one or more contiguous nucleotides were excised. (SO:ke)
499
+ # The point at which one or more contiguous nucleotides were excised.
256
500
  # (http://purl.obolibrary.org/obo/SO_0000159)
257
501
  def self.deletion
258
502
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159')
259
503
  end
260
504
 
261
- # A modified RNA base in which adenine has been methylated. (SO:ke)
505
+ # A modified base in which adenine has been methylated.
262
506
  # (http://purl.obolibrary.org/obo/SO_0000161)
263
- def self.methylated_A
507
+ def self.methylated_adenine
264
508
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161')
265
509
  end
266
510
 
267
- # Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. (SO:cjm, SO:ke)
511
+ # Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
268
512
  # (http://purl.obolibrary.org/obo/SO_0000162)
269
513
  def self.splice_site
270
514
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162')
271
515
  end
272
516
 
273
- # Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. (http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
517
+ # Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
274
518
  # (http://purl.obolibrary.org/obo/SO_0000163)
275
519
  def self.five_prime_cis_splice_site
276
520
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163')
277
521
  end
278
522
 
279
- # Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. (http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke)
523
+ # Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
280
524
  # (http://purl.obolibrary.org/obo/SO_0000164)
281
525
  def self.three_prime_cis_splice_site
282
526
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164')
283
527
  end
284
528
 
285
- # A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
529
+ # A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
286
530
  # (http://purl.obolibrary.org/obo/SO_0000165)
287
531
  def self.enhancer
288
532
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165')
289
533
  end
290
534
 
291
- # A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. (SO:regcreative)
535
+ # A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
292
536
  # (http://purl.obolibrary.org/obo/SO_0000167)
293
537
  def self.promoter
294
538
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167')
295
539
  end
296
540
 
297
- # A nucleotide match against a sequence from another organism. (SO:ma)
541
+ # A nucleotide match against a sequence from another organism.
298
542
  # (http://purl.obolibrary.org/obo/SO_0000177)
299
543
  def self.cross_genome_match
300
544
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177')
301
545
  end
302
546
 
303
- # A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. (SO:ma)
547
+ # A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
304
548
  # (http://purl.obolibrary.org/obo/SO_0000178)
305
549
  def self.operon
306
550
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178')
307
551
  end
308
552
 
309
- # The start of the clone insert. (SO:ke)
553
+ # The start of the clone insert.
310
554
  # (http://purl.obolibrary.org/obo/SO_0000179)
311
555
  def self.clone_insert_start
312
556
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000179')
313
557
  end
314
558
 
315
- # A match against a translated sequence. (SO:ke)
559
+ # A match against a translated sequence.
316
560
  # (http://purl.obolibrary.org/obo/SO_0000181)
317
561
  def self.translated_nucleotide_match
318
562
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181')
319
563
  end
320
564
 
321
- # A region of the gene which is not transcribed. (SO:ke)
565
+ # A region of the gene which is not transcribed.
322
566
  # (http://purl.obolibrary.org/obo/SO_0000183)
323
567
  def self.non_transcribed_region
324
568
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183')
325
569
  end
326
570
 
327
- # A transcript that in its initial state requires modification to be functional. (SO:ma)
571
+ # A transcript that in its initial state requires modification to be functional.
328
572
  # (http://purl.obolibrary.org/obo/SO_0000185)
329
573
  def self.primary_transcript
330
574
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185')
331
575
  end
332
576
 
333
- # A group of characterized repeat sequences. (SO:ke)
577
+ # A group of characterized repeat sequences.
334
578
  # (http://purl.obolibrary.org/obo/SO_0000187)
335
579
  def self.repeat_family
336
580
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000187')
337
581
  end
338
582
 
339
- # A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
583
+ # A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
340
584
  # (http://purl.obolibrary.org/obo/SO_0000188)
341
585
  def self.intron
342
586
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188')
343
587
  end
344
588
 
345
- # A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. (GOC:pj)
589
+ # A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
346
590
  # (http://purl.obolibrary.org/obo/SO_0000193)
347
591
  def self.RFLP_fragment
348
592
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193')
349
593
  end
350
594
 
351
- # An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). (SO:ke)
595
+ # An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
352
596
  # (http://purl.obolibrary.org/obo/SO_0000195)
353
597
  def self.coding_exon
354
598
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195')
355
599
  end
356
600
 
357
- # The sequence of the five_prime_coding_exon that codes for protein. (SO:cjm)
601
+ # The sequence of the five_prime_coding_exon that codes for protein.
358
602
  # (http://purl.obolibrary.org/obo/SO_0000196)
359
603
  def self.five_prime_coding_exon_coding_region
360
604
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000196')
361
605
  end
362
606
 
363
- # The sequence of the three_prime_coding_exon that codes for protein. (SO:cjm)
607
+ # The sequence of the three_prime_coding_exon that codes for protein.
364
608
  # (http://purl.obolibrary.org/obo/SO_0000197)
365
609
  def self.three_prime_coding_exon_coding_region
366
610
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000197')
367
611
  end
368
612
 
369
- # An exon that does not contain any codons. (SO:ke)
613
+ # An exon that does not contain any codons.
370
614
  # (http://purl.obolibrary.org/obo/SO_0000198)
371
615
  def self.noncoding_exon
372
616
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000198')
373
617
  end
374
618
 
375
- # The 5' most coding exon. (SO:ke)
619
+ # The 5' most coding exon.
376
620
  # (http://purl.obolibrary.org/obo/SO_0000200)
377
621
  def self.five_prime_coding_exon
378
622
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000200')
379
623
  end
380
624
 
381
- # Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. (SO:ke)
625
+ # Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
382
626
  # (http://purl.obolibrary.org/obo/SO_0000203)
383
627
  def self.UTR
384
628
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203')
385
629
  end
386
630
 
387
- # A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
631
+ # A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
388
632
  # (http://purl.obolibrary.org/obo/SO_0000204)
389
633
  def self.five_prime_UTR
390
634
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204')
391
635
  end
392
636
 
393
- # A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
637
+ # A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
394
638
  # (http://purl.obolibrary.org/obo/SO_0000205)
395
639
  def self.three_prime_UTR
396
640
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205')
397
641
  end
398
642
 
399
- # A primary transcript encoding a ribosomal RNA. (SO:ke)
643
+ # A primary transcript encoding a ribosomal RNA.
400
644
  # (http://purl.obolibrary.org/obo/SO_0000209)
401
645
  def self.rRNA_primary_transcript
402
646
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209')
403
647
  end
404
648
 
405
- # A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. (SO:ke)
649
+ # A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
406
650
  # (http://purl.obolibrary.org/obo/SO_0000233)
407
651
  def self.mature_transcript
408
652
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000233')
409
653
  end
410
654
 
411
- # Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. (SO:ma)
655
+ # Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
412
656
  # (http://purl.obolibrary.org/obo/SO_0000234)
413
657
  def self.mRNA
414
658
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234')
415
659
  end
416
660
 
417
- # A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. (SO:ke)
661
+ # A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
418
662
  # (http://purl.obolibrary.org/obo/SO_0000235)
419
663
  def self.TF_binding_site
420
664
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235')
421
665
  end
422
666
 
423
- # The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. (SGD:rb, SO:ma)
667
+ # The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
424
668
  # (http://purl.obolibrary.org/obo/SO_0000236)
425
669
  def self.ORF
426
670
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236')
427
671
  end
428
672
 
429
- # The sequences extending on either side of a specific region. (SO:ke)
673
+ # The sequences extending on either side of a specific region.
430
674
  # (http://purl.obolibrary.org/obo/SO_0000239)
431
675
  def self.flanking_region
432
676
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239')
433
677
  end
434
678
 
435
- # RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732)
679
+ # RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
436
680
  # (http://purl.obolibrary.org/obo/SO_0000252)
437
681
  def self.rRNA
438
682
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000252')
439
683
  end
440
684
 
441
- # Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732)
685
+ # Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
442
686
  # (http://purl.obolibrary.org/obo/SO_0000253)
443
687
  def self.tRNA
444
688
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000253')
445
689
  end
446
690
 
447
- # A small nuclear RNA molecule involved in pre-mRNA splicing and processing. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems)
691
+ # A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
448
692
  # (http://purl.obolibrary.org/obo/SO_0000274)
449
693
  def self.snRNA
450
694
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274')
451
695
  end
452
696
 
453
- # A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. (GOC:kgc)
697
+ # A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
454
698
  # (http://purl.obolibrary.org/obo/SO_0000275)
455
699
  def self.snoRNA
456
700
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275')
457
701
  end
458
702
 
459
- # Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. (PMID:12592000)
703
+ # Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
460
704
  # (http://purl.obolibrary.org/obo/SO_0000276)
461
705
  def self.miRNA
462
706
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000276')
463
707
  end
464
708
 
465
- # A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem. (http://www.informatics.jax.org/silver/glossary.shtml)
709
+ # A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
466
710
  # (http://purl.obolibrary.org/obo/SO_0000289)
467
711
  def self.microsatellite
468
712
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289')
469
713
  end
470
714
 
471
- # The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. (SO:ke)
715
+ # The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
472
716
  # (http://purl.obolibrary.org/obo/SO_0000294)
473
717
  def self.inverted_repeat
474
718
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294')
475
719
  end
476
720
 
477
- # The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
721
+ # The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
478
722
  # (http://purl.obolibrary.org/obo/SO_0000296)
479
723
  def self.origin_of_replication
480
724
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296')
481
725
  end
482
726
 
483
- # Part of the primary transcript that is clipped off during processing. (SO:ke)
727
+ # Part of the primary transcript that is clipped off during processing.
484
728
  # (http://purl.obolibrary.org/obo/SO_0000303)
485
729
  def self.clip
486
730
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000303')
487
731
  end
488
732
 
489
- # A modified nucleotide, i.e. a nucleotide other than A, T, C. G. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
733
+ # A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
490
734
  # (http://purl.obolibrary.org/obo/SO_0000305)
491
- def self.modified_base
735
+ def self.modified_DNA_base
492
736
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305')
493
737
  end
494
738
 
495
- # A nucleotide modified by methylation. (SO:ke)
739
+ # A nucleotide modified by methylation.
496
740
  # (http://purl.obolibrary.org/obo/SO_0000306)
497
- def self.methylated_base_feature
741
+ def self.methylated_DNA_base_feature
498
742
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306')
499
743
  end
500
744
 
501
- # Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. (SO:rd)
745
+ # Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
502
746
  # (http://purl.obolibrary.org/obo/SO_0000307)
503
747
  def self.CpG_island
504
748
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307')
505
749
  end
506
750
 
507
- # A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. (SO:ke)
751
+ # A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
508
752
  # (http://purl.obolibrary.org/obo/SO_0000314)
509
753
  def self.direct_repeat
510
754
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314')
511
755
  end
512
756
 
513
- # The first base where RNA polymerase begins to synthesize the RNA transcript. (SO:ke)
757
+ # The first base where RNA polymerase begins to synthesize the RNA transcript.
514
758
  # (http://purl.obolibrary.org/obo/SO_0000315)
515
759
  def self.TSS
516
760
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315')
517
761
  end
518
762
 
519
- # A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. (SO:ma)
763
+ # A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
520
764
  # (http://purl.obolibrary.org/obo/SO_0000316)
521
765
  def self.CDS
522
766
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316')
523
767
  end
524
768
 
525
- # First codon to be translated by a ribosome. (SO:ke)
769
+ # First codon to be translated by a ribosome.
526
770
  # (http://purl.obolibrary.org/obo/SO_0000318)
527
771
  def self.start_codon
528
772
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000318')
529
773
  end
530
774
 
531
- # In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. (SO:ke)
775
+ # In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
532
776
  # (http://purl.obolibrary.org/obo/SO_0000319)
533
777
  def self.stop_codon
534
778
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319')
535
779
  end
536
780
 
537
- # A nucleotide sequence that may be used to identify a larger sequence. (SO:ke)
781
+ # A nucleotide sequence that may be used to identify a larger sequence.
538
782
  # (http://purl.obolibrary.org/obo/SO_0000324)
539
783
  def self.tag
540
784
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324')
541
785
  end
542
786
 
543
- # A primary transcript encoding a large ribosomal subunit RNA. (SO:ke)
787
+ # A primary transcript encoding a large ribosomal subunit RNA.
544
788
  # (http://purl.obolibrary.org/obo/SO_0000325)
545
789
  def self.rRNA_large_subunit_primary_transcript
546
790
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000325')
547
791
  end
548
792
 
549
- # A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract)
793
+ # A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
550
794
  # (http://purl.obolibrary.org/obo/SO_0000326)
551
795
  def self.SAGE_tag
552
796
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326')
553
797
  end
554
798
 
555
- # Region of sequence similarity by descent from a common ancestor. (SO:ke)
799
+ # Region of sequence similarity by descent from a common ancestor.
556
800
  # (http://purl.obolibrary.org/obo/SO_0000330)
557
801
  def self.conserved_region
558
802
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330')
559
803
  end
560
804
 
561
- # Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. (http://www.biospace.com)
805
+ # Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
562
806
  # (http://purl.obolibrary.org/obo/SO_0000331)
563
807
  def self.STS
564
808
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331')
565
809
  end
566
810
 
567
- # Coding region of sequence similarity by descent from a common ancestor. (SO:ke)
811
+ # Coding region of sequence similarity by descent from a common ancestor.
568
812
  # (http://purl.obolibrary.org/obo/SO_0000332)
569
813
  def self.coding_conserved_region
570
814
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332')
571
815
  end
572
816
 
573
- # The boundary between two exons in a processed transcript. (SO:ke)
817
+ # The boundary between two exons in a processed transcript.
574
818
  # (http://purl.obolibrary.org/obo/SO_0000333)
575
819
  def self.exon_junction
576
820
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000333')
577
821
  end
578
822
 
579
- # Non-coding region of sequence similarity by descent from a common ancestor. (SO:ke)
823
+ # Non-coding region of sequence similarity by descent from a common ancestor.
580
824
  # (http://purl.obolibrary.org/obo/SO_0000334)
581
825
  def self.nc_conserved_region
582
826
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000334')
@@ -588,955 +832,961 @@ class SOFA
588
832
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000336')
589
833
  end
590
834
 
591
- # A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. (SO:rd)
835
+ # A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
592
836
  # (http://purl.obolibrary.org/obo/SO_0000337)
593
837
  def self.RNAi_reagent
594
838
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337')
595
839
  end
596
840
 
597
- # Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. (SO:ma)
841
+ # Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
598
842
  # (http://purl.obolibrary.org/obo/SO_0000340)
599
843
  def self.chromosome
600
844
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340')
601
845
  end
602
846
 
603
- # A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. (SO:ma)
847
+ # A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
604
848
  # (http://purl.obolibrary.org/obo/SO_0000341)
605
849
  def self.chromosome_band
606
850
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341')
607
851
  end
608
852
 
609
- # A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. (SO:ke)
853
+ # A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
610
854
  # (http://purl.obolibrary.org/obo/SO_0000343)
611
855
  def self.match
612
856
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343')
613
857
  end
614
858
 
615
- # Region of a transcript that regulates splicing. (SO:ke)
859
+ # Region of a transcript that regulates splicing.
616
860
  # (http://purl.obolibrary.org/obo/SO_0000344)
617
861
  def self.splice_enhancer
618
862
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344')
619
863
  end
620
864
 
621
- # A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. (SO:ke)
865
+ # A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
622
866
  # (http://purl.obolibrary.org/obo/SO_0000345)
623
867
  def self.EST
624
868
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000345')
625
869
  end
626
870
 
627
- # A match against a nucleotide sequence. (SO:ke)
871
+ # A match against a nucleotide sequence.
628
872
  # (http://purl.obolibrary.org/obo/SO_0000347)
629
873
  def self.nucleotide_match
630
874
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347')
631
875
  end
632
876
 
633
- # A match against a protein sequence. (SO:ke)
877
+ # A match against a protein sequence.
634
878
  # (http://purl.obolibrary.org/obo/SO_0000349)
635
879
  def self.protein_match
636
880
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349')
637
881
  end
638
882
 
639
- # A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. (SO:ma)
883
+ # A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
640
884
  # (http://purl.obolibrary.org/obo/SO_0000353)
641
885
  def self.sequence_assembly
642
886
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353')
643
887
  end
644
888
 
645
- # A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. (http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke)
889
+ # A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
646
890
  # (http://purl.obolibrary.org/obo/SO_0000360)
647
891
  def self.codon
648
892
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360')
649
893
  end
650
894
 
651
- # The junction where an insertion occurred. (SO:ke)
895
+ # The junction where an insertion occurred.
652
896
  # (http://purl.obolibrary.org/obo/SO_0000366)
653
897
  def self.insertion_site
654
898
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366')
655
899
  end
656
900
 
657
- # The junction in a genome where a transposable_element has inserted. (SO:ke)
901
+ # The junction in a genome where a transposable_element has inserted.
658
902
  # (http://purl.obolibrary.org/obo/SO_0000368)
659
903
  def self.transposable_element_insertion_site
660
904
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368')
661
905
  end
662
906
 
663
- # A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. (SO:ma)
907
+ # A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
664
908
  # (http://purl.obolibrary.org/obo/SO_0000370)
665
909
  def self.small_regulatory_ncRNA
666
910
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000370')
667
911
  end
668
912
 
669
- # An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. (RSC:cb)
913
+ # An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
670
914
  # (http://purl.obolibrary.org/obo/SO_0000372)
671
915
  def self.enzymatic_RNA
672
916
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372')
673
917
  end
674
918
 
675
- # An RNA with catalytic activity. (SO:ma)
919
+ # An RNA with catalytic activity.
676
920
  # (http://purl.obolibrary.org/obo/SO_0000374)
677
921
  def self.ribozyme
678
922
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374')
679
923
  end
680
924
 
681
- # 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002)
925
+ # 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
682
926
  # (http://purl.obolibrary.org/obo/SO_0000375)
683
927
  def self.rRNA_5_8S
684
928
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375')
685
929
  end
686
930
 
687
- # A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. (PMID:2436805)
931
+ # A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
688
932
  # (http://purl.obolibrary.org/obo/SO_0000380)
689
933
  def self.hammerhead_ribozyme
690
934
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380')
691
935
  end
692
936
 
693
- # The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030)
937
+ # The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
694
938
  # (http://purl.obolibrary.org/obo/SO_0000385)
695
939
  def self.RNase_MRP_RNA
696
940
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385')
697
941
  end
698
942
 
699
- # The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010)
943
+ # The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
700
944
  # (http://purl.obolibrary.org/obo/SO_0000386)
701
945
  def self.RNase_P_RNA
702
946
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386')
703
947
  end
704
948
 
705
- # The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025)
949
+ # The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
706
950
  # (http://purl.obolibrary.org/obo/SO_0000390)
707
951
  def self.telomerase_RNA
708
952
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390')
709
953
  end
710
954
 
711
- # U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003)
955
+ # U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
712
956
  # (http://purl.obolibrary.org/obo/SO_0000391)
713
957
  def self.U1_snRNA
714
958
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391')
715
959
  end
716
960
 
717
- # U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004)
961
+ # U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
718
962
  # (http://purl.obolibrary.org/obo/SO_0000392)
719
963
  def self.U2_snRNA
720
964
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392')
721
965
  end
722
966
 
723
- # U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
967
+ # U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
724
968
  # (http://purl.obolibrary.org/obo/SO_0000393)
725
969
  def self.U4_snRNA
726
970
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000393')
727
971
  end
728
972
 
729
- # An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). (PMID:=12409455)
973
+ # An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
730
974
  # (http://purl.obolibrary.org/obo/SO_0000394)
731
975
  def self.U4atac_snRNA
732
976
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394')
733
977
  end
734
978
 
735
- # U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020)
979
+ # U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
736
980
  # (http://purl.obolibrary.org/obo/SO_0000395)
737
981
  def self.U5_snRNA
738
982
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395')
739
983
  end
740
984
 
741
- # U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015)
985
+ # U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
742
986
  # (http://purl.obolibrary.org/obo/SO_0000396)
743
987
  def self.U6_snRNA
744
988
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000396')
745
989
  end
746
990
 
747
- # U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract)
991
+ # U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
748
992
  # (http://purl.obolibrary.org/obo/SO_0000397)
749
993
  def self.U6atac_snRNA
750
994
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397')
751
995
  end
752
996
 
753
- # U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. (PMID:9622129)
997
+ # U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
754
998
  # (http://purl.obolibrary.org/obo/SO_0000398)
755
999
  def self.U11_snRNA
756
1000
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398')
757
1001
  end
758
1002
 
759
- # The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007)
1003
+ # The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
760
1004
  # (http://purl.obolibrary.org/obo/SO_0000399)
761
1005
  def self.U12_snRNA
762
1006
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000399')
763
1007
  end
764
1008
 
765
- # U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119)
1009
+ # U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
766
1010
  # (http://purl.obolibrary.org/obo/SO_0000403)
767
1011
  def self.U14_snoRNA
768
1012
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403')
769
1013
  end
770
1014
 
771
- # A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006)
1015
+ # A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
772
1016
  # (http://purl.obolibrary.org/obo/SO_0000404)
773
1017
  def self.vault_RNA
774
1018
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404')
775
1019
  end
776
1020
 
777
- # Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019)
1021
+ # Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
778
1022
  # (http://purl.obolibrary.org/obo/SO_0000405)
779
1023
  def self.Y_RNA
780
1024
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405')
781
1025
  end
782
1026
 
783
- # A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. (SO:ke)
1027
+ # A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
784
1028
  # (http://purl.obolibrary.org/obo/SO_0000407)
785
1029
  def self.rRNA_18S
786
1030
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407')
787
1031
  end
788
1032
 
789
- # A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. (EBIBS:GAR, SO:ke)
1033
+ # A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
790
1034
  # (http://purl.obolibrary.org/obo/SO_0000409)
791
1035
  def self.binding_site
792
1036
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409')
793
1037
  end
794
1038
 
795
- # A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. (SO:ke)
1039
+ # A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
796
1040
  # (http://purl.obolibrary.org/obo/SO_0000410)
797
1041
  def self.protein_binding_site
798
1042
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410')
799
1043
  end
800
1044
 
801
- # A region of polynucleotide sequence produced by digestion with a restriction endonuclease. (SO:ke)
1045
+ # A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
802
1046
  # (http://purl.obolibrary.org/obo/SO_0000412)
803
1047
  def self.restriction_fragment
804
1048
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412')
805
1049
  end
806
1050
 
807
- # A region where the sequence differs from that of a specified sequence. (SO:ke)
1051
+ # A region where the sequence differs from that of a specified sequence.
808
1052
  # (http://purl.obolibrary.org/obo/SO_0000413)
809
1053
  def self.sequence_difference
810
1054
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000413')
811
1055
  end
812
1056
 
813
- # The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
1057
+ # The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
814
1058
  # (http://purl.obolibrary.org/obo/SO_0000418)
815
1059
  def self.signal_peptide
816
1060
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000418')
817
1061
  end
818
1062
 
819
- # The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. (EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb)
1063
+ # The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
820
1064
  # (http://purl.obolibrary.org/obo/SO_0000419)
821
1065
  def self.mature_protein_region
822
1066
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000419')
823
1067
  end
824
1068
 
825
- # A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. (SO:ma)
1069
+ # A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
826
1070
  # (http://purl.obolibrary.org/obo/SO_0000436)
827
1071
  def self.ARS
828
1072
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436')
829
1073
  end
830
1074
 
831
- # A single stranded oligonucleotide. (SO:ke)
1075
+ # A single stranded oligonucleotide.
832
1076
  # (http://purl.obolibrary.org/obo/SO_0000441)
833
1077
  def self.ss_oligo
834
1078
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441')
835
1079
  end
836
1080
 
837
- # A double stranded oligonucleotide. (SO:ke)
1081
+ # A double stranded oligonucleotide.
838
1082
  # (http://purl.obolibrary.org/obo/SO_0000442)
839
1083
  def self.ds_oligo
840
1084
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442')
841
1085
  end
842
1086
 
843
- # A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. (http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284)
1087
+ # A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
844
1088
  # (http://purl.obolibrary.org/obo/SO_0000454)
845
1089
  def self.rasiRNA
846
1090
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454')
847
1091
  end
848
1092
 
849
- # A non-functional descendent of a functional entity. (SO:cjm)
1093
+ # A non-functional descendent of a functional entity.
850
1094
  # (http://purl.obolibrary.org/obo/SO_0000462)
851
1095
  def self.pseudogenic_region
852
1096
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000462')
853
1097
  end
854
1098
 
855
- # A non-functional descendant of an exon. (SO:ke)
1099
+ # A non-functional descendant of an exon.
856
1100
  # (http://purl.obolibrary.org/obo/SO_0000464)
857
1101
  def self.decayed_exon
858
1102
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000464')
859
1103
  end
860
1104
 
861
- # One of the pieces of sequence that make up a golden path. (SO:rd)
1105
+ # One of the pieces of sequence that make up a golden path.
862
1106
  # (http://purl.obolibrary.org/obo/SO_0000468)
863
1107
  def self.golden_path_fragment
864
1108
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000468')
865
1109
  end
866
1110
 
867
- # A set of regions which overlap with minimal polymorphism to form a linear sequence. (SO:cjm)
1111
+ # A set of regions which overlap with minimal polymorphism to form a linear sequence.
868
1112
  # (http://purl.obolibrary.org/obo/SO_0000472)
869
1113
  def self.tiling_path
870
1114
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472')
871
1115
  end
872
1116
 
873
- # A piece of sequence that makes up a tiling_path (SO:0000472). (SO:ke)
1117
+ # A piece of sequence that makes up a tiling_path (SO:0000472).
874
1118
  # (http://purl.obolibrary.org/obo/SO_0000474)
875
1119
  def self.tiling_path_fragment
876
1120
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000474')
877
1121
  end
878
1122
 
879
- # A primary transcript that is never translated into a protein. (SO:ke)
1123
+ # A primary transcript that is never translated into a protein.
880
1124
  # (http://purl.obolibrary.org/obo/SO_0000483)
881
1125
  def self.nc_primary_transcript
882
1126
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483')
883
1127
  end
884
1128
 
885
- # The sequence of the 3' exon that is not coding. (SO:ke)
1129
+ # The sequence of the 3' exon that is not coding.
886
1130
  # (http://purl.obolibrary.org/obo/SO_0000484)
887
1131
  def self.three_prime_coding_exon_noncoding_region
888
1132
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000484')
889
1133
  end
890
1134
 
891
- # The sequence of the 5' exon preceding the start codon. (SO:ke)
1135
+ # The sequence of the 5' exon preceding the start codon.
892
1136
  # (http://purl.obolibrary.org/obo/SO_0000486)
893
1137
  def self.five_prime_coding_exon_noncoding_region
894
1138
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000486')
895
1139
  end
896
1140
 
897
- # A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. (SO:ke)
1141
+ # A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
898
1142
  # (http://purl.obolibrary.org/obo/SO_0000499)
899
1143
  def self.virtual_sequence
900
1144
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499')
901
1145
  end
902
1146
 
903
- # A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. (SO:ke)
1147
+ # A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
904
1148
  # (http://purl.obolibrary.org/obo/SO_0000502)
905
1149
  def self.transcribed_region
906
1150
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000502')
907
1151
  end
908
1152
 
909
- # The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
1153
+ # The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
910
1154
  # (http://purl.obolibrary.org/obo/SO_0000551)
911
1155
  def self.polyA_signal_sequence
912
1156
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000551')
913
1157
  end
914
1158
 
915
- # The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
1159
+ # The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
916
1160
  # (http://purl.obolibrary.org/obo/SO_0000553)
917
1161
  def self.polyA_site
918
1162
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000553')
919
1163
  end
920
1164
 
921
- # A region of chromosome where the spindle fibers attach during mitosis and meiosis. (SO:ke)
1165
+ # A region of chromosome where the spindle fibers attach during mitosis and meiosis.
922
1166
  # (http://purl.obolibrary.org/obo/SO_0000577)
923
1167
  def self.centromere
924
1168
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577')
925
1169
  end
926
1170
 
927
- # A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. (http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html)
1171
+ # A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
928
1172
  # (http://purl.obolibrary.org/obo/SO_0000581)
929
1173
  def self.cap
930
1174
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581')
931
1175
  end
932
1176
 
933
- # Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028)
1177
+ # Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
934
1178
  # (http://purl.obolibrary.org/obo/SO_0000587)
935
1179
  def self.group_I_intron
936
1180
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000587')
937
1181
  end
938
1182
 
939
- # A self spliced intron. (SO:ke)
1183
+ # A self spliced intron.
940
1184
  # (http://purl.obolibrary.org/obo/SO_0000588)
941
1185
  def self.autocatalytically_spliced_intron
942
1186
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588')
943
1187
  end
944
1188
 
945
- # The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017)
1189
+ # The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
946
1190
  # (http://purl.obolibrary.org/obo/SO_0000590)
947
1191
  def self.SRP_RNA
948
1192
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000590')
949
1193
  end
950
1194
 
951
- # Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. (http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html)
1195
+ # Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
952
1196
  # (http://purl.obolibrary.org/obo/SO_0000593)
953
1197
  def self.C_D_box_snoRNA
954
1198
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593')
955
1199
  end
956
1200
 
957
- # A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. (http://www.rna.ucla.edu/index.html)
1201
+ # A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
958
1202
  # (http://purl.obolibrary.org/obo/SO_0000602)
959
1203
  def self.guide_RNA
960
1204
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602')
961
1205
  end
962
1206
 
963
- # Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. (http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml)
1207
+ # Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
964
1208
  # (http://purl.obolibrary.org/obo/SO_0000603)
965
1209
  def self.group_II_intron
966
1210
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603')
967
1211
  end
968
1212
 
969
- # A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. (SO:cjm)
1213
+ # A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
970
1214
  # (http://purl.obolibrary.org/obo/SO_0000605)
971
1215
  def self.intergenic_region
972
1216
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605')
973
1217
  end
974
1218
 
975
- # Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. (SO:ke)
1219
+ # Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
976
1220
  # (http://purl.obolibrary.org/obo/SO_0000610)
977
1221
  def self.polyA_sequence
978
1222
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000610')
979
1223
  end
980
1224
 
981
- # A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. (SO:ke)
1225
+ # A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
982
1226
  # (http://purl.obolibrary.org/obo/SO_0000611)
983
1227
  def self.branch_site
984
1228
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611')
985
1229
  end
986
1230
 
987
- # The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. (http://nar.oupjournals.org/cgi/content/full/25/4/888)
1231
+ # The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
988
1232
  # (http://purl.obolibrary.org/obo/SO_0000612)
989
1233
  def self.polypyrimidine_tract
990
1234
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612')
991
1235
  end
992
1236
 
993
- # The base where transcription ends. (SO:ke)
1237
+ # The base where transcription ends.
994
1238
  # (http://purl.obolibrary.org/obo/SO_0000616)
995
1239
  def self.transcription_end_site
996
1240
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000616')
997
1241
  end
998
1242
 
999
- # A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. (SO:ma)
1243
+ # A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
1000
1244
  # (http://purl.obolibrary.org/obo/SO_0000624)
1001
1245
  def self.telomere
1002
1246
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624')
1003
1247
  end
1004
1248
 
1005
- # A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. (SO:ke)
1249
+ # A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
1006
1250
  # (http://purl.obolibrary.org/obo/SO_0000625)
1007
1251
  def self.silencer
1008
1252
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625')
1009
1253
  end
1010
1254
 
1011
- # A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. (SO:regcreative)
1255
+ # A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
1012
1256
  # (http://purl.obolibrary.org/obo/SO_0000627)
1013
1257
  def self.insulator
1014
1258
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627')
1015
1259
  end
1016
1260
 
1261
+ # -- No comment or description provided. --
1262
+ # (http://purl.obolibrary.org/obo/SO_0000628)
1017
1263
  def self.chromosomal_structural_element
1018
1264
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628')
1019
1265
  end
1020
1266
 
1021
- # A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. (http://www.informatics.jax.org/silver/glossary.shtml)
1267
+ # A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
1022
1268
  # (http://purl.obolibrary.org/obo/SO_0000643)
1023
1269
  def self.minisatellite
1024
1270
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643')
1025
1271
  end
1026
1272
 
1027
- # Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. (SO:ke)
1273
+ # Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
1028
1274
  # (http://purl.obolibrary.org/obo/SO_0000644)
1029
1275
  def self.antisense_RNA
1030
1276
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000644')
1031
1277
  end
1032
1278
 
1033
- # The reverse complement of the primary transcript. (SO:ke)
1279
+ # The reverse complement of the primary transcript.
1034
1280
  # (http://purl.obolibrary.org/obo/SO_0000645)
1035
1281
  def self.antisense_primary_transcript
1036
1282
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645')
1037
1283
  end
1038
1284
 
1039
- # A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. (PMID:12592000)
1285
+ # A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
1040
1286
  # (http://purl.obolibrary.org/obo/SO_0000646)
1041
1287
  def self.siRNA
1042
1288
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646')
1043
1289
  end
1044
1290
 
1045
- # Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. (PMID:11081512)
1291
+ # Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans.
1046
1292
  # (http://purl.obolibrary.org/obo/SO_0000649)
1047
1293
  def self.stRNA
1048
1294
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000649')
1049
1295
  end
1050
1296
 
1051
- # Ribosomal RNA transcript that structures the small subunit of the ribosome. (SO:ke)
1297
+ # Ribosomal RNA transcript that structures the small subunit of the ribosome.
1052
1298
  # (http://purl.obolibrary.org/obo/SO_0000650)
1053
1299
  def self.small_subunit_rRNA
1054
1300
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650')
1055
1301
  end
1056
1302
 
1057
- # Ribosomal RNA transcript that structures the large subunit of the ribosome. (SO:ke)
1303
+ # Ribosomal RNA transcript that structures the large subunit of the ribosome.
1058
1304
  # (http://purl.obolibrary.org/obo/SO_0000651)
1059
1305
  def self.large_subunit_rRNA
1060
1306
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651')
1061
1307
  end
1062
1308
 
1063
- # 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription. (http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001)
1309
+ # 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
1064
1310
  # (http://purl.obolibrary.org/obo/SO_0000652)
1065
1311
  def self.rRNA_5S
1066
1312
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000652')
1067
1313
  end
1068
1314
 
1069
- # A component of the large ribosomal subunit. (SO:ke)
1315
+ # A component of the large ribosomal subunit.
1070
1316
  # (http://purl.obolibrary.org/obo/SO_0000653)
1071
1317
  def self.rRNA_28S
1072
1318
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000653')
1073
1319
  end
1074
1320
 
1075
- # An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. (SO:ke)
1321
+ # An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
1076
1322
  # (http://purl.obolibrary.org/obo/SO_0000655)
1077
1323
  def self.ncRNA
1078
1324
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655')
1079
1325
  end
1080
1326
 
1081
- # A region of sequence containing one or more repeat units. (SO:ke)
1327
+ # A region of sequence containing one or more repeat units.
1082
1328
  # (http://purl.obolibrary.org/obo/SO_0000657)
1083
1329
  def self.repeat_region
1084
1330
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657')
1085
1331
  end
1086
1332
 
1087
- # A repeat that is located at dispersed sites in the genome. (SO:ke)
1333
+ # A repeat that is located at dispersed sites in the genome.
1088
1334
  # (http://purl.obolibrary.org/obo/SO_0000658)
1089
1335
  def self.dispersed_repeat
1090
1336
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000658')
1091
1337
  end
1092
1338
 
1093
- # An intron which is spliced by the spliceosome. (SO:ke)
1339
+ # An intron which is spliced by the spliceosome.
1094
1340
  # (http://purl.obolibrary.org/obo/SO_0000662)
1095
1341
  def self.spliceosomal_intron
1096
1342
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000662')
1097
1343
  end
1098
1344
 
1099
- # The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. (SO:ke)
1345
+ # The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
1100
1346
  # (http://purl.obolibrary.org/obo/SO_0000667)
1101
1347
  def self.insertion
1102
1348
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000667')
1103
1349
  end
1104
1350
 
1105
- # A match against an EST sequence. (SO:ke)
1351
+ # A match against an EST sequence.
1106
1352
  # (http://purl.obolibrary.org/obo/SO_0000668)
1107
1353
  def self.EST_match
1108
1354
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000668')
1109
1355
  end
1110
1356
 
1111
- # An RNA synthesized on a DNA or RNA template by an RNA polymerase. (SO:ma)
1357
+ # An RNA synthesized on a DNA or RNA template by an RNA polymerase.
1112
1358
  # (http://purl.obolibrary.org/obo/SO_0000673)
1113
1359
  def self.transcript
1114
1360
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673')
1115
1361
  end
1116
1362
 
1117
- # A region of nucleotide sequence targeted by a nuclease enzyme. (SO:ma)
1363
+ # A region of nucleotide sequence targeted by a nuclease enzyme.
1118
1364
  # (http://purl.obolibrary.org/obo/SO_0000684)
1119
1365
  def self.nuclease_sensitive_site
1120
1366
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000684')
1121
1367
  end
1122
1368
 
1123
- # The space between two bases in a sequence which marks the position where a deletion has occurred. (SO:ke)
1369
+ # The space between two bases in a sequence which marks the position where a deletion has occurred.
1124
1370
  # (http://purl.obolibrary.org/obo/SO_0000687)
1125
1371
  def self.deletion_junction
1126
1372
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000687')
1127
1373
  end
1128
1374
 
1129
- # A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. (SO:ls)
1375
+ # A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
1130
1376
  # (http://purl.obolibrary.org/obo/SO_0000688)
1131
1377
  def self.golden_path
1132
1378
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000688')
1133
1379
  end
1134
1380
 
1135
- # A match against cDNA sequence. (SO:ke)
1381
+ # A match against cDNA sequence.
1136
1382
  # (http://purl.obolibrary.org/obo/SO_0000689)
1137
1383
  def self.cDNA_match
1138
1384
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000689')
1139
1385
  end
1140
1386
 
1141
- # SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. (SO:cb)
1387
+ # SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
1142
1388
  # (http://purl.obolibrary.org/obo/SO_0000694)
1143
1389
  def self.SNP
1144
1390
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000694')
1145
1391
  end
1146
1392
 
1147
- # A sequence used in experiment. (SO:ke)
1393
+ # A sequence used in experiment.
1148
1394
  # (http://purl.obolibrary.org/obo/SO_0000695)
1149
1395
  def self.reagent
1150
1396
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695')
1151
1397
  end
1152
1398
 
1153
- # A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. (SO:ma)
1399
+ # A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
1154
1400
  # (http://purl.obolibrary.org/obo/SO_0000696)
1155
1401
  def self.oligo
1156
1402
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696')
1157
1403
  end
1158
1404
 
1159
- # A sequence_feature with an extent of zero. (SO:ke)
1405
+ # A sequence_feature with an extent of zero.
1160
1406
  # (http://purl.obolibrary.org/obo/SO_0000699)
1161
1407
  def self.junction
1162
1408
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699')
1163
1409
  end
1164
1410
 
1165
- # A comment about the sequence. (SO:ke)
1411
+ # A comment about the sequence.
1166
1412
  # (http://purl.obolibrary.org/obo/SO_0000700)
1167
1413
  def self.remark
1168
1414
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700')
1169
1415
  end
1170
1416
 
1171
- # A region of sequence where the validity of the base calling is questionable. (SO:ke)
1417
+ # A region of sequence where the validity of the base calling is questionable.
1172
1418
  # (http://purl.obolibrary.org/obo/SO_0000701)
1173
1419
  def self.possible_base_call_error
1174
1420
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000701')
1175
1421
  end
1176
1422
 
1177
- # A region of sequence where there may have been an error in the assembly. (SO:ke)
1423
+ # A region of sequence where there may have been an error in the assembly.
1178
1424
  # (http://purl.obolibrary.org/obo/SO_0000702)
1179
1425
  def self.possible_assembly_error
1180
1426
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000702')
1181
1427
  end
1182
1428
 
1183
- # A region of sequence implicated in an experimental result. (SO:ke)
1429
+ # A region of sequence implicated in an experimental result.
1184
1430
  # (http://purl.obolibrary.org/obo/SO_0000703)
1185
1431
  def self.experimental_result_region
1186
1432
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000703')
1187
1433
  end
1188
1434
 
1189
- # A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. (SO:immuno_workshop)
1435
+ # A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
1190
1436
  # (http://purl.obolibrary.org/obo/SO_0000704)
1191
1437
  def self.gene
1192
1438
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000704')
1193
1439
  end
1194
1440
 
1195
- # Two or more adjcent copies of a region (of length greater than 1). (SO:ke)
1441
+ # Two or more adjcent copies of a region (of length greater than 1).
1196
1442
  # (http://purl.obolibrary.org/obo/SO_0000705)
1197
1443
  def self.tandem_repeat
1198
1444
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705')
1199
1445
  end
1200
1446
 
1201
- # The 3' splice site of the acceptor primary transcript. (SO:ke)
1447
+ # The 3' splice site of the acceptor primary transcript.
1202
1448
  # (http://purl.obolibrary.org/obo/SO_0000706)
1203
1449
  def self.trans_splice_acceptor_site
1204
1450
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000706')
1205
1451
  end
1206
1452
 
1207
- # A region of nucleotide sequence corresponding to a known motif. (SO:ke)
1453
+ # A region of nucleotide sequence corresponding to a known motif.
1208
1454
  # (http://purl.obolibrary.org/obo/SO_0000714)
1209
1455
  def self.nucleotide_motif
1210
1456
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000714')
1211
1457
  end
1212
1458
 
1213
- # A motif that is active in RNA sequence. (SO:ke)
1459
+ # A motif that is active in RNA sequence.
1214
1460
  # (http://purl.obolibrary.org/obo/SO_0000715)
1215
1461
  def self.RNA_motif
1216
1462
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715')
1217
1463
  end
1218
1464
 
1219
- # A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. (SGD:rb)
1465
+ # A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
1220
1466
  # (http://purl.obolibrary.org/obo/SO_0000717)
1221
1467
  def self.reading_frame
1222
1468
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717')
1223
1469
  end
1224
1470
 
1225
- # An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. (FB:WG)
1471
+ # An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
1226
1472
  # (http://purl.obolibrary.org/obo/SO_0000719)
1227
1473
  def self.ultracontig
1228
1474
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000719')
1229
1475
  end
1230
1476
 
1231
- # A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
1477
+ # A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
1232
1478
  # (http://purl.obolibrary.org/obo/SO_0000724)
1233
1479
  def self.oriT
1234
1480
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000724')
1235
1481
  end
1236
1482
 
1237
- # The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). (http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html)
1483
+ # The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
1238
1484
  # (http://purl.obolibrary.org/obo/SO_0000725)
1239
1485
  def self.transit_peptide
1240
1486
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000725')
1241
1487
  end
1242
1488
 
1243
- # A regulatory_region where more than 1 TF_binding_site together are regulatorily active. (SO:SG)
1489
+ # A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.
1244
1490
  # (http://purl.obolibrary.org/obo/SO_0000727)
1245
1491
  def self.CRM
1246
1492
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727')
1247
1493
  end
1248
1494
 
1249
- # A gap in the sequence of known length. The unknown bases are filled in with N's. (SO:ke)
1495
+ # A gap in the sequence of known length. The unknown bases are filled in with N's.
1250
1496
  # (http://purl.obolibrary.org/obo/SO_0000730)
1251
1497
  def self.gap
1252
1498
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000730')
1253
1499
  end
1254
1500
 
1501
+ # -- No comment or description provided. --
1502
+ # (http://purl.obolibrary.org/obo/SO_0000752)
1255
1503
  def self.gene_group_regulatory_region
1256
1504
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000752')
1257
1505
  end
1258
1506
 
1259
- # The region of sequence that has been inserted and is being propagated by the clone. (SO:ke)
1507
+ # The region of sequence that has been inserted and is being propagated by the clone.
1260
1508
  # (http://purl.obolibrary.org/obo/SO_0000753)
1261
1509
  def self.clone_insert
1262
1510
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000753')
1263
1511
  end
1264
1512
 
1265
- # A non functional descendent of an rRNA. (SO:ke)
1513
+ # A non functional descendent of an rRNA.
1266
1514
  # (http://purl.obolibrary.org/obo/SO_0000777)
1267
1515
  def self.pseudogenic_rRNA
1268
1516
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000777')
1269
1517
  end
1270
1518
 
1271
- # A non functional descendent of a tRNA. (SO:ke)
1519
+ # A non functional descendent of a tRNA.
1272
1520
  # (http://purl.obolibrary.org/obo/SO_0000778)
1273
1521
  def self.pseudogenic_tRNA
1274
1522
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000778')
1275
1523
  end
1276
1524
 
1277
- # A region of a chromosome. (SO:ke)
1525
+ # A region of a chromosome.
1278
1526
  # (http://purl.obolibrary.org/obo/SO_0000830)
1279
1527
  def self.chromosome_part
1280
1528
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830')
1281
1529
  end
1282
1530
 
1283
- # A region of a gene. (SO:ke)
1531
+ # A region of a gene.
1284
1532
  # (http://purl.obolibrary.org/obo/SO_0000831)
1285
1533
  def self.gene_member_region
1286
1534
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000831')
1287
1535
  end
1288
1536
 
1289
- # A region of a transcript. (SO:ke)
1537
+ # A region of a transcript.
1290
1538
  # (http://purl.obolibrary.org/obo/SO_0000833)
1291
1539
  def self.transcript_region
1292
1540
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833')
1293
1541
  end
1294
1542
 
1295
- # A region of a mature transcript. (SO:ke)
1543
+ # A region of a mature transcript.
1296
1544
  # (http://purl.obolibrary.org/obo/SO_0000834)
1297
1545
  def self.mature_transcript_region
1298
1546
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000834')
1299
1547
  end
1300
1548
 
1301
- # A part of a primary transcript. (SO:ke)
1549
+ # A part of a primary transcript.
1302
1550
  # (http://purl.obolibrary.org/obo/SO_0000835)
1303
1551
  def self.primary_transcript_region
1304
1552
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835')
1305
1553
  end
1306
1554
 
1307
- # A region of an mRNA. (SO:cb)
1555
+ # A region of an mRNA.
1308
1556
  # (http://purl.obolibrary.org/obo/SO_0000836)
1309
1557
  def self.mRNA_region
1310
1558
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836')
1311
1559
  end
1312
1560
 
1313
- # A region of UTR. (SO:ke)
1561
+ # A region of UTR.
1314
1562
  # (http://purl.obolibrary.org/obo/SO_0000837)
1315
1563
  def self.UTR_region
1316
1564
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000837')
1317
1565
  end
1318
1566
 
1319
- # Biological sequence region that can be assigned to a specific subsequence of a polypeptide. (SO:GAR, SO:ke)
1567
+ # Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
1320
1568
  # (http://purl.obolibrary.org/obo/SO_0000839)
1321
1569
  def self.polypeptide_region
1322
1570
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000839')
1323
1571
  end
1324
1572
 
1325
- # A region within an intron. (SO:ke)
1573
+ # A region within an intron.
1326
1574
  # (http://purl.obolibrary.org/obo/SO_0000841)
1327
1575
  def self.spliceosomal_intron_region
1328
1576
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841')
1329
1577
  end
1330
1578
 
1579
+ # -- No comment or description provided. --
1580
+ # (http://purl.obolibrary.org/obo/SO_0000842)
1331
1581
  def self.gene_component_region
1332
1582
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842')
1333
1583
  end
1334
1584
 
1335
- # A region of a CDS. (SO:cb)
1585
+ # A region of a CDS.
1336
1586
  # (http://purl.obolibrary.org/obo/SO_0000851)
1337
1587
  def self.CDS_region
1338
1588
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851')
1339
1589
  end
1340
1590
 
1341
- # A region of an exon. (RSC:cb)
1591
+ # A region of an exon.
1342
1592
  # (http://purl.obolibrary.org/obo/SO_0000852)
1343
1593
  def self.exon_region
1344
1594
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000852')
1345
1595
  end
1346
1596
 
1347
- # A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. (SO:ke)
1597
+ # A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
1348
1598
  # (http://purl.obolibrary.org/obo/SO_0001000)
1349
1599
  def self.rRNA_16S
1350
1600
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001000')
1351
1601
  end
1352
1602
 
1353
- # A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. (SO:ke)
1603
+ # A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
1354
1604
  # (http://purl.obolibrary.org/obo/SO_0001001)
1355
1605
  def self.rRNA_23S
1356
1606
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001001')
1357
1607
  end
1358
1608
 
1359
- # A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. (RSC:cb)
1609
+ # A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
1360
1610
  # (http://purl.obolibrary.org/obo/SO_0001002)
1361
1611
  def self.rRNA_25S
1362
1612
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001002')
1363
1613
  end
1364
1614
 
1365
- # A variation that increases or decreases the copy number of a given region. (SO:ke)
1615
+ # A variation that increases or decreases the copy number of a given region.
1366
1616
  # (http://purl.obolibrary.org/obo/SO_0001019)
1367
1617
  def self.copy_number_variation
1368
1618
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001019')
1369
1619
  end
1370
1620
 
1371
- # A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome. (PMID:14681355)
1621
+ # A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
1372
1622
  # (http://purl.obolibrary.org/obo/SO_0001037)
1373
1623
  def self.mobile_genetic_element
1374
1624
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001037')
1375
1625
  end
1376
1626
 
1377
- # An MGE that is integrated into the host chromosome. (SO:ke)
1627
+ # An MGE that is integrated into the host chromosome.
1378
1628
  # (http://purl.obolibrary.org/obo/SO_0001039)
1379
1629
  def self.integrated_mobile_genetic_element
1380
1630
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039')
1381
1631
  end
1382
1632
 
1383
- # A regulatory_region that modulates the transcription of a gene or genes. (SO:regcreative)
1633
+ # A regulatory_region that modulates the transcription of a gene or genes.
1384
1634
  # (http://purl.obolibrary.org/obo/SO_0001055)
1385
1635
  def self.transcriptional_cis_regulatory_region
1386
1636
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055')
1387
1637
  end
1388
1638
 
1389
- # A regulatory_region that modulates splicing. (SO:ke)
1639
+ # A regulatory_region that modulates splicing.
1390
1640
  # (http://purl.obolibrary.org/obo/SO_0001056)
1391
1641
  def self.splicing_regulatory_region
1392
1642
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056')
1393
1643
  end
1394
1644
 
1395
- # A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. (SO:ke)
1645
+ # A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
1396
1646
  # (http://purl.obolibrary.org/obo/SO_0001059)
1397
1647
  def self.sequence_alteration
1398
1648
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001059')
1399
1649
  end
1400
1650
 
1401
- # An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. (EBIBS:GAR)
1651
+ # An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
1402
1652
  # (http://purl.obolibrary.org/obo/SO_0001063)
1403
1653
  def self.immature_peptide_region
1404
1654
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001063')
1405
1655
  end
1406
1656
 
1407
- # The maximal intersection of exon and UTR. (SO:ke)
1657
+ # The maximal intersection of exon and UTR.
1408
1658
  # (http://purl.obolibrary.org/obo/SO_0001214)
1409
1659
  def self.noncoding_region_of_exon
1410
1660
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001214')
1411
1661
  end
1412
1662
 
1413
- # The region of an exon that encodes for protein sequence. (SO:ke)
1663
+ # The region of an exon that encodes for protein sequence.
1414
1664
  # (http://purl.obolibrary.org/obo/SO_0001215)
1415
1665
  def self.coding_region_of_exon
1416
1666
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001215')
1417
1667
  end
1418
1668
 
1419
- # A region containing at least one unique origin of replication and a unique termination site. (ISBN:0716719207)
1669
+ # A region containing at least one unique origin of replication and a unique termination site.
1420
1670
  # (http://purl.obolibrary.org/obo/SO_0001235)
1421
1671
  def self.replicon
1422
1672
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235')
1423
1673
  end
1424
1674
 
1425
- # A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. (SO:ke)
1675
+ # A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
1426
1676
  # (http://purl.obolibrary.org/obo/SO_0001236)
1427
1677
  def self.base
1428
1678
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001236')
1429
1679
  end
1430
1680
 
1431
- # A region of the genome of known length that is composed by ordering and aligning two or more different regions. (SO:ke)
1681
+ # A region of the genome of known length that is composed by ordering and aligning two or more different regions.
1432
1682
  # (http://purl.obolibrary.org/obo/SO_0001248)
1433
1683
  def self.assembly
1434
1684
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001248')
1435
1685
  end
1436
1686
 
1437
- # A region which is intended for use in an experiment. (SO:cb)
1687
+ # A region which is intended for use in an experiment.
1438
1688
  # (http://purl.obolibrary.org/obo/SO_0001409)
1439
1689
  def self.biomaterial_region
1440
1690
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001409')
1441
1691
  end
1442
1692
 
1443
- # A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. (SO:cb)
1693
+ # A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
1444
1694
  # (http://purl.obolibrary.org/obo/SO_0001410)
1445
1695
  def self.experimental_feature
1446
1696
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410')
1447
1697
  end
1448
1698
 
1449
- # A region defined by its disposition to be involved in a biological process. (SO:cb)
1699
+ # A region defined by its disposition to be involved in a biological process.
1450
1700
  # (http://purl.obolibrary.org/obo/SO_0001411)
1451
1701
  def self.biological_region
1452
1702
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411')
1453
1703
  end
1454
1704
 
1455
- # A region that is defined according to its relations with other regions within the same sequence. (SO:cb)
1705
+ # A region that is defined according to its relations with other regions within the same sequence.
1456
1706
  # (http://purl.obolibrary.org/obo/SO_0001412)
1457
1707
  def self.topologically_defined_region
1458
1708
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412')
1459
1709
  end
1460
1710
 
1461
- # Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. (SO:cjm, SO:ke)
1711
+ # Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
1462
1712
  # (http://purl.obolibrary.org/obo/SO_0001419)
1463
1713
  def self.cis_splice_site
1464
1714
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419')
1465
1715
  end
1466
1716
 
1467
- # Primary transcript region bordering trans-splice junction. (SO:ke)
1717
+ # Primary transcript region bordering trans-splice junction.
1468
1718
  # (http://purl.obolibrary.org/obo/SO_0001420)
1469
1719
  def self.trans_splice_site
1470
1720
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001420')
1471
1721
  end
1472
1722
 
1473
- # SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. (SO:bm)
1723
+ # SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
1474
1724
  # (http://purl.obolibrary.org/obo/SO_0001483)
1475
1725
  def self.SNV
1476
1726
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001483')
1477
1727
  end
1478
1728
 
1479
- # A region of peptide sequence used to target the polypeptide molecule to a specific organelle. (SO:ke)
1729
+ # A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
1480
1730
  # (http://purl.obolibrary.org/obo/SO_0001527)
1481
1731
  def self.peptide_localization_signal
1482
1732
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001527')
1483
1733
  end
1484
1734
 
1485
- # A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. (SO:ke)
1735
+ # A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
1486
1736
  # (http://purl.obolibrary.org/obo/SO_0001647)
1487
1737
  def self.kozak_sequence
1488
1738
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001647')
1489
1739
  end
1490
1740
 
1491
- # A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. (SO:ke)
1741
+ # A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
1492
1742
  # (http://purl.obolibrary.org/obo/SO_0001654)
1493
1743
  def self.nucleotide_to_protein_binding_site
1494
1744
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654')
1495
1745
  end
1496
1746
 
1497
- # A regulatory region that is involved in the control of the process of transcription. (SO:ke)
1747
+ # A regulatory region that is involved in the control of the process of transcription.
1498
1748
  # (http://purl.obolibrary.org/obo/SO_0001679)
1499
1749
  def self.transcription_regulatory_region
1500
1750
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679')
1501
1751
  end
1502
1752
 
1503
- # A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. (http://en.wikipedia.org/wiki/Sequence_motif)
1753
+ # A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
1504
1754
  # (http://purl.obolibrary.org/obo/SO_0001683)
1505
1755
  def self.sequence_motif
1506
1756
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001683')
1507
1757
  end
1508
1758
 
1509
- # A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. (http://en.wikipedia.org/wiki/Epigenetics, SO:ke)
1759
+ # A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
1510
1760
  # (http://purl.obolibrary.org/obo/SO_0001720)
1511
1761
  def self.epigenetically_modified_region
1512
1762
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720')
1513
1763
  end
1514
1764
 
1515
- # An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). (SO:ke)
1765
+ # An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
1516
1766
  # (http://purl.obolibrary.org/obo/SO_0001790)
1517
1767
  def self.paired_end_fragment
1518
1768
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001790')
1519
1769
  end
1520
1770
 
1521
- # A region of sequence that is involved in the control of a biological process. (SO:ke)
1771
+ # A region of sequence that is involved in the control of a biological process.
1522
1772
  # (http://purl.obolibrary.org/obo/SO_0005836)
1523
1773
  def self.regulatory_region
1524
1774
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005836')
1525
1775
  end
1526
1776
 
1527
- # A collection of related genes. (SO:ma)
1777
+ # A collection of related genes.
1528
1778
  # (http://purl.obolibrary.org/obo/SO_0005855)
1529
1779
  def self.gene_group
1530
1780
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855')
1531
1781
  end
1532
1782
 
1533
- # The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation. (EBIBS:GAR)
1783
+ # The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
1534
1784
  # (http://purl.obolibrary.org/obo/SO_0100011)
1535
1785
  def self.cleaved_peptide_region
1536
1786
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_0100011')
1537
1787
  end
1538
1788
 
1539
- # A sequence alteration where the length of the change in the variant is the same as that of the reference. (SO:ke)
1789
+ # A sequence alteration where the length of the change in the variant is the same as that of the reference.
1540
1790
  # (http://purl.obolibrary.org/obo/SO_1000002)
1541
1791
  def self.substitution
1542
1792
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000002')
@@ -1548,25 +1798,25 @@ class SOFA
1548
1798
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000005')
1549
1799
  end
1550
1800
 
1551
- # A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. (SO:immuno_workshop)
1801
+ # A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
1552
1802
  # (http://purl.obolibrary.org/obo/SO_1000008)
1553
1803
  def self.point_mutation
1554
1804
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000008')
1555
1805
  end
1556
1806
 
1557
- # A continuous nucleotide sequence is inverted in the same position. (EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html)
1807
+ # A continuous nucleotide sequence is inverted in the same position.
1558
1808
  # (http://purl.obolibrary.org/obo/SO_1000036)
1559
1809
  def self.inversion
1560
1810
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1000036')
1561
1811
  end
1562
1812
 
1563
- # A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal. (ISBN:0198506732)
1813
+ # A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
1564
1814
  # (http://purl.obolibrary.org/obo/SO_1001284)
1565
1815
  def self.regulon
1566
1816
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_1001284')
1567
1817
  end
1568
1818
 
1569
- # The sequence referred to by an entry in a databank such as Genbank or SwissProt. (SO:ke)
1819
+ # The sequence referred to by an entry in a databank such as Genbank or SwissProt.
1570
1820
  # (http://purl.obolibrary.org/obo/SO_2000061)
1571
1821
  def self.databank_entry
1572
1822
  return RDF::URI.new('http://purl.obolibrary.org/obo/SO_2000061')
@@ -1576,55 +1826,157 @@ class SOFA
1576
1826
  #
1577
1827
  # +uri+:: URI that is tested for being an object property
1578
1828
  def self.is_object_property?(uri)
1579
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:adjacent_to') then
1829
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/part_of') then
1580
1830
  return true
1581
1831
  end
1582
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature') then
1832
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#adjacent_to') then
1583
1833
  return true
1584
1834
  end
1585
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contained_by') then
1835
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#associated_with') then
1586
1836
  return true
1587
1837
  end
1588
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:contains') then
1838
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#complete_evidence_for_feature') then
1589
1839
  return true
1590
1840
  end
1591
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:derives_from') then
1841
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#connects_on') then
1592
1842
  return true
1593
1843
  end
1594
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') then
1844
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contained_by') then
1595
1845
  return true
1596
1846
  end
1597
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part') then
1847
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#contains') then
1598
1848
  return true
1599
1849
  end
1600
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part') then
1850
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#derives_from') then
1601
1851
  return true
1602
1852
  end
1603
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') then
1853
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#disconnected_from') then
1604
1854
  return true
1605
1855
  end
1606
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of') then
1856
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_from') then
1607
1857
  return true
1608
1858
  end
1609
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of') then
1859
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#edited_to') then
1610
1860
  return true
1611
1861
  end
1612
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of') then
1862
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#evidence_for_feature') then
1613
1863
  return true
1614
1864
  end
1615
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to') then
1865
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#exemplar_of') then
1616
1866
  return true
1617
1867
  end
1618
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to') then
1868
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finished_by') then
1619
1869
  return true
1620
1870
  end
1621
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') then
1871
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#finishes') then
1622
1872
  return true
1623
1873
  end
1624
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature') then
1874
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#gained') then
1625
1875
  return true
1626
1876
  end
1627
- if uri == RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to') then
1877
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#genome_of') then
1878
+ return true
1879
+ end
1880
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guided_by') then
1881
+ return true
1882
+ end
1883
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#guides') then
1884
+ return true
1885
+ end
1886
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_integral_part') then
1887
+ return true
1888
+ end
1889
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_origin') then
1890
+ return true
1891
+ end
1892
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_part') then
1893
+ return true
1894
+ end
1895
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#has_quality') then
1896
+ return true
1897
+ end
1898
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#homologous_to') then
1899
+ return true
1900
+ end
1901
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#integral_part_of') then
1902
+ return true
1903
+ end
1904
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#is_consecutive_sequence_of') then
1905
+ return true
1906
+ end
1907
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#lost') then
1908
+ return true
1909
+ end
1910
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#maximally_overlaps') then
1911
+ return true
1912
+ end
1913
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#member_of') then
1914
+ return true
1915
+ end
1916
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#non_functional_homolog_of') then
1917
+ return true
1918
+ end
1919
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#orthologous_to') then
1920
+ return true
1921
+ end
1922
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#overlaps') then
1923
+ return true
1924
+ end
1925
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#paralogous_to') then
1926
+ return true
1927
+ end
1928
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#part_of') then
1929
+ return true
1930
+ end
1931
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#partial_evidence_for_feature') then
1932
+ return true
1933
+ end
1934
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#position_of') then
1935
+ return true
1936
+ end
1937
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_from') then
1938
+ return true
1939
+ end
1940
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#processed_into') then
1941
+ return true
1942
+ end
1943
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_from') then
1944
+ return true
1945
+ end
1946
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#recombined_to') then
1947
+ return true
1948
+ end
1949
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#sequence_of') then
1950
+ return true
1951
+ end
1952
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#similar_to') then
1953
+ return true
1954
+ end
1955
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#started_by') then
1956
+ return true
1957
+ end
1958
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#starts') then
1959
+ return true
1960
+ end
1961
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_from') then
1962
+ return true
1963
+ end
1964
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#trans_spliced_to') then
1965
+ return true
1966
+ end
1967
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_from') then
1968
+ return true
1969
+ end
1970
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#transcribed_to') then
1971
+ return true
1972
+ end
1973
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translates_to') then
1974
+ return true
1975
+ end
1976
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#translation_of') then
1977
+ return true
1978
+ end
1979
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/SOFA_2_5_2.obo#variant_of') then
1628
1980
  return true
1629
1981
  end
1630
1982
  return false
@@ -2404,6 +2756,9 @@ class SOFA
2404
2756
  #
2405
2757
  # +uri+:: URI that is tested for being a named individual
2406
2758
  def self.is_named_individual?(uri)
2759
+ if uri == RDF::URI.new('http://purl.obolibrary.org/obo/anonymous#variant_of') then
2760
+ return true
2761
+ end
2407
2762
  return false
2408
2763
  end
2409
2764
 
@@ -2430,7 +2785,7 @@ class SOFA
2430
2785
  end
2431
2786
 
2432
2787
  private
2433
- @@parent_properties = { RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:complete_evidence_for_feature') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_integral_part') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:has_part') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:similar_to') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:integral_part_of') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:member_of') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:part_of') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:non_functional_homolog_of') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:orthologous_to') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:paralogous_to') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:homologous_to') , RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:partial_evidence_for_feature') => RDF::URI.new('http://purl.obolibrary.org/obo/http_//purl.org/obo/owl:evidence_for_feature') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000001') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000110') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000004') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000705') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000006') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000057') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000752') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000059') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001654') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000101') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000102') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000112') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000113') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001039') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000114') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000120') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000139') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000833') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000151') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000695') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000159') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000161') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000162') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000163') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000164') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001419') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000165') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000167') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000177') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000178') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0005855') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000181') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000183') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000842') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000193') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000198') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000147') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000200') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000195') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000204') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000205') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000203') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000234') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000233') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000235') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000236') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000717') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000239') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001412') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000289') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000294') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000303') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001720') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000306') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000305') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000307') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000314') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000657') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000315') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000316') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000836') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000318') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000319') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000325') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000209') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000326') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000331') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000324') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000332') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000334') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000330') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000337') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000340') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001235') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000341') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001410') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000344') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001056') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000347') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000349') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000343') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001248') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000360') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000851') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000699') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000368') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000366') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000370') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000673') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000374') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000372') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000375') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000651') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000380') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000715') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000385') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000386') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000390') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000391') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000392') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000393') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000394') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000395') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000396') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000397') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000398') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000399') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000274') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000403') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000404') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000405') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000407') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000650') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000410') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000409') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000412') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000143') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000413') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000700') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000436') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000296') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000441') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000442') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000696') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000454') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000462') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000472') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000483') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000499') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000353') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000551') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001679') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000577') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000581') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000587') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000188') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000593') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000275') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000602') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000603') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000588') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000605') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001411') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000611') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000612') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000841') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000616') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000835') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000624') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000625') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000727') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000627') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0001055') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000628') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000830') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000643') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000005') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000645') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000185') , RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000646') => RDF::URI.new('http://purl.obolibrary.org/obo/SO_0000655') , 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2435
2790
  end
2436
2791